bluuebunny/crossref_metadata_2025_split huggingface dataset:
The fitness landscape of TEM-1 β-lactamase is stratified and inverted by sublethal concentrations of cefotaxime
Authors: Farr Andrew D. , Pesce Diego , Zwart Mark P. , de Visser J. Arjan G. M. 
Published: July 2022

AbstractAdaptive evolutionary processes are constrained by the availability of mutations which cause a fitness benefit – a concept that may be illustrated by ‘fitness landscapes’ which map the relationship of genotype space with fitness. Experimentally derived landscapes have demonstrated a predictability to evolution by identifying limited ‘mutational routes’ that evolution by natural selection may take between low and high-fitness genotypes. However, such studies often utilise indirect measures to determine fitness. We estimated the competitive fitness of each mutant relative to all of its single-mutation neighbours to describe the fitness landscape of three mutations in a β-lactamase enzyme at sub-lethal concentrations of the antibiotic cefotaxime in a structured and unstructured environment. We found that in the unstructured environment the antibiotic selected for higher-resistance types – but with an equivalent fitness for subsets of mutants, despite substantial variation in resistance – resulting in a stratified fitness landscape. In contrast, in a structured environment with low antibiotic concentration, antibiotic-susceptible genotypes had a relative fitness advantage, which was associated with antibiotic-induced filamentation. These results cast doubt that highly resistant genotypes have a unique selective advantage in environments with sub-inhibitory concentrations of antibiotics, and demonstrate that direct fitness measures are required for meaningful predictions of the accessibility of evolutionary routes.ImportanceThe evolution of antibiotic resistant bacterial populations underpins the ongoing antibiotic-resistance crisis. We aim to understand how antibiotic-degrading enzymes can evolve to cause increased resistance, how this process is constrained and whether it can be predictable. To this end we performed competition experiments with a combinatorially-complete set of mutants of a β-lactamase gene subject to sub-inhibitory concentrations of the antibiotic cefotaxime. While some mutants confer their hosts with high resistance to cefotaxime, in competition these mutants do not always confer a selective advantage. Similarly, we identified conditions involving spatial structure where mutations causing high resistance result in a selective disadvantage. Together, this work suggests that the relationship between resistance level and fitness at sub-inhibitory concentrations is complex; predicting the evolution of antibiotic resistance requires knowledge of the conditions that select for resistant genotypes and the selective advantage evolved types have over their predecessors.
SARS-CoV-2 infection dynamics and genomic surveillance reveals early variant transmission in urban wastewater
Authors: Lamba Sanjay , Sutharsan G , Daroch Namrta , Paul Kiran , Joshi Soumya Gopal , Darshan S , Annamalai N , Vishwanath S , Mishra Rakesh , Ramakrishnan Uma , Ishtiaq Farah 
Published: July 2022

AbstractEnvironmental surveillance (ES) of a pathogen is crucial for understanding the community load of disease. As an early warning system, ES for SARS-CoV-2 has complemented routine diagnostic surveillance by capturing near real-time virus circulation at a population level. In this longitudinal study in 28 sewershed sites in Bangalore city, we quantified SARS-CoV-2 RNA to track infection dynamics and provide evidence of change in the relative abundance of emerging variants. We describe an early warning system using the exponentially weighted moving average control chart and demonstrate how SARS-CoV-2 RNA concentrations in wastewater correlated with clinically diagnosed new COVID-19 cases, with the trends appearing 8–14 days earlier in wastewater than in clinical data. This was further corroborated by showing that the estimated number of infections is strongly correlated with SARS-CoV-2 RNA copies detected in the wastewater. Using a deconvolution matrix, we detected emerging variants of concern up to two months earlier in wastewater samples. In addition, we found a huge diversity in variants detected in wastewater compared to clinical samples. Our study highlights that quantifying viral titres, correlating it with a known number of cases in the area, and combined with genomic surveillance helps in tracking VOCs over time and space, enabling timely and making informed policy decisions.
Investigation of in-phase bilateral exercise effects on corticospinal plasticity in relapsing remitting multiple sclerosis: a multiple baseline design
Authors: Sokratous Dimitris , Charalambous Charalambos C. , Zamba-Papanicolaou Eleni , Michailidou Kyriaki , Konstantinou Nikos 
Published: July 2022

