bluuebunny/crossref_metadata_2025 huggingface dataset:
Excessive Dietary Fructose Aggravates Heart Failure via Impairing Myocardial Fatty Acid Oxidation Metabolism in Diet Induced Obese Mouse
Authors: Zhang Yufeng , Xue Yuzhou , Gong Qifan , Xu Jingshen , Wang Shuaikang , Zhu Min , Wang Jinhui , Song Zhiqiang , Zhang Shuxian , Wang Hu , Jin Ling , Hua Kun , Yang Xiubin , Li Jianping , Li Jin , Xu Ming , Huang He
Published: May 2024

Background

An unhealthy diet and a sedentary lifestyle increase the prevalence of cardiometabolic syndrome. Several cardiovascular diseases (CVDs) have been highly linked to excessive added sugar intake, which alters whole-body metabolism, including heart tissue. However, whether specific added sugars can cause and aggravate severe heart dysfunction is still unknown.

Methods

We examined the association between CVDs and added sugar intake using statistical analyses and Mendelian randomization (MR). Then, we evaluated the effect of added sugar on mouse heart function employing a diet-induced obese (DIO) model with transverse aortic constriction (TAC) challenge. We measured the fatty acid and fructose metabolic flux in mouse hearts employing a mass spectrometry-basedin vivodouble stable isotopic labeling (DSIL) technique. The results of animal models were also confirmed in aortic stenosis (AS) patient samples.

Results

Statistical analyses and MR estimation on public databases indicated that added sugars, especially fructose, are associated with a high risk of heart failure. Feeding on either ingested or drunk fructose could aggravate heart failure and diastolic and systolic dysfunction in TAC challenged DIO mice. Mechanistically, excessive dietary intake of fructose could suppress heart fatty acid oxidation (FAO) metabolism via both shrinkage of the flux rate of FAO and inhibition of the AMPK-ACC axis. Activation of AMPK or deactivation of ACC could limit such heart dysfunction and myocardial hypertrophy. We also obtained plasma from 27 patients with AS and determined that the high fructose level instead of glucose or sucrose was linked to left ventricular ejection fractions (LVEF) and fractional shortening (FS) decline.

Conclusions

Findings from epidemiological statistical analyses and investigations of animal models suggested the harmful effect of excessive fructose intake on heart function. Fructose could directly alter heart metabolism by suppressing FAO. Our results implied that targeting AMPK-ACC mediation could effectively attenuate excessive fructose-induced heart failure in DIO mice.
Mucociliary Clearance is Impaired in Small Airways of Cystic Fibrosis Pigs
Authors: Stewart Carley G. , Hilkin Brieanna M. , Gansemer Nicholas D. , Dick David W. , Sunderland John J. , Stoltz David A. , Abou Alaiwa Mahmoud H. , Zabner Joseph
Published: May 2024

Rationale

Cystic fibrosis is a genetic disorder characterized by recurrent airway infections, inflammation, and progressive decline in lung function. Autopsy and spirometry data suggest that cystic fibrosis may start in the small airways which, due to the fractal nature of the airways, account for most of the airway tree surface area. However, they are not easily accessible for testing.

Objectives

Here, we tested the hypothesis that mucociliary clearance is abnormal in the small airways of newborn cystic fibrosis pigs.

Methods

Current mucociliary clearance assays are limited therefore we developed a dynamic positron emission tomography scan assay with high spatial and temporal resolution. Each study was accompanied by a high-resolution computed tomography scan that helped identify the thin outer region of the lung that contained small airways.

Measurements and Main Results

Clearance of aerosolized [68Ga]macro aggregated albumin from distal airways occurred within minutes after delivery and followed a two-phase process. In cystic fibrosis pigs, both early and late clearance rates were slower. Stimulation of the cystic fibrosis airways with the purinergic agonist UTP further impaired late clearance. Only 1 cystic fibrosis pig treated with UTP out of 6 cleared more than 20% of the delivered dose.

Conclusions

These data indicate that mucociliary transport in the small airways is fast and can easily be missed if the acquisition is not fast enough. The data also indicate that mucociliary transport is impaired in small airways of cystic fibrosis pigs. This defect is exacerbated by stimulation of mucus secretions with purinergic agonists.
The interaction between social determinants of health, health behaviors, and child’s intellectual developmental diagnosis
Authors: Tchoua Phoebe P. , Clarke Emily , Wasser Heather , Agrawal Seema , Scothorn Rebecca , Thompson Kelsey , Schenkelberg Michaela , Willis Erik A.
Published: May 2024

INTRODUCTION

Social determinants of health (SDOH) may impact caregivers’ ability to implement evidence-based health practices at home during early childhood, especially in families with children with intellectual and developmental disabilities (IDD). Therefore, we examined the influence of SDOH and children’s diagnosis (typically developing [TD], Down syndrome [DS], autism) on caregiver’s self-report of meeting evidence-based health practices.

METHODS

Caregivers (n=172) of children ages 2-6 years (TD: n=93, DS: n=40, autism: n=39) completed an online survey on SDOH and health practices related to child nutrition (CN), physical activity (PA), outdoor play (OP), and screen time (ST). A total SDOH score was computed by assigning 1 point for each favorable SDOH metric (range 0-13). Linear regressions were used to examine associations between SDOH and CN, PA, OP, ST health practices and the moderating effect of IDD diagnosis.

