bluuebunny/crossref_metadata_2025 huggingface dataset:
Eelgrass (Zosteraspp.) associated phytomyxids are host-specific congeneric parasites and predominant eukaryotes in the eelgrass rhizosphere on a global scale
Authors: Kolátková Viktorie , Mooney Megan , Kelly Kate , Hineva Elitsa , Gawryluk Ryan M. R. , Elliott Joel
Published: March 2023

Together with increasing environmental and anthropogenic pressures, pathogenic diseases are one of important factors contributing to the ongoing decline of seagrass meadows worldwide; yet the diversity and ecology of the microorganisms acknowledged as seagrass parasites remain critically understudied. Here we investigate phytomyxid parasites (Rhizaria: Endomyxa: Phytomyxea) of three different eelgrass (Zosteraspp.) species found in the Northern hemisphere. We present molecular evidence thatPlasmodiophora bicaudata, a long-recognized parasite of dwarf eelgrass taxa, is closely related to the novel phytomyxid recently discovered in root hairs ofZostera marina, and together they form a distinct clade within the order Phagomyxida, proposed here asFeldmanniellagen. nov. A full life cycle is systematically described in a phagomyxid representative for the first time, proving its conformity with the generalized phytomyxid life history, despite previous uncertainties. The presence of primary infection stages in nearly all collected eelgrass specimens, and subsequent analysis of amplicon sequences from a globalZ. marinadataset, reveal phytomyxids to be ubiquitous and one of the predominant microeukaryotes associated with eelgrass roots on a global scale. Our discoveries challenge the current view of Phytomyxea as rare entities in seagrass meadows and suggest their generally low pathogenicity in natural ecosystems.

Originality-Significance Statement

This study addresses a group of microbial parasites critically understudied in the marine environment. It presents complex evidence that Phytomyxea - obligate intracellular biotrophs previously considered to be rare entities in the oceans, are in fact ubiquitous endobionts of seagrasses of the genusZostera– foundation species and important primary producers in coastal areas worldwide. Our work represents a significant contribution to the fields of aquatic microbiology and seagrass ecology and is seminal to understanding the biology of Phytomyxea outside of terrestrial ecosystems.
Structural characterization of stem cell factors Oct4, Sox2, Nanog and Esrrb disordered domains, and a method to identify their phospho-dependent binding partners
Authors: Chafiaa Bouguechtouli , Ghouil Rania , Alik Ania , Florent Dingli , Damarys Loew , Francois-Xavier Theillet
Published: March 2023

The combined expression of a handful of pluripotency transcription factors (PluriTFs) in somatic cells can generate induced pluripotent stem cells (iPSCs). Here, we report the structural characterization of disordered regions contained in four important PluriTFs, namely Oct4, Sox2, Nanog and Esrrb. Moreover, many post-translational modifications (PTMs) have been detected on PluriTFs, whose roles are not yet characterized. To help in their study, we also present a method i) to produce well-characterized phosphorylation states of PluriTFs, using NMR analysis, and ii) to use them for pull-downs in stem cell extracts analyzed by quantitative proteomics to identify of Sox2 binders.
Vaccine induction of CD4-mimicking broadly neutralizing antibody precursors in macaques
Authors: Saunders Kevin O. , Counts James , Stalls Victoria , Edwards Robert , Manne Kartik , Lu Xiaozhi , Thakur Bhishem , Mansouri Katayoun , Chen Yue , Parks Rob , Barr Maggie , Sutherland Laura , Bal Joena , Havill Nicholas , Chen Haiyan , Machiele Emily , Jamieson Nolan , Hora Bhavna , Kopp Megan , Janowska Katarzyna , Anasti Kara , Jiang Chuancang , Venkatayogi Sravani , Eaton Amanda , Henderson Rory , Barbosa Christopher , Alam S. Munir , Santra Sampa , Weissman Drew , Moody M. Anthony , Cain Derek W. , Tam Ying , Lewis Mark , Williams Wilton B. , Wiehe Kevin , Montefiori David , Acharya Priyamvada , Haynes Barton F.
Published: March 2023

The CD4 binding site (CD4bs) is a conserved epitope on HIV-1 envelope (Env) that can be targeted by protective broadly neutralizing antibodies (bnAbs). HIV-1 vaccines have not elicited CD4bs bnAbs for many reasons, including the CD4bs is occluded by glycans, immunogen expansion of appropriate naïve B cells, and selection of functional antibody mutations. Here, we demonstrate immunization of macaques with a CD4bs-targeting immunogen elicits neutralizing bnAb precursors with structural and genetic features of CD4-mimicking bnAbs. Structures of the CD4bs nAbs bound to HIV-1 Env demonstrated binding angles similar to human bnAbs and heavy chain second complementarity determining region-dependent binding characteristic of all known human CD4-mimicking bnAbs. Macaque nAbs were derived from variable and joining gene segments orthologous to the genes of human VH1-46-class bnAbs. This vaccine study initiated the B cells from which derive CD4bs bnAbs in primates, accomplishing the key first step in development of an effective HIV-1 vaccine.
Nanopore sequencing of antibiotic-resistantKlebsiella pneumoniaeJRCGR1 isolate from Pakistan and country scale pan-genomics
Authors: Basharat Zarrin , Nisa Zaib un , Irfan Muhammad , Khan Rao Muhammad Abid , Karim Asad , Aurongzeb Muhammad , Hassan Syed Shah
Published: March 2023