AbstractRelapsing-remitting multiple sclerosis is the most common type of multiple sclerosis characterized by periods of relapses and generating various motor symptoms. These symptoms are associated with the corticospinal tract integrity, which is quantified by means of corticospinal plasticity which can be probed via transcranial magnetic stimulation and assessed with motor threshold, motor evoked potential and central motor conduction time. Several factors, such as exercise and interlimb coordination, can influence corticospinal plasticity. Previous work in healthy and in stroke patients showed that the greatest improvement in corticospinal plasticity occurred during in-phase bilateral arm exercises. Altered corticospinal plasticity due to bilateral cortical lesions is common in multiple sclerosis, yet, the impact of these type of exercises in this cohort is unclear. The aim of this concurrent multiple baseline design study is to investigate the effects of in-phase bilateral exercises on corticospinal plasticity and on clinical measures using transcranial magnetic stimulation and standardized clinical assessment, in five people with relapsing-remitting multiple sclerosis. The intervention protocol will last for 12 consecutive weeks (30-60 minutes /session x 3 sessions/week) and include in-phase bilateral movements of the upper limbs, adapted to different sports activities and to functional training. To define functional relation between the intervention and the results on corticospinal plasticity (i.e., resting motor threshold, motor evoked potential amplitude, latency) and on clinical measures (i.e., balance, gait, bilateral hand dexterity and strength, cognitive function), we will perform a visual analysis followed by multilevel modelling and the single case educational design-specific mean difference in order to estimate the magnitude of the effect size across cases. We assume that possible effects from our study, will introduce a type of exercise that will be effective during the disease progression.
Therapeutic potential of IL6R blockade for the treatment of sepsis and sepsis-related death: Findings from a Mendelian randomisation study
Authors: Hamilton Fergus , Thomas Matt , Arnold David , Palmer Tom , Moran Ed , Mentzer Alexander J , Maskell Nick , Baillie Kenneth , Summers Charlotte , Hingorani Aroon , MacGowan Alasdair , Khandakar Golam M , Mitchell Ruth , Smith George Davey , Ghazal Peter , Timpson Nicholas J 
Published: July 2022

IntroductionSepsis is characterised by dysregulated, life-threatening immune responses, which are thought to be driven by cytokines such as interleukin-6 (IL-6). Genetic variants in IL6R known to downregulate IL-6 signalling are associated with improved COVID-19 outcomes, a finding later confirmed in randomised trials of IL-6 receptor antagonists (IL6RA). We hypothesised that blockade of IL6R could also improve outcomes in sepsis.MethodsWe performed a Mendelian randomisation analysis using single nucleotide polymorphisms (SNPs) in and near IL6R to evaluate the likely causal effects of IL6R blockade on sepsis, sepsis severity, other infections, and COVID-19. We weighted SNPs by their effect on CRP and combined results across them in inverse variance weighted meta-analysis, proxying the effect of IL6RA. Our outcomes were measured in UK Biobank, FinnGen, the COVID-19 Host Genetics Initiative (HGI), and the GenOSept and GainS consortium. We performed several sensitivity analyses to test assumptions of our methods, including utilising variants around CRP in a similar analysis.ResultsIn the UK Biobank cohort (N=485,825, including 11,643 with sepsis), IL6R blockade was associated with a decreased risk of sepsis (OR=0.80; 95% CI 0.66-0.96, per unit of natural log transformed CRP decrease). The size of this effect increased with severity, with larger effects on 28-day sepsis mortality (OR=0.74; 95% CI 0.38-0.70); critical care admission with sepsis (OR=0.48, 95% CI 0.30-0.78) and critical care death with sepsis (OR=0.37, 95% CI 0.14 - 0.98) Similar associations were seen with severe respiratory infection: OR for pneumonia in critical care 0.69 (95% CI 0.49 - 0.97) and for sepsis survival in critical care (OR=0.22; 95% CI 0.04- 1.31) in the GainS and GenOSept consortium. We also confirm the previously reported protective effect of IL6R blockade on severe COVID-19 (OR=0.69, 95% 0.57 - 0.84) in the COVID-19 HGI, which was of similar magnitude to that seen in sepsis. Sensitivity analyses did not alter our primary results.ConclusionsIL6R blockade is causally associated with reduced incidence of sepsis, sepsis related critical care admission, and sepsis related mortality. These effects are comparable in size to the effect seen in severe COVID-19, where IL-6 receptor antagonists were shown to improve survival. This data suggests a randomised trial of IL-6 receptor antagonists in sepsis should be considered.
A custom library construction method for super-resolution ribosome profiling in Arabidopsis
Authors: Wu Hsin-Yen Larry , Hsu Polly Yingshan 
Published: July 2022

