bluuebunny/crossref_metadata_2025_split huggingface dataset:
COVID-19 Case and Mortality Surveillance using Daily SARS-CoV-2 in Wastewater Samples adjusting for Meteorological Conditions and Sample pH
Authors: Abelson Samantha , Penso Johnathon , Alsuliman Bader , Babler Kristina , Sharkey Mark , Stevenson Mario , Grills George , Mason Christopher E. , Solo-Gabriele Helena , Kumar Naresh 
Published: July 2023

ABSTRACTBackgroundWastewater monitoring is increasingly used for community surveillance of infectious diseases, especially after the COVID-19 pandemic as the genomic footprints of pathogens shed by infected individuals can be traced in the environment. However, detection and concentration of pathogens in the environmental samples and their efficacy in predicting infectious diseases can be influenced by meteorological conditions and quality of samples.ObjectivesThis research examines whether meteorological conditions and sample pH affect SARS-CoV-2 concentrations in wastewater samples, and whether the association of SARS-CoV-2 with COVID-19 cases and mortality improves when adjusted for meteorological conditions and sample pH value in Miami-Dade County, FL.MethodsDaily wastewater samples were collected from Miami-Dade Wastewater Treatment Plant in Key Biscayne, Florida from August 2021 to August 2022. The samples were analyzed for pH and spiked with OC43. RNA was extracted from the concentrated wastewater sample and SARS-CoV-2 was quantified using qPCR. COVID-19 and mortality data were acquired from the Centers for Disease Control and Prevention (CDC) and meteorological data from the National Climatic Data Center. COVID-19 case and mortality rates were modelled with respect to time-lagged wastewater SARS-CoV-2 adjusting for meteorological conditions, and sample pH value and OC43 recovery.ResultsTemperature, dew point, pH values and OC43 recovery showed significant associations with wastewater SARS-CoV-2. Time-lagged wastewater SARS-CoV-2 showed significant associations with COVID-19 case and mortality incidence rates. This association improved when wastewater SARS-CoV-2 levels were adjusted for (or instrumented on) meteorological conditions, OC43 recovery, and sample pH. A 0.47% change in COVID-19 case incidence rate was associated with 1% change in wastewater SARS-CoV-2 (β ∼ 0.47; 95% CI = 0.29 – 0.64; p < 0.001). A 0.12 % change in COVID-19 mortality rate was associated with 1 % change in SARS-CoV-2 in wastewater 44 days prior. A 0.07% decline in COVID-19 mortality rate was associated with a unit increase in ambient temperature 28 days prior.DiscussionTime lagged wastewater SARS-CoV-2 (and its adjustment for sample pH and RNA recovery) and meteorological conditions can be used for the surveillance of COVID-19 case and mortality. These findings can be extrapolated to improve the surveillance of other infectious diseases by proactive measurements of infectious agent(s) in the wastewater samples, adjusting for meteorological conditions and sample pH value.
Determining the importance of the stringent response for methicillin-resistantStaphylococcus aureusvirulence using a zebrafish model of infection
Authors: Choudhury Naznin R. , Urwin Lucy , Salamaga Bartłomiej , Prince Lynne R. , Renshaw Stephen A. , Corrigan Rebecca M. 
Published: July 2023

