bluuebunny/crossref_metadata_2025_split huggingface dataset:
Rare coding variants inNOX4link high superoxide levels to psoriatic arthritis mutilans
Authors: Wang Sailan , Nikamo Pernilla , Laasonen Leena , Gudbjornsson Bjorn , Ejstrup Leif , Iversen Lars , Lindqvist Ulla , Alm Jessica J. , Eisfeldt Jesper , Zheng Xiaowei , Catrina Sergiu-Bogdan , Taylan Fulya , Vaz Raquel , Ståhle Mona , Tapia-Paez Isabel 
Published: June 2023

SummaryPsoriatic arthritis mutilans (PAM) is the rarest and most severe form of psoriatic arthritis. PAM is characterized by erosions of the small joints of hands and feet and osteolysis leading to joint disruption. Despite its severity, the underlying mechanisms are unknown, and no candidate susceptibility genes have hitherto been identified. We aimed to investigate the genetic basis of PAM. We performed massive parallel sequencing of sixty-one patients’ genomes from the PAM Nordic cohort. We validated the rare variants found by Sanger sequencing and genotyped additional psoriasis, psoriatic arthritis, and control cohorts. We then tested the role of the variants usingin vivoandin vitromodels. We found rare variants with a minor allele frequency (MAF) below 0.0001 in the NADPH oxidase 4 (NOX4) in four patients.In silicopredictions show that the identified variants are potentially damaging. NOXs are the only enzymes producing reactive oxygen species (ROS). ROS are highly reactive molecules important role in the regulation of signal transduction. NOX4 is specifically involved in the differentiation of osteoclasts, the cells implicated in bone resorption. Functional follow-up studies using cell culture, zebrafish models, and measurement of ROS in patients uncovered that theNOX4variants found in this study increase the levels of ROS both invitroandin vivo.We proposeNOX4as the first candidate susceptibility gene for PAM. Our study links high levels of ROS caused byNOX4variants to the development of PAM, opening the possibility for a potential therapeutic target.
Intraspecific genetic variation is critical to robust toxicological predictions of aquatic contaminants
Authors: Shahmohamadloo René S. , Rudman Seth M. , Clare Catherine I. , Westrick Judy A. , Wang Xueqi , De Meester Luc , Fryxell John M. 
Published: June 2023

AbstractEnvironmental risk assessment is a critical tool for protecting aquatic life and its effectiveness is predicated on predicting how natural populations respond to contaminants. Yet, routine toxicity testing typically examines only one genotype, which may render risk assessments inaccurate as populations are most often composed of genetically distinct individuals. To determine the importance of intraspecific variation in the translation of toxicity testing to populations, we quantified the magnitude of genetic variation within 20Daphnia magnaclones derived from one lake using whole genome sequencing and phenotypic assays. We repeated these assays across two exposure levels of microcystins, a cosmopolitan and lethal aquatic contaminant produced by harmful algal blooms. We found considerable intraspecific genetic variation in survival, growth, and reproduction, which was amplified by microcystins exposure. Finally, using simulations we demonstrate that the common practice of employing a single genotype to calculate toxicity tolerance failed to produce an estimate within the 95% confidence interval over half of the time. These results illuminate the importance of incorporating intraspecific genetic variation into toxicity testing to reliably predict how natural populations will respond to aquatic contaminants.
Genomes of historical specimens reveal multiple invasions of LTR retrotransposons inDrosophila melanogasterpopulations during the 19thcentury
Authors: Scarpa Almorò , Pianezza Riccardo , Wierzbicki Filip , Kofler Robert 
Published: June 2023