RESULTS

Most caregivers were non-Hispanic White (84.3%), female (76.7%), 18-35 years old (55.2%), and married (89.5%). The DS group had the lowest SDOH score (mean = 8.4±1.0) compared to autism (mean = 10.1±1.0) and TD (mean = 11.0±0.9). No family scored 100% in evidence-based practices for any health practice. SDOH score was significantly associated with evidence-based practices met score for CN (b = 1.94, 95% CI = 0.84, 3.04; p = 0.001) and PA (b = 4.86, 95% CI = 2.92, 6.79; p <0.0001). Moderation analysis showed no association in the DS and autism groups between SDOH score and CN percent total score, or between SDOH score and CN, PA, and OP for percent evidence-based practices met. SDOH score was also not associated with OP percent total score for the DS group.

CONCLUSIONS

This study highlights the differential influence of SDOH on caregivers’ implementing health practices in families with children of different IDD diagnoses. Future research is needed to understand impacts of SDOH on non-typically developing children.
In-brain construction of receptor-based protease sensors by coupling ligand-directed chemistry and click chemistry
Authors: Sakamoto Seiji , Shiraiwa Kazuki , Wang Mengchu , Ishikawa Mamoru , Nonaka Hiroshi , Hamachi Itaru
Published: May 2024

The chemical modification of natural proteins in living systems is highly desirable toward the cutting-edge research in chemistry-biology interface. Recent advances in bioorthogonal protein modification have enabled the production of chemically functional proteins in cultured cell systems. However, few methods are applicablein vivobecause of the complexity of the three-dimensional constructs of living systems with diverse, heterogeneous cell populations and flow systems filled with tissue fluids. Here, we report a genetic engineering-free method to modify receptor proteins with various probes in the living mouse brain by combining in-brain ligand-directed chemistry with bioorthogonal click chemistry, and propose a chemical guideline for the reaction design. The rapid and selective tethering of a set of fluorescent peptides to AMPA-type glutamate receptors (AMPARs) allowed the construction of receptor-based fluorescent sensors. These probes enabled mapping of the activity of matrix metalloproteinase-9 proximal to AMPARs in the living brain to be realized with high spatial resolution. Our strategy provides new opportunities for the precise analysis of particularin vivomicroenvironments that has not been able to be addressed by conventional methods. Such analysis should contribute to the understanding of the molecular basis for complicatedin vivoevents, such as the regulation of neuroplasticity, the most important challenge in neuroscience.
The sensory shark: high-quality morphological, genomic and transcriptomic data for the small-spotted catsharkScyliorhinus caniculareveal the molecular bases of sensory organ evolution in jawed vertebrates
Authors: Mayeur H. , Leyhr J. , Mulley J. , Leurs N. , Michel L. , Sharma K. , Lagadec R. , Aury J.-M. , Osborne O.G. , Mulhair P. , Poulain J. , Mangenot S. , Mead D. , Smith M. , Corton C. , Oliver K. , Skelton J. , Betteridge E. , Dolucan J. , Dudchenko O. , Omer A.D. , Weisz D. , Aiden E.L. , McCarthy S. , Sims Y. , Torrance J. , Tracey A. , Howe K. , Baril T , Hayward A. , Martinand-Mari C. , Sanchez S. , Haitina T. , Martin K. , Korsching S.I. , Mazan S. , Debiais-Thibaud M.
Published: May 2024

Cartilaginous fishes (chimaeras and elasmobranchs -sharks, skates and rays) hold a key phylogenetic position to explore the origin and diversifications of jawed vertebrates. Here, we report and integrate reference genomic, transcriptomic and morphological data in the small-spotted catsharkScyliorhinus caniculato shed light on the evolution of sensory organs. We first characterise general aspects of the catshark genome, confirming the high conservation of genome organisation across cartilaginous fishes, and investigate population genomic signatures. Taking advantage of a dense sampling of transcriptomic data, we also identify gene signatures for all major organs, including chondrichthyan specializations, and evaluate expression diversifications between paralogs within major gene families involved in sensory functions. Finally, we combine these data with 3D synchrotron imaging andin situgene expression analyses to explore chondrichthyan-specific traits and more general evolutionary trends of sensory systems. This approach brings to light, among others, novel markers of the ampullae of Lorenzini electro-sensory cells, a duplication hotspot for crystallin genes conserved in jawed vertebrates, and a new metazoan clade of the Transient-receptor potential (TRP) family. These resources and results, obtained in an experimentally tractable chondrichthyan model, open new avenues to integrate multiomics analyses for the study of elasmobranchs and jawed vertebrates.
Stand Age and Climate Change Effects on Carbon Increments and Stock Dynamics
Authors: Vangi Elia , Dalmonech Daniela , Morichetti Mauro , Grieco Elisa , Giannetti Francesca , D’Amico Giovanni , Nakhavali Mahdi (Andre) , Chirici Gherardo , Collalti Alessio
Published: May 2024

