bluuebunny/crossref_metadata_2025_split huggingface dataset:
A comprehensive single cell data analysis of in lymphoblastoid cells reveals the role of Super-enhancers in maintaining EBV latency
Authors: Yan Bingyu , Wang Chong , Chakravorty Srishti , Zhang Zonghao , Kadadi Simran D. , Zhuang Yuxin , Sirit Isabella , Hu Yonghua , Jung Minwoo , Sahoo Subhransu , Wang Luopin , Shao Kunming , Anderson Nicole L. , Trujillo-Ochoa Jorge L. , Liu Xing , Olson Matthew R. , Afzali Behdad , Zhao Bo , Kazemian Majid 
Published: August 2022

AbstractWe probed the lifecycle of EBV on a cell-by-cell basis using single cell RNA sequencing (scRNA-seq) data from nine publicly available lymphoblastoid cell lines (LCL). While the majority of LCLs comprised cells containing EBV in the latent phase, two other clusters of cells were clearly evident and were distinguished by distinct expression of host and viral genes. Notably, both were high expressors of EBV LMP1/BNLF2 and BZLF1 compared to another cluster that expressed neither gene. The two novel clusters differed from each other in their expression of EBV lytic genes, including glycoprotein gene GP350. The first cluster, comprising GP350−LMP1hi cells, expressed high levels of HIF1A and was transcriptionally regulated by HIF1-α. Treatment of LCLs with Pevonedistat, a drug that enhances HIF1-α signaling, markedly induced this cluster. The second cluster, containing GP350+LMP1hi cells, expressed EBV lytic genes. Host genes that are controlled by super-enhancers (SEs), such as transcription factors MYC and IRF4, had the lowest expression in this cluster. Functionally, the expression of genes regulated by MYC and IRF4 in GP350+LMP1hi cells were lower compared to other cells. Indeed, induction of EBV lytic reactivation in EBV+ AKATA reduced the expression of these SE-regulated genes. Furthermore, CRISPR-mediated perturbation of the MYC or IRF4 SEs in LCLs induced the lytic EBV gene expression, suggesting that host SEs and/or SE target genes are required for maintenance of EBV latency. Collectively, our study revealed EBV associated heterogeneity among LCLs that may have functional consequence on host and viral biology.ImportanceEpstein-Barr virus (EBV) establishes a life-long latency program within host cells. As such, EBV immortalized lymphoblastoid cells (LCLs) often carry the latent EBV genome and only a small percentage of LCLs containing lytic EBV. However, the cellular programs that distinguish latent from lytic cells and the heterogeneity of cells in latent or lytic phases remains poorly explored. To explore these unknowns, we reanalyzed publicly available single cell RNA-seq data from nine LCLs. This approach permitted the simultaneous study of cells in both latent and lytic phases. We identified three cell populations with distinct lytic/latent activity and further characterized the transcriptomes of these cells. We also identified a new role of super-enhancers in regulating EBV lytic replication. Collectively, our studies revealed EBV associated heterogeneity among LCLs that contribute to EBV life cycle and biology.
Genetic differences between 129S substrains affect antiretroviral immune responses
Authors: Zhang Robert Z. , Mele Vincent , Robben Lia , Kane Melissa 
Published: August 2022

AbstractInbred mouse lines vary in their ability to mount protective antiretroviral immune responses, and even closely related strains can exhibit opposing phenotypes upon retroviral infection. Here, we found that 129S mice inherit a previously unknown mechanism for the production of anti-murine leukemia virus (MLV) antibodies and control of infection. The resistant phenotype is controlled by two dominant loci that are independent from known MLV-resistance genes. We also show that production of anti-MLV antibodies in 129S7, but not 129S1 mice is independent of interferon gamma (IFNγ) signaling. Thus, our data indicate that 129S mice inherit an unknown mechanism for control of MLV infection and demonstrate that there is genetic variability in 129S substrains that affects their ability to mount antiviral immune responses.ImportanceUnderstanding the genetic basis for production of protective antiviral immune responses is crucial for the development of novel vaccines and adjuvants. Additionally, characterizing the genetic and phenotypic variability in inbred mice has implications for the selection of strains for targeted mutagenesis, choice of controls, and for broader understanding of the requirements for protective immunity.
Resting State Functional Connectivity Demonstrates Increased Segregation in Bilateral Temporal Lobe Epilepsy
Authors: Lucas Alfredo , Cornblath Eli J. , Sinha Nishant , Hadar Peter , Caciagli Lorenzo , Keller Simon S. , Bonilha Leonardo , Shinohara Russell T. , Stein Joel M. , Das Sandhitsu , Gleichgerrcht Ezequiel , Davis Kathryn A. 
Published: August 2022

