bluuebunny/crossref_metadata_2025_split huggingface dataset:
EyeG2P: an automated variant filtering approach improves efficiency of diagnostic genomic testing for inherited ophthalmic disorders
Authors: Lenassi Eva , Carvalho Ana , Thormann Anja , Fletcher Tracy , Hardcastle Claire , Hunt Sarah E , Sergouniotis Panagiotis I , Michaelides Michel , Webster Andrew R , Cunningham F , Ramsden Simon , FitzPatrick David R , Black Graeme CM , Ellingford Jamie M 
Published: July 2021

AbstractPurposeThe widespread adoption of genomic testing for individuals with ophthalmic disorders has increased demand on diagnostic genomic services for these conditions. Moreover, the clinical utility of a molecular diagnosis for individuals with inherited ophthalmic disorders is increasingly placing pressure on the speed and accuracy of genomic testing.MethodsWe created EyeG2P, a publically available resource to assist diagnostic filtering of genomic datasets for ophthalmic conditions, utilising the Ensembl Variant Effect Predictor. We assessed the sensitivity of EyeG2P for 1234 individuals with a broad range of conditions, who had previously received a confirmed molecular diagnosis through routine genomic diagnostic approaches. For a prospective cohort of 83 individuals, we also assessed the precision of EyeG2P in comparision to routine genomic diagnostic approaches.ResultsWe observed that EyeG2P had a 99.5% sensitivity for genomic variants previously identified as a molecular diagnosis for 1234 individuals. EyeG2P enabled a significant increase in precision in comparison to routine testing strategies (p<0.001), with an increased precision in variant analysis of 35% per individual, on average.ConclusionAutomated filtering of genomic variants through EyeG2P can increase the efficiency of diagnostic testing for individuals with a broad range of inherited ophthalmic disorders.
Challenges to self-isolation among contacts of cases of COVID-19: a national telephone survey in Wales
Authors: Isherwood Kate R , Kyle Richard G , Gray Benjamin J , Davies Alisha R 
Published: July 2021

ABSTRACTObjectivesTo identify the specific challenges of self-isolation experienced by population sub-groups to better target and tailor support.DesignThe Contact Adherence Behavioural Insights Study (CABINS) was a 15-minute telephone survey of confirmed contacts of cases of COVID-19 identified through the national NHS Wales Test Trace Protect (TTP) database.MethodsConfirmed contacts of cases of COVID-19 reached by TTP completed a 15-minute telephone survey (N = 2,027). Binary logistic regression models adjusted for age, gender, living alone, survey round, deprivation quintile (defined by the Welsh Index of Multiple Deprivation) and income precarity (financial security) determined which population sub-groups were more likely to experience challenges during self-isolation.ResultsYounger people (aged 18-29 years) were 3 times more likely to report mental health concerns (Adjusted Odds Ratio [aOR]: 3.16, 95% Confidence Interval [CI]: 2.05-4.86) and 2 times more likely to report loneliness (aOR: 1.96, CI: 1.37-2.81) compared to people aged over 60 years. Women were 1.5 times more likely to experience mental health concerns (aOR: 1.51, 95% CI: 1.20-1.92) compared to men. People with high/very high levels of income precarity were 8 times more likely to report financial challenges (aOR: 7.73, CI: 5.10-11.74) and 3 times more likely to report mental health concerns than their more financially secure counterparts (aOR: 3.08, CI: 2.22-4.28).ConclusionsSelf-isolation is particularly challenging for those with younger people, women and precarious incomes. Providing enhanced emotional, financial and social support and signposting to these groups is required to minimise the harms of self-isolation.What is already known on this subject?Self-isolation after notification as a contact of a positive case of COVID-19 is essential to prevent the spread of the disease. However, self-isolation can be challenging and adherence is dependent upon a range of psychological, social and economic factors.Emerging data suggests that the COVID-19 pandemic is having disproportionate impact on those on lower incomes and those of lower socio-economic status.What does this study add?The most common challenges faced to self-isolation were wanting to see family and friends, followed by a lack of exercise.Individuals with some income precarity were more than 7 times more likely to report financial concerns and 3 times more likely to report mental health concerns as a challenge to self-isolation than those who were financially secure.Interventions to support individuals to self-isolate needs to be targeted at groups most susceptible to experiencing challenges to self-isolation for infectious diseases. Our research suggests that the use of income precarity questions as a screening tool is important to direct financial and practical support through contact tracing systems.
An anti-ACVR1 antibody exacerbates heterotopic ossification by fibro/adipogenic progenitors in fibrodysplasia ossificans progressiva mice
Authors: Lees-Shepard John B. , Stoessel Sean J. , Chandler Julian , Bouchard Keith , Bento Patricia , Apuzzo Lorraine N. , Devarakonda Parvathi M. , Hunter Jeffrey W. , Goldhamer David J. 
Published: July 2021