Carbon assimilation and wood production are influenced by environmental conditions and endogenous factors, such as species auto-ecology, age, and hierarchical position within the forest structure. Disentangling the intricate relationships between those factors is more pressing than ever due to climate change’s pressure. We employed the 3D-CMCC-FEM model to simulate undisturbed forests of different ages under four climate change scenarios (plus one no climate change) from five Earth System Models. In this context, carbon stocks and increment were simulated via total car-bon woody stocks and mean annual increment, which depends mainly on climate trends. We find greater differences among different age cohorts under the same scenario than in different climate scenarios under the same age class. Increasing temperature and changes in precipitation patterns led to a decline in above-ground biomass in spruce stands, espe-cially in the older age classes. On the contrary, the results show that beech forests at DK-Sor will maintain and even increase C-storage rates under most RCP scenarios. Scots pine forests show an intermediate behavior with a stable stock capacity over time and in different scenarios but with decreasing mean volume annual increment. These results confirm current observations worldwide that indicate a stronger climate-related decline in conifers forests than in broadleaves.
Hypothalamus-specific NSCs derived from hPSCs ameliorate age-associated dysfunction upon transplantation into aged mouse hypothalamus
Authors: Sulistio Yanuar Alan , Lee Yuna , Pieknell Kelvin , Hong Sebin , Kim Jumi , Seok Min Jong , Lee Na-Kyung , Park Kyu-Sang , Hong Taeui , Choi Suyeon , Kim Ki Woo , Yang Dong Joo , Park Woong-Yang , Han Kyung Yeon , Yoon Seul Gi , Kim Il Yong , Seong Je Kyung , Lee Tae Yong , Kim Min Sung , Kim Min Soo , Lee Sang-Hun
Published: May 2024

The hypothalamus is the brain region that regulates systemic body metabolism and multiple functions in other brain regions. In adult mice, the hypothalamus harbors neural stem/precursor cell (NSC)-like cells. Along with the dysregulation of body metabolism and physiology that occurs during aging, the NSC population in the hypothalamus declines with age. Here, we introduce a novel protocol that yields scalable and storable hypothalamus-specific NSCs (htNSCs) from human pluripotent stem cells (hPSCs). Implanting htNSCs into the medio-basal hypothalami of aged mice conspicuously ameliorated age-related declines in metabolic fitness, physical capacity, and cognitive function and produced corresponding histologic changes in various body tissues. Single transcriptome and immunohistochemical analyses of the grafted hypothalamic tissues showed that the anti-aging effects were attained by correcting glial NF-κB, TNF-α, and NLRP3 inflammasome pathways. Collectively, our findings support the potential of anti- or healthy aging therapies that target htNSCs and hypothalamic inflammation.

One Sentence Summary

hPSC-derived hypothalamus NSCs mitigate age-associated physiological decline upon transplantation into the hypothalamus of aged mice.
Genomic factors shaping codon usage across the Saccharomycotina subphylum
Authors: Zavala Bryan , Dineen Lauren , Fisher Kaitlin J. , Opulente Dana A. , Harrison Marie-Claire , Wolters John F. , Shen Xing-Xing , Zhou Xiaofan , Groenewald Marizeth , Hittinger Chris Todd , Rokas Antonis , LaBella Abigail Leavitt
Published: May 2024

Codon usage bias, or the unequal use of synonymous codons, is observed across genes, genomes, and between species. The biased use of synonymous codons has been implicated in many cellular functions, such as translation dynamics and transcript stability, but can also be shaped by neutral forces. The Saccharomycotina, the fungal subphylum containing the yeastsSaccharomyces cerevisiaeandCandida albicans, has been a model system for studying codon usage. We characterized codon usage across 1,154 strains from 1,051 species to gain insight into the biases, molecular mechanisms, evolution, and genomic features contributing to codon usage patterns across the subphylum. We found evidence of a general preference for A/T-ending codons and correlations between codon usage bias, GC content, and tRNA-ome size. Codon usage bias is also distinct between the 12 orders within the subphylum to such a degree that yeasts can be classified into orders with an accuracy greater than 90% using a machine learning algorithm trained on codon usage. We also characterized the degree to which codon usage bias is impacted by translational selection. Interestingly, the degree of translational selection was influenced by a combination of genome features and assembly metrics that included the number of coding sequences, BUSCO count, and genome length. Our analysis also revealed an extreme bias in codon usage in the Saccharomycodales associated with a lack of predicted arginine tRNAs. The order contains 24 species, and 23 are computationally predicted to lack tRNAs that decode CGN codons, leaving only the AGN codons to encode arginine. Analysis of Saccharomycodales gene expression, tRNA sequences, and codon evolution suggests that extreme avoidance of the CGN codons is associated with a decline in arginine tRNA function. Codon usage bias within the Saccharomycotina is generally consistent with previous investigations in fungi, which show a role for both genomic features and GC bias in shaping codon usage. However, we find cases of extreme codon usage preference and avoidance along yeast lineages, suggesting additional forces may be shaping the evolution of specific codons.
A dedicated caller forDUX4rearrangements from whole-genome sequencing data
Authors: Grobecker Pascal , Berri Stefano , Peden John F. , Chow Kai-Jie , Fielding Claire , Armogida Ivana , Northen Helen , McBride David J. , Campbell Peter J. , Becq Jennifer , Ryan Sarra L. , Bentley David R. , Harrison Christine J. , Moorman Anthony V. , Ross Mark T. , Mijuskovic Martina
Published: May 2024

Rearrangements involving theDUX4gene (DUX4-r) define a subtype of paediatric and adult acute lymphoblastic leukaemia (ALL) with a favourable outcome. Currently, there is no ‘standard of care’ diagnostic method for their confident identification. Here, we present an open-source software tool designed to detectDUX4-r from short-read, whole-genome sequencing (WGS) data. Evaluation on a cohort of 210 paediatric ALL cases showed that our method detects all known, as well as previously unidentified, cases ofIGH::DUX4and rearrangements with other partner genes. These findings demonstrate the possibility of robustly detectingDUX4-r using WGS in the routine clinical setting.
A sequential, RNA-derived, modified adenosine pathway safeguards cellular metabolism
Authors: Ogawa Akiko , Watanabe Satoshi , Kawakami Tomoyoshi , Tsai Allen Yi-Lun , Fuse Jirio , Araki Kimi , Sawa Shinichiro , Inaba Kenji , Wei Fan-Yan
Published: May 2024