Klebsiella pneumoniaeis a gram-negative, encapsulated, non-motile bacterium that can cause damage to human lungs. Antibiotic resistance of this strain requires constant monitoring and for this purpose, Oxford nanopore mediated whole genome sequencing was done for a strain acquired from the pleural fluid of a diabetic patient suffering from chronic kidney disease. A genome of 5.98 MB was obtained, with 8,869 CDSs and 110 RNAs. Around 96 proteins were seen as involved in virulence, disease or defense, while 25 antibiotic resistance genes were identified. Pan-genome was inferred as open, with 12,857 and 1,303 CDSs forming respective accessory and core genome of antibiotic resistant Pakistani strains (n=168) of this species. Apart from notable antimicrobial resistance genes like beta-lactamases, a gene conferring resistance to colistin was also mined. To the best of our knowledge, this is first report of nanopore mediated long read sequencing of a hypermucoviscous virulentK. pneumoniaefrom Pakistan.
Oceanographic drivers of legal-sized male Dungeness crab in the California Current System
Authors: Bani Ridouan , Punt André E. , Holland Daniel S. , Tolimieri Nick , Richerson Kate , Haltuch Melissa A. , Mantua Nathan J. , Oken Kiva L.
Published: March 2023

We investigate environmental drivers of pre-season abundance of US West Coast legal-sized male Dungeness crab (Cancer magister), with the goal of developing an environmental index that can be used to forecast crab abundance in advance of the fishery. A conceptual life history approach is used to generate life-stage-specific and spatio-temporally-specific mechanistic hypotheses regarding oceanographic variables that influence survival at each life stage. Linear models are fit using the logarithms of pre-season abundance estimates of the coastal population of legal-sized male Dungeness crab as the dependent variable and environmental drivers from outputs developed using a regional oceanographic model for the California Current System as the independent environmental variables. Using different model selection methods, we show that the so-called ‘best’ models differ substantially among model selection approaches, illustrating the need to carefully choose performance metrics for model selection. Since our goal was to forecast crab abundance, we selected the ‘best’ model using a cross-validation metric that accounts for the time-series nature of the data. The resulting ‘best’ models suggest that the mechanisms that drive preseason abundance differ among regions widely recognized for spatially and seasonally varying dominant physical processes. We found that the processes determining pre-season abundance of legal-sized male Dungeness crab could be identified with sufficient precision to enable a predictive skill, suggesting that the predictions may be useful for management purposes. Moreover, we found that transport (within and between regions), as well as temperature were likely drivers of pre-season abundance, highlighting that future studies should focus on multiple processes.
Validation of a multiplex microsphere immunoassay for detection ofTrypanosoma cruziantibodies in dogs
Authors: Rodriguez Carlos A. , Busselman Rachel E. , Shen Huifeng , Saunders Ashley B. , Tarleton Rick , Hamer Sarah A.
Published: March 2023

The vector-borne protozoan parasiteTrypanosoma cruzicauses Chagas disease in humans, dogs, and many other mammalian hosts. Canine Chagas disease is increasingly diagnosed in dogs of the southern US where triatomine insect vectors occur, and there are limited veterinary diagnostic options; currently, only the indirect fluorescent antibody (IFA) test is offered at a single accredited diagnostic laboratory. This study evaluated a multiplex microsphere immunoassay (MIA) for detecting antibodies againstT. cruziin dogs and compared with existing serological methods to establish cut-off values and relative sensitivity/specificity. Dog sera (n=135) which were previously characterized using the IFA and off-label use of two commercial rapid assays were tested on the multiplex MIA against 12 different antigens: nineT. cruziantigens, a negative control recombinant protein (green fluorescent protein), aLeishmaniaantigen, and a canine parvovirus antigen (used as an antibody control given near-ubiquitous parvovirus vaccination). For each sample, the ratio of median fluorescence intensity (MFI) for eachT. cruziantigen to that of GFP was calculated. Samples with an antigen/GFP ratio greater than 4 standard deviations above the mean of 25 known negative sera were considered positive on that antigen. Samples testing positive on 2 or more antigens were considered positive forT. cruziantibodies. Compared to the IFA, the multiplex MIA demonstrated a relative sensitivity of 100% and specificity of 96.97%. Given its precision, high-throughput format, potential for automation, and lack of subjective interpretation, the multiplex MIA should be considered a valid and improved assay forT. cruziantibodies in dogs.
Predicting the feasibility of targeting a conserved region on the S2 domain of the SARS-CoV-2 spike protein
Authors: Garg Pranav , Hsueh Shawn C. C. , Plotkin Steven S.
Published: March 2023