AbstractFibrodysplasia ossificans progressiva (FOP) is a rare genetic disease characterized by progressive and catastrophic heterotopic ossification (HO) of skeletal muscle and associated soft tissues. FOP is caused by dominantly acting mutations in the bone morphogenetic protein (BMP) type I receptor, ACVR1 (also known as ALK2), the most prevalent of which is an arginine to histidine substitution [ACVR1(R206H)] in the glycine-serine rich intracellular domain of the receptor. A fundamental pathological consequence of FOP-causing ACVR1 receptor mutations is to enable activin A to initiate canonical BMP signaling in responsive progenitors, which drives skeletogenic commitment and HO. With the clear targets of activin A and ACVR1 identified, development of antibody therapeutics to prevent ligand-receptor interactions is an interventional approach currently being explored. Here, we developed a monoclonal blocking antibody (JAB0505) to the extracellular domain of ACVR1 and tested its ability to inhibit HO in established FOP mouse models. JAB0505 inhibited BMP-dependent gene expression in wild-type and ACVR1(R206H)-overexpressing cell lines. Strikingly, however, JAB0505 treatment markedly exacerbated injury-induced HO in two independent FOP mouse models in which ACVR1(R206H) was either broadly expressed, or more selectively expressed in fibro/adipogenic progenitors (FAPs). JAB0505 drove HO even under conditions of activin A inhibition, indicating that JAB0505 has receptor agonist activity. JAB0505-treated mice exhibited multiple, distinct foci of heterotopic lesions, suggesting an atypically broad anatomical domain of FAP recruitment to endochondral ossification. In addition, skeletogenic differentiation was both delayed and prolonged, and this was accompanied by dysregulation of FAP population growth. Collectively, alterations in the growth and differentiative properties of FAPs and FAP-derived skeletal cells are implicated in the aggravated HO phenotype. These data raise serious safety and efficacy concerns for the use of anti-ACVR1 antibodies to treat FOP patients.
Spatial and temporal localization of cell wall associated pili in Enterococcus faecalis
Authors: Choo Pei Yi , Wang Charles Y. , VanNieuwenhze Michael S. , Kline Kimberly A. 
Published: July 2021

AbstractEnterococcus faecalis relies upon a number of cell wall-associated proteins for virulence. One virulence factor is the sortase-assembled endocarditis and biofilm associated pilus (Ebp), an important factor for biofilm formation in vitro and in vivo. The current paradigm for sortase-assembled pilus biogenesis in Gram-positive bacteria is that the pilus sortase covalently links pilus monomers prior to recognition, while the housekeeping sortase cleaves at the LPXTG motif within the terminal pilin subunit, and subsequently attaches assembled pilus fiber to the growing cell wall at sites of new cell wall synthesis. While the cell wall anchoring mechanism and polymerization of Ebp is well characterized, less is known about the spatial and temporal deposition of this protein on the cell surface. We followed the distribution of Ebp and peptidoglycan (PG) throughout the E. faecalis cell cycle via immunofluorescence microscopy and fluorescent D-amino acids (FDAA) staining. Surprisingly, cell surface Ebp did not co-localize with newly synthesized PG. Instead, surface-anchored Ebp was localized to the cell hemisphere but never at the septum where new cell wall is deposited. In addition, the older hemisphere of the E. faecalis diplococcus were completely saturated with Ebp, while Ebp appeared as two foci directly adjacent to the nascent septum in the newer hemisphere. A similar localization pattern was observed for another cell wall anchored substrate by sortase A, aggregation substance (AS), suggesting that this may be a general rule for all SrtA substrates in E. faecalis. When cell wall synthesis was inhibited by ramoplanin, an antibiotic that binds and sequesters lipid II cell wall precursors, new Ebp deposition at the cell surface was not disrupted. These data suggest an alternative paradigm for sortase substrate deposition in E. faecalis, in which Ebp are anchored directly onto un-crosslinked cell wall, independent of new PG synthesis.
A protocol for good quality genomic DNA isolation from formalin-fixed paraffin-embedded tissues without using commercial kits
Authors: Talukdar Fazlur Rahman , Abramović Irena , Cuenin Cyrille , Carreira Christine , Gangane Nitin , Sincic Nino , Herceg Zdenko 
Published: July 2021