RNA contains diverse post-transcriptional modifications and its catabolic breakdown yields numerous modified nucleosides that must be properly processed, but the molecular mechanism is largely unknown. Here, we show that three RNA-derived modified adenosines,N6-methyladenosine (m6A),N6,N6-dimethyladenosine (m6,6A), andN6-isopentenyladenosine (i6A), are sequentially metabolized to inosine monophosphate (IMP) to prevent their intrinsic cytotoxicity. These modified adenosines are phosphorylated by adenosine kinase (ADK) followed by adenosine deaminase-like (ADAL)-mediated deamination in both plants and animals. ADAL knockout mice accumulateN6-modified AMPs that allosterically inhibit AMP-activated protein kinase (AMPK), leading to dysregulation of glucose metabolism. Furthermore, ADK deficiency, reported in patients with severe metabolic defects, induces aberrant elevation of m6A/m6,6A/i6A, disrupting lipid metabolism and causing early death in mouse models. The findings unveil a fundamental mechanism by which cells alleviate the toxicity of modified adenosines, and that connects modified adenosines to human disease.

In brief

RNA catabolism yields diverse nucleosides with modifications attached. Three RNA-derived modified adenosines (m6A, m6,6A, and i6A) are intrinsically toxic and subjected to sequential metabolism to yield inosine monophosphate. Dysregulation of this pathway impairs energy balance and contributes to metabolic diseases.

Highlights

Cytotoxic RNA catabolism-derived modified adenosines undergo sequential metabolism

m6A, m6,6A, and i6A are phosphorylated by ADK then deaminated by ADAL to IMP

m6AMP, m6,6AMP, and i6AMP allosterically inhibit AMP-mediated AMPK activation

Loss of ADK causes the accumulation of m6A, m6,6A, and i6A, and abnormal lipid metabolism, which can lead to genetic disease
Subtilase SBT5.2 inactivates flagellin immunogenicity in the plant apoplast
Authors: Buscaill Pierre , Sanguankiattichai Nattapong , Kaschani Farnusch , Huang Jie , Mooney Brian C. , Li Yuge , Lyu Joy , Sueldo Daniela , Kaiser Markus , van der Hoorn Renier A. L.
Published: May 2024

Most angiosperm plants recognise the flg22 epitope in bacterial flagellin via homologs of cell surface receptor FLS2 and mount pattern-triggered immune responses. However, flg22 is buried within the flagellin protein indicating that proteases might be required for flg22 release. Here, we demonstrate the extracellular subtilase SBT5.2 not only releases flg22, but also inactivates the immunogenicity of flagellin and flg22 by cleaving within the flg22 epitope, consistent with previous reports that flg22 is unstable in the apoplast. The prolonged lifetime of flg22 insbt5.2mutant plants results in increased bacterial immunity in priming assays, indicating that SBT5.2 counterbalances flagellin immunogenicity to provide spatial-temporal control and restrict costly immune responses and that bacteria take advantage of the host proteolytic machinery to avoid detection by flagellin having a protease-sensitive flg22 epitope.
The structure of the SufS-SufE complex reveals interactions driving protected persulfide transfer in iron-sulfur cluster biogenesis
Authors: Gogar Rajleen K. , Chhikara Nidhi , Vo Minh , Gilbert Nathaniel C. , Dunkle Jack A. , Frantom Patrick A.
Published: May 2024

Fe-S clusters are critical cofactors for redox chemistry in all organisms. The cysteine desulfurase, SufS, provides sulfur in the SUF Fe-S cluster bioassembly pathway. SufS is a dimeric, PLP-dependent enzyme that uses cysteine as a substrate to generate alanine and a covalent persulfide on an active site cysteine residue. SufS enzymes are activated by an accessory transpersulfurase protein, either SufE or SufU depending on the organism, which accepts the persulfide product and delivers it to downstream partners for Fe-S assembly. Here, usingE. coliproteins, we present the first X-ray crystal structure of a SufS/SufE complex. There is a 1:1 stoichiometry with each monomeric unit of the EcSufS dimer bound to one EcSufE subunit, though one EcSufE is rotated ∼7° closer to the EcSufS active site. EcSufE makes clear interactions with the α16 helix of EcSufS and site-directed mutants of several α16 residues were deficient in EcSufE binding. Analysis of the EcSufE structure showed a loss of electron density at the EcSufS/EcSufE interface for a flexible loop containing the highly conserved residue R119. An R119A EcSufE variant binds EcSufS but is not active in cysteine desulfurase assays and fails to support Fe-S cluster bioassembly in vivo.35S-transfer assays suggest that R119A EcSufE can receive a persulfide, suggesting the residue may function in a release mechanism. The structure of the EcSufS/EcSufE complex allows for comparison with other cysteine desulfurases to understand mechanisms of protected persulfide transfer across protein interfaces.
T cells regulate intestinal motility and shape enteric neuronal responses to intestinal microbiota
Authors: de Souza Patricia Rodrigues Marques , Keenan Catherine M. , Wallace Laurie E. , Habibyan Yasaman Bahojb , Davoli-Ferreira Marcela , Ohland Christina , Vicentini Fernando A. , McCoy Kathy D. , Sharkey Keith A.
Published: May 2024