The efficacy of vaccines against the SARS-CoV-2 virus significantly declines with the emergence of mutant strains, prompting investigation into the feasibility of targeting highly conserved but often cryptic regions on the S2 domain of spike protein. Using tools from molecular dynamics, we find that this conserved S2 epitope located in the central helices below the receptor binding domains is unlikely to be exposed by dynamic fluctuations without any external facilitating factors, in spite of previous computational evidence suggesting transient exposure of this region. Furthermore, glycans inhibit opening dynamics, and thus stabilize spike in addition to immunologically shielding the protein surface, again in contrast to previous computational findings. Though the S2 epitope region examined here is central to large scale conformational changes during viral entry, free energy landscape analysis obtained using the path coordinate formalism reveals no inherent “loaded spring” effect, suggesting that a vaccine immunogen would tend to present the epitope in a pre-fusion-like conformation and may be effective in neutralization. These findings contribute to a deeper understanding of the dynamic origins of the function of the spike protein, as well as further characterizing the feasibility of the S2 epitope as a therapeutic target.
Opportunities to sustain a multi-country quality of care network: lessons on the actions of four countries Bangladesh, Ethiopia, Malawi, and Uganda
Authors: Lemma Seblewengel , Daniels-Howell Callie , Tufa Asebe Amenu , Sarker Mithun , Akter Kohenour , Nakidde Catherine , Seruwagi Gloria , Dube Albert , Mwandira Kondwani ,   The QCN Evaluation group, Taye Desalegn Bekele , English Mike , Shawar Yusra Ribhi , Mwaba Kasonde , Djellouli Nehla , Colbourn Tim , Marchant Tanya
Published: March 2023

The Quality of Care Network (QCN) is a global initiative that was established in 2017 under the leadership of WHO in 11 low-and-middle income countries to improve maternal, newborn, and child health. The vision was that the Quality of Care Network would be embedded within member countries and continued beyond the initial implementation period: that the Network would be sustained. This paper investigated the experience of actions taken to sustain QCN in four Network countries (Bangladesh, Ethiopia, Malawi, and Uganda) and reports on lessons learned. Multiple iterative rounds of data collection were conducted through qualitative interviews with global and national stakeholders, and non-participatory observation of health facilities and meetings. A total of 241 interviews, 42 facility and four meeting observations were carried out. We conducted a thematic analysis of all data using a framework approach that defined six critical actions that can be taken to promote sustainability. The analysis revealed that these critical actions were present with varying degrees in each of the four countries. Although vulnerabilities were observed, there was good evidence to support that actions were taken to institutionalize the innovation within the health system, to motivate micro-level actors, plan opportunities for reflection and adaptation from the outset, and to support strong government ownership. Two actions were largely absent and weakened confidence in future sustainability: managing financial uncertainties and fostering community ownership.

Evidence from four countries suggested that the QCN model would not be sustained in its original format, largely because of financial vulnerability and insufficient time to embed the innovation at the sub-national level. But especially the efforts made to institutionalize the innovation in existing systems meant that some characteristics of QCN may be carried forward within broader government quality improvement initiatives.
A hybrid approach to scalable real-world data curation by machine learning and human experts
Authors: Waskom Michael L. , Tan Katherine , Wiberg Holly , Cohen Aaron B. , Wittmershaus Brett , Shapiro Will
Published: March 2023

Objective

Machine learning has the potential to increase the scale of real-world data curated from electronic health records, but maintaining a high standard of data quality is important to avoid biasing downstream analyses. To increase scale without compromising quality, we propose a hybrid data curation methodology that employs both manual abstraction by clinical experts and automated extraction by machine learning models.

Materials and Methods

Our methodology makes the determination about when to employ manual abstraction using a confidence score associated with each model output. We describe a process for selecting confidence thresholds based on simulations validated against a reference-standard labeled dataset. To establish the fitness of our methodology for retrospective research, we apply it to a multi-variable cohort selection task on a large real-world oncology database.

Results

Only small amounts of manual abstraction are required for hybrid curation to achieve expert-level error rates. In fact, the hybrid methodology can even reduce error rates relative to manual abstraction in some cases. We further demonstrate that demographic characteristics of a research cohort defined using hybrid variables are comparable to one curated with conventional methods.

Discussion

Our methodology is general and makes few assumptions about the clinical variable or machine learning model. A key requirement is the availability of reference standard labels for calibrating the tradeoff between abstraction effort and data quality.

Conclusion

Incorporating machine learning into real-world data curation using hybrid methodology holds the promise to scale practicable cohort sizes while maintaining data fitness for research purposes.
Systemic inflammation and subsequent risk of amyotrophic lateral sclerosis: prospective cohort study
Authors: Batty G. David , Kivimäki Mika , Frank Philipp , Gale Catharine R. , Wright Liam
Published: March 2023

Importance

While systemic inflammation has been implicated in the aetiology of selected neurodegenerative disorders, its role in the development of amyotrophic lateral sclerosis (ALS) is untested.

Objective

To quantify the relationship of C-reactive protein (CRP), an acute-phase reactant and marker of systemic inflammation, with ALS occurrence.

Design, Setting, Participants

UK Biobank, a prospective cohort study of 502,649 participants who were aged 37 to 73 years when examined at research centres between 2006 and 2010.

Exposure

Venous blood was collected at baseline in the full cohort and assayed for CRP. Repeat measurement was made 3-7 years later in a representative subgroup (N=14,514) enabling correction for regression dilution.

Main Outcome(s) and Measure(s)

ALS as ascertained via national hospitalisation and mortality registries. We computed multi-variable hazard ratios with accompanying 95% confidence intervals for log-transformed CRP expressed as standard deviation and tertiles.