ABSTRACTDNA isolation from formalin-fixed paraffin-embedded (FFPE) tissues for molecular analysis has become a frequent procedure in cancer research. However, the yield or quality of the isolated DNA is often compromised, and commercial kits are used to overcome this to some extent. We developed a new protocol (IARCp) to improve better quality and yield of DNA from FFPE tissues without using any commercial kit. To evaluate the IARCp’s performance, we compared the quality and yield of DNA with two commercial kits, namely NucleoSpin® DNA FFPE XS (MN) and QIAamp DNA Micro (QG) isolation kit. Total DNA yield for QG ranged from 120.0 – 282.0 ng (mean 216.5 ng), for MN: 213.6 – 394.2 ng (mean 319.1 ng), and with IARCp the yield was much higher ranging from 775.5 – 1896.9 ng (mean 1517.8 ng). Moreover, IARCp has also performed well in qualitative assessments. Overall, IARCp represents a novel approach to DNA isolation from FFPE which results in good quality and significant amounts of DNA suitable for many downstream genome-wide and targeted molecular analyses. Our proposed protocol does not require the use of any commercial kits for isolating DNA from FFPE tissues, making it suitable to implement in low-resource settings such as low and middle-income countries (LMICs).
Genomic rearrangements have consequences for introgression breeding as revealed by genome assemblies of wild and cultivated lentil species
Authors: Ramsay Larissa , Koh Chu Shin , Kagale Sateesh , Gao Dongying , Kaur Sukhjiwan , Haile Teketel , Gela Tadesse S. , Chen Li-An , Cao Zhe , Konkin David J. , Toegelová Helena , Doležel Jaroslav , Rosen Benjamin D. , Stonehouse Robert , Humann Jodi L. , Main Dorrie , Coyne Clarice J. , McGee Rebecca J. , Cook Douglas R. , Varma Penmetsa R. , Vandenberg Albert , Chan Crystal , Banniza Sabine , Edwards David , Bayer Philipp E. , Batley Jacqueline , Udupa Sripada M. , Bett Kirstin E. 
Published: July 2021

AbstractUnderstanding the genomic relationship between wild and cultivated genomes would facilitate access to the untapped variability found in crop wild relatives. We developed genome assemblies of a cultivated lentil (Lens culinaris) as well as a wild relative (L. ervoides). Comparative analyses revealed large-scale structural rearrangements and additional repetitive DNA in the cultivated genome, resulting in regions of reduced recombination, segregation distortion and permanent heterozygosity in the offspring of a cross between the two species. These novel findings provide plant breeders with better insight into how best to approach accessing the novel variability available in wild relatives.
Trait-trait relationships and tradeoffs vary with genome size in prokaryotes
Authors: Beier Sara , Werner Johannes , Bouvier Thierry , Mouquet Nicolas , Violle Cyrille 
Published: July 2021

AbstractWe report genomic traits that have been associated with the life history of prokaryotes and highlight conflicting findings concerning earlier observed trait correlations and tradeoffs. In order to address possible explanations for these contradictions we examined trait-trait variations of 11 genomic traits from ~ 18,000 sequenced genomes. The studied trait-trait variations suggested: (i) the predominance of two resistance and resilience-related orthogonal axes and (ii) at least in free living species with large effective population sizes whose evolution is little affected by genetic drift an overlap between a resilience axis and an axis of resource usage efficiency. These findings imply that resistance associated traits of prokaryotes are globally decoupled from resilience related traits and in the case of free-living communities also from resource use efficiencies associated traits. However, further inspection of pairwise scatterplots showed that resistance and resilience traits tended to be positively related for genomes up to roughly five million base pairs and negatively for larger genomes. This in turn may preclude a globally consistent assignment of prokaryote genomic traits to the competitor - stress-tolerator - ruderal (CSR) schema that sorts species depending on their location along disturbance and productivity gradients into three ecological strategies and may serve as an explanation for conflicting findings from earlier studies. All reviewed genomic traits featured significant phylogenetic signals and we propose that our trait table can be applied to extrapolate genomic traits from taxonomic marker genes. This will enable to empirically evaluate the assembly of these genomic traits in prokaryotic communities from different habitats and under different productivity and disturbance scenarios as predicted via the resistance-resilience framework formulated here.
Determination of the Two-Component Systems regulatory network reveals core and accessory regulations across Pseudomonas aeruginosa lineages
Authors: Trouillon Julian , Imbert Lionel , Villard Anne-Marie , Vernet Thierry , Attrée Ina , Elsen Sylvie 
Published: July 2021

