bluuebunny/crossref_metadata_2025 huggingface dataset:
Relationships among Physical Activity Bone Mineral Density and Body Composition in Obese and Athletes
Authors: Suttho Dutsadee , Apibantaweesakul Sudarat , Soponputthaporn Jatesupa , Hemapaibun Salintip , Santipongphibool Maitee , Tengcharoenkul Chatchaya
Published: December 2024

Background: Osteoporosis is a significant global public health issue, increasingly affecting younger individuals and placing substantial economic burdens on society. Risk factors vary, with non-modifiable ones like age and ethnicity, as well as modifiable factors including corticosteroid use, caffeine intake, and reduced exercise. This study examines the relationship between bone density, body components, and physical activity (PA) in enhancing bone health, particularly in obese athletes.Methods: The 66 participants aged 18 to 30 were classified into two groups: 34 obese and 32 athletes. Measured parameters included body composition through bioelectrical impedance analysis, and bone mineral density (BMD) via quantitative ultrasound, while PA was assessed using the International PA Questionnaire.Results: Our findings revealed a significant positive correlation between BMD and PA (r=0.284, P=0.023). Additionally, PA demonstrated strong negative correlations with body mass index (BMI), fat mass, and visceral fat (r=-0.738, r=-0.733, and r=-0.704 respectively, all P<0.001). In contrast, no significant correlation was observed between PA and lean mass (r=0.065, P=0.609). BMD was negatively associated with BMI and visceral fat, while a robust correlation between basal metabolic rate and lean mass was evident.Conclusions: A study comparing athletes involved in high-impact sports indicated that these athletes maintained adequate BMD for their chronological age (Z-score≥-2.0). Moreover, a significant difference in BMD was observed when comparing the athletes to the obese group(P=0.018).
Making yogurt with the ant holobiont uncovers bacteria, acids, and enzymes for food fermentation
Authors: Sinotte Veronica M. , Ramos-Viana Verónica , Vásquez Diego Prado , Sirakova Sevgi Mutlu , Valerón Nabila Rodríguez , Cuesta-Maté Ana , Taylor Parkins Shannara K. , Giecko Julia , Velasco Esther Merino , Zilber David , Munk Rasmus , Andersen Sandra B. , Dunn Robert R. , Jahn Leonie J.
Published: December 2024

Milk fermentation has a rich history in which food culture, the environment, and microbes intersect. However, the biocultural origins of fermentation practices and microbes have largely been replaced by industrial processes. Here, we consider a historical fermentation originating from Turkey and Bulgaria – ant yogurt. We revisit the traditional practices and modern gastronomic applications that use red wood ants (Formica rufagroup) to initiate milk fermentation. Subsequently, we characterize the ants and experimental ant-derived yogurts. We uncover that the ant holobiont, which consists of the ants and their microbes, contributes key acids and enzymes to fermentation. Metabarcoding and culturing revealed that lactic and acetic acid bacteria, including species related to conventional sourdough, originate from the live ants and proliferate in the milk. The ants and bacteria consequently introduce formic, lactic, and acetic acid, advantageous for yogurt acidification and coagulation. Last, proteases with the potential to act on casein may alter yogurt texture and are produced by the ants and bacteria. The ant holobiont thus catalyses fermentation akin to the microbial consortia in other ferments. Our findings highlight the value of integrating traditional, gastronomic, and biological frameworks to uncover the origins and applications of microbes for fermented foods.
ANALYSIS OF SELF-CARE FACTORS IN HYPERTENSION PATIENTS IN COMMUNITY SETTINGS
Authors: Dewi Ni Putu Ayu Ratna , Pandin Moses Glorino Rumambo , Nursalam  , Agustini Ni Luh Putu Inca Buntari , Wahyuni Ni Wayan Sri , Putra Komang Ardidhana Nugraha
Published: December 2024

Background

Controlling blood pressure in hypertensive patients is one of the most important interventions in preventing complications, reducing morbidity, and premature mortality. Patients must practice hypertension self-care to prevent the disease’s frequent recurrence from deteriorating their health and to maintain effective behavior.