AbstractTemporal lobe epilepsy (TLE) is the most common type of focal epilepsy. An increasingly identified subset of patients with TLE consists of those who show bilaterally independent temporal lobe involvement during seizures. Bilateral TLE (BiTLE) remains understudied, likely due to its complex underlying pathophysiology and heterogeneous clinical presentation.In this study, using a multicenter resting state functional MRI (rs-fMRI) dataset, we constructed whole brain functional networks of 19 patients with BiTLE, and compared them to those of 75 patients with unilateral TLE (UTLE). We quantified resting-state, whole-brain topological properties using metrics derived from network theory, including clustering coefficient, global efficiency, participation coefficient, and modularity. For each metric, we computed an average across all brain regions, and iterated this process across network densities ranging from 0.10-0.50. Curves of network density versus each network metric were compared between groups. Finally, we derived a combined metric, which we term the “integration-segregation axis”, by combining whole brain average clustering coefficient and global efficiency curves and applying principal component analysis (PCA)-based dimensionality reduction.Compared to UTLE, BiTLE had decreased global efficiency (p=0.026), increased whole brain average clustering coefficient (p=0.035), and decreased whole brain average participation coefficient across a range of network densities (p=0.001). Modularity maximization yielded a larger number of smaller communities in BiTLE than in UTLE (p=0.016). Differences in network properties separate BiTLE and UTLE along the integration-segregation axis: 68% of patients with BiTLE were identified within the high segregation region, while only 41% of the UTLE patients were identified in the same region (p=0.042). Along the integration-segregation axis, UTLE patients with poor surgical outcomes were more similar to BiTLE than those with good surgical outcomes (p=0.72).Increased interictal whole brain network segregation, as measured by rs-fMRI, is specific to BiTLE, and may assist in non-invasively identifying this patient population prior to intracranial EEG or device implantation.
Longitudinal neonatal brain development and socio-demographic correlates of infant outcomes following preterm birth
Authors: Vanes Lucy , Fenn-Moltu Sunniva , Hadaya Laila , Fitzgibbon Sean , Cordero-Grande Lucilio , Price Anthony , Chew Andrew , Falconer Shona , Arichi Tomoki , Counsell Serena J. , Hajnal Joseph V. , Batalle Dafnis , Edwards A. David , Nosarti Chiara 
Published: August 2022

AbstractPreterm birth results in premature exposure of the brain to the extrauterine environment during a critical period of neurodevelopment. Consequently, infants born preterm are at a heightened risk of adverse behavioural outcomes in later life. We characterise longitudinal development of neonatal regional brain volume and functional connectivity in the first weeks following preterm birth, sociodemographic factors, and their respective relationships to psychomotor outcomes and psychopathology in toddlerhood. We study 121 preterm infants preterm who underwent magnetic resonance imaging shortly after birth, at term-equivalent age, or both. Longitudinal regional brain volume and functional connectivity were modelled as a function of psychopathology and psychomotor outcomes at 18 months. Better psychomotor functioning in toddlerhood was associated with greater relative right cerebellar volume and a more rapid decrease over time of sensorimotor degree centrality in the neonatal period. In contrast, increased 18-month psychopathology was associated with a more rapid decrease in relative regional subcortical volume. Furthermore, while socio-economic deprivation was related to both psychopathology and psychomotor outcomes, cognitively stimulating parenting predicted psychopathology only. Our study highlights the importance of longitudinal imaging to better predict toddler outcomes following preterm birth, as well as disparate environmental influences on separable facets of behavioural development in this population.
Real-time analysis of the cancer genome and fragmentome from plasma and urine short and long cell-free DNA using Nanopore sequencing
Authors: van der Pol Ymke , Tantyo Normastuti Adhini , Evander Nils , Hentschel Anouk E. , Ramaker Jip , Bahce Idris , Nieuwenhuijzen Jakko A. , Steenbergen Renske D.M. , Pegtel D. Michiel , Moldovan Norbert , Mouliere Florent 
Published: August 2022