AbstractTransposable element invasions have a profound impact on the evolution of genomes and phenotype. It is thus an important open question on how often such TE invasions occur. Based on strains sampled at different times, previous work showed that four different TE families invadedD. melanogasterduring the 20thcentury. Here we utilize the genomes of historical specimens to extend this work by another 100 years. We found that the LTR retrotransposons Blood, Opus and 412 spread inD. melanogasterin the 19thcentury. These invasions were found to constitute second waves, as degraded fragments were found for all three TEs. We show that two of the three invasions, Opus and 412, led to pronounced geographic heterogeneity, likely due to founder effects during the invasions. Finally, we identified species from the simulans complex as the likely origin of the TEs. In total, seven TE families invadedD. melanogasterduring the last 200 years, increasing the genome size by 1.2 Mbp. Based on the analysis of strains and specimens sampled at different times, we provide a detailed timeline of TE invasions, makingD. melanogasterthe first organism where we could infer the invasion history of TEs during the last two centuries.
Scattered differentiation of unlinked loci across the genome underlines ecological divergence of the selfing grassBrachypodium stacei
Authors: Mu Wenjie , Li Kexin , Yang Yongzhi , Breiman Adina , Yang Jiao , Wu Ying , Wu Shuang , Zhu Mingjia , Liu Jianquan , Nevo Eviatar , Catalan Pilar 
Published: June 2023

AbstractEcological divergence without geographic isolation, as an early speciation process that may lead finally to reproductive isolation through natural selection, remains one of the most interesting issues in evolutionary biology. However, the patterns of the underlying genetic divergences across the genome vary between different groups. Here we report thatBrachypodium stacei, an inbreeding grass species, has been involved in sympatric ecological divergence without geographic isolation. Genomic, transcriptomic, and metabolomic analyses suggest that diploidB. staceidiverged sympatrically in two slopes with contrasting biomes at Evolution Canyon I (ECI), Mount Carmel, Israel, where gene flow has continued freely but reduced with the time. This ecological divergence involved the scattered divergence of many unlinked loci across the total genome that include both coding and non-coding regions. We also identified significantly differential expressions of ABA signaling pathway genes, and contrasting metabolome composition between the arid-vsforest-adaptedB. staceiECI populations. These results suggest that many small loci involved in environmental responses act additively to account for the ecological usages of this species in contrasted environments with gene flow.SignificanceEcological divergence provides evidence for the origin of species through natural selection that has governed evolutionists’ attention since Darwin. In this study, we present multiple-omics analyses of two plant populations growing sympatrically in contrasted environments and revealed their distinct differentiation across all examined data. These two populations share the most recent ancestor compared with other populations and their divergence started in the early Holocene. We revealed that gene flow had continued but with a progressive reduction over time. The genetic divergences are scattered across the total genome involving many unlinked coding and non-coding regions. These findings highlight the significance of natural selection in the ecological divergence that may finally lead to species formation without geographic isolation.
Estimating individuals’ exposure to predation risk in group-living baboons,Papio anubis
Authors: Suire Alexandre , Kunita Itsuki , Harel Roi , Crofoot Margaret , Mutinda Mathew , Kamau Maureen , Hassel James M. , Murray Suzan , Matsumoto-Oda Akiko 
Published: June 2023

AbstractIn environments with multiple predators, the vulnerabilities attached to the spatial positions of group-living prey are not uniform and depend on the hunting styles of the predators. Coursing predators, mainly canids and hyenas, follow their prey over long distances and attack open areas, making individuals at the edge of the group more dangerous than those at the center (marginal predation). In contrast, ambush predators, mainly cats, approach their prey undetected and appear randomly anywhere in the group; therefore, isolated individuals are at a greater risk of predation. However, identifying individuals at high risk of predation requires the simultaneous recording of predator locations and direct observation of predation events, which are both difficult. Therefore, several theoretical methods have been proposed to assess predation risk (predation risk proxies). In a group of wild anubis baboons exposed to predation by leopards, lions, and hyenas, we calculated predation risk proxies using movement data collected from global positioning system (GPS) collars and found that adult males were on the edge of the group with a higher risk of predation (Hypothesis 1). In addition, adult males were more isolated within this group (Hypothesis 2). None of the predation risks differed among the other age-sex classes. The most dominant male was expected to be in the safety center of the group (Hypothesis 3) but was isolated on the periphery, like the other males. Therefore, we discussed why adult males were more peripheral and isolated.
Modeling the 3D structure and conformational dynamics of very large RNAs using coarse-grained molecular simulations
Authors: Henderson Aaron N. , McDonnell Robert T. , Elcock Adrian H. 
Published: June 2023