AbstractStaphylococcus aureusis a bacterial pathogen that poses a major threat to human health. The ability of this bacterium to adapt to stresses encountered in the host is essential for disease. The stringent response is a signalling pathway utilised by all bacteria to alarm cells when stressed, and has been linked to the virulence of a number of species. This signalling pathway is controlled by the nucleotide alarmones guanosine tetra-(ppGpp) and pentaphosphate (pppGpp: collectively termed (p)ppGpp), produced inS. aureusby three synthetase enzymes: Rel, RelP and RelQ. Here, we used a triple (p)ppGpp synthetase mutant ((p)ppGpp0) to examine the importance of this signalling network for the survival and virulence ofS. aureus in vivo. Using an established zebrafish larval infection model, we observed that infection with (p)ppGpp0resulted in attenuated virulence, which was not due to a reduced ability of the mutant to replicatein vivo. Of the three (p)ppGpp synthetases, Rel was established as key during infection, but roles for RelP and RelQ were also observed. Zebrafish myeloid cell depletion restored the virulence of (p)ppGpp0during systemic infection, indicating that (p)ppGpp is important for survival within host phagocytes. Primary macrophages infection studies, followed byin vitrotolerance assays to key innate immune effectors, demonstrated that (p)ppGpp0was more susceptible to stressors found within the intracellular macrophage environment, with roles for all three synthetases implicated. Lastly, the absence of CodY, a transcription factor linked to the stringent response, significantly increased the tolerance ofS. aureusto phagolysosomal-like stressorsin vitro, but had no impactin vivo. Taken together, these results define the importance of the stringent response forS. aureusinfection, revealing that (p)ppGpp produced by all three synthetases is required for bacterial survival within the host environment by mediating adaptation to the phagolysosome.
reanalyzerGSE: tackling the everlasting lack of reproducibility and reanalyses in transcriptomics
Authors: Ruiz José L , Terrón-Camero Laura C , Castillo-González Julia , Fernández-Rengel Iván , Delgado Mario , Gonzalez-Rey Elena , Andrés-León Eduardo 
Published: July 2023

ABSTRACTSummaryIn the current context of transcriptomics democratization, there is an unprecedented surge in the number of studies and datasets. However, advances are hampered by aspects such as the reproducibility crisis, and lack of standardization, in particular with scarce reanalyses of secondary data. reanalyzerGSE, is a user-friendly pipeline that aims to be an all-in-one automatic solution for locally available transcriptomic data and those found in public repositories, thereby encouraging data reuse. With its modular and expandable design, reanalyzerGSE combines cutting-edge software to effectively address simple and complex transcriptomic studies ensuring standardization, up to date reference genome, reproducibility, and flexibility for researchers.Availability and implementationThe reanalyzerGSE open-source code and test data are freely available at bothhttps://github.com/BioinfoIPBLN/reanalyzerGSEand 10.5281/zenodo.XXXX under the GPL3 license.Supplementary dataare available.
Feeding behaviour, species associations and natural diets of 10 Cyprinid fish species from South-West Sri Lanka
Authors: Kortmulder Koenraad , van der Wiele Peter 
Published: July 2023

AbstractSri Lanka has been a favored region for studies of fish assemblages in tropical streams. Food, habitats, reproduction and species segregation have been in focus. The present paper introduces a new approach, comparing feeding behavior of 10 indigenous cyprinid species as observed in aquaria under standardized conditions. It is found that species with similar feeding habits (as to substrate preferences and some characteristics of snapping and processing) are largely separated in their typical habitats in the wild. This conclusion is similar to what others, working with largely the same species in the same region, have found, namely that co-existing species differ in their food preferences. But our conclusion was arrived at independently on the basis of different data. Advantages of behavior studies in this context are discussed, such as identification of evolutionary adaptations in behavior and added information onwherein their common habitat co-occurring species collect certain food items that are commonly found in gut content analyses.
Eye lens organoids going simple: characterization of a new 3-dimensional organoid model for lens development and pathology
Authors: Duot Matthieu , Viel Roselyne , Viet Justine , Le Goff-Gaillard Catherine , Paillard Luc , Lachke Salil A. , Gautier-Courteille Carole , Reboutier David 
Published: July 2023