Results

In an analytical sample of 400,884 individuals (218,203 women), a mean follow-up of 12 years gave rise to 231 hospitalisations and 223 deaths ascribed to ALS. After adjustment for covariates which included health behaviours, comorbidity, and socio-economic status, a one standard deviation higher log-CRP was associated with elevated rates of both ALS mortality (hazard ratios; 95% confidence intervals: 1.32; 1.13, 1.53) and hospitalisations (1.20; 1.00, 1.39). There was evidence of dose-response effects across tertiles of CRP for both outcomes (p for trend≤0.05). Correction for regression dilution led to a strengthening of the relationship with CRP for both mortality (1.62; 1.27, 2.08) and hospitalisations (1.37; 1.05, 1.76) ascribed to ALS.

Conclusions and Relevance

Higher levels of CRP, a blood-based biomarker widely captured in clinical practice, were associated with a higher subsequent risk of ALS.

Key Points

Question

Is C-reactive protein (CRP), a marker of systemic inflammation widely used in clinical practice, associated with later risk of amyotrophic lateral sclerosis (ALS)?

Findings

Following 11 years disease surveillance in 400,884 individuals (218,203 women), after adjustment for covariates and correction for regression dilution, a one standard deviation higher CRP levels were associations with both mortality (hazard ratio; 95% confidence interval: 1.62; 1.27, 2.08) and hospitalisations (1.37; 1.05, 1.76) ascribed to ALS.

Meaning

In the present study, CRP has a dose-response relationship with the risk of later ALS.
An Explainable Host Genetic Severity Predictor Model for COVID-19 Patients
Authors: Onoja Anthony , Raimondi Francesco , Nanni Mirco
Published: March 2023

Understanding the COVID-19 severity and why it differs significantly among patients is a thing of concern to the scientific community. The major contribution of this study arises from the use of a voting ensemble host genetic severity predictor (HGSP) model we developed by combining several state-of-the-art machine learning algorithms (decision tree-based models: Random Forest and XGBoost classifiers). These models were trained using a genetic Whole Exome Sequencing (WES) dataset and clinical covariates (age and gender) formulated from a 5-fold stratified cross-validation computational strategy to randomly split the dataset to overcome model instability. Our study validated the HGSP model based on the 18 features (i.e., 16 identified candidate genetic variants and 2 covariates) identified from a prior study. We provided post-hoc model explanations through the ExplainerDashboard - an open-source python library framework, allowing for deeper insight into the prediction results. We applied the Enrichr and OpenTarget genetics bioinformatic interactive tools to associate the genetic variants for plausible biological insights, and domain interpretations such as pathways, ontologies, and disease/drugs. Through an unsupervised clustering of the SHAP feature importance values, we visualized the complex genetic mechanisms. Our findings show that while age and gender mainly influence COVID-19 severity, a specific group of patients experiences severity due to complex genetic interactions.
Quantitative analysis of insecticides in long-lasting insecticidal nets using liquid chromatography mass spectrometry (LC-MS) and X-ray fluorescence (XRF) spectroscopy
Authors: Koinari Melanie , Bubun Nakei , Wilson David , Anetul Evodia , Timinao Lincoln , Johnson Petrina , Daly Norelle , Laman Moses , Freeman Tim , Karl Stephan
Published: March 2023

Background

Long lasting insecticidal nets (LLIN) are a key vector control tool used for the prevention of malaria. Active ingredient (AI) measurements in LLIN are essential for evaluating their quality and effectiveness. The main aim of the present study was to determine the utility of X-ray fluorescence (XRF) spectroscopy as a suitable in-field tool for total AI quantification in LLINs.

Methods

New and unused LLIN samples containing deltamethrin (PermaNet® 2.0, n = 35) and alpha-cypermethrin (SafeNet®, n = 43) were obtained from batches delivered to PNG for mass distribution. Insecticides were extracted from the LLINs using a simple extraction technique and quantified using liquid chromatography mass spectrometry (LC-MS). The LC-MS results were correlated with in-field XRF spectroscopy measurements on the same nets. Operators were blinded towards the identity of the nets. Bioefficacy of the LLIN samples was tested using WHO cone bioassays and test results were correlated with total AI content.

Results

The results indicate a close agreement between the quantitative XRF and LC-MS. Interestingly, the total AI content was negatively correlated with bioefficacy in PermaNet® 2.0 (especially, in recently manufactured nets). In contrast, AI content was positively correlated with bioefficacy in SafeNet®. These results indicate that the chemical content analysis in predelivery inspections does not always predict bioefficacy well.

Conclusion

XRF is a promising in-field method for quantification of both deltamethrin and alpha-cypermethrin coated LLINs. Since total AI content is not always a predictor of the efficacy of LLINs to kill mosquitoes, bioefficacy measurements should be included in predelivery inspections.
Genome wide association study based on clustering by obesity-related variables shed light on a genetic architecture of obesity in Japanese and UK population
Authors: Takahashi Ippei , Ohseto Hisashi , Ueno Fumihiko , Onuma Tomomi , Narita Akira , Obara Taku , Ishikuro Mami , Murakami Keiko , Noda Aoi , Hozawa Atsushi , Sugawara Junichi , Tamiya Gen , Kuriyama Shinichi
Published: March 2023

Background

Many loci associated with obesity have been reported in previous genome-wide association studies (GWASs). However, it remains unclear whether variants at all these loci contributed to onset of obesity or whether one or a few variants cause obesity when obesity is a genetically heterogeneous population.

Objective

To investigate the genetic architecture of obesity by clustering a population with obesity into clusters using obesity-related factors.