The gut microbiota and immune system maintain intestinal homeostasis and regulate gut physiology in concert with the enteric nervous system (ENS). However, the underlying mechanisms remain incompletely understood. Using wildtype and T-cell deficient germ-free mice colonized with segmented filamentous bacteria (SFB) or specific pathogen-free (SPF) microbiota, we studied immune regulation of the ENS and intestinal motility. Colonization markedly increased Th17 cells and Treg expressing RORγ+T cells in both the ileum and colon of wildtype mice. T cells were necessary for the normalization of intestinal motility after colonization by SPF microbiota, and for SFB to restore neuronal density in the ENS of the ileum of germ-free mice. T cells were also required for neurogenic responses in myenteric neurons of the ileum, but not the colon, and for regulating the levels of nestin expression. The cytokines IL-1β and IL-17A mediate the enteric neurogenic response to an SPF microbiota but were not involved in the regulation of intestinal motility. Together, our findings provide new insights into the microbiota-neuroimmune dialogue that regulates intestinal physiology.
Chicken cecal microbial functional capacity and resistome differ by age and barn disinfection practice
Authors: Fan Yi , Ju Tingting , Bhardwaj Tulika , Korver Douglas R. , Willing Benjamin P.
Published: May 2024

Chemical disinfectants and water-wash methods are widely employed in sanitizing broiler chicken barns. Previous studies showed that chemical disinfectants affect environmental microbial composition and antibiotic resistance genes (ARGs). However, little is known regarding how barn disinfection treatments impact the chicken gut resistome and microbial functionality. The current study compared the effects of chemical disinfection and water-wash method on the gut microbiome and resistome of commercial broilers using a crossover experimental design after 2 production cycles at 7 barns. Shotgun metagenomic sequencing performed on cecal contents collected at day 7 and 30 also allowed evaluation of age-associated characteristics of microbiome. Age of the chickens had the largest effects on the resistome, with younger birds having increased relative abundance of total ARGs (P<0.05) and differences in resistance mechanism, however, functional and resistome differences were also identified by barn sanitation practice. At day 7, chickens in chemically-disinfected barns had decreased functional capacity related to amino acid synthesis compared to the water-wash group. Additionally, genes related to stringent response were enriched in chickens raised under chemically-disinfected condition (FDR-P<0.05), suggesting selection for stress resistance. Consistently, lower abundance of genetic pathways encoding amino acid biosynthesis associated with cecalHelicobacter pullorumwas observed in the disinfection group at day 30 compared to the water-wash group, with the same pattern in short-chain fatty acid biosynthesis (FDR-P<0.05). Overall, while the use of disinfectants in barn sanitation slightly affected the relative abundance of some ARGs in the gut, age had a dominant effect on the microbial functionality and resistome.

Importance

This is the first study to evaluate the effect of sanitation practices on microbial functional capacity and resistome of chickens in a commercial setting. It is also amongst the biggest metagenomics studies on the gut microbiome of broiler chickens. It provides new insights into the changes in resistance profiles with age that agree with other studies examining maturation of the microbiome in other species. Finally, the current study provides valuable insights for informing industry sanitation practices and future studies on broiler gut microbiome and resistome.
Convergence and horizontal gene transfer drive the evolution of anaerobic methanotrophy in archaea
Authors: Woods Philip H. , Speth Daan R. , Laso-Pérez Rafael , Utter Daniel R. , Ruff S. Emil , Orphan Victoria J.
Published: May 2024

1

Despite their large environmental impact and multiple independent emergences, the processes leading to the evolution of anaerobic methanotrophic archaea (ANME) remain unclear. This work uses comparative metagenomics of a recently evolved but understudied ANME group, ‘CandidatusMethanovorans’ (ANME-3) to identify evolutionary processes and innovations at work in ANME which may be obscured in earlier evolved lineages. Within members ofMethanovorans, we identified convergent evolution in carbon and energy metabolic genes as likely drivers of ANME evolution. We also identified erosion of genes required for methylotrophic methanogenesis along with horizontal acquisition of multi-heme cytochromes and other loci uniquely associated with ANME. The assembly and comparative analysis of multiple Methanovorans genomes offers important functional context for understanding the niche-defining metabolic differences between methane-oxidizing ANME and their methanogen relatives. Furthermore, this work illustrates the multiple evolutionary modes at play in the transition to a novel and globally important metabolic niche.
Designing DNA With Tunable Regulatory Activity Using Discrete Diffusion
Authors: Sarkar Anirban , Tang Ziqi , Zhao Chris , Koo Peter
Published: May 2024

Engineering regulatory DNA sequences with precise activity levels in specific cell types hold immense potential for medicine and biotechnology. However, the vast combinatorial space of possible sequences and the complex regulatory grammars governing gene regulation have proven challenging for existing approaches. Supervised deep learning models that score sequences proposed by local search algorithms ignore the global structure of functional sequence space. While diffusion-based generative models have shown promise in learning these distributions, their application to regulatory DNA has been limited. Evaluating the quality of generated sequences also remains challenging due to a lack of a unified framework that characterizes key properties of regulatory DNA. Here we introduce DNA Discrete Diffusion (D3), a generative framework for conditionally sampling regulatory sequences with targeted functional activity levels. We develop a comprehensive suite of evaluation metrics that assess the functional similarity, sequence similarity, and regulatory composition of generated sequences. Through benchmarking on three high-quality functional genomics datasets spanning human promoters and fly enhancers, we demonstrate that D3 outperforms existing methods in capturing the diversity of cis-regulatory grammars and generating sequences that more accurately reflect the properties of genomic regulatory DNA. Furthermore, we show that D3-generated sequences can effectively augment supervised models and improve their predictive performance, even in data-limited scenarios.
Deep mutational scanning of H5 hemagglutinin to inform influenza virus surveillance
Authors: Dadonaite Bernadeta , Ahn Jenny J , Ort Jordan T , Yu Jin , Furey Colleen , Dosey Annie , Hannon William W , Baker Amy Vincent , Webby Richard J , King Neil P , Liu Yan , Hensley Scott E , Peacock Thomas P , Moncla Louise H , Bloom Jesse D
Published: May 2024

