bluuebunny/crossref_metadata_2025 huggingface dataset:
Compound heterozygous mutations in the kinase domain of IKKα lead to immunodeficiency and immune dysregulation
Authors: Riller Quentin , Sorin Boris , Courteille Charline , Ho-Nhat Duong , Voyer Tom Le , Debray Jean-Christophe , Stolzenberg Marie-Claude , Pellé Olivier , Becquard Thomas , Riestra María Rodrigo , Berteloot Laureline , Migaud Mélanie , Delage Laure , Jeanpierre Marie , Boussard Charlotte , Brunaud Camille , Magérus Aude , Michel Victor , Roux Camille , Picard Capucine , Masson Cécile , Bole-Feysot Christine , Cagnard Nicolas , Corneau Aurélien , Meyts Isabelle , Baud Véronique , Casanova Jean-Laurent , Fischer Alain , Dejardin Emmanuel , Puel Anne , Boulanger Cécile , Neven Bénédicte , Rieux-Laucat Frédéric
Published: May 2024

IKKα, encoded byCHUK, is crucial in the non-canonical NF-κB pathway and part of the IKK complex activating the canonical pathway alongside IKKβ. Absence of IKKα cause fetal encasement syndrome in human, fatal in utero, while an impaired IKKα-NIK interaction was reported in a single patient and cause combined immunodeficiency. Here, we describe compound heterozygous variants in the kinase domain of IKKα in a female patient with hypogammaglobulinemia, recurrent lung infections, and Hay-Wells syndrome-like features. We showed that both variants were loss-of-function. Non-canonical NF-κB activation was profoundly diminished in stromal and immune cells while the canonical pathway was partially impaired. Reintroducing wild-typeCHUKrestored non-canonical NF-κB activation. The patient had neutralizing autoantibodies against type I IFN, akin to non-canonical NF-κB pathway deficiencies. Thus, this is the first case of bi-allelicCHUKmutations disrupting IKKα kinase function, broadening non-canonical NF-κB defect understanding and suggesting IKKα’s role in canonical NF-κB target gene expression in human.
Impact of Covid-19 on Bangladeshi university students mental health: ML and DL analysis
Authors: Atique Md Monir Ahammod Bin , Bappi Md Ilias , Kim Kyungbeak , Choi Kwanghoon , Ahamad Md Martuza , Reza Khondaker Masfiq
Published: May 2024

The Covid-19 outbreak has adversely influenced university students across the world both physically and psychologically. The psychological struggle faced by students, is effected by various factors, including disruptions to daily routines and academic activities, increased reliance on smartphones and the internet, limited social interaction, and confinement to their homes. These impediments reflect a broader issue of imbalance in cognitive health status among them during the pandemic. In Bangladesh, despite having the necessary population to study, understanding the impact of Covid-19 on the mental health status of university students has been limited. Hence, it is imperative to diagnose mental health issues and deal with the underlying reasons in order to enhance students’ psychological well-being, which leads to academic achievement. Nowadays, Artificial Intelligence (AI) based prediction models have the potential to play a crucial role in predicting mental state early. The purpose of the study is to explore the following effects of the pandemic on the mental health of Bangladeshi university students using Machine Learning (ML) and Deep Learning (DL) techniques. A reliable AI prediction system requires real-world data, that was collected by a survey through a Google form (online questionnaires) among 400 students of 16 universities, and the respondents were 253. In this paper, after data preprocessing, ten widely known ML and four DL models were developed to automatically and accurately predict mental well-being during or after the Covid-19 circumstance. According to our findings, the Random Forest (RF) algorithm and Siamese Neural Networks (SNNs) outperformed other models in terms of accuracy (86% and 75%). Additionally, Chi-Square test was conducted, which revealed the five most common and significant predictors (“Stable family income”, “Disruption of daily life”, “Own income”, “Sleep status”, and “Fear of getting infected with Covid-19”) of psychological health conditions. Overall, this work could assist university administrations, government agencies, and health specialists in taking appropriate measures to understand and maintain students’ mental health. This research also suggests proper monitoring, government support, and social awareness during and after the worldwide epidemic to keep an excellent mental health state of university students.
Safety and effects of acetylated and butyrylated high amylose maize starch in recently diagnosed youths with type 1 diabetes; a Pilot Study
Authors: Ismail Heba M , Liu Jianyun , Netherland Michael , Evans-Molina Carmella , DiMeglio Linda A
Published: May 2024

Acetylated and butyrylated high amylose starch (HAMS-AB) is a prebiotic shown to be effective in type 1 diabetes (T1D) prevention in mouse models and is safe in adults with established T1D. HAMS-AB alters the gut microbiome profile with increased bacterial fermenters that produce short chain fatty acids (SCFAs) with anti-inflammatory and immune-modulatory effects. We performed a pilot study using a cross-over design to assess the safety and efficacy of 4 weeks of oral HAMS-AB consumption by recently diagnosed (< 2 years of diagnosis) youths with T1D. Seven individuals completed the study. The mean±SD age was 15.0±1.2 years, diabetes duration 19.5±6.3 months, 5/7 were female and 4/7 were White, all with a BMI of < 85th%. The prebiotic was safe. Following prebiotic intake, gut microbiome changes were seen, including a notable increase in the relative abundance of fermenters such as Bifidobacterium and Faecalibacterium. Treatment was also associated with changes in bacterial functional pathways associated with either improved energy metabolism (upregulation of tyrosine metabolism) or anti-inflammatory effects (reduced geraniol degradation). There were no differences in stool SCFA levels. Plasma metabolites associated with improved glycemia, such as hippurate, were significantly increased after treatment and there were positive and significant changes in the immune regulatory function of mucosal associated invariant T cells. There was a significant decrease in the area under the curve glucose but not C-peptide, as measured during a mixed meal tolerance testing, following the prebiotic consumption. In summary, the prebiotic HAMS-AB was safe in adolescents with T1D and showed promising effects on the gut microbiome composition, function and immune regulatory function.
Impact of Executive and Adaptive function on functional outcomes in adults with Maple Syrup Urine Disease
Authors: Gold Jessica I , Strong Alanna , Gold Nina B , Yudkoff Marc , Szalda Dava , Jan Sophia , Schwartz Lisa A , Ganetzky Rebecca
Published: May 2024