Objective

Analyze the factors that influence the implementation of self-care in hypertensive patients.

Method

Cross-sectional using the purposive sampling technique involving 120 respondents. The study was conducted in the working area of the Gianyar 1 Health Center, Bali, Indonesia. Data collection utilized the Indonesian version of the High Blood Pressure self-care profile questionnaire. Analysis included univariate, bivariate using chi-square, and multivariate using multinomial logistic regression.

Results

A long history of suffering from hypertension has an effect on behavior; education has an effect on motivation; and education and work have an effect on self-efficacy.

Conclusion

The article emphasizes the importance of holistic treatments in managing high blood pressure, with a focus on patient engagement to improve taking care of themselves with focused education and support systems. The outcomes align with the axiological dimension of philosophy by highlighting practical values that enhance patients’ autonomy and quality of life through education and supportive systems. Further, the research makes an empirical contribution by providing a comprehensive knowledge of self-care characteristics, which can be used to develop culturally appropriate and patient-focused intervention techniques.
Role of personalized predictions for people with prediabetes: disseminating patient-centered estimates of benefit
Authors: Olchanski Natalia , Ciemins Elizabeth L. , Cuddeback John , Colangelo Francis , Koenig Carolyn , Kent David M.
Published: December 2024

Background

To assess acceptability and feasibility of incorporating individualized risk prediction into clinical assessment, decision making, and communication of risk of type 2 diabetes and prevention recommendations.

Methods

We integrated a prediction model into the clinical workflow at a US health care organization. We conducted patient and provider focus groups and pre- and post-dissemination surveys and assessed the effect on referrals to and enrollment in the Diabetes Prevention Program, among 2,775 patients with prediabetes who had primary care visits between May 2018 and December 2020.

Results

Among patients with prediabetes seen in primary care during the study period, 79% had a calculation with the risk prediction model completed. After implementation of the risk prediction model, prevention intervention rates increased, with 62.3% of high-risk patients receiving an intervention within 1 year.

Conclusions

Used at the point of care during a shared decision-making discussion between the patient and provider, the diabetes risk calculator helped providers prioritize patients for diabetes prevention interventions, facilitated communication, and successfully improved rates of engagement in their care among patients with prediabetes.
Sublethal pesticide exposure decreases mating and disrupts chemical signaling in a beneficial pollinator
Authors: Derstine Nathan , Murray Cameron , Purnell Freddy S , Amsalem Etya
Published: December 2024

Pesticides provide vital protection against insect pests and the diseases they vector but are simultaneously implicated in the drastic worldwide decline of beneficial insect populations. Convincing evidence suggests that even sublethal pesticide exposure has detrimental effects on both individual- and colony-level traits, but the mechanisms mediating these effects remained poorly understood. Here, we use bumble bees to examine how sublethal exposure to pesticides affects mating, a key life history event shared by nearly all insects, and whether these impacts are mediated via impaired sexual communication. In insects, mate location and copulation are primarily regulated through chemical signals and rely on both the production and perception of semiochemicals. We show through behavioral bioassays that mating success is reduced in bumble bee gynes after exposure to field-relevant sublethal doses of imidacloprid, and that this effect is likely mediated through a disruption of both the production and perception of semiochemicals. Semiochemical production was altered in gyne and male cuticular hydrocarbons (CHCs), but not in exocrine glands where sex pheromones are presumably produced (i.e., gyne mandibular glands and male labial glands). Male responsiveness to gyne mandibular gland secretion was reduced, but not the queen responsiveness to the male labial secretion. In addition, pesticide exposure reduced queen fat body lipid stores and male sperm quality. Overall, the exposure to imidacloprid affected the fitness and CHCs of both sexes and the antennal responses of males to gynes. Together, our findings identify disruption of chemical signaling as the mechanism through which sublethal pesticide exposure reduces mating success.
Tuning the contractility and deformation modes of active actin-based assemblies in vitro: from 2D active networks to liquid crystal drops
Authors: Stam Samantha , Huntley Steven , Feigeles Carolyn A. , Armstrong Veronica J. , Cheves Margaret A. , Rubin Sam , Weirich Kimberly L.
Published: December 2024