H5 influenza is a potential pandemic threat. Previous studies have identified molecular phenotypes of the viral hemagglutinin (HA) protein that contribute to pandemic risk, including cell entry, receptor preference, HA stability, and reduced neutralization by polyclonal sera. Here we use pseudovirus deep mutational scanning to measure how all mutations to a clade 2.3.4.4b H5 HA affect each phenotype. We identify mutations that allow HA to better bind a2-6-linked sialic acids, and show that some viruses already carry mutations that stabilize HA. We also identify recent viral strains with reduced neutralization to sera elicited by candidate vaccine virus. Overall, the systematic nature of deep mutational scanning combined with the safety of pseudoviruses enables comprehensive characterization of mutations to inform surveillance of H5 influenza.
ATP and glutamate coordinate contractions in the freshwater spongeEphydatia muelleri
Authors: Ho Vanessa R , Goss Greg G , Leys Sally P
Published: May 2024

Sponges (phylumPorifera) are an early diverging animal lineage that lacks both conventional nervous and muscular systems, and yet they are able to produce coordinated whole-body contractions in response to disturbances. Little is known about the underlying signaling mechanisms in coordinating such responses. Previous studies demonstrated that sponges respond specifically to neuroactive chemicals such as L-glutamate and γ-amino-butyric acid (GABA), which trigger and prevent contractions respectively. Genes for purinergic P2X-like receptors are present in several sponge genomes, leading us to ask whether ATP works with glutamate to coordinate contractions in sponges as it does in other animal nervous systems. Using pharmacological approaches on the freshwater spongeEphydatia muelleri, we show that ATP is involved in coordinating contractions. Bath applications of ATP cause a rapid, sustained expansion of the excurrent canals in a dose-dependent manner. Complete contractions occur when ATP is added in the presence of apyrase, an enzyme that hydrolyzes ATP. Applying ADP, the first metabolic product of ATP hydrolysis, triggers complete contractions, whereas AMP, the subsequent metabolite, does not trigger a response. Blocking ATP from binding and activating P2X receptors with pyridoxalphosphate-6-azophenyl-2’,4’-disulfonic acid (PPADS) prevents both glutamate- and ATP-triggered contractions, suggesting that ATP works downstream of glutamate. Bioinformatic analysis revealed two P2X receptor sequences, one which groups with other vertebrate P2X receptors. Altogether, our results confirm that purinergic signaling by ATP is involved in coordinating contractions in the freshwater sponge suggesting a role of ATP-mediated signaling that predates the evolution of the nervous system and multicellularity in animals.

Summary statement

Nerveless sponges coordinate a sneeze-like reflex using glutamate and ATP signaling to expel water from the body.
Stearoyl coenzyme A desaturase 1 (SCD1) regulates foot-and-mouth disease virus replication by modulating host cell lipid metabolism and 2C-mediated replication complex formation
Authors: Lv Bonan , Yuan Yuncong , Yang Zhuang , Wang Xingran , Hu Jianjun , Sun Yidan , Du Hang , Liu Xuemei , Duan Huimin , Ding Ruyi , Pan Zishu , Tang Xiao-Feng , Shen Chao
Published: May 2024

The life cycle of foot-and-mouth disease virus (FMDV) is tightly regulated by host cell lipid metabolism. In a previous study, we successfully established a BHK-21 cell model (BHK-Op) for persistent FMDV infection by single-cell clone selection and isolated a virus-negative cell line (BHK-VEC cells) from high-passage BHK-Op cells. BHK-VEC cells could be not infected with FMDV. By conforming the transcriptome data of BHK-VEC cells and BHK-21 cells, we identified that the stearoyl coenzyme A desaturase 1 (SCD1), a key enzyme for the fatty acid metabolism, regulates FMDV replication. SCD1 overexpression or exogenous addition of oleic acid (OA), a product of SCD1 enzyme activity, promoted or upregulated FMDV replication in BHK-21 cells or SCD1 knockdown cells, respectively. Interestingly, overexpression of SCD1 or exogenous addition of OA restored the FMDV infection and replication in BHK-VEC cells. Exogenous addition of OA also promoted FMDV replication in BHK-Op. SCD1 recruited the nonstructural FMDV protein 2C to the detergent-resistant membrane located in the perinuclear nucleus to form replication complex. Inhibition of SCD1 enzyme activity resulted in significantly decreased number of FMDV replication complexes with also abnormal morphology. Importantly, inhibition of SCD1 enzyme activity effectively suppressed replication of other positive-sense RNA viruses, such as REO176, PV1 and EV71. Our results demonstrated that, as a key host regulator of RNA virus replication, SCD1 is a potential target for developing novel drugs against positive-sense RNA virus infection.
Linking regulatory variants to target genes by integrating single-cell multiome methods and genomic distance
Authors: Dorans Elizabeth , Jagadeesh Karthik , Dey Kushal , Price Alkes L.
Published: May 2024