Purpose

Successful transition to adulthood requires intact executive and adaptive function. These neurocognitive domains, critical for independence, are frequently impaired in inherited metabolic disorders (IMD), though predictive clinical and biochemical factors are lacking. Standardized assessments linking neurocognitive status with functional outcomes are needed to improve prognostication and tailor support for affected emerging adults.

Methods

Maple Syrup Urine Disease (MSUD), a relatively prevalent IMD, is primarily diagnosed in the first week of life through newborn screening. Despite early intervention, executive and adaptive dysfunction persist. We designed a remote, interactive battery of neurocognitive and functional assessments for adults (≥21 years) with MSUD to correlate neurocognition and long-term outcomes.

Results

Assessments completed by 28 adults with MSUD (23 diagnosed after symptom onset) show a wide range in educational attainment, employment, and residence. Executive function, and adaptive function were significantly impaired in adults with MSUD compared to controls. Executive and adaptive deficits correlated negatively with obtaining skills needed for adult-oriented healthcare or independent living. Clinical history did not predict functional outcomes, but neurocognitive assessments suggest the benefits of pre-symptomatic diagnosis.

Conclusion

Independent adulthood is attainable for individuals with MSUD. Routine, targeted assessment of neurocognition may improve long-term functional outcomes in IMD.
Developing an Indicator for Age-Friendly Communities: The Japan Gerontological Evaluation Study
Authors: Fujihara Satoko , Noguchi Taiji , Ide Kazushige , Jeong Seungwon , Kondo Katsunori , Ojima Toshiyuki
Published: May 2024

Background

Age-friendly communities (AFCs) aim to create inclusive societies for older people. Despite the World Health Organization (WHO)’s emphasis on incorporating dementia-friendliness across all phases, including planning, implementation, monitoring, evaluation, and scale-up, there are very few community-level indicators that incorporate dementia-friendly elements.

Objective

To develop a community-level AFC indicator based on WHO AFC guidelines incorporating dementia-friendly elements, and examine its validity and reliability.

Design

A repeated cross-sectional study using data from the 2016 and 2019 waves of the Japan Gerontological Evaluation Study.

Setting and Subjects

Data were collected from 61 school districts in 16 Japanese municipalities, involving 45,162 individuals aged ≥65 years in 2016, and 39,313 in 2019. The 2016 and 2019 datasets were the development and retest samples, respectively.

Methods

After identifying 23 candidate items according to the WHO AFC guidelines and expert reviews, data were aggregated by school district. Exploratory factor analysis on the 2016 data helped derive factor structure, confirming reproducibility with the 2019 data. Internal consistency and test-retest reliability were evaluated.

Results

The final 17-item indicator comprised three subscales:Social inclusion and dementia-friendliness(7 items, α = 0.86),Social engagement and communication(5 items, α = 0.78), andAge-friendly physical environment(5 items, α = 0.82). The structure showed adequate test-retest reliability (r = 0.71–0.79; ICC = 0.67–0.78).

Conclusions

A valid and reliable 17-item community-level indicator was developed, which aligns with the WHO framework and also incorporates dementia-friendly elements. This indicator is useful for monitoring and evaluating to promote the AFC and dementia-friendly communities.
Association of daily steps with incident non-alcoholic fatty liver disease: Evidence from the UK Biobank cohort
Authors: Fulda Evelynne S. , Portas Laura , Harper Charlie , Preiss David , Bennett Derrick , Doherty Aiden
Published: May 2024

Background

Low physical activity (PA) has been shown to be associated with higher risk of non-alcoholic fatty liver disease (NAFLD). However, the strength and shape of this association are currently uncertain due to a reliance on self-reported PA measures. This report aims to investigate the relationship of PA with NAFLD using accelerometer-derived step count from a large prospective cohort study.

Methods

The wrist-worn accelerometer sub-study of the UK Biobank (N=∼100,000) was used to characterise median daily step count over a seven-day period. NAFLD cases were ascertained via record linkage with hospital inpatient data and death registers or by using a measure of liver fat from imaging. Cox proportional hazards models were employed to assess the association between step count and NAFLD, adjusting for age, sociodemographic, and lifestyle factors. Mediation analyses were conducted.

Results

Among 91,031 participants (709,440 person-years of follow-up), there were 762 incident NAFLD cases. Higher step count was log-linearly and inversely associated with risk of NAFLD. A 1000 step increase (representing 10 minutes of walking) was associated with a 12% (95% CI: 10%–14%) lower hazard of NAFLD. When using imaging to identify NAFLD, a 1,000-step increase was associated with a 6% (95% CI: 6%–7%) lower risk. There was evidence for some mediation by adiposity.