AbstractThe ocular lens, along with the cornea, focuses light on the retina to generate sharp images. Opacification of the lens, or cataract, is the leading cause of blindness worldwide. Presently, the best approach for cataract treatment is to surgically remove the diseased lens and replace it with an artificial implant. Although effective, this is costly and can have post-surgical complications. Toward identifying alternate treatments, it is imperative to develop organoid models relevant for lens studies and anti-cataract drug screening. Here, we demonstrate that by culturing mouse lens epithelial cells under defined 3-dimensional (3D) culture conditions, it is possible to generate organoids that display optical properties and recapitulate many aspects of lens organization at the tissue, cellular and transcriptomic levels. These 3D cultured lens organoids can be rapidly produced in large amounts. High-throughput RNA-sequencing (RNA-seq) on specific organoid regions isolated by laser capture microdissection (LCM) and immunofluorescence assays demonstrate that these lens organoids display spatiotemporal expression of key lens genes,e.g.,Jag1,Pax6,Prox1,Hsf4andCryab. Further, these lens organoids are amenable to induction of opacities. Finally, knockdown of a cataract-linked RNA-binding protein encoding gene,Celf1, induces opacities in these organoids, indicating their use in rapidly screening for genes functionally relevant to lens biology and cataract. In sum, this lens organoid model represents a compelling new tool to advance the understanding of lens biology and pathology, and can find future use in the rapid screening of compounds aimed at preventing and/or treating cataract.
Unbiased counting of whole proteins with nanopores over the full dynamic range of a proteome: a computational study
Authors: Sampath G. 
Published: July 2023

AbstractA computational model is presented for nanopore-based counting of intact single protein molecules in a sample regardless of the number of copies. It is based on measurable quantities and low detector bandwidths and can be applied to the full dynamic range of a proteome without the need for proteolysis or complex protein separation methods. Denatured unfolded whole protein molecules are assumed to translocate through a nanopore via electrophoresis and diffusion. A low solution pH helps keep the required detector bandwidth B in the 10-20 KHz range. An incremental Fokker-Planck drift-diffusion model is used to calculate two measurable quantities: 1) the total time (in the precision range set by B) for a protein to translocate through the pore, computed from the mean incremental translocation times of residues exiting the pore in succession; and 2) the volumes of protein segments inside the pore during translocation (used here as a proxy for the current blockade signal level) over alternate time blocks of width 1/2B. These are used to obtain volume-based string codes for each protein, substrings thereof as protein identifiers, and, if multiple copies are present, the copy number for a protein. This is a non-destructive single-molecule label-free alternative to mass spectrometry (MS) and other methods based on antibodies or optical tagging, it does not use any sequence identity information. Computational results are presented for the human proteome (Uniprot id UP000005640_9606; 20598 curated proteins). Total translocation times for the entire proteome (one copy per protein) are found to be in the tens of minutes. Over 80% of the proteome can be identified; higher percentages are possible by comparing whole proteins based on their string codes and total translocation times. Extrapolation of these results to a parallel 1000 pore array suggests that ∼109individual protein molecules can be counted in 15-20 hours.
Stand age diversity and climate change affects forests’ resilience and stability, although unevenly
Authors: Vangi Elia , Dalmonech Daniela , Cioccolo Elisa , Marano Gina , Bianchini Leonardo , Puchi Paulina F. , Grieco Elisa , Cescatti Alessandro , Colantoni Andrea , Chirici Gherardo , Collalti Alessio 
Published: July 2023

AbstractStand age significantly influences the functioning of forest ecosystems by shaping structural and physiological plant traits, affecting water and carbon budgets. Forest age distribution is determined by the interplay of tree mortality and regeneration, influenced by both natural and anthropogenic disturbances. Thus, human-driven alteration of tree age distribution presents an underexplored avenue for enhancing forest stability and resilience. In our study, we investigated how age distribution impacts the stability and resilience of the forest carbon budget under both current and future climate conditions. We employed a biogeochemical model on three historically managed forest stands, projecting their future as undisturbed systems, i.e., left at their natural evolution with no management interventions. The model, driven by climate data from five Earth System Models under four representative climate scenarios and one baseline scenario, spanned 11 age classes for each stand. Our findings indicate that Net Primary Production (NPP) peaks in the young and middle-aged classes (16- to 50-year-old), aligning with ecological theories, regardless of the climate scenario. Under climate change, the beech forest exhibited an increase in NPP and maintained stability across all age classes, while resilience remained constant with rising atmospheric CO2and temperatures. However, NPP declined under climate change scenarios for the Norway spruce and Scots pine sites. In these coniferous forests, stability and resilience were more influenced. These results underscore the necessity of accounting for age classes and species-specific reactions in evaluating the impacts of climate change on forest stability and resilience. We, therefore, advocate for customized management strategies that enhance the adaptability of forests to changing climatic conditions, taking into account the diverse responses of different species and age groups to climate.
Endocytosis Inhibitors Block SARS-CoV-2 Pseudoparticle Infection of Mink Lung Epithelium
Authors: Song Ann , Phandthong Rattapol , Talbot Prue 
Published: July 2023