Actin cytoskeleton-based materials are widely investigated as model cellular materials to elucidate physical mechanisms of cell mechanics, such as shape regulation and force production, as well as intriguing soft polymeric materials. In this method, we detail creating actin-based assembliesin vitrousing purified protein for fluorescence microscopy studies. We polymerize long actin filaments in a sample chamber and use a polymer depletant to crowd filaments into a 2D-entangled network against a surface passivated with a surfactant layer. Adding skeletal muscle myosin II filaments in the presence of ATP induces contraction of the actin network. By bundling actin filaments with cross-linker, we tune the contractility of the assembly, transitioning from a material that buckles to a material that slides at the microscale. By reducing the length of the actin filaments through co-polymerizing actin in the presence of capping protein, we tune the material from being a 2D network to a liquid crystal. Cross-linking of dispersed short actin filaments results in 3D liquid crystal droplet formation.
Identification of potent HSV antivirals using 3D bioprinted human skin equivalents
Authors: Ellison S. Tori , Hayman Ian , Derr Kristy , Derr Paige , Frebert Shayne , Itkin Zina , Shen Min , Jones Anthony , Olson Wendy , Corey Lawrence , Wald Anna , Johnston Christine , Fong Youyi , Ferrer Marc , Zhu Jia
Published: December 2024

Herpes simplex virus (HSV) infection has worldwide public health concerns and lifelong medical impacts. The standard therapy, acyclovir, has limited efficacy in preventing HSV subclinical virus shedding, and drug resistance occurs in immunocompromised patients, highlighting the need for novel therapeutics. HSV infection manifests in the skin epidermal layer, but current drug discovery utilizes Vero cells and fibroblasts monolayer cultures, capturing neitherin vivorelevance nor tissue environment. To bridge the gap, we established 3D bioprinted human skin equivalents that recapitulate skin architecture in a 96-well plate format amenable for antiviral screening and preclinical testing. Screening a library of 738 compounds with broad targets and mechanisms of action, we identified potent antivirals, including most of the known anti-HSV compounds, validating the translational relevance of our assay. Acyclovir was dramatically less potent for inhibiting HSV in keratinocytes compared to donor-matched fibroblasts. In contrast, antivirals against HSV helicase/primase or host replication pathways displayed similar potency across cell types and donor sources in 2D and 3D models. The reduced potency of acyclovir in keratinocytes, the primary cell type encountered by HSV reactivation, helps explain the limited benefit acyclovir and its congeners play in reducing sexual transmission. Finally, we demonstrated that our 3D bioprinted skin platform can integrate patient-derived cells, facilitating the incorporation of variable genetic backgrounds early into drug testing. Thus, these data indicate that the 3D bioprinted human skin equivalent assay platform provides a more physiologically relevant approach to identifying potential antivirals for HSV-directed drug development.

One Sentence Summary

High-throughput screen using 3D bioprinted human skin equivalents to identify antivirals against HSV and evaluate cell-type specific effects.
Caliber of zebrafish touch-sensory axons is dynamic in vivo
Authors: Ching Kaitlin , Sagasti Alvaro
Published: December 2024

Cell shape is crucial to cell function, particularly in neurons. The cross-sectional diameter, also known as caliber, of axons and dendrites is an important parameter of neuron shape, best appreciated for its influence on the speed of action potential propagation. Many studies of axon caliber focus on cell-wide regulation and assume that caliber is static. Here, we have characterized local variation and dynamics of axon caliber in vivo using the peripheral axons of zebrafish touch-sensing neurons at embryonic stages, prior to sex determination. To obtain absolute measurements of caliber in vivo, we paired sparse membrane labeling with super- resolution microscopy of neurons in live fish. We observed that axon segments had varicose or “pearled” morphologies, and thus vary in caliber along their length, consistent with reports from mammalian systems. Sister axon segments originating from the most proximal branch point in the axon arbor had average calibers that were uncorrelated with each other. Axon caliber also tapered across the branch point. Varicosities and caliber, overall, were dynamic on the timescale of minutes, and dynamicity changed over the course of development. By measuring the caliber of axons adjacent to dividing epithelial cells, we found that skin cell division is one aspect of the cellular microenvironment that may drive local differences and dynamics in axon caliber. Our findings support the possibility that spatial and temporal variation in axon caliber could significantly influence neuronal physiology.