Conclusion

Physical activity, a modifiable risk factor, is log-linearly and inversely associated with NAFLD. This association was only partially explained by adiposity. These findings from a large cohort study may have important implications for strategies to lower NAFLD risk.
Gut Microbiome Multi-Omics and Cognitive Function in the Hispanic Community Health Study/Study of Latinos- Investigation of Neurocognitive Aging
Authors: Palacios Natalia , Gordon Scott , Wang Tao , Burk Robert , Qi Qibin , Huttenhower Curtis , Gonzalez Hector M. , Knight Robert , De Carli Charles , Daviglus Marta , Lamar Melissa , Telavera Gregory , Tarraf Wassim , Kosciolek Tomasz , Cai Jianwen , Kaplan Robert C.
Published: May 2024

STRUCTURED ABSTRACT

INTRODUCTION

Weconducted a study within the Hispanic Community Health Study/Study of Latinos- Investigation of Neurocognitive Aging (HCHS/SOL-INCA) cohort to examine the association between gut microbiome and cognitive function.

METHODS

We analyzed the fecal metagenomes of 2,471 HCHS/SOL-INCA participants to, cross-sectionally, identify microbial taxonomic and functional features associated with global cognitive function. Omnibus (PERMANOVA) and feature-wise analyses (MaAsLin2) were conducted to identify microbiome-cognition associations, and specific microbial species and pathways (Kyoto Encyclopedia of Genes and Genomes (KEGG modules) associated with cognition.

RESULTS

Eubacteriumspecies(E. siraeumandE. eligens), were associated with better cognition. Several KEGG modules, most strongly Ornithine, Serine biosynthesis and Urea Cycle, were associated with worse cognition.

DISCUSSION

In a large Hispanic/Latino cohort, we identified several microbial taxa and KEGG pathways associated with cognition.
Assessing the impact of Enhanced-Case-Finding on tuberculosis incidence and transmission in The Gambia using epidemiological and phylodynamic approaches
Authors: Gehre Florian , Oko Francis , Ofori-Anyinam Boatema , Meehan Conor J. , Windels Etthel M. , Joof Ken , Faal Tutty , Mendy Francis , Jobarteh Tijan , Gitteh Ensa , Riley Abi Janet , Sarr-Kuyateh Binta , Okoi Catherine , Demba Edward , Del-Alorse William , Mlaga Kodjovi , Sambou Basil , Kanuteh Fatoumatta , Lette Koduh , Muhammad Abdul Khalie , Agbla Shadrac , Mulders Wim , Donkor Simon , Jeffries David , Roca Anna , D’Alessandro Umberto , Antonio Martin , Adetifa Ifedayo , de Jong Bouke C.
Published: May 2024

Background

Most tuberculosis (TB) cases in The Gambia are notified in the Greater Banjul Area (GBA). We conducted an Enhanced-Case-Finding (ECF) intervention in the GBA and determined its effect on TB incidence and ongoing TB transmission.

Methods

This was a cluster randomized trial in which randomly assigned intervention areas of grouped settlements received three rounds of an ECF strategy consisting of sensitization followed by auramine microscopy, whereas TB patients in control areas continued to be identified through passive case finding. The primary outcome was TB incidence rate. To exclude that an increase in notified cases, followed by a decrease in notified cases, would hide the future impact of the intervention, we tested for changes in transmission dynamics using both genetic clustering and phylodynamic methods.

Results

No significant difference in TB incidence rates, transmission clustering or effective reproductive number was detected between intervention and control areas.

Conclusion

Although we did not find evidence for decreased TB incidence nor TB transmission through the ECF strategy used, this approach is an examplar of how both classical epidemiology and genomic phylodynamics approaches can be integrated to better assess public health intervention outcomes.
Diagnostics for detection and surveillance of priority epidemic-prone diseases in Africa: an assessment of testing capacity and laboratory strengthening needs
Authors: Ashenafi Aytenew , Sule Olajumoke , Peter Trevor , Mashate Silver , Otieno Osborn , Kebede Yenew , Oio John , Kao Kekeletso , Carter Jane , Whistler Toni , Ndlovu Nqobile , Kebede Yenew
Published: May 2024

In 2023, Africa experienced 180 public health emergencies, of which 90% were infectious diseases and 75% were related to zoonotic diseases. Testing capacity for epidemic-prone diseases is essential to enable rapid and accurate identification of causative agents, and for action to prevent disease spread. Moreover, testing is pivotal in monitoring disease transmission, evaluating public health interventions, and informing targeted resource allocation during outbreaks. An online, self-assessment survey was conducted in African Union Member States to identify major challenges in testing for epidemic-prone diseases. The survey assessed current capacity for diagnosing priority epidemic-prone diseases at different laboratory levels. It explored challenges in establishing and maintaining testing capacity to improve outbreak response and mitigate public health impact. Survey data analysed diagnostic capacity for priority infectious diseases, diagnostic technologies in use, existing surveillance programmes and challenges limiting diagnostic capacity, by country. The survey result from 15 Member States who responded to the survey, showed high variability in testing capacity and technologies across countries and diverse factors limiting testing capacity for certain priority diseases like dengue and Crimean-Congo haemorrhagic fever. At the same time, there is better diagnostic capacity for coronavirus disease 2019 (COVID-19), polio, and measles due to previous investments. Unfortunately, many countries are not utilising multiplex testing, despite its potential to improve diagnostic access. The challenges of limited laboratory capacity for testing future outbreaks are indeed significant. Recent disease outbreaks in Africa have underscored the urgent need to strengthen diagnostic capacity and introduce cost-effective technologies. Small sample sizes and differing disease prioritisation within each country limited the analysis. These findings suggest the benefits of evaluating laboratory testing capacity for epidemic-prone diseases and highlight the importance of effectively addressing challenges to detect diseases and prevent future pandemics.
Genome-wide association studies in a large Korean cohort identify novel quantitative trait loci for 36 traits and illuminate their genetic architectures
Authors: Jee Yon Ho , Wang Ying , Jung Keum Ji , Lee Ji-Young , Kimm Heejin , Duan Rui , Price Alkes L. , Martin Alicia R. , Kraft Peter
Published: May 2024