AbstractWe describe a computational approach to building and simulating realistic 3D models of very large RNA molecules (>1000 nucleotides) at a resolution of one “bead” per nucleotide. The method starts with a predicted secondary structure and uses several stages of energy minimization and Brownian dynamics (BD) simulation to build 3D models. A key step in the protocol is the temporary addition of a 4thspatial dimension that allows all predicted helical elements to become disentangled from each other in an effectively automated way. We then use the resulting 3D models as input to Brownian dynamics simulations that include hydrodynamic interactions (HIs) that allow the diffusive properties of the RNA to be modelled as well as enabling its conformational dynamics to be simulated. To validate the dynamics part of the method, we first show that when applied to small RNAs with known 3D structures the BD-HI simulation models accurately reproduce their experimental hydrodynamic radii (Rh). We then apply the modelling and simulation protocol to a variety of RNAs for which experimental Rh values have been reported ranging in size from 85 to 3569 nucleotides. We show that the 3D models, when used in BD-HI simulations, produce hydrodynamic radii that are usually in good agreement with experimental estimates for RNAs that do not contain tertiary contacts that persist even under very low salt conditions. Finally, we show that sampling of the conformational dynamics of large RNAs on timescales of 100 µs is computationally feasible with BD-HI simulations.
Sex-specific mechanisms of cerebral microvascular BKCadysfunction in a mouse model of Alzheimer’s disease
Authors: Silva Josiane F. , Polk Felipe D. , Martin Paige E. , Thai Stephenie H. , Savu Andrea , Gonzales Matthew , Kath Allison M. , Gee Michael T. , Pires Paulo W. 
Published: June 2023

AbstractBackgroundCerebral microvascular dysfunction and nitro-oxidative stress are present in patients with Alzheimer’s disease (AD) and may contribute to disease progression and severity. Large conductance Ca2+-activated K+channels (BKCa) play an essential role in vasodilatory responses and maintenance of myogenic tone in resistance arteries. BKCaimpairment can lead to microvascular dysfunction and hemodynamic deficits in the brain. We hypothesized that reduced BKCafunction in cerebral arteries mediates microvascular and neurovascular responses in the5x-FADmodel of AD.MethodsBKCaactivity in the cerebral microcirculation was assessed by patch clamp electrophysiology and pressure myography, in situ Ca2+sparks by spinning disk confocal microscopy, hemodynamics by laser speckle contrast imaging. Molecular and biochemical analyses were conducted by affinity-purification assays, qPCR, Western blots and immunofluorescence.ResultsWe observed that pial arteries from 5-6 months-old male and female5x-FADmice exhibited a hyper-contractile phenotype than wild-type (WT) littermates, which was linked to lower vascular BKCaactivity and reduced open probability. In males, BKCadysfunction is likely a consequence of an observed lower expression of the pore-forming subunit BKαand blunted frequency of Ca2+sparks, which are required for BKCaactivity. However, in females, impaired BKCafunction is, in part, a consequence of reversible nitro-oxidative changes in the BKαsubunit, which reduces its open probability and regulation of vascular tone. We further show that BKCafunction is involved in neurovascular coupling in mice, and its dysfunction is linked to neurovascular dysfunction in the model.ConclusionThese data highlight the central role played by BKCain cerebral microvascular and neurovascular regulation, as well as sex-dependent mechanisms underlying its dysfunction in a mouse model of AD.
The full spectrum of OCT1 (SLC22A1) mutations bridges transporter biophysics to drug pharmacogenomics
Authors: Yee Sook Wah , Macdonald Christian , Mitrovic Darko , Zhou Xujia , Koleske Megan L. , Yang Jia , Silva Dina Buitrago , Grimes Patrick Rockefeller , Trinidad Donovan , More Swati S. , Kachuri Linda , Witte John S. , Delemotte Lucie , Giacomini Kathleen M. , Coyote-Maestas Willow 
Published: June 2023