Methods that analyze single-cell paired RNA-seq and ATAC-seq multiome data have shown great promise in linking regulatory elements to genes. However, existing methods differ in their modeling assumptions and approaches to account for biological and technical noise—leading to low concordance in their linking scores—and do not capture the effects of genomic distance. We propose pgBoost, an integrative modeling framework that trains a non-linear combination of existing linking strategies (including genomic distance) on fine-mapped eQTL data to assign a probabilistic score to each candidate SNP-gene link. We applied pgBoost to single-cell multiome data from 85k cells representing 6 major immune/blood cell types. pgBoost attained higher enrichment for fine-mapped eSNP-eGene pairs (e.g. 21x at distance >10kb) than existing methods (1.2-10x; p-value for difference = 5e-13 vs. distance-based method and < 4e-35 for each other method), with larger improvements at larger distances (e.g. 35x vs. 0.89-6.6x at distance >100kb; p-value for difference < 0.002 vs. each other method). pgBoost also outperformed existing methods in enrichment for CRISPR-validated links (e.g. 4.8x vs. 1.6-4.1x at distance >10kb; p-value for difference = 0.25 vs. distance-based method and < 2e-5 for each other method), with larger improvements at larger distances (e.g. 15x vs. 1.6-2.5x at distance >100kb; p-value for difference < 0.009 for each other method). Similar improvements in enrichment were observed for links derived from Activity-By-Contact (ABC) scores and GWAS data. We further determined that restricting pgBoost to features from a focal cell type improved the identification of SNP-gene links relevant to that cell type. We highlight several examples where pgBoost linked fine-mapped GWAS variants to experimentally validated or biologically plausible target genes that were not implicated by other methods. In conclusion, a non-linear combination of linking strategies, including genomic distance, improves power to identify target genes underlying GWAS associations.
Investigating psychobiological causes and mechanisms in functional seizures and functional motor symptoms: Study protocol
Authors: Pick Susannah , David Anthony S. , Edwards Mark J. , Goldstein Laura H. , Hodsoll John , Merritt Millman L. S. , Nicholson Timothy R. , Reinders A.A.T.S. , Stanton Biba , Winston Joel S. , Mehta Mitul A. , Chalder Trudie , Hotopf Matthew
Published: May 2024

Introduction

Advances have been made in understanding the aetiology of functional neurological disorder (FND); however, its pathophysiological mechanisms have not been definitively demonstrated. Evidence suggests interacting roles for altered emotional processing and interoception, elevated autonomic arousal, and dissociation, but there is limited evidence demonstrating their causal influence on specific FND symptoms. Our superordinate aim is to elucidate potentially shared and distinct aetiological factors and mechanisms in two common FND subtypes, functional seizures (FS) and functional motor symptoms (FMS).

Methods

This study has a multimodal, mixed between- and within-groups design. The target sample is 50 individuals with FS, 50 with FMS, 50 clinical controls (anxiety/depression), and 50 healthy controls. Potential aetiological factors (e.g., adverse life events, physical/mental health symptoms, dissociative tendencies, interoceptive insight/sensibility) will be assessed with a detailed medical history interview and self-report questionnaires. A laboratory session will include a neurocognitive battery, psychophysiological testing, cardiac interoception and time estimation tasks and an isometric handgrip task. A subsample will undergo magnetic resonance imaging, including structural, resting-state and task-based scans combined with psychophysiological recording. Remote monitoring with ecological momentary assessment and wearables will measure variability in FND symptoms and in patients’ daily lives and their potential predictors/correlates for ≥2 weeks. Longitudinal follow-ups at 3, 6, and 12-months will monitor longer-term outcomes in the clinical groups.

Discussion

This study employs multimodal research methods to rigorously examine several putative mechanisms in FND, at subjective/experiential, behavioural, and physiological levels. The study will test causal hypotheses about the role of altered emotional processing, autonomic arousal, dissociation and interoception in the initiation or exacerbation of FND symptoms, directly comparing these processes in FS and FMS to healthy and clinical controls. This is the first study of its kind, with potential to reveal important targets for prevention and treatment of FND in future.
Early detection of anastomotic leakage in upper gastrointestinal surgery
Authors: Merboth Felix , Sonntag Friederike , Sonntag Katharina , Reißfelder Christoph , Stange Daniel E. , Weitz Jürgen , Bogner Andreas
Published: May 2024

Background

Although surgical methods for upper gastrointestinal tract cancer continue to advance with the aim of reducing the incidence of anastomotic leakage (AL), it remains a prevalent and serious complication. Therefore, early identification of patients at high risk for AL is necessary for timely therapeutic measures.

Methods

We retrospectively identified patients with AL who underwent elective gastric/esophageal resection at our department between 2005 and 2017. Using propensity score matching, a comparison group without AL but with comparable baseline characteristics was developed. Several previously published risk scores (o-POSSUM, E-PASS, Steyerberg, NUn score) were calculated, and their predictive accuracy for presence of AL was compared.

Results

Steyerberg Risk Score, o-POSSUM, and E-PASS were found to be unsuitable for early detection of an anastomotic problem. However, an increased NUn score on the fourth to seventh postoperative day was independently associated with the presence of AL. The test accuracy (0.631-0.714), sensitivity (28.9%-50.5%), and specificity (72.5%-89.5%) were marginally satisfactory. When only C-reactive protein levels were considered, similar test accuracy (0.629-0.717), sensitivity (47.5%-69.9%), and specificity values (51.5%-81.6%) were observed using a cut-off of 150 mg/l.