Genome-wide association studies (GWAS) have been predominantly conducted in populations of European ancestry, limiting opportunities for biological discovery in diverse populations. We report GWAS findings from 153,950 individuals across 36 quantitative traits in the Korean Cancer Prevention Study-II (KCPS2) Biobank. We discovered 301 novel genetic loci in KCPS2, including an association between thyroid-stimulating hormone and CD36. Meta-analysis with the Korean Genome and Epidemiology Study, Biobank Japan, Taiwan Biobank, and UK Biobank identified 4,588 loci that were not significant in any contributing GWAS. We describe differences in genetic architectures across these East Asian and European samples. We also highlight East Asian specific associations, including a known pleiotropic missense variant in ALDH2, which fine-mapping identified as a likely causal variant for a diverse set of traits. Our findings provide insights into the genetic architecture of complex traits in East Asian populations and highlight how broadening the population diversity of GWAS samples can aid discovery.
Inferring causal cell types of human diseases and risk variants from candidate regulatory elements
Authors: Kim Artem , Zhang Zixuan , Legros Come , Lu Zeyun , de Smith Adam , Moore Jill E. , Mancuso Nicholas , Gazal Steven
Published: May 2024

The heritability of human diseases is extremely enriched in candidate regulatory elements (cRE) from disease-relevant cell types. Critical next steps are to infer which and how many cell types are truly causal for a disease (after accounting for co-regulation across cell types), and to understand how individual variants impact disease risk through single or multiple causal cell types. Here, we propose CT-FM and CT-FM-SNP, two methods that leverage cell-type-specific cREs to fine-map causal cell types for a trait and for its candidate causal variants, respectively. We applied CT-FM to 63 GWAS summary statistics (averageN= 417K) using nearly one thousand cRE annotations, primarily coming from ENCODE4. CT-FM inferred 81 causal cell types with corresponding SNP-annotations explaining a high fraction of trait SNP-heritability (∼2/3 of the SNP-heritability explained by existing cREs), identified 16 traits with multiple causal cell types, highlighted cell-disease relationships consistent with known biology, and uncovered previously unexplored cellular mechanisms in psychiatric and immune-related diseases. Finally, we applied CT-FM-SNP to 39 UK Biobank traits and predicted high confidence causal cell types for 2,798 candidate causal non-coding SNPs. Our results suggest that most SNPs impact a phenotype through a single cell type, and that pleiotropic SNPs target different cell types depending on the phenotype context. Altogether, CT-FM and CT-FM-SNP shed light on how genetic variants act collectively and individually at the cellular level to impact disease risk.
Identifying a Heterogeneous Effect of Atrial Fibrillation Screening in Older Adults: A Secondary Analysis of the VITAL-AF Trial
Authors: Shah Sachin J , Iyer Jay M. , Agha Leila , Chang Yuchiao , Ashburner Jeffrey M. , Atlas Steven J. , McManus David D. , Ellinor Patrick T. , Lubitz Steven A. , Singer Daniel E.
Published: May 2024

Background

One-time atrial fibrillation (AF) screening trials have produced mixed results; however, it is unclear if there is a subset for whom screening is effective. Identifying such a subgroup would support targeted screening.

Methods

We conducted a secondary analysis of VITAL-AF, a randomized trial of one-time, single-lead ECG screening during primary care visits. We tested two approaches to identify a subgroup where screening is effective. First, we developed an effect-based model using a T-learner. Specifically, we separately predicted the likelihood of AF diagnosis under screening and usual care conditions; the difference in probabilities was the predicted screening effect. Second, we used a validated AF risk model to test for a heterogeneous screening effect. We used interaction testing to determine if observed AF diagnosis rates in the screening and usual care groups differed when stratified by decile of the predicted screening effect and predicted AF risk.

Results

Baseline characteristics were similar between the screening (n=15187) and usual care (n=15078) groups (mean age 74 years, 59% female). In the effect-based analysis, in the highest decile of predicted screening effectiveness (n=3026), AF diagnosis rates were higher in the screening group (6.50 vs. 3.06 per 100 person-years, rate difference 3.45, 95%CI 1.62 to 5.28). In this group, the mean age was 84 years and 68% were female. The risk-based analysis did not identify a subgroup where screening was more effective. Predicted screening effectiveness and predicted baseline AF risk were poorly correlated (Spearman coefficient 0.13).