AbstractMembrane transporters play a fundamental role in the tissue distribution of endogenous compounds and xenobiotics and are major determinants of efficacy and side effects profiles. Polymorphisms within these drug transporters result in inter-individual variation in drug response, with some patients not responding to the recommended dosage of drug whereas others experience catastrophic side effects. For example, variants within the major hepatic Human organic cation transporter OCT1 (SLC22A1) can change endogenous organic cations and many prescription drug levels. To understand how variants mechanistically impact drug uptake, we systematically study how all known and possible single missense and single amino acid deletion variants impact expression and substrate uptake of OCT1. We find that human variants primarily disrupt function via folding rather than substrate uptake. Our study revealed that the major determinants of folding reside in the first 300 amino acids, including the first 6 transmembrane domains and the extracellular domain (ECD) with a stabilizing and highly conserved stabilizing helical motif making key interactions between the ECD and transmembrane domains. Using the functional data combined with computational approaches, we determine and validate a structure-function model of OCT1s conformational ensemble without experimental structures. Using this model and molecular dynamic simulations of key mutants, we determine biophysical mechanisms for how specific human variants alter transport phenotypes. We identify differences in frequencies of reduced function alleles across populations with East Asians vs European populations having the lowest and highest frequency of reduced function variants, respectively. Mining human population databases reveals that reduced function alleles of OCT1 identified in this study associate significantly with high LDL cholesterol levels. Our general approach broadly applied could transform the landscape of precision medicine by producing a mechanistic basis for understanding the effects of human mutations on disease and drug response.
Boundary Bypass Activity in theAbdominal-BRegion of theDrosophilaBithorax Complex is Position Dependent and Regulated
Authors: Kyrchanova Olga , Ibragimov Airat , Postika Nikolay , Georgiev Pavel , Schedl Paul 
Published: June 2023

ABSTRACTExpression ofAbdominal-B(Abd-B) in abdominal segments A5–A8 is controlled by four regulatory domains,iab-5 – iab-8. Each domain has an initiator element (which sets the activity state), elements that maintain this state and tissue-specific enhancers. To ensure their functional autonomy, each domain is bracketed by boundary elements (Mcp,Fab-7,Fab-7andFab-8). In addition to blocking crosstalk between adjacent regulatory domains, theFabboundaries must also have bypass activity so the relevant regulatory domains can “jump over” intervening boundaries and activate theAbd-Bpromoter. In the studies reported here we have investigated the parameters governing bypass activity. We find that the bypass elements in theFab-7andFab-8boundaries must be located in the regulatory domain that is responsible for drivingAbd-Bexpression. We suggest that bypass activity may also be subject to regulation.Summary StatementBoundaries separatingAbd-Bregulatory domains block crosstalk between domains and mediate their interactions withAbd-B. The latter function is location but not orientation dependent.
Benefits and limits of biological nitrification inhibitors for plant N uptake and the environment
Authors: Kuppe Christian W. , Postma Johannes A. 
Published: June 2023

ABSTRACTDoes root-exudation of biological nitrification inhibitors (BNIs) facilitate nitrogen (N) uptake and reduce pollution by N loss to the environment? We modeled the spatial-temporal dynamics of nitrifiers, ammonium, nitrate, and BNIs around a root and simulated root N uptake and net rhizosphere N loss over the plant’s life cycle. We determined the sensitivity of N uptake and loss to variation in the parameters, testing a broad range of soil-plant-microbial conditions.An increase in BNI exudation reduces net N loss and, under most conditions, plant N uptake. BNIs decrease uptake in the case of (1) low ammonium concentrations, (2) high ammonium adsorption to the soil, (3) rapid nitrate-or slow ammonium uptake by the plant, and (4) a slowly growing or fast-declining nitrifier population.Bactericidal inhibitors facilitate uptake more than bacteriostatic ones. Some nitrification, however, is necessary to maximize uptake by both ammonium and nitrate transporter systems. Selection for increased BNI exudation should co-select for improved ammonium uptake. BNIs can reduce N uptake, which may explain why not all species exude BNIs but have a generally positive effect on the environment by increasing rhizosphere N retention.
Long-term cytotoxic NK cells with broad anti-tumour capacity proliferate selectively, without exhaustion, after BCG priming and extremely low doses of cytokines
Authors: Felgueres María-José , Esteso Gloria , García-Jiménez Álvaro F. , Dopazo Ana , Martínez-Piñeiro Luis , Reyburn Hugh T. , Valés-Gómez Mar 
Published: June 2023