SUMMARYPseudomonas aeruginosa possesses one of the most complex bacterial regulatory networks, which largely contributes to its success as a human opportunistic pathogen. However, most of its transcription factors (TFs) are still uncharacterized and the potential intra-species variability in regulatory networks has been mostly ignored so far. Here, to provide a first global view of the two-component systems (TCSs) regulatory network in P. aeruginosa, we produced and purified all DNA-binding TCS response regulators (RRs) and used DAP-seq to map the genome-wide binding sites of these 55 TFs across the three major P. aeruginosa lineages. The resulting networks encompass about 40% of all genes in each strain and contain numerous new important regulatory interactions across most major physiological processes, including virulence and antibiotic resistance. Strikingly, the comparison between the three representative strains shows that about half of the detected targets are specific to only one or two of the tested strains, revealing a previously unknown large functional diversity of TFs within a single species. Three main mechanisms were found to drive this diversity, including differences in accessory genome content, as exemplified by the strain-specific plasmid in the IHMA87 outlier strain which harbors numerous binding sites of chromosomally-encoded RRs. Additionally, most RRs display potential auto-regulation or RR-RR cross-regulation, bringing to light the vast complexity of this network. Overall, we provide the first complete delineation of the TCS regulatory network in P. aeruginosa that will represent an important resource for future studies on this pathogen.
Malaria parasite evades mosquito immunity by glutaminyl cyclase mediated protein modification
Authors: Kolli Surendra Kumar , Molina-Cruz Alvaro , Araki Tamasa , van Geurten Fiona J.A. , Ramesar Jai , Chevalley-Maurel Severine , Kroeze Hans J , Bezemer Sacha , de Korne Clarize , Withers Roxanne , Raytselis Nadia , El Hebieshy Angela F. , Kim Robert Q , Child Matthew , Kakuta Soichiro , Hisaeda Hajime , Kobayashi Hirotaka , Annoura Takeshi , Hensbergen Paul J. , Franke-Fayard Blandine M. , Barillas-Mury Carolina , Scheeren Ferenc A. , Janse Chris J. 
Published: July 2021

AbstractGlutaminyl cyclase (QC) modifies N-terminal glutamine or glutamic acid residues of target proteins into cyclic pyroglutamic acid (pGlu). Here, we report the biochemical and functional analysis of Plasmodium QC. We show that Plasmodium sporozoites of QC-null mutants are recognized by the mosquito immune system and melanized when they reach the hemocoel. Sporozoite numbers in salivary glands are also reduced in mosquitoes infected with QC-null or QC catalytically-dead mutants. This phenotype can be rescued by genetic complementation or by disrupting mosquito hemocytes or melanization immune responses. Mutation of a single QC-target glutamine of the major sporozoite surface protein (CSP) also results in immune recognition of sporozoites. These findings reveal QC-mediated post-translational modification of surface proteins as a major mechanism of mosquito immune evasion by Plasmodium sporozoites.
The human neuronal receptor NgR1 bridges reovirus capsid proteins to initiate infection
Authors: Sutherland Danica M. , Strebl Michael , Koehler Melanie , Welsh Olivia L. , Yu Xinzhe , Hu Liya , dos Santos Natividade Rita , Knowlton Jonathan J. , Taylor Gwen M. , Moreno Rodolfo A. , Wörz Patrick , Lonergan Zachary R. , Aravamudhan Pavithra , Guzman-Cardozo Camila , Alsteens David , Wang Zhao , Prasad B. V. V. , Stehle Thilo , Dermody Terence S. 
Published: July 2021