Significance Statement

Axon caliber directly influences how quickly neurons send messages to other cells and likely plays a role in neurons’ overall health. In the peripheral nervous system, where neurons cover particularly long distances, cell shape can determine whether an animal successfully executes behaviors such as escape responses. We found that axon caliber can vary between locations within the same cell and is highly dynamic. Taking these variations into account may allow neuroscientists to better estimate transmission speeds for cells in neural circuits. We observed that axon caliber is distorted when nearby skin cells change shape. Thus, cells not classically considered part of the nervous system can also contribute to caliber dynamics, broadening our view of axon caliber determinants.
MEGA-FISH: multi-omics extensible GPU-accelerated FISH processing framework for huge-scale spatial omics
Authors: Ito Yuma , Tomimatsu Kosuke , Nagasaki Masao , Ochiai Hiroshi , Ohkawa Yasuyuki
Published: December 2024

Spatial omics enables comprehensive mapping of cell types and states in their spatial context, providing profound insights into cellular communication and tissue organization. However, analyzing large tissue sections, especially crucial for clinical applications, remains a significant challenge due to the computational demands of current image processing methods. To overcome these limitations, we developed MEGA-FISH, a flexible, GPU-accelerated Python framework optimized for large-scale spatial omics image analysis. Benchmarking on simulated and tissue images demonstrated that MEGA-FISH achieved high accuracy in spot detection while significantly reducing processing times compared with established tools. The framework’s adaptable computational capabilities optimize resource allocation (e.g., GPU or multi-core CPU) for diverse tasks, and its scalable architecture enables integration with advanced imaging and segmentation techniques. By bridging cutting-edge imaging methods and single-cell analysis, MEGA-FISH provides an efficient platform for multi-modal analysis and advances research and clinical applications of spatial omics at organ and organism scales.
ActinoMation: a literate programming approach for medium-throughput robotic conjugation ofStreptomycesspp
Authors: Møller Tenna Alexiadis , Booth Thom , Shaw Simon , Møller Vilhelm Krarup , Frandsen Rasmus J.N. , Weber Tilmann
Published: December 2024

The genusStreptomycesare valuable producers of antibiotics and other pharmaceutically important bioactive compounds. Advances in molecular engineering tools, such as CRISPR, has provided some access to the metabolic potential ofStreptomyces, but efficient genetic engineering of strains is hindered by laborious and slow manual transformation protocols. In this paper, we present a semi-automated medium-throughput workflow for the introduction of recombinant DNA intoStreptomycesspp. using the affordable and open-sourced Opentrons (OT-2) robotics platform. To increase the accessibility of the workflow we provide an open-source protocol-creator, ActinoMation. ActinoMation is a literate programming environment using Python in Jupyter Notebook. We validated the method by transformingStreptomyces coelicolor(M1152 and M1146),S. albidoflavus(J1047), andS. venezuelae(DSM40230) with the plasmids pSETGUS and pIJ12551. We demonstrate conjugation efficiencies of 3.33*10−3for M1152 with pSETGUS and pIJ12551; 2.96*10−3for M1146 with pSETGUS and pIJ12551; 1.21*10−5for J1047 with pSETGUS and 4.70*10−4with pIJ12551, and 4.97*10−2for DSM40230 with pSETGUS and 6.13*10−2with pIJ12551 with a false positive rate between 8.33% and 54.54%. Automation of the conjugation workflow improves consistency when handling large sample sizes that facilitates easy reproducibility on a larger scale.
Interaction of osteoprotegerin with fibulin-1 is essential for extracellular matrix deposition in fibrotic lung tissue
Authors: Liu Y , Habibie H. , Borghuis Theo , Liu Gang , Hansbro Philip M , Melgert B.N. , Burgess J.K.
Published: December 2024