AbstractBackground:Natural killer (NK) cell-based immunotherapies, currently under investigation, appear to be safe, efficient treatments in patients with haematological tumours. Nevertheless, the short-lived nature of these cells combined with the need to infuse large number of cells for efficient tumour elimination represent important challenges for the development of NK cell-based therapies. Although NK cell anti-tumour activity is regulated by cytokines, constant stimulation together with the immunosuppressive tumour environment can result in NK cell exhaustion. Therefore, improved approaches to produce highly cytotoxic and longer-lived NK cells are of considerable clinical interest.Methods:Peripheral blood mononuclear cells (PBMC) are primedin vitrowith a pulse of eitherBacillus Calmette-Guérin(BCG) vaccine or a cell wall extract ofM. bovis, followed by weekly stimulations with low doses of IL12, 15 and 21. The phenotype and anti-tumour fitness of the activated NK cell culture were examined using scRNA-seq, flow cytometry and functional assays, including degranulation, specific cytotoxicity and IFNγ release.Results:we describe a novel strategy for the generation of long-lived activated NK cells capable of killing a broad range of solid tumours. A unique subset of cytotoxic NK cells (CD56highCD16+NKG2A+) specifically proliferatedin vitro, and was further expanded without functional exhaustion under minimal survival cytokine combinations. Mycobacterial cell-wall fractions also activated NK cells that recognised tumours efficiently, and proliferated well, and this approach has the advantage that no live bacteria are present in the cultures.Conclusions:We propose that BCG-priming to expand anti-tumour NK cells, without cell sorting, could be a scalable and economical basis for the development of safe and universal cellular immunotherapies against solid tumours.Key messagesAdoptive therapy with sorted NK cells grown in IL12, 15, 18 are being tested in clinical trials, but are only efficient for haematological tumours. In addition, their survivalin vivois limited. Here, we define culture conditions that drive the selective proliferation of long-lived natural killer (NK) cells, without the need of cell sorting, in minimal doses of cytokines, after priming with BCG or mycobacteria components. BCG-primed NK cells grow and maintain effective cytotoxic function against a variety of solid tumoursin vitro, without exhaustion for at least 28 days of culture. This new approach provides the basis for the generation of innate adoptive cell therapy tools.
Vγ9+Vδ2+Tcell-mediated purging ofListeria monocytogenes-infected epithelial cells requires butyrophilin 3A genes
Authors: Fischer Katrin , Bradlerova Michaela , Decker Thomas , Supper Verena 
Published: June 2023

AbstractIntracellular bacteria produce antigens, which serve as potent activators of γδ T cells. Phosphoantigens are presented via a complex of Butyrophilins (BTN) to signal infection to human Vγ9+Vδ2+ T cells. Here, we established an in vitro system allowing for studies of Vγ9+Vδ2+ T cell activity in coculture with epithelial cells infected with the intracellular bacterial pathogenListeria monocytogenes. We report that the Vγ9+Vδ2+ T cells efficiently purge such cultures from infected cells. This effector function requires the expression of members of the BTN3A family on epithelial cells. Specifically, the BTN3A1 and BTN3A3 are redundant in their ability to present antigen to Vγ9+Vδ2+ T cells. Since BTN3A1 is the only BTN3A associated with phosphoantigen presentation our study suggests that BTN3A3 may present different classes of antigens to mediate Vγ9+Vδ2+ T cell effector function against L. monocytogenes-infected epithelia.