Conclusions

The NUn score showed no superiority over CRP values in the prediction of AL. Therefore, further diagnostics should be carried out from the fourth postoperative day if the CRP is > 150 mg/l. However, large-scale registry studies and artificial intelligence may aid in more appropriate determination of patient-specific risks in the future.
Body image and appearance distress among military veterans and civilians with an injury-related visible difference: A comparison study
Authors: Keeling Mary , Harcourt Diana , White Paul , Evans Sarah , Williams Victoria S. , Kiff James , Williamson Heidi
Published: May 2024

Injuries sustained during military conflict can significantly impact appearance. Yet, little is known about the psychosocial experiences of veterans with conflict-related appearance-altering injuries (AAI) and whether current civilian interventions are appropriate for veterans. To inform the development of acceptable and effective support for veterans with appearance–related psychosocial difficulties, this study aimed to identify factors associated with psychosocial adjustment to an altered appearance among both veterans and civilians with AAI. A cross-sectional online survey study was conducted. N = 121 veterans and N = 197 civilians who had sustained AAI took part. Multivariable regression was used to examine factors related to adjustment in the two groups. Overall, both groups reported similar experiences, with some key exceptions. Veterans reported significantly greater depression and Post Traumatic Stress Disorder, significantly lower Body Image (BI) psychological flexibility, BI life engagement, and higher perceived appearance-related stigma. BI psychological flexibility was identified as a key predictor of appearance-related outcomes in both groups. Self-compassion predicted social anxiety and depression symptoms in both groups, but only appearance outcomes among civilians. Based on these identified associated factors, it is suggested that both groups, but particularly veterans, may benefit from an Acceptance and Commitment Therapy-based intervention, including explicit self-compassion activities, and practical social skills training.
Prevalence and determinants of tobacco use among school-going adolescents in 53 African countries: evidence from Global Youth Tobacco Surveys
Authors: Pokothoane Retselisitsoe , Agerfa Terefe Gelibo , Miderho Christus Cito , Mdege Noreen Dadirai
Published: May 2024

Introduction

Tobacco use typically begins during adolescence. There is a lack of comprehensive evidence on the use of different tobacco products among adolescents in Africa.

Aims and Methods

We used the most recent Global Youth Tobacco Surveys data from 53 African countries, covering 2003 – 2020, to estimate the overall and gender-specific prevalence of each type of tobacco product by country, Africa region, World Bank income group, and age group. We further used independent logit regression models to assess the determinants of the use of different types of tobacco products. The datasets covered 204,537 primary/secondary school- going adolescents aged 11 - 17 years. Pooled prevalence estimates were computed using the individual-level data.

Results

The overall prevalence of any tobacco use among African adolescents was 14.3% [95% CI: 13.5, 15.3]. Specifically, the prevalence for cigarette smoking was 6.4% [95% CI: 5.9, 7.0], for other smoked tobacco was 6.7% [95% CI: 6.0, 7.4], for smokeless tobacco use was 6.4% [95% CI: 5.9, 6.9], and for shisha smoking was 5.2% [95% CI: 4.4, 6.1]. The prevalence of dual use of smoked and smokeless tobacco was 3.0% [95% CI: 2.8, 3.2], and that of shisha and cigarettes was 1.5% [95% CI: 1.2, 2.0]. The prevalence of any tobacco use was higher among boys (17.4%) than girls (10.6%). Exposure to anti-tobacco smoking messages, exposure to smoking at home and school, the age restriction to tobacco purchases, and peer pressure were positively associated with the tobacco use, irrespective of product type. Being a female was a protective factor of tobacco use for almost all products. Country-level factors such as predominant religion, African region, and World Bank income group were significant factors only for cigarettes and shisha smoking.

Conclusions

The prevalence of tobacco use among African adolescents aged 11 - 17 years is high, but similar across different tobacco products. Peer pressure and school environment significantly influence adolescents’ decisions to participate in tobacco use. Policymakers could prioritize implementing large pictorial health warnings about tobacco dangers covering the entire packaging of different products.

IMPLICATIONS

African countries and regions need to strengthen tobacco control policies that are most effective in reducing tobacco consumption among young people, such as increasing tobacco taxes, textual and graphic health warnings and banning tobacco industry influence: advertising and any sponsorships. It is also important to have comprehensive surveillance systems that monitor the use of the whole range of tobacco and nicotine products overtime.
The ARC Toolbox: Artificial Languages with Rhythmicity Control
Authors: Titone Lorenzo , Milosevic Nikola , Meyer Lars
Published: May 2024

Statistical learning is the ability to extract and retain statistical regularities from the environment. In language, extracting statistical regularities—so-called transitional probabilities, TPs—is crucial for segmenting speech and learning new words. To investigate whether neural activity synchronizes with these statistical patterns, so-called neural frequency-tagging paradigms have been employed. Here, brain activity is recorded while a stream of syllables is presented at one fixed rate (e.g., 3.3 Hz) and rhythmic patterns of low-TP events are present at a different rate (e.g., 1.1 Hz). Such studies report neural tracking of both syllables and TPs; that is, for both acoustic and abstract events, respectively. However, recent criticism pointed out that the possible confounding of acoustic and abstract rhythms limits the interpretability of this work. Here, we present a new Python toolbox that minimizes this confounding by creatingArtificial languages with Rhythmicity Controls(ARC). ARC features a phonological rhythmicity index (PRI) to quantify the confounding periodicity of phonological features at the TP rate. It implements a pseudo-random-walk approach to ensure unconfounded TP stationarity throughout streams of arbitrary length. We provide a step-by-step guide to generate artificial pseudowords based on a pre-specified syllable inventory and create controlled lexicon streams. Simulation results show that ARC lexicons minimize PRI and TP variance, not only relative to sets of random syllable groups, but also to benchmarking sets of artificial languages used in the prior literature. ARC should be used by future work in order to suppress the confounding of acoustics and TPs in artificial language learning experiments.