Conclusions

In a secondary analysis of the VITAL-AF trial, we identified a small subgroup where one-time screening was associated with increased AF diagnoses using an effect-based approach. In this study, predicted AF risk was a poor proxy for predicted screening effectiveness. These data caution against the assumption that high AF risk is necessarily correlated with high screening effectiveness.
Oxygen-based autoregulation indices associated with clinical outcomes and spreading depolarization in aSAH
Authors: Carlson Andrew P , Jones Thomas , Zhu Yiliang , Desai Masoom , Alsarah Ali , Shuttleworth C. William
Published: May 2024

Background

Impairment in cerebral autoregulation has been proposed as a potentially targetable factor in patients with aneurysmal subarachnoid hemorrhage (aSAH), however there are different continuous measures that can be used to calculate the state of autoregulation. In addition, it has previously been proposed that there may be an association of impaired autoregulation with the occurrence of spreading depolarization (SD) events.

Methods

Subjects with invasive multimodal monitoring and aSAH were enrolled in an observational study. Autoregulation indices were prospectively calculated from this database as a 10 second moving correlation coefficient between various cerebral blood flow (CBF) surrogates and mean arterial pressure (MAP). In subjects with subdural ECoG (electrocorticography) monitoring, SD was also scored. Associations between clinical outcomes using the mRS (modified Rankin Scale) and occurrence of either isolated or clustered SD was assessed.

Results

320 subjects were included, 47 of whom also had ECoG SD monitoring. As expected, baseline severity factors such as mFS and WFNS (World Federation of Neurosurgical Societies scale) were strongly associated with the clinical outcome. SD probability was related to blood pressure in a triphasic pattern with a linear increase in probability below MAP of ∼100mmHg.

Autoregulation indices were available for intracranial pressure (ICP) measurements (PRx), PbtO2 from Licox (ORx), perfusion from the Bowman perfusion probe (CBFRx), and cerebral oxygen saturation measured by near infrared spectroscopy (OSRx). Only worse ORx and OSRx were associated with worse clinical outcomes. ORx and OSRx also were found to both increase in the hour prior to SD for both sporadic and clustered SD.

Conclusions

Impairment in autoregulation in aSAH is associated with worse clinical outcomes and occurrence of SD when using ORx and OSRx. Impaired autoregulation precedes SD occurrence. Targeting the optimal MAP or cerebral perfusion pressure in patients with aSAH should use ORx and/or OSRx as the input function rather than intracranial pressure.
Microbial education plays a crucial role in harnessing the beneficial properties of microbiota for infectious disease protection inCrassostrea gigas
Authors: Dantan Luc , Carcassonne Prunelle , Dégremont Lionel , Morga Benjamin , Travers Marie-Agnès , Petton Bruno , Mege Mickael , Maurouard Elise , Allienne Jean-François , Courtay Gaëlle , Romatif Océane , Pouzadoux Juliette , Lami Raphaël , Intertaglia Laurent , Gueguen Yannick , Vidal-Dupiol Jeremie , Toulza Eve , Cosseau Céline
Published: May 2024

Background

Recently, the frequency and severity of marine diseases have increased in association with global changes, and molluscs of economic interest are particularly concerned. Among them, the Pacific oyster (Crassostrea gigas) production faces challenges from several diseases such as the Pacific Oyster Mortality Syndrome (POMS) or vibriosis. Various strategies such as genetic selection or immune priming have been developed to fight some of these infectious diseases. The microbial education, which consist of exposing the host immune system to beneficial microorganisms during early life stages is a promising approach against diseases. This study explores the concept of microbial education using controlled and pathogen-free bacterial communities and assesses its protective effects against POMS andVibrio aestuarianusinfections, highlighting potential applications in oyster production.

Results

We demonstrate that it is possible to educate the oyster immune system by adding microorganisms during the larval stage. Adding culture based bacterial mixes to larvae protects only against the POMS disease while adding whole microbial communities from oyster donors protects against both POMS and vibriosis. The efficiency of the immune protection depends both on oyster origin and on the composition of the bacterial mixes used for exposure. No preferential protection was observed when the oysters were stimulated with their sympatric strains. We further show that the added bacteria were not maintained in the oyster microbiota after the exposure, but this bacterial addition induced long term changes in the microbiota composition and oyster immune gene expression.

Conclusion

Our study reveals successful immune system education of oysters by introducing beneficial micro-organisms during the larval stage. We improved the long-term resistance of oysters against critical diseases (POMS disease andVibrio aestuarianusinfections) highlighting the potential of microbial education in aquaculture.
A benchmark comparison of CRISPRn guide-RNA design algorithms and generation of small single and dual-targeting libraries to boost screening efficiency
Authors: Lukasiak Sebastian , Kalinka Alex , Gupta Nikhil , Papadopoulos Angelos , Saeed Khalid , McDermott Ultan , Hannon Gregory J , Ross-Thriepland Douglas , Walter David
Published: May 2024

Genome-wide CRISPR sgRNA libraries have emerged as transformative tools to systematically probe gene function. While these libraries have been iterated over time to be more efficient, their large size limits their use in some applications. Here, we benchmarked publicly available genome-wide single-targeting sgRNA libraries and evaluated dual targeting as a strategy for pooled CRISPR loss-of-function screens. We leveraged this data to design two minimal genome-wide human CRISPR-Cas9 libraries that are 50% smaller than other libraries and that preserve specificity and sensitivity, thus enabling broader deployment at scale.
Wings expansion inDrosophila melanogaster
Authors: Hadjaje Simon , Andrade-Silva Ignacio , Dalbe Marie-Julie , Clément Raphaël , Marthelot Joel
Published: May 2024