AbstractCell-free DNA (cfDNA) can be isolated from blood and/or urine of cancer patients and analyzed with sequencing. Unfortunately, most conventional short-read sequencing methods are technically challenging, labor intensive and time consuming, requiring several days but more typically weeks to obtain interpretable data which are limited by a bias for short cfDNA fragments.Here, we demonstrate that with Oxford Nanopore Technologies sequencing we can achieve economical and ultra-fast delivery of clinical data from liquid biopsies.Our ‘ITSFASTR’ approach is able to deliver copy number aberrations, and cfDNA fragmentation profiles in less than 24 hours from sample collection. The tumorderived cfDNA fraction calculated from lung cancer patient plasma and urine from bladder cancer patients was highly correlated (R=0.98) to the tumor fraction calculated from conventional short-read sequencing of the same samples. cfDNA size profile and fragmentation patterns in plasma and urine exhibited the typical cfDNA features yet with a significantly higher proportion of fragments that exceed 300bp, exhibiting similar tumor fraction than shorter size fragments. Notably, comprehensive fragment-end composition and nucleosome profiling near transcription start sites can be determined from the same data.We propose that ITSFASTR is the first point-of-care solution for obtaining genomic and fragmentomic results from liquid biopsies.
Risk factors for COVID-19 hospitalization or death during the first Omicron surge in adults: a large population-based case-control study
Authors: Lo TKT , Usman Hussain , Sikdar Khokan C. , Strong David , James Samantha , Ross Jordan , Saxinger Lynora M. 
Published: August 2022

AbstractBackgroundDescription of risk factors of severe acute COVID-19 outcomes with the consideration of vaccination status in the era of the Omicron variant of concern are limited.ObjectivesTo examine the association of age, sex, underlying medical conditions, and COVID-19 vaccination with hospitalization, intensive-care unit (ICU) admission, or death due to the disease, using data from a period when Omicron was the dominant strain.MethodsA population-based case-control study based on administrative health data, that included confirmed COVID-19 patients during January (2022) in Alberta, Canada. Patients who were non-residents, without the provincial healthcare insurance coverage, or ≤18 years of age were excluded. Patients with any severe outcome were the cases; and those without any hospitalization, ICU admission, or death were controls. Adjusted odds ratios, of the explanatory factors of a severe outcome, were estimated using a logistic regression model.ResultsThere were 90,989 COVID-19 patients included in the analysis; 2% had severe outcomes and 98% were included in the control group. Overall, more COVID patients were found in the younger age-groups (72.0% ≤49 years old), females (56.5%), with no underlying conditions (59.5%), and fully vaccinated patients (90.4%). However, the adjusted odds ratios were highest in the 70–79 age group (28.32; 95% CI 20.6–38.9) or among ≥80 years old (29.8; 21.6–41.0), males (1.4; 1.3–1.6); unvaccinated (16.1; 13.8–18.8), or patients with ≥3 underlying conditions (13.1; 10.9–15.8).ConclusionHigher risk of severe acute COVID-19 outcomes were associated with older age, the male sex, and increased number of underlying medical conditions. Unvaccination or undervaccination remained as the greatest modifiable risk factor in prevention of severe COVID outcomes. These findings help inform medical decisions and allocation of scarce healthcare resources.
Keeping up with the pathogens: Improved antimicrobial resistance detection and prediction fromPseudomonasaeruginosa genomes
Authors: Madden Danielle E. , Baird Timothy , Bell Scott C. , McCarthy Kate L. , Price Erin P. , Sarovich Derek S. 
Published: August 2022

AbstractBackgroundAntimicrobial resistance (AMR) is an intensifying threat that requires urgent mitigation to avoid a post-antibiotic era. The ESKAPE pathogen,Pseudomonas aeruginosa, represents one of the greatest AMR concerns due to increasing multi- and pan-drug resistance rates. Shotgun sequencing is quickly gaining traction forin silicoAMR profiling due to its unambiguity and transferability; however, accurate and comprehensive AMR prediction fromP. aeruginosagenomes remains an unsolved problem.MethodsWe first curated the most comprehensive database yet of knownP. aeruginosaAMR variants. Next, we performed comparative genomics and microbial genome-wide association study analysis across a Global isolate Dataset (n=1877) with paired antimicrobial phenotype and genomic data to identify novel AMR variants. Finally, the performance of ourP. aeruginosaAMR database, implemented in our ARDaP software, was compared with three previously publishedin silicoAMR gene detection or phenotype prediction tools – abritAMR, AMRFinderPlus, ResFinder – across both the Global Dataset and an analysis-naïve Validation Dataset (n=102).ResultsOur AMR database comprises 3639 mobile AMR genes and 733 AMR-conferring chromosomal variants, including 75 chromosomal variants not previously reported, and 284 chromosomal variants that we show are unlikely to confer AMR. Our pipeline achieved a genotype-phenotype balanced accuracy (bACC) of 85% and 81% across 10 clinically relevant antibiotics when tested against the Global and Validation Datasets, respectively, vs. just 56% and 54% with abritAMR, 58% and 54% with AMRFinderPlus, and 60% and 53% with ResFinder.ConclusionsOur ARDaP software and associated AMR variant database provides the most accurate tool yet for predicting AMR phenotypes inP. aeruginosa, far surpassing the performance of current tools. Implementation of our ARDaP-compatible database for routine AMR prediction fromP. aeruginosagenomes and metagenomes will improve AMR identification, addressing a critical facet in combatting this treatment-refractory pathogen. However, knowledge gaps remain in our understanding of theP. aeruginosaresistome, particularly the basis of colistin AMR.
Structural and Dynamic Basis of DNA Capture and Translocation by Mitochondrial Twinkle Helicase
Authors: Li Zhuo , Kaur Parminder , Lo Chen-Yu , Chopra Neil , Smith Jamie , Wang Hong , Gao Yang 
Published: August 2022