ABSTRACTHuman Nogo-66 receptor 1 (NgR1) is a receptor for mammalian orthoreoviruses (reoviruses), but the mechanism of virus-receptor engagement is unknown. NgR1 binds a variety of structurally dissimilar ligands in the adult central nervous system (CNS) to inhibit axon outgrowth. Disruption of ligand binding to NgR1 and subsequent signaling can improve neuron regrowth, making NgR1 an important therapeutic target for diverse conditions such as spinal crush injuries and Alzheimer disease. To elucidate how NgR1 mediates cell binding and entry of reovirus, we defined the affinity of interaction between virus and receptor, determined the structure of the virus-receptor complex, and identified residues in the receptor required for virus binding and infection. These studies revealed that NgR1 sequences in a central concave region of the molecule establish a bridge between two copies of the viral capsid protein, σ3. This unusual binding interface produces high-avidity interactions between virus and receptor and likely primes early entry steps. NgR1 sequences engaged by reovirus also are required for NgR1 binding to ligands expressed by neurons and oligodendrocytes. These studies redefine models of reovirus cell-attachment and highlight the evolution of viruses to engage multiple receptors using distinct capsid components.
Regulation of neuronal progenitor delamination by dynein-driven post-Golgi apical transport
Authors: Brault J.B. , Bardin S. , Lampic M. , Carpentieri J.A. , Coquand L. , Penisson M. , Lachuer Hugo , Victoria G.S. , Baloul S. , Boncompain G. , Miserey-Lenkei S. , Fraisier V. , Francis F. , Perez F. , Goud B. , Baffet A. D. 
Published: July 2021

AbstractRadial glial (RG) cells are the neural stem cells of the developing neocortex. Apical RG (aRG) cells can delaminate to generate basal RG (bRG) cells, a cell type associated with human brain expansion. Here, we report that this delamination is regulated by the post-Golgi secretory pathway. Using in situ subcellular live imaging, we show that post-Golgi transport of RAB6+ vesicles occurs toward the minus ends of microtubules and depends on dynein. We demonstrate that the apical determinant Crumbs3 (CRB3) is also transported by dynein. Double knockout of RAB6A/A’ and RAB6B impairs apical localization of CRB3, and induces a retraction of aRG cell apical process, leading to delamination and ectopic division. These defects are phenocopied by knock-out of the dynein activator LIS1. Overall, our results identify a RAB6-dynein-LIS1 complex for Golgi to apical surface transport in aRG cells, and highlights the role of this pathway in the maintenance of neuroepithelial integrity.
Mechanosensitivity of nucleocytoplasmic transport
Authors: Andreu Ion , Granero-Moya Ignasi , Chahare Nimesh R. , Clein Kessem , Jordàn Marc Molina , Beedle Amy E. M. , Elosegui-Artola Alberto , Trepat Xavier , Raveh Barak , Roca-Cusachs Pere 
Published: July 2021

AbstractMechanical force controls fundamental cellular processes in health and disease, and increasing evidence shows that the nucleus both experiences and senses applied forces. Here we show that nuclear forces differentially control passive and facilitated nucleocytoplasmic transport, setting the rules for the mechanosensitivity of shuttling proteins. We demonstrate that nuclear force increases permeability across nuclear pore complexes, with a dependence on molecular weight that is stronger for passive than facilitated diffusion. Due to this differential effect, force leads to the translocation into or out of the nucleus of cargoes within a given range of molecular weight and affinity for nuclear transport receptors. Further, we show that the mechanosensitivity of several transcriptional regulators can be both explained by this mechanism, and engineered exogenously by introducing appropriate nuclear localization signals. Our work sets a novel framework to understand mechanically induced signalling, with potential general applicability across signalling pathways and pathophysiological scenarios.One sentence summaryForce application to the nucleus leads to nuclear accumulation of proteins by differentially affecting passive versus facilitated nucleocytoplasmic transport.
DNA mismatch and damage detection using a FRET-based assay for monitoring the loading of multiple MutS sliding clamps
Authors: Kunetsky Vladislav , Storozhuk Olha , Brouwer Gwendolyn , Laffeber Charlie , Dillingham Mark S. , Lebbink Joyce , Friedhoff Peter 
Published: July 2021

ABSTRACTWe developed a sensitive, homogeneous fluorescence assay for the detection of DNA mismatches and DNA damage based on the mismatch repair (MMR) protein MutS. The assay is based on Förster resonance energy transfer (FRET) between SYBR Green I (SG), non-covalently bound to DNA, and Alexa Fluor 647 (AF647) conjugated to MutS. In contrast to previous assays using only the mismatch binding activity of MutS, we exploited the ATP-dependent loading of multiple MutS sliding clamps provoked by mismatch/damage to the DNA, which increases the overall sensitivity of the assay. The assay was validated using a well-characterized 3 kb circular DNA containing a single G/T mismatch. We also demonstrate that treatment of long (multiple kb) DNA with various chemical or physical agents including non-denaturing bisulfite conversion of cytosine to uracil, cisplatin modification or ultraviolet light (UVC) results in changes in the DNA that can be detected by the FRET-based MutS biosensor.