During their final transformation, insects emerge from the pupal case and deploy their wings within minutes. The wings deploy from a compact origami structure, to form a planar, rigid and functional blade that allows the insect to fly. The deployment is powered by a rapid increase in internal pressure, and by the subsequent flow of hemolymph into the deployable wing structure. Using a combination of imaging techniques, we characterize the internal and external structure of the wing inDrosophila melanogaster, the unfolding kinematics at the organ scale, and the hemolymph flow during deployment. We find that beyond the mere unfolding of the macroscopic folds, wing deployment also involves an expansion of cell surface and the unfolding of microscopic wrinkles in the cuticle enveloping the wing. A quantitative computational model, incorporating mechanical measurements of the viscoelastic properties and microstructure of the wing, predicts the existence of an operating point for deployment and captures the dynamics of expansion. This model suggests that insects exploit material and geometric nonlinearities to achieve rapid and efficient reconfiguration of soft deployable structures.
Machine Learning and Directed Evolution of Base Editing Enzymes
Authors: Perrotta Ramiro M. , Vinke Svenja , Ferreira Raphaël , Moret Michaël , Mahas Ahmed , Chiappino-Pepe Anush , Riedmayr Lisa M. , Mehra Anna-Thérèse , Lehmann Louisa S. , Church George M.
Published: May 2024

As we enter the era of CRISPR medicines, base editors (BEs) emerged as one of the most promising tools to treat genetic associated diseases. However, unintended bystander editing beyond the target nucleotide poses a challenge to their translation into effective therapies. While many efforts have been made in the design of a universal enzyme with minimal bystander editing, the context dependent activity represents a major challenge for base editing-based therapies. In this work, we designed a sequence-specific guide RNA library with 3’-extensions and detected guides that were able to reduce bystander and increase editing efficiency in a context dependent manner. The best candidate was later used for phage assisted non-continuous evolution to find a new generation of precise base editors. Simultaneously, we use protein language models trained on massive protein sequence datasets to find the evolutionarily plausible mutational patterns that can improve deaminase activity and precision. Both strategies provide a collection of precise TadA variants that not only drastically reduced bystander edits, but also was not in detriment of on-target activity. Our findings introduce a guide/enzyme parallel engineering pipeline, which lays the foundation for the development of new personalized genome editing strategies, ultimately enhancing the safety and precision of this groundbreaking technology.
Phase synchrony between prefrontal noradrenergic and cholinergic signals indexes inhibitory control
Authors: Liu Yuxiang (Andy) , Nong Yuhan , Feng Jiesi , Li Guochuan , Sajda Paul , Li Yulong , Wang Qi
Published: May 2024

Inhibitory control is a critical executive function that allows animals to suppress their impulsive behavior in order to achieve certain goals or avoid punishment. We investigated norepinephrine (NE) and acetylcholine (ACh) dynamics and population neuronal activity in the prefrontal cortex (PFC) during inhibitory control. Using fluorescent sensors to measure extracellular levels of NE and ACh, we simultaneously recorded prefrontal NE and ACh dynamics in mice performing inhibitory control tasks. The prefrontal NE and ACh signals exhibited strong coherence at 0.4-0.8 Hz. Although inhibition of locus coeruleus (LC) neurons projecting to the PFC impaired inhibitory control, inhibiting LC neurons projecting to the basal forebrain (BF) caused a more profound impairment, despite an approximately 30% overlap between LC neurons projecting to the PFC and BF, as revealed by our tracing studies. The inhibition of LC neurons projecting to the BF did not diminish the difference in prefrontal NE/ACh signals between successful and failed trials; instead, it abolished the difference in NE-ACh phase synchrony between successful and failed trials, indicating that NE-ACh phase synchrony is a task-relevant neuromodulatory feature. Chemogenetic inhibition of cholinergic neurons that project to the LC region did not impair inhibitory control, nor did it abolish the difference in NE-ACh phase synchrony between successful or failed trials, further confirming the relevance of NE-ACh phase synchrony to inhibitory control. To understand the possible effect of NE-ACh synchrony on prefrontal population activity, we employed Neuropixels to record from the PFC during inhibitory control. The inhibition of LC neurons projecting to the BF not only reduced the number of prefrontal neurons encoding inhibitory control, but also disrupted population firing patterns representing inhibitory control, as revealed by a demixed principal component (dPCA) analysis. Taken together, these findings suggest that the LC modulates inhibitory control through its collective effect with cholinergic systems on population activity in the prefrontal cortex. Our results further indicate that NE-ACh phase synchrony is a critical neuromodulatory feature with important implications for cognitive control.
Cryo-EM structures of a bathy phytochrome histidine kinase reveal a unique light-dependent activation mechanism
Authors: Bódizs Szabolcs , Mészáros Petra , Grunewald Lukas , Takala Heikki , Westenhoff Sebastian
Published: May 2024

Phytochromes are photoreceptor proteins in plants, fungi and bacteria. They can adopt two photochromic states with differential biochemical responses. The structural changes transducing the signal from the chromophore to the biochemical output modules are poorly understood due to challenges in capturing structures of the dynamic, full-length protein. Here, we present the first cryo-electron microscopy structures of the phytochrome fromPseudomonas aeruginosa(PaBphP) in its resting Pfr and photoactivated Pr state. The kinase-active Pr state has an asymmetric, dimeric structure, whereas the kinase-inactive Pfr state opens up. This behaviour is different from other known phytochromes and we explain it with the unusually short connection between the photosensory and output modules. Multiple sequence alignment of this region suggests evolutionary optimisation for different modes of signal transduction in sensor proteins. The results establish a new mechanism for light-sensing by phytochrome histidine kinases and provide input for the design of optogenetic phytochrome variants.
Emergence and evolution of heterocyte glycolipid biosynthesis enabled specialized nitrogen fixation in cyanobacteria
Authors: Pérez Gallego Ruth , von Meijenfeldt F. A. Bastiaan , Bale Nicole J. , Sinninghe Damsté Jaap S. , Villanueva Laura
Published: May 2024