AbstractRibosome profiling (aka Ribo-seq) is the deep sequencing of ribosome footprints (RFs). It maps and quantifies ribosome occupancy on mRNA, which enables the identification of coding regions and the accurate quantification of translation efficiency. We previously optimized the Ribo-seq method in Arabidopsis and tomato (Hsu et al., 2016; Wu et al., 2019; Wu and Hsu, 2022) to obtain precise RFs with strong 3-nucleotide periodicity, a feature displayed by actively translating ribosomes and a benchmark of high-quality Ribo-seq (Brar and Weissman, 2015). This strong periodicity allowed us to confidently define numerous unannotated translation events across plants (Hsu et al., 2016; Wu et al., 2019; Wu and Hsu, 2022). Recently, several key commercial reagents used in our methods were discontinued; thus, there is an urgent need to develop a new protocol. Here, we report an updated protocol that adapts two custom library construction methods (McGlincy and Ingolia, 2017; Li et al., 2021) for plants. We applied this new protocol to Arabidopsis seedlings and obtained high-quality data. We describe our step-by-step method and discuss crucial considerations for Ribo-seq experiments. We also provide a bioinformatic pipeline to perform essential quality control analyses on Ribo-seq data. Our approach should be readily applicable to other plant species with minimal modifications.
Fc effector activity and neutralization against SARS-CoV-2 BA.4 is compromised in convalescent sera, regardless of the infecting variant
Authors: Richardson Simone I. , Kgagudi Prudence , Manamela Nelia P. , Kaldine Haajira , Venter Elizabeth M. , Pillay Thanusha , Lambson Bronwen E. , van der Mescht Mieke A. , Hermanus Tandile , de Beer Zelda , de Villiers Talita Roma , Bodenstein Annie , van den Berg Gretha , du Pisanie Marizane , Burgers Wendy A. , Ntusi Ntobeko A.B. , Ueckermann Veronica , Rossouw Theresa M. , Boswell Michael T. , Moore Penny L. 
Published: July 2022

SummaryThe SARS-CoV-2 Omicron BA.1 variant, which exhibits high level neutralization resistance, has since evolved into several sub-lineages including BA.4 and BA.5, which have dominated the fifth wave of infection in South Africa. Here we assessed the sensitivity of BA.4 to neutralization and antibody dependent cellular cytotoxicity (ADCC) in convalescent donors infected with four previous variants of SARS-CoV-2, as well as in post-vaccination breakthrough infections (BTIs) caused by Delta or BA.1. We confirm that BA.4 shows high level resistance to neutralization, regardless of the infecting variant. However, breakthrough infections, which trigger potent neutralization, retained activity against BA.4, albeit at reduced titers. Fold reduction of neutralization in BTIs was lower than that seen in unvaccinated convalescent donors, suggesting maturation of neutralizing responses to become more resilient against VOCs in hybrid immunity. BA.4 sensitivity to ADCC was reduced but remained detectable in both convalescent donors and in BTIs. Overall, the high neutralization resistance of BA.4, even to antibodies from BA.1 infections, provides an immunological mechanism for the rapid spread of BA.4 immediately after a BA.1-dominated wave. Furthermore, although ADCC activity against BA.4 was reduced, residual activity may nonetheless contribute to the protection from disease.
Mutagenesis Induced by Protonation of Single-Stranded DNA is Linked to Glycolytic Sugar Metabolism
Authors: Gelova Suzana P. , Chan Kin 
Published: July 2022