Idiopathic pulmonary fibrosis (IPF) is a progressive, fatal lung disease with an unclear cause and no cure. Osteoprotegerin (OPG), a well-known regulator of bone extracellular matrix (ECM), is increased in pulmonary fibrosis and this is associated with lower lung function and IPF progression. Fibulin-1, a key ECM protein, is increased in lung fibroblasts and lung tissues from patients with IPF and high levels are predictive of a poor prognosis for these patients. We found a positive correlation between levels of OPG and fibulin-1 in serum from patients with IPF, but it is unknown if these proteins interact. This study aimed at investigating interactions between OPG and fibulin-1 in lung fibrosis, hypothesizing that OPG may form a complex with fibulin-1 thereby possibly influencing lung fibrosis.

We investigated intracellular interactions between OPG and fibulin-1 in human lung fibroblasts, showing neither OPG nor fibulin-1 expression were dependent on each other. However, OPG protein deposition was significantly decreased in lung tissues of fibulin-1 knockout mice (fibulin-1−/−)compared to controls suggesting extracellular interactions. Subsequently, we detected colocalization of both proteins in both IPF and control lung tissues using immunofluorescence, with both of them also colocalizing with latent TGFβ binding protein 1 (LTBP1). Proximity ligation analyses confirmed close proximity of OPG to fibulin-1 and fibulin-1 to LTBP1, particularly in the interstitial regions of both control and IPF lung tissue, but not OPG and LTBP1.

In conclusion, we found that OPG, fibulin-1 and LTBP1 seem to form a complex, with fibulin-1 playing a bridging role between OPG and LTBP1, in the extracellular environment. This complex may play a regulatory role in deposition of extracellular matrix in lung tissue.
Accessing the specific capacity of TIL-derived CD8 T-cells to suppress tumor recurrence in resectable HBV-HCC patients
Authors: Kah Janine , Staffeldt Lisa , Mattert Gregor , Volz Tassilo , Schulze Kornelius , Heumann Asmus , Voß Maximillian , Hoell Marie-Charlotte , Goebel Meike , Peine Sven , Dandri Maura , Lüth Stefan
Published: December 2024

Background

Hepatocellular carcinoma represents a significant global health challenge, affecting over a million patients annually, arising mainly from chronic liver diseases, with a majority being related to viral infections. However, despite the groundbreaking clinical results of immune checkpoint blockades and adoptive cell therapies, we still face non-responders accompanied by high rebound rates after resection. Considering that the main concern is to overcome a highly specialized immunosuppressive tumor microenvironment of the individual patient, the characterization of the particular tumor microenvironment and the source of the immune cells used in ACT is of immense importance. Approved ACT therapies mainly use modified peripheral blood cells from individuals. At the same time, tumor-infiltrating lymphocytes are underrepresented even if they have garnered interest due to their potential to target tumor-specific antigens more effectively.

Methods

In this study, we employed allogenic and autologous immune cell sources for expansion and stimulation, resulting in adoptive T-cell transfer experiments determining the effector cell differentiation and the related anti-tumor effects by the possible implementation of re-stimulation.

Results

We determined a high success rate in expanding and stimulating tumor-infiltrating lymphocytes with consistent CD8 T-cell fractions from HCC patients. To showcase the effectiveness of stimulated T-cells from different sources, we generated cell lines derived from the margin and center of an HBV-induced HCC with a highly immune-suppressive TME. We found effective immune responses supported by cell death induction, ferroptosis, proptosis and apoptosis triggered by all sources of T-cells depending on the area of derived tumor cells.