Paleontological and phylogenomic observations have shed light on the evolution of cyanobacteria. Nevertheless, the emergence of heterocytes, specialized cells for nitrogen fixation, remains unclear. Heterocytes are surrounded by heterocyte glycolipids (HGs), which contribute to protection of the nitrogenase enzyme from oxygen. Here, by comprehensive HG identification and screening of HG biosynthesis genes throughout cyanobacteria, we identify HG analogs produced by specific and distantly related non-heterocytous cyanobacteria. These structurally less complex molecules probably acted as precursors of HGs, suggesting that HGs arose after a genomic reorganization and expansion of ancestral biosynthetic machinery, enabling the rise of cyanobacterial heterocytes in an increasingly oxygenated atmosphere. Subsequently, HG chemical structure evolved convergently in response to environmental pressures. Our results open a new chapter in the potential use of diagenetic products of HGs and HG analogs as fossils for reconstructing the evolution of multicellularity and division of labor in cyanobacteria.
Epigenetic delineation of the earliest cardiac lineage segregation by single-cell multi-omics
Authors: Xie Peng , Jiang Xu , He Jingjing , Pan Qingyun , Yang Zhongzhou , Zheng Yanying , Fan Wenli , Wu Chen , Zheng Weiheng , Fang Ke , Si Shuhan , Zhu Shiqi , Yang Yi , Zhong Tao P. , Yang Zhongzhou , Wei Ke , Xie Wei , Jing Naihe , Luo Zhuojuan , Lin Chengqi
Published: May 2024

The mammalian heart is formed from multiple mesoderm-derived cell lineages. However, it remains largely unknown when and how the specification of mesoderm towards cardiac lineages is determined. Here, we systematically depict the transcriptional trajectories toward cardiomyocyte in early mouse embryo, and characterize the epigenetic landscapes underlying the early mesodermal lineage specification by single-cell multi-omics analyses. The analyses also reveal distinct core regulatory networks (CRN) in controlling specification of mesodermal lineages. We further demonstrate the essential role HAND1 and FOXF1 in driving the earliest cardiac progenitors specification. These key transcription factors occupy at distinct enhancers, but function synergistically and hierarchically to regulate the expression of cardiac-specific genes. In addition, HAND1 is required for exiting from the nascent mesoderm program, while FOXF1 is essential for driving cardiac differentiation during MJH specification. Our findings establish transcriptional and epigenetic determinants specifying the early cardiac lineage, providing insights for the investigation of congenital heart defects.
Mechanism of TAX1BP1 recruitment in aggrephagy to switch from cargo collection to sequestration
Authors: Bauer Bernd , Idinger Jonas , Schuschnig Martina , Ferrari Luca , Martens Sascha
Published: May 2024

Autophagy mediates the degradation of harmful material within lysosomes. In aggrephagy, the pathway mediating the degradation of aggregated, ubiquitinated proteins, this cargo material is collected in larger condensates prior to its sequestration by autophagosomes. In this process, SQSTM1/p62 and NBR1 drive cargo condensation, while TAX1BP1, which binds to NBR1 recruits the autophagy machinery to facilitate autophagosome biogenesis at the condensates. The mechanistic basis for the TAX1BP1 mediated switch from cargo collection to its sequestration is unclear. Here we show that TAX1BP1 is not a constitutive component of the condensates. Its recruitment correlates with the induction of autophagosome biogenesis. TAX1BP1 is sufficient to recruit the TBK1 kinase via the SINTBAD adapter. We define the NBR1 - TAX1BP1 binding site, which is adjacent to the GABARAP/LC3 interaction site and demonstrate that the recruitment of TAX1BP1 to cargo mimetics can be enhanced by an increased ubiquitin load. Our study suggests that autophagosome biogenesis is initiated once sufficient cargo is collected in the condensates.
Denitrification genotypes of endospore-forming Bacillota
Authors: Bell Emma , Chen Jianwei , Fustic Milovan , Hubert Casey RJ
Published: May 2024

Denitrification is a key metabolic process in the global nitrogen cycle and is performed by taxonomically diverse microorganisms. Despite the widespread importance of this metabolism, challenges remain in identifying denitrifying populations and predicting their metabolic end-products based on their genotype. Here, genome-resolved metagenomics was used to explore the denitrification genotype of Bacillota enriched in nitrate-amended high temperature incubations with confirmed N2O and N2 production. A set of 12 hidden Markov models (HMMs) was created to target the diversity of denitrification genes in members of the phylum Bacillota. Genomic potential for complete denitrification was found in five metagenome-assembled genomes (MAGs) from nitrate-amended enrichments, including two novel members of the Brevibacillaceae family. Genomes of complete denitrifiers encode N2O reductase (nos) gene clusters with clade II-type nosZ and often include multiple variants of the nitric oxide reductase (nor) gene. The HMM set applied to all genomes of Bacillota from the Genome Taxonomy Database (GTDB) identified 17 genera inferred to contain complete denitrifiers based on their gene content. Among complete denitrifiers it was common for three distinct nitric oxide reductases to be present (qNOR, bNOR and sNOR) which may reflect the metabolic adaptability of Bacillota in environments with variable redox conditions.
CellSeg3D: self-supervised 3D cell segmentation for fluorescence microscopy
Authors: Achard Cyril , Kousi Timokleia , Frey Markus , Vidal Maxime , Paychère Yves , Hofmann Colin , Iqbal Asim , Hausmann Sebastien B. , Pagès Stéphane , Mathis Mackenzie Weygandt
Published: May 2024