AbstractMutagenesis can be thought of as random, in the sense that the occurrence of each mutational event cannot be predicted with precision in space or time. However, when sufficiently large numbers of mutations are analyzed, recurrent patterns of base changes called mutational signatures can be identified. To date, some 60 single base substitution or SBS signatures have been derived from analysis of cancer genomics data. We recently reported that the ubiquitous signature SBS5 matches the pattern of single nucleotide polymorphisms (SNPs) in humans and has analogs in many species. Using a temperature-sensitive single-stranded DNA mutation reporter system, we also showed that a similar mutational pattern in yeast is dependent on error-prone translesion DNA synthesis and glycolytic sugar metabolism. Here, we further investigated mechanisms that are responsible for this form of mutagenesis in yeast. We first confirmed that excess sugar metabolism leads to increased mutation rate, which was detectable by fluctuation assay. We then ruled out a significant role for aerobic respiration in SBS5-like mutagenesis by observing that petite and wild-type cells did not exhibit statistical differences in mutation frequencies. Since glycolysis is known to produce excess protons, we then investigated the effects of experimental manipulations on pH and mutagenesis. We hypothesized that yeast metabolizing 8% glucose would produce more excess protons than cells metabolizing 2% glucose. Consistent with this, cells metabolizing 8% glucose had lower intracellular and extracellular pH values. Similarly, deletion ofvma3(encoding a vacuolar H+-ATPase subunit) increased mutagenesis. We also found that treating cells with edelfosine (which renders membranes more permeable, including to protons) or culturing in low pH media increased mutagenesis. Altogether, our results agree with multiple biochemical studies showing that protonation of nitrogenous bases can alter base pairing so as to stabilize some mispairs, and shed new light on a common form of intrinsic mutagenesis.Graphical Abstract
Substrate binding and lipid-mediated allostery in the human organic anion transporter 1 at the atomic-scale
Authors: Janaszkiewicz Angelika , Tóth Ágota , Faucher Quentin , Arnion Hélène , Védrenne Nicolas , Guellec Chantal Barin-Le , Marquet Pierre , Meo Florent Di 
Published: July 2022

AbstractThe Organic Anion Transporter 1 is a membrane transporter known for its central role in drug elimination by the kidney.hOAT1 is an antiporter translocating substrate in exchange forα-ketoglutarate. The understanding ofhOAT1 structure and function remains limited due to the absence of resolved structure ofhOAT1. Benefiting from conserved structural and functional patterns shared with other Major Facilitator Superfamily transporters, the present study intended to investigate fragments ofhOAT1 transport function and modulation of its activity in order to make a step forward the understanding of its transport cycle.μs-long molecular dynamics simulation ofhOAT1 were carried out suggesting two plausible binding sites for a typical substrate, adefovir, in line with experimental observations. The well-known B-like motif binding site was observed in line with previous studies. However, we here propose a new inner binding cavity which is expected to be involved in substrate translocation event. Binding modes ofhOAT1 co-substrateα-ketoglutarate were also investigated suggesting that it may binds to highly conserved intracellular motifs. We here hypothesize thatα-ketoglutarate may disrupt the pseudo-symmetrical intracellular charge-relay system which in turn may participate to the destabilisation of OF conformation. Investigations regarding allosteric communications alonghOAT1 also suggest that substrate binding event might modulate the dynamics of intracellular charge relay system, assisted by surrounding lipids as active partners. We here proposed a structural rationalisation of transport impairments observed for two single nucleotide polymorphisms, p.Arg50His and p.Arg454Gln suggesting that the present model may be used to transport dysfunctions arising fromhOAT1 mutations.HighlightsAdefovir has at least two binding pockets onhOAT1 in the outward-facing conformation.The highly conserved B-motif within MFS is strongly involved in substrate binding.α-Ketoglutarate binds to the intracellular domain ofhOAT1 and destabilizes its OF conformation.The lipid membrane bilayer plays an active role in the allosteric communication between intracellular and extracellular domains ofhOAT1.Graphical AbstractThe present work (from left): (i) reveals binding modes of adefovir (top) andα-ketoglutarate (bottom) tohOAT1; (ii) maps Single Nucleotide Polymorphisms on outward-facing (top) and inward-facing (bottom) conformation ofhOAT1; (iii) asses the allosteric effect of lipidic environment and presence of substrates.
How do tuna schools associate to dFADs? A study using echo-sounder buoys to identify global patterns
Authors: Navarro-García Manuel , Precioso Daniel , Gavira-O’Neill Kathryn , Torres-Barrán Alberto , Gordo David , Gallego Víctor , Gómez-Ullate David 
Published: July 2022