Methods

This study was based on the Tohoku Medical Megabank Project Birth and Three-Generation Cohort Study and the Community-Based Cohort Study. As the Step-1, a GWAS with body mass index (BMI) as an outcome was performed for all 48,365 eligible participants. As the Step-2, we then assigned the 13,067/48,365 participants with obesity (BMI ≥ 25 kg/m2) using the k-prototype to 5 clusters. Obesity-related factors (such as age, nutrient intake, physical activity, sleep duration, difference between weight at age 20 and current weight, smoking, alcohol drinking, psychological distress, and birth weight) were used for clustering. Subsequently, participants in each cluster and those with a BMI < 25 kg/m2were combined, and GWASs were performed according to the 5 clusters. Additionally, a sub-analysis using data from the UK Biobank was conducted to compare the results.

Results

The Step-1 detected 18 genes, most of which were reportedly associated with obesity or obesity-related topics in previous studies. The result of Step-2, of the 18 genes detected in Step-1,LINC01741, CRYZL2P-SEC16B, andSEC16Bwere significantly related to Cluster 2,FTO, PMAIP1, andMC4Rto Cluster 3, andBDNF, BDNF-AS, LINC00678, andKIF18Ato Clusters 4 and 5. In the sub-analysis, a similar phenomenon was observed in which separate obesity-related genes were detected for each cluster.

Conclusions

Our data support the notion that a decreased sample size with increased homogeneity may reveal insights into the genetic architecture of obesity.
Grey and white matter metrics demonstrate distinct and complementary prediction of differences in cognitive performance in children: Findings from ABCD (N= 11 876)
Authors: Michel Lea C. , McCormick Ethan M. , Kievit Rogier A.
Published: March 2023

Individual differences in cognitive performance in childhood are a key predictor of significant life outcomes such as educational attainment and mental health. Differences in cognitive ability are governed in part by variations in brain structure. However, studies commonly focus on either grey or white matter metrics in humans, leaving open the key question as to whether grey or white matter microstructure play distinct or complementary roles supporting cognitive performance.

To compare the role of grey and white matter in supporting cognitive performance, we used regularized structural equation models to predict cognitive performance with grey and white matter measures. Specifically, we compared how grey matter (volume, cortical thickness and surface area) and white matter measures (volume, fractional anisotropy and mean diffusivity) predicted individual differences in cognitive performance. The models were tested in 11,876 children (ABCD Study, 5680 female; 6196 male) at 10 years old.

We found that grey and white matter metrics bring partly non-overlapping information to predict cognitive performance. The models with only grey or white matter explained respectively 15.4% and 12.4% of the variance in cognitive performance, while the combined model explained 19.0%. Zooming in we additionally found that different metrics within grey and white matter had different predictive power, and that the tracts/regions that were most predictive of cognitive performance differed across metric.

These results show that studies focusing on a single metric in either grey or white matter to study the link between brain structure and cognitive performance are missing a key part of the equation.

Significance Statement

This paper enriches the recent debates on the challenges of linking variation in brain structure to phenotypic differences (Marek et al., 2022). We demonstrate that using latent variables (to improve power), structural equation modelling (to allow greater flexibility in linking brain to behaviour), and by simultaneously incorporating multiple measures of grey and white matter in a large sample, we demonstrate relatively strong and robust brain-behaviour associations, which highlight the complementarity of grey and white matter metrics in predicting cognitive performance as well as the importance of incorporating the full complexity of these associations over 1-to-1 linkages. This finding should lead researchers to consider integrating both grey and white matter measures when demonstrating a more comprehensive picture of brain-cognition relationships.
Demographic Modeling of Admixed Latin American Populations from Whole Genomes
Authors: Medina-Muñoz Santiago G. , Ortega-Del Vecchyo Diego , Cruz-Hervert Luis Pablo , Ferreyra-Reyes Leticia , García-García Lourdes , Moreno-Estrada Andrés , Ragsdale Aaron P.
Published: March 2023

Demographic models of Latin American populations often fail to fully capture their complex evolutionary history, which has been shaped by both recent admixture and deeper-in-time demographic events. To address this gap, we used high-coverage whole genome data from Indigenous American ancestries in present-day Mexico and existing genomes from across Latin America to infer multiple demographic models that capture the impact of different timescales on genetic diversity. Our approach, which combines analyses of allele frequencies and ancestry tract length distributions, represents a significant improvement over current models in predicting patterns of genetic variation in admixed Latin American populations. We jointly modeled the contribution of European, African, East Asian, and Indigenous American ancestries into present-day Latin American populations to capture the historical demographic events that have shaped genetic variation. Our inferred demographic histories are consistent across different genomic regions and annotations, suggesting that our inferences are robust to the potential effects of linked selection. In conjunction with published distributions of fitness effects for new nonsynonymous mutations in humans, we show in large-scale simulations that our models recover important features of both neutral and deleterious variation. By providing a more realistic framework for understanding the evolutionary history of Latin American populations, our models can help address the historical under-representation of admixed groups in genomics research, and can be a valuable resource for future studies of populations with complex admixture and demographic histories.
Climate Change Factors Interactively Shift Peatland Functional Microbial Composition in a Whole-Ecosystem Warming Experiment
Authors: Kilner Christopher L. , Carrell Alyssa A. , Wieczynski Daniel J. , Votzke Samantha , DeWitt Katrina , Yammine Andrea , Shaw Jonathan , Pelletier Dale A. , Weston David J. , Gibert Jean P.
Published: March 2023