Understanding the complex three-dimensional structure of cells is crucial across many disciplines in biology and especially in neuroscience. Here, we introduce a set of models including a 3D transformer (SwinUNetR) and a novel 3D self-supervised learning method (WNet3D) designed to address the inherent complexity of generating 3D ground truth data and quantifying nuclei in 3D volumes. We developed a Python package called CellSeg3D that provides access to these models in Jupyter Notebooks and in a napari GUI plugin. Recognizing the scarcity of high-quality 3D ground truth data, we created a fully human-annotated mesoSPIM dataset to advance evaluation and benchmarking in the field. To assess model performance, we benchmarked our approach across four diverse datasets: the newly developed mesoSPIM dataset, a 3D platynereis-ISH-Nuclei confocal dataset, a separate 3D platynereis-Nuclei light-sheet dataset, and a challenging and densely packed Mouse-Skull-Nuclei confocal dataset. We demonstrate that our self-supervised model, WNet3D – trained without any ground truth labels – achieve performance on par with state-of-the-art supervised methods, paving the way for broader applications in label-scarce biological contexts.
A stochastic RNA editing process targets a limited number of sites in individualDrosophilaglutamatergic motoneurons
Authors: Crane Andrés B. , Jetti Suresh K. , Littleton J. Troy
Published: May 2024

RNA editing is a post-transcriptional source of protein diversity and occurs across the animal kingdom. Given the complete profile of mRNA targets and their editing rate in individual cells is unclear, we analyzed single cell RNA transcriptomes fromDrosophilalarval tonic and phasic glutamatergic motoneuron subtypes to determine the most highly edited targets and identify cell-type specific editing. From ∼15,000 genes encoded in the genome, 316 high confidence A-to-I canonical RNA edit sites were identified, with 102 causing missense amino acid changes in proteins regulating membrane excitability, synaptic transmission, and cellular function. Some sites showed 100% editing in single neurons as observed with mRNAs encoding mammalian AMPA receptors. However, most sites were edited at lower levels and generated variable expression of edited and unedited mRNAs within individual neurons. Together, these data provide insights into how the RNA editing landscape alters protein function to modulate the properties of two well-characterized neuronal populations inDrosophila.
New highly selective antivirals for Chikungunya Virus identified from the screening of a drug-like compound library
Authors: Castro Eliana F. , Álvarez Diego E.
Published: May 2024

Chikungunya fever is a mosquito-borne disease caused by Chikungunya virus (CHIKV). Treatment of CHIKV infections is currently supportive and does not limit viral replication or symptoms of persistent chronic arthritis. Although there are multiple compounds reported as antivirals active against CHIKVin vitro, there are still no effective and safe antivirals. Thus, active research aims at the identification of new chemical structures with antiviral activity. Here, we report the screen of the Pandemic Response Box library of small molecules against a fully infectious CHIKV reporter virus. Our screening approach successfully identified previously reported CHIKV antiviral compounds within this library and further expanded potentially active hits, supporting the use of reporter-virus-based assays in high-throughput screening format as a reliable tool for antiviral drug discovery. Four molecules were identified as potential drug candidates against CHIKV: MMV1634402 (Brilacidin) and MMV102270 (Diphyllin), which were previously shown to present broad-spectrum antiviral activities, in addition to MMV1578574 (Eravacycline), and the antifungal MMV689401 (Fluopicolide), for which their antiviral potential is uncovered here.
Structural insights intoPseudomonas aeruginosalysine-specific uptake mechanism for extremely low pH regulation
Authors: Bicer Deniz , Matsuoka Rei , Moumbock Aurélien F. A. , Sukumar Preethi , Cheruvara Harish , Quigley Andrew , Pardon Els , Steyaert Jan , Henderson Peter J.F. , Caffrey Martin , Griese Julia J. , Nji Emmanuel
Published: May 2024

Under conditions of extremely low pH, in addition to transporting lysine, bacterial lysine-specific permease (LysP) interacts with the transcriptional regulator CadC to upregulatecadBAoperon expression.cadBAencodes CadA, which decarboxylates lysine to cadaverine, and CadB, which exports cadaverine to the environment to reduce acidity. This process is crucial for survival of pathogenic bacteria in their hosts. Here, we report the inward-occluded (3.2 – 5.3 Å) cryo-EM structure ofPseudomonas aeruginosaLysP bound to L-lysine and in complex with a nanobody. L-lysine is coordinated by hydrophobic stacking, cation-π interactions and hydrogen bonding mostly with polar uncharged LysP residues. LysP reconstituted into liposomes showed robust and specific transport of L-lysine with the transport being inhibited by L-4-thialysine (S-2-aminoethyl-L-cysteine). These findings inform our understanding of the specific recognition, inhibition, and transport mechanism of L-lysine by LysP, which will have important ramifications for the design of antibiotics to target bacterial LysP.