AbstractBased on the data gathered by echo-sounder buoys attached to drifting Fish Aggregating Devices (dFADs) across tropical oceans, the current study applies a Machine Learning protocol to examine the temporal trends of tuna schools’ association to drifting objects. Using a binary output, metrics typically used in the literature were adapted to account for the fact that the entire tuna aggregation under the dFAD was considered. The median time it took tuna to colonize the dFADs for the first time varied between 25 and 43 days, depending on the ocean, and the longest soak and colonization times were registered in the Pacific Ocean. The tuna schools’ Continuous Residence Times were generally shorter than Continuous Absence Times (median values between 5 and 7 days, and 9 and 11 days, respectively), in line with the results found by previous studies. Using a regression output, two novel metrics, namely aggregation time and disaggregation time, were estimated to obtain further insight into the symmetry of the aggregation process. Across all oceans, the time it took for the tuna aggregation to depart from the dFADs was not significantly longer than the time it took for the aggregation to form. The value of these results in the context of the “ecological trap” hypothesis is discussed, and further analyses to enrich and make use of this data source are proposed.
Power and precision: Evaluation and recommendations of quantitative trait analysis methods for RNA expression levels in the Hybrid Rat Diversity Panel
Authors: Pattee Jack , Vanderlinden Lauren A. , Mahaffey Spencer , Hoffman Paula , Tabakoff Boris , Saba Laura M 
Published: July 2022

AbstractThe Hybrid Rat Diversity Panel (HRDP) is a stable and well-characterized set of more than 90 inbred rat strains that can be leveraged for systems genetics approaches to understanding the genetic and genomic variation associated with complex disease. The HRDP exhibits substantial between-strain diversity while retaining substantial within-strain isogenicity, allowing for the precise mapping of genetic variation associated with complex phenotypes and providing statistical power to identify associated variants. In order to robustly identify associated genetic variants, it is important to account for the population structure induced by inbreeding. To this end, we investigate the performance of various plausible approaches towards modeling quantitative traits in the HRDP and quantify their operating characteristics. Towards facilitating study planning and design, we conduct extensive simulations to investigate the power of genetic association analyses in the HRDP, and characterize the impressive attained power.
Epistasis reduces fitness costs of influenza A virus escape from stem-binding antibodies
Authors: Lee Chung-Young , Caceres C. Joaquin , Geiger Ginger , Seibert Brittany , Faccin Flavio Cargnin , Gay L. Claire , Ferreri Lucas M. , Kaul Drishti , Wrammert Jens , Tan Gene S. , Perez Daniel R. , Lowen Anice C. 
Published: July 2022

AbstractThe hemagglutinin (HA) stem region is a major target of universal influenza vaccine efforts owing to the presence of highly conserved epitopes across multiple influenza A virus strains and subtypes. To explore the potential impact of vaccine-induced immunity targeting the HA stem, we examined the fitness effects of viral escape from stem-binding broadly neutralizing antibodies (stem-bnAbs). Recombinant viruses containing each individual antibody escape substitution showed diminished replication compared to wild-type virus, indicating that stem-bnAb escape incurred fitness costs. A second-site mutation in the HA head domain (N133D) reduced the fitness effects observed in primary cell cultures and likely enabled the selection of escape mutations. This putative permissive mutation was not, however, sufficient to ease fitness costs in a ferret transmission model. Taken together, these data suggest that viral escape from stem-bnAbs is costly but highlight the potential for epistatic interactions to enable evolution within the functionally constrained HA stem domain.