AbstractBoth spill over and spill back of SARS-CoV-2 virus have been reported on mink farms in Europe and the United States. Zoonosis is a public health concern as dangerous mutated forms of the virus could be introduced into the human population through spillback. The purpose of our study was to determine the SARS-CoV-2 entry mechanism using mink lung epithelial cell line (Mv1Lu) and to block entry with drug inhibitors. Mv1Lu cells were susceptible to SARS-CoV-2 viral pseudoparticle infection, validating them as a suitable disease model for COVID-19. Inhibitors of TMPRSS2 and of endocytosis, two pathways of viral entry, were tested to identify those that blocked infection. Dyngo4a, a small molecule endocytosis inhibitor, significantly reduced infection, while TMPRSS2 inhibitors had minimal impact, supporting the conclusion that the entry of the SARS-CoV-2 virus into Mv1Lu cells occurs primarily through endocytosis. The small molecule inhibitors that were effective in this study could potentially be used therapeutically to prevent SARS-CoV-2 infection in mink populations. This study will facilitate the development of therapeutics to prevent zoonotic transmission of SARS-CoV-2 variants to other animals, including humans.
Mechanical stress combines with planar polarised patterning during metaphase to orient embryonic epithelial cell divisions
Authors: Blanchard Guy B. , Scarpa Elena , Muresan Leila , Sanson Bénédicte 
Published: July 2023

SummaryThe orientation of cell division (OCD) in the plane of epithelia drives tissue morphogenesis and relaxes stresses, with errors leading to pathologies. Stress anisotropy, cell elongation and planar polarisation can all contribute to the OCD, but it is unclear how these interactin vivo.In the planar polarisedDrosophilaembryonic ectoderm during axis elongation, planar OCD is highly variable. We show that both a temporary reversal of tissue stress anisotropy and local compression from neighbouring dividing cells re-orient mitotic spindles during metaphase, independently of interphase cell elongation. Isotropic cells align their OCD to the anterior-posterior (AP) embryonic axis, mediated by tissue-wide planar polarised Myosin II, while the spindle of elongated cells is sterically constrained to cell long axes.Thus AP-patterning ensures that cell division combines with cell rearrangement to extend the body axis, except when strong local stress anisotropy is dissipated by cells dividing according to their elongation.
Structural basis for auto-inhibition and activation of a short prokaryotic Argonaute associated TIR-APAZ defense system
Authors: Guo Lijie , Huang Pingping , Li Zhaoxin , Shin Young-Cheul , Yan Purui , Lu Meiling , Chen Meirong , Xiao Yibei 
Published: July 2023

AbstractShort prokaryotic Ago accounts for most prokaryotic Argonaute (pAgo) and is involved in defending bacteria against invading nucleic acids. Short prokaryotic Ago associated with APAZ-TIR (SPARTA) has been shown to oligomerize and deplete NAD+upon guide-mediated target DNA recognition. However, the molecular basis of SPARTA inhibition and activation remains unknown. Here we determine the cryo-EM structures ofCrenotalea thermophilaSPARTA in its inhibited, transient, as well as activated states. The SPARTA is auto-inhibited by its acidic tail, which occupies the guide-target binding channel. Guide mediated target binding expels this acidic tail and triggers substantial conformational changes to expose Ago-Ago dimerization interface. As a result, SPARTA assembles into an active TIR-APAZ4/short Ago4octamer, where the four TIR domains are rearranged and packed to form NADase active sites. Together with biochemical evidence, our results provide a panoramic vision explaining SPARTA auto-inhibition and activation, and expand understanding of pAgo mediated bacterial defense systems.
Collaborative Cross mice have diverse phenotypic responses to infection with Methicillin-resistantStaphylococcus aureusUSA300
Authors: Nagarajan Aravindh , Scoggin Kristin , Gupta Jyotsana , Aminian Manuchehr , Garry Adams L. , Kirby Michael , Threadgill David , Andrews-Polymenis Helene 
Published: July 2023