ABSTRACTTwinkle is the sole helicase responsible for mitochondrial DNA replication. Twinkle can selfload onto and unwind mitochondrial DNA. Nearly 60 mutations on Twinkle have been linked to human mitochondrial diseases. Using cryo-electron microscopy (cryo-EM) and High-speed atomic force microscope (HS-AFM), we obtained the atomic-resolution structure of a vertebrate Twinkle homolog with DNA and captured in real-time how Twinkle is self-loaded onto DNA. Our data highlight the essential role of the non-catalytic N-terminal domain of Twinkle. The N-terminal domain interacts with the helicase domain to stabilize Twinkle hexamers during translocation and the new domain-domain interface is a hotspot for disease-related mutations. The N-terminal domains can protrude approximately 5 nm to capture nearby DNA and initialize Twinkle loading onto DNA. Moreover, structural analysis and subunit doping experiments suggest that Twinkle hydrolyzes ATP stochastically, which explains the low efficiency of Twinkle DNA unwinding and implicates additional regulations of Twinkle during mitochondrial DNA replication.
Transcriptome and chromatin accessibility mapping reveals a type I Interferon response triggered by Mycobacterium tuberculosis infection
Authors: Madden Katrina , El Hamra Rayan , Berton Stefania , Alvarez Gonzalo G. , Blais Alexandre , Sun Jim 
Published: August 2022

ABSTRACTTuberculosis, a deadly infectious lung disease caused by Mycobacterium tuberculosis (Mtb), remains the leading cause of bacterial disease-related deaths worldwide. The success of Mtb as a human pathogen depends on its ability to manipulate host immune response pathways, many of which are regulated by epigenetic mechanisms that control the accessibility of chromatin to the transcriptional machinery. Recent reports suggest that host phosphatases, such as PPM1A, may play a role in the regulation of chromatin accessibility during bacterial infections. However, changes in genome-wide chromatin accessibility during Mtb infection and whether PPM1A plays a role in this process remains unknown. Using combinatorial chromatin accessibility (ATAC-seq) and transcriptomics (RNA-seq) profiling of wild-type (WT), PPM1A knockout (ΔPPM1A) and PPM1A overexpressing (PPM1A+) macrophages, we demonstrate that Mtb infection induces global chromatin remodeling consistent with changes in gene expression signatures. The strongest concordant chromatin accessibility and gene expression signature triggered by Mtb infection was enriched for genes involved in the type I interferon (IFN) signaling pathways. Modulation of PPM1A expression results in altered chromatin accessibility signatures during Mtb infection that are reflected in the total number, chromosome location and directionality of change. Transcription factor motif analysis revealed an enrichment for transcription factors involved in the type I IFN pathway during Mtb infection, including IRF4, MEF2A, and JDP2. In contrast, both deletion and overexpression of PPM1A produced unique transcription factor enrichment signatures linked to the genomic regions with altered chromatin accessibility. Our study demonstrates that altered type I IFN responses in Mtb-infected macrophages occurs as a result of genome-wide changes in chromatin accessibility, and that PPM1A likely plays a role in a subset of these signatures.
Phosphorylation of the Smooth Muscle Master Splicing Regulator RBPMS Regulates its Splicing Activity
Authors: Barnhart Michael D. , Yang Yi , Nakagaki-Silva Erick E. , Hammond Thomas H. , Pizzinga Mariavittoria , Gooding Clare , Stott Katherine , Smith Christopher W.J. 
Published: August 2022