Microbes affect the global carbon cycle that influences climate change and are in turn influenced by environmental change. Here, we use data from a long-term whole-ecosystem warming experiment at a boreal peatland to answer how temperature and CO2jointly influence communities of abundant, diverse, yet poorly understood, non-fungi microbial Eukaryotes (protists). These microbes influence ecosystem function directly through photosynthesis and respiration, and indirectly, through predation on decomposers (bacteria, fungi). Using a combination of high-throughput fluid imaging and 18S amplicon sequencing, we report large climate-induced, community-wide shifts in the community functional composition of these microbes (size, shape, metabolism) that could alter overall function in peatlands. Importantly, we demonstrate a taxonomic convergence but a functional divergence in response to warming and elevated CO2with most environmental responses being contingent on organismal size: warming effects on functional composition are reversed by elevated CO2and amplified in larger microbes but not smaller ones. These findings show how the interactive effects of warming and rising CO2could alter the structure and function of peatland microbial food webs — a fragile ecosystem that stores 25% of terrestrial carbon and is increasingly threatened by human exploitation.
Chimeric and mutant CARD9 constructs enable analyses of conserved and diverged autoinhibition mechanisms in the CARD-CC protein family
Authors: Staal Jens , Driege Yasmine , Van Gaever Femke , Steels Jill , Beyaert Rudi
Published: March 2023

CARD9, -10, -11 and -14 all belong to the CARD-coiled coil (CC) protein family and originated from a single common ancestral protein early in vertebrate evolution. All four proteins form CARD-CC/BCL10/MALT1 (CBM) complexes leading to NF-κB activation after upstream phosphorylation by various protein kinase C (PKC) isoforms. CBM complex signaling is critical for innate and adaptive immunity, but aberrant activation can cause autoimmune or autoinflammatory diseases, or be oncogenic. CARD9 shows a superior auto-inhibition with very low spontaneous activity when overexpressed in HEK293T cells. In contrast, the poor auto-inhibition of other CARD-CC family proteins, especially CARD10 (CARMA3) and CARD14 (CARMA2), is hampering characterization of upstream activators or activating mutations in overexpression studies. We grafted different domains from CARD10, -11 and 14 on CARD9 to generate chimeric CARD9 backbones for functional characterization of activating mutants using NF-κB reporter gene activation in HEK293T cells as readout. CARD11 (CARMA1) activity was not further reduced by grafting on CARD9 backbones. The chimeric CARD9 approach was subsequently validated by using several known disease-associated mutations in CARD10 and CARD14, and additional screening allowed us to identify several novel activating natural variants in human CARD9 and CARD10. Using Genebass as a resource of exome-based disease association statistics, we found that activated alleles of CARD9 correlate with irritable bowel syndrome (IBS), constipation, osteoarthritis, fibromyalgia, insomnia, anxiety and depression, which can occur as comorbidities.
Computational modeling of reinforcement learning and functional neuroimaging of probabilistic reversal dissociates compulsive behaviors in Gambling and Cocaine Use Disorders
Authors: Zühlsdorff Katharina , Verdejo-Román Juan , Clark Luke , Albein-Urios Natalia , Soriano-Mas Carles , Cardinal Rudolf N. , Robbins Trevor W. , Dalley Jeffrey W. , Verdejo-García Antonio , Kanen Jonathan W.
Published: March 2023

Cognitive flexibility refers to the ability to adjust to changes in the environment and is essential for adaptive behavior. It can be investigated using laboratory tests such as probabilistic reversal learning (PRL). In individuals with both Cocaine Use Disorder (CUD) and Gambling Disorder (GD), overall impairments in PRL flexibility are observed. However, it is poorly understood whether this impairment depends on the same brain mechanisms in cocaine and gambling addictions. Reinforcement learning (RL) is the process by which rewarding or punishing feedback from the environment is used to adjust behavior, to maximise reward and minimise punishment. Using RL models, a deeper mechanistic explanation of the latent processes underlying cognitive flexibility can be gained. Here, we report results from a re-analysis of PRL data from control participants (n=18) and individuals with either GD (n=18) or CUD (n=20) using a hierarchical Bayesian RL approach. We observed significantly reduced ‘stimulus stickiness’ (i.e., stimulus-bound perseveration) in GD, which may reflect increased exploratory behavior that is insensitive to outcomes. RL parameters were unaffected in CUD. We relate the behavioral findings to their underlying neural substrates through an analysis of task-based fMRI data. We report differences in tracking reward and punishment expected values (EV) in individuals with GD compared to controls, with greater activity during reward EV tracking in the cingulate gyrus and amygdala. In CUD, we observed reduced responses to positive punishment prediction errors (PPE) and increased activity following negative PPEs in the superior frontal gyrus compared to controls. Thus, an RL framework serves to differentiate behavior in a probabilistic learning paradigm in two compulsive disorders, GD and CUD.
Pioneer factor Foxa2 mediates chromatin conformation changes in ligand-dependent activation of nuclear receptor FXR
Authors: Hao Yi , Han Lu , Wu Anqi , Bochkis Irina M.
Published: March 2023