AbstractStaphylococcus aureus(S. aureus) is an opportunistic pathogen causing diseases ranging from mild skin infections to life threatening conditions, including endocarditis, pneumonia, and sepsis. To identify host genes modulating this host-pathogen interaction, we infected 25 Collaborative Cross (CC) mouse strains with methicillin-resistantS. aureus(MRSA) and monitored disease progression for seven days using a surgically implanted telemetry system. CC strains varied widely in their response to intravenous MRSA infection. We identified eight ‘susceptible’ CC strains with high bacterial load, tissue damage, and reduced survival. Among the surviving strains, six with minimal colonization were classified as ‘resistant’, while the remaining six tolerated higher organ colonization (‘tolerant’). The kidney was the most heavily colonized organ, but liver, spleen and lung colonization were better correlated with reduced survival. Resistant strains had higher pre-infection circulating neutrophils and lower post-infection tissue damage compared to susceptible and tolerant strains. We identified four CC strains with sexual dimorphism: all females survived the study period while all males met our euthanasia criteria earlier. In these CC strains, males had more baseline circulating monocytes and red blood cells. We identified several CC strains that may be useful as new models for endocarditis, myocarditis, pneumonia, and resistance to MRSA infection. Quantitative Trait Locus (QTL) analysis identified two significant loci, on Chromosomes 18 and 3, involved in early susceptibility and late survival after infection. We prioritizedNpc1andIfi44lgenes as the strongest candidates influencing survival using variant analysis and mRNA expression data from kidneys within these intervals.Author SummaryMethicillin-resistantStaphylococcus aureusis a human opportunistic pathogen that can cause life-threatening diseases. To study the influence of host genetics on the outcome of MRSA infection, we infected a collection of genetically diverse mice. We identified different phenotypes for survival, organ colonization, and tissue damage, and classified CC strains into MRSA susceptible, tolerant, and resistant categories. We identified several parameters that correlated with these phenotypes. Four CC strains exhibited strong sexual dimorphism in infection outcome: females lived longer, and males had higher baseline circulating monocytes and red blood cells. Several of the CC strains we characterize may represent better animal models for diseases caused by MRSA. QTL analysis identified two genes,Npc1andIfi44l, as strong candidates for involvement in early susceptibility and late survival after MRSA infection. Our data suggests a strong involvement of host genetics in MRSA infection outcome.
Cotton Microbiome Profiling and Cotton Leaf Curl Disease (CLCuD) Suppression through Microbial Consortia associated withGossypium arboreum
Authors: Aqueel Rhea , Badar Ayesha , Roy Nazish , Mushtaq Qandeel , Ali Aimen Fatima , Bashir Aftab , Ijaz Umer Zeeshan , Malik Kauser Abdulla 
Published: July 2023

AbstractThe failure of breeding strategies has caused scientists to shift to other means where the new approach involves exploring the microbiome to modulate plant defense mechanisms against CLCuD. The cotton microbiome of CLCuD-resistant varieties may harbor a multitude of bacterial genera that significantly contribute to disease resistance and provide information on metabolic pathways that differ between the susceptible and resistant varieties. The current study aimed to explore the microbiome of CLCuD-susceptibleGossypium hirsutumand CLCuD-resistantGossypium arboreum. Microbial community surveys performed using 16S rRNA gene amplification revealed thatPseudomonasinhabited the rhizosphere whileBacilluswas predominantly found in the phyllosphere of CLCuV-tolerantG. arboreum. The study was done for the leaf endophyte, leaf epiphyte, rhizosphere, and root endophyte of the two cotton species. Furthermore, our disease incidence assay using pot experiments has revealed mechanistic insights through salicylic acid-producingSerratia spp. andFictibacillus spp. isolated from CLCuD-resistantG. arboreum, which exhibited viral disease suppression and induced systemic resistance in CLCuD susceptibleG. hirsutum.