ABSTRACTWe previously identified RBPMS as a master regulator of alternative splicing in differentiated smooth muscle cells (SMCs). RBPMS is transcriptionally downregulated during SMC dedifferentiation, but we hypothesized that RBPMS protein activity might be acutely downregulated by post-translational modifications. Publicly available phosphoproteomic datasets reveal that Thr113 and Thr118 immediately adjacent to the RRM domain are commonly both phosphorylated. An RBPMS T113/118 phosphomimetic T/E mutant showed decreased splicing regulatory activity both in transfected cells and in a cell-free in vitro assay, while a non-phosphorylatable T/A mutant retained full activity. Loss of splicing activity was associated with a modest reduction in RNA affinity but significantly reduced RNA binding in nuclear extract. A lower degree of oligomerization of the T/E mutant might cause lower avidity of multivalent RNA binding. However, NMR analysis also revealed that the T113/118E peptide acts as an RNA mimic which can loop back and antagonize RNA-binding by the RRM domain. Finally, we identified ERK2 as the most likely kinase responsible for phosphorylation at Thr113 and Thr118. Collectively, our data identify a potential mechanism for rapid modulation of the SMC splicing program in response to external signals during the vascular injury response and atherogenesis.
Designing a Cas9/gRNA-assisted quantitative Real-Time PCR (CARP) assay for identification of point mutations leading to rifampicin resistance in the human pathogen Mycobacterium tuberculosis
Authors: Augustin Linus , Agarwal Nisheeth 
Published: August 2022

AbstractA simple, rapid and low-cost diagnostic test, which can detect both the drug-sensitive and the drug-resistant tuberculosis (TB) cases is the need of the hour. Here, we developed a Cas9/gRNA-assisted quantitative Real-Time PCR (qRT-PCR) (CARP) assay to detect single nucleotide mutations causing drug resistance in the TB pathogen, Mycobacterium tuberculosis (Mtb). Guide RNAs (gRNAs) were designed against S531 and H526 positions in the rifampicin (RIF)-resistance-determining region (RR-DR) of the Mtb rpoB gene that exhibit frequent mutations in the RR clinical isolates of Mtb. Conditions were optimised for in vitro Cas9 cleavage such that single nucleotide changes at these positions can be recognised by Cas9/gRNA complex with 100% specificity. Further estimation of Cas9/gRNA-based cleavage of target DNA by qRT-PCR led to rapid detection of drug-resistant sequences. The newly designed CARP assay holds a great deal of promise in the diagnosis and prognosis of patients suffering from TB, in a cost-effective manner.
Turnover of the extracellular polymeric matrix in an EBPR microbial community
Authors: Tomás-Martínez Sergio , Zwolsman Erwin J. , Merlier Franck , Pabst Martin , Lin Yuemei , van Loosdrecht Mark C.M. , Weissbrodt David G. 
Published: August 2022

AbstractPolyphosphate accumulating organisms (PAOs) are responsible for enhanced biological phosphate removal (EBPR) from wastewater, where they grow embedded in a matrix of extracellular polymeric substances (EPS). EPS comprise a mixture of biopolymers like polysaccharides or (glyco)proteins. Despite previous studies, little is known about the dynamics of EPS in mixed cultures, and their production by PAOs and potential consumption by flanking microbes. EPS are biodegradable and have been suggested to be a substrate for other organisms in the community. Studying EPS turnover can help elucidate their biosynthesis and biodegradation cycles. We analyzed the turnover of proteins and polysaccharides in the EPS of an enrichment culture of PAOs relative to the turnover of internal proteins. An anaerobic-aerobic sequencing batch reactor (SBR) simulating EBPR conditions was operated to enrich for PAOs. After achieving a stable culture, carbon source was switched to uniformly 13C-labelled acetate. Samples were collected at the end of each aerobic phase. EPS were extracted by alkaline treatment. 13C enrichment in proteins and sugars (after hydrolysis of polysaccharides) in the extracted EPS were measured by mass spectrometry. The average turnover rate of sugars and proteins (0.167 and 0.192 d-1 respectively) was higher than the expected value based on the solid removal rate (0.132 d-1), and no significant difference was observed between intracellular and secreted proteins. This indicates that EPS from the PAO enriched community is not selectively degraded by flanking populations under stable EBPR process conditions. Instead, we observed general decay of biomass, which corresponds to a value of 0.048 d-1.Graphical abstractKey points- Proteins showed a higher turnover rate than carbohydrates.- Turnover of EPS was similar to the turnover of intracellular proteins.- EPS is not preferentially consumed by flanking populations.