ABSTACT

Activation of nuclear receptors, a family of ligand-dependent transcription factors, is used extensively in development of drug targets. We have previously shown that pioneer factor Foxa2 opens chromatin for binding of nuclear receptors FXR and LXRα during acute ligand activation. FXR is activated by bile acids and deletion of Foxa2 in the liver results in intrahepatic cholestasis. We hypothesized that Foxa2 also enables chromatin conformational changes during ligand activation. We performed Foxa2 HiChIP to assess Foxa2-dependent long-range interactions in mouse livers treated with either vehicle control or FXR agonist GW4064. HiChIP contact analysis shows that global chromatin interactions are dramatically increased during FXR activation. Ligand-treated livers exhibit extensive redistribution of topological associated domains (TAD and substantial increase in Foxa2-anchored loops, suggesting Foxa2 is involved in dynamic chromatin conformational changes. We demonstrate that chromatin conformation, including genome-wide interactions, TADs, intra-chromosomal and inter-chromosomal Foxa2-anchored loops, drastically changes upon addition of FXR agonist. Hence, we determine a novel role for Foxa2 in enabling these conformational changes, extending its function in bile acid metabolism.
Matrix and analysis metadata standards (MAMS) to facilitate harmonization and reproducibility of single-cell data
Authors: Wang Yichen , Sarfraz Irzam , Teh Wei Kheng , Sokolov Artem , Herb Brian R. , Creasy Heather H. , Virshup Isaac , Dries Ruben , Degatano Kylee , Mahurkar Anup , Schnell Daniel J. , Madrigal Pedro , Hilton Jason , Gehlenborg Nils , Tickle Timothy , Campbell Joshua D.
Published: March 2023

A large number of genomic and imaging datasets are being produced by consortia that seek to characterize healthy and disease tissues at single-cell resolution. While much effort has been devoted to capturing information related to biospecimen information and experimental procedures, the metadata standards that describe data matrices and the analysis workflows that produced them are relatively lacking. Detailed metadata schema related to data analysis are needed to facilitate sharing and interoperability across groups and to promote data provenance for reproducibility. To address this need, we developed the Matrix and Analysis Metadata Standards (MAMS) to serve as a resource for data coordinating centers and tool developers. We first curated several simple and complex use cases to characterize the types of feature-observation matrices (FOMs), annotations, and analysis metadata produced in different workflows. Based on these use cases, metadata fields were defined to describe the data contained within each matrix including those related to processing, modality, and subsets. Suggested terms were created for the majority of fields to aid in harmonization of metadata terms across groups. Additional provenance metadata fields were also defined to describe the software and workflows that produced each FOM. Finally, we developed a simple list-like schema that can be used to store MAMS information and implemented in multiple formats. Overall, MAMS can be used as a guide to harmonize analysis-related metadata which will ultimately facilitate integration of datasets across tools and consortia. MAMS specifications, use cases, and examples can be found at https://github.com/single-cell-mams/mams/.
DNA-PK and the TRF2 iDDR inhibit MRN-initiated resection at leading-end telomeres
Authors: Myler Logan R. , Toia Beatrice , Vaughan Cara K. , Takai Kaori , Matei Andreea M. , Wu Peng , Paull Tanya T. , de Lange Titia , Lottersberger Francisca
Published: March 2023

Telomeres replicated by leading-strand synthesis lack the 3’ overhang required for telomere protection. Surprisingly, resection of these blunt telomere is initiated by the telomere-specific 5’ exonuclease Apollo rather than the Mre11-Rad50-Nbs1 (MRN) complex, the nuclease that acts at DNA breaks. Without Apollo, leading-end telomeres undergo fusion, which, as demonstrated here, are mediated by alternative End Joining. Here, we show that DNA-PK and TRF2 coordinate the repression of MRN at blunt telomeres. DNA-PK represses an MRN-dependent long range resection at blunt telomeres, while the endonuclease activity of MRN/CtIP, which could cleave DNA-PK off of blunt telomere ends, is inhibitedin vitroandin vivoby the iDDR of TRF2. AlphaFold-Multimer predicts a conserved association of the iDDR with Rad50 potentially interfering with CtIP binding and MRN endonuclease activation. We propose that repression of MRN-mediated resection is a conserved aspect of telomere maintenance and represents an ancient feature of DNA-PK and the iDDR.
Symbiotic acacia ants drive nesting behavior by birds in an African savanna
Authors: Ema Lujan , Nielsen Ryen , Short Zoe , Wicks Samuel , Watetu Wilson Nderitu , Khasoha Leo M. , Palmer Todd M. , Goheen Jacob R. , Alston Jesse M.
Published: March 2023

Mutualisms between plants and ants are common features of tropical ecosystems around the globe and can have cascading effects on interactions with the ecological communities in which they occur. In an African savanna, we assessed whether acacia ants influence nest site selection by tree-nesting birds. Birds selected nest sites in trees inhabited by ant species that vigorously defend against browsing mammals. Future research could address the extent to which hatching and fledging rates depend on the species of ant symbiont, and why ants tolerate nesting birds but not other tree associates (especially insects).
Mitochondrial haplotype and mito-nuclear matching drive somatic mutation and selection throughout aging
Authors: Serrano Isabel M. , Hirose Misa , Valentine Charles C. , Roesner Sharon , Schmidt Elizabeth , Pratt Gabriel , Williams Lindsey , Salk Jesse , Ibrahim Saleh , Sudmant Peter H.
Published: March 2023

Mitochondrial genomes co-evolve with the nuclear genome over evolutionary timescales and are shaped by selection in the female germline. Here, we investigate how mismatching between nuclear and mitochondrial ancestry impacts the somatic evolution of the mt-genome in different tissues throughout aging. We used ultra-sensitive Duplex Sequencing to profile ∼2.5 million mt-genomes across five mitochondrial haplotypes and three tissues in young and aged mice, cataloging ∼1.2 million mitochondrial somatic and ultra low frequency inherited mutations, of which 81,097 are unique. We identify haplotype-specific mutational patterns and several mutational hotspots, including at the Light Strand Origin of Replication, which consistently exhibits the highest mutation frequency. We show that rodents exhibit a distinct mitochondrial somatic mutational spectrum compared to primates with a surfeit of reactive oxygen species-associated G>T/C>A mutations, and that somatic mutations in protein coding genes exhibit signatures of negative selection. Lastly, we identify an extensive enrichment in somatic reversion mutations that “re-align” mito-nuclear ancestry within an organism’s lifespan. Together, our findings demonstrate that mitochondrial genomes are a dynamically evolving subcellular population shaped by somatic mutation and selection throughout organismal lifetimes.
Unfolded Protein Response Factor ATF6 Augments T Helper Cell Responses and Promotes Mixed Granulocytic Airway Inflammation
Authors: Wu Dandan , Zhang Xing , Zimmerly Kourtney M. , Wang Ruoning , Wang Chunqing , Wu Xiang , Liu Meilian , Yang Xuexian O.
Published: March 2023

The unfolded protein response (UPR) is associated with the risk of asthma, including treatment- refractory severe asthma. Several recent studies demonstrated a pathogenic role of activating transcription factor 6α (ATF6α or ATF6), one of the essential arms of UPR, in airway structural cells. However, its role in T helper (TH) cells has not been well examined. In this study, we found that ATF6 was selectively induced by STAT6 and STAT3 in TH2 and TH17 cells, respectively. ATF6 upregulated UPR genes and promoted the differentiation and cytokine secretion of TH2 and TH17 cells. T cell-specificAtf6-deficiency impaired TH2 and TH17 responsesin vitroandin vivoand attenuated mixed granulocytic experimental asthma. ATF6 inhibitor Ceapin A7 suppressed ATF6 downstream gene expression and TH cell cytokine expression in both murine and human memory CD4+T cells. At the chronic stage of asthma, administration of Ceapin A7 lessened TH2 and TH17 responsesin vivo, leading to alleviation of both airway neutrophilia and eosinophilia. Thus, our results demonstrate a critical role of ATF6 in TH2 and TH17 cell-driven mixed granulocytic airway disease, suggesting a novel option to combat steroid-resistant mixed and even T2-low endotypes of asthma by targeting ATF6.
Evaluation of Antinociceptive and Anti-Inflammatory Activities of Solvent Fraction of the Roots ofEchinops keberichoMesfin (Asteraceae) In Mice Model
Authors: Tadesse Tesfaye Yimer , Dagnew Samuel Berihun , Yiblet Tesfagegn Gobezie , Addis Getu Tesfaw , Kiflie Zemene Demelash
Published: March 2023

Background

Since ancient times, pain and inflammation have been treated using herbal remedies, which are essentially a stockroom of phytochemical components. Due to the numerous adverse effects of the already available anti-pain and anti-inflammatory medications, the search for new potential pharmaceuticals used to relieve pain and inflammation from natural sources is an ongoing process. The present study was therefore, aimed at investigating the antinociceptive and antiinflammatory activities of the solvent fractions of the roots ofE. keberichoM. in mice model.

Methods

Successive maceration was used as a method of extraction using solvents of increasing polarity: methanol and water. The crude extract was then further fractionated using distilled water, ethyl acetate, and chloroform. Each solvent fraction was then evaluated for its peripheral analgesic activities using an acetic acid-induced writing test and central analgesic activities using the hot plate method. The acute and chronic anti-inflammatory activities of the solvent fractions were detected using carrageenan induced paw edema and cotton pellet ear granuloma respectively. The detected doses were 100mg/kg, 200mg/kg, and 400mg/kg. The positive control groups received ASA (150mg/kg) for the writing test, morphine (10mg/kg) for the hot plate method, diclofenac Na for carrageenan induced paw edema and dexamethasone (10mg/kg) for granuloma, while the negative control group received distilled water.

Result

EA fraction at all test doses employed (100mg/kg, 200mg/kg and 400mg/kg) showed statistical significant (p < 0.05, p < 0.01, p < 0.001 respectively) analgesic effects in both chemical and thermal induced pain stimuli in dose dependant manner. Likewise, EA fraction also exhibited anti-inflammatory activities on carrageenan induced paw edema and cotton pellet-induced granuloma in a dose-dependent manner. The AQ fraction on the other hand produced statistical significant (p < 0.05, p < 0.012) analgesic and anti-inflammatory activities at the doses of 200mg/kg and 400mg/kg, while the CH fraction exhibited statistical significant (p < 0.05) analgesic and anti-inflammatory activity at the dose of 400mg/kg.

Conclusion

In general, the data obtained from the present study elucidated that the solvent fractions possessed significant analgesic and anti-inflammatory activities and recommended further investigations.