Conclusion

Effector T-cell fractions derived from tumor-infiltrating lymphocytes present a viable source for cell-based immune therapy combined with immune checkpoint inhibitors in HCC patients, especially after resection, to suppress rebound strategies of the parental tumor on an individual level.
Cited4a limits cardiomyocyte dedifferentiation and proliferation during zebrafish heart regeneration
Authors: Forman-Rubinsky Rachel , Feng Wei , Schlegel Brent T. , Paul Angela , Zuppo Daniel , Kedziora Katarzyna , Stoltz Donna , Watkins Simon , Rajasundaram Dhivyaa , Li Guang , Tsang Michael
Published: December 2024

Cardiac regeneration involves the interplay of complex interactions between many different cell types, including cardiomyocytes. The exact mechanism that enables cardiomyocytes to undergo dedifferentiation and proliferation to replace lost cells has been intensely studied. Here we report a single nuclear RNA sequencing profile of the injured zebrafish heart and identify distinct cardiomyocyte populations in the injured heart. These cardiomyocyte populations have diverse functions, including stress response, myofibril assembly, proliferation and contraction. The contracting cardiomyocyte population also involves the activation of maturation pathways as an early response to injury. This intriguing finding suggests that constant maintenance of a distinctive terminally differentiated cardiomyocyte population is important for cardiac function during regeneration. To test this hypothesis, we determined thatcited4a,a p300/CBP transcriptional coactivator, is induced after injury in the mature cardiomyocyte population. Moreover, loss-of-cited4amutants presented increased dedifferentiation, proliferation and accelerated heart regeneration. Thus, suppressing cardiomyocyte maturation pathway activity in injured hearts could be an approach to promote heart regeneration.
Brain responses vary in duration - modeling strategies and challenges
Authors: Skukies René , Schepers Judith , Ehinger Benedikt
Published: December 2024

Typically, event-related brain responses are calculated invariant to the underlying event duration, even in cases where event durations observably vary: with reaction times, fixation durations, word lengths, or varying stimulus durations. Additionally, an often co-occurring consequence of differing event durations is a variable overlap of the responses to subsequent events. While the problem of overlap e.g. in fMRI and EEG is successfully addressed using linear deconvolution, it is unclear whether deconvolution and duration covariate modeling can be jointly used, as both are dependent on the same inter-event-distance variability. Here, we first show that failing to explicitly account for event durations can lead to spurious results and thus are important to consider. Next, we propose and compare several methods based on multiple regression to explicitly account for stimulus durations. Using simulations, we find that non-linear spline regression of the duration effect outperforms other candidate approaches. Finally, we show that non-linear event duration modeling is compatible with linear overlap correction in time, making it a flexible and appropriate tool to model overlapping brain signals. This allows us to reconcile the analysis of stimulus responses with e.g. condition-biased reaction times, condition-biased stimulus duration, or fixation-related activity with condition-biased fixation durations. While in this paper we focus on EEG analyses, these findings generalize to LFPs, fMRI BOLD-responses, pupil dilation responses, and other overlapping signals.
The monomer/dimer switch modulates the activity of plant adenosine kinase
Authors: Kopecny David Jaroslav , Vigouroux Armelle , Belicek Jakub , Kopecna Martina , Koncitikova Radka , Friedecka Jaroslava , Mik Vaclav , Humplik Jan Frantisek , Le Berre Marine , Plancqueel Stephane , Strnad Miroslav , von Schwartzenberg Klaus , Novak Ondrej , Morera Solange , Kopecny David
Published: December 2024

Adenosine undergoes ATP-dependent phosphorylation catalyzed by adenosine kinase (ADK). In plants, ADK also phosphorylates cytokinin ribosides, transport forms of the hormone. Here, we investigated the substrate preferences, oligomeric states and structures of ADKs from moss (Physcomitrella patens) and maize (Zea mays) alongside metabolomic and phenotypic analyses. We showed that dexamethasone-inducible ZmADK overexpressor lines in Arabidopsis can benefit from a higher number of lateral roots and larger root areas under nitrogen starvation. We discovered that maize and moss enzymes can form dimers upon increasing protein concentration, setting them apart from the monomeric human and protozoal ADKs. Structural and kinetic analyses revealed a catalytically inactive unique dimer. Within the dimer, both active sites are mutually blocked. The activity of moss ADKs, exhibiting a higher propensity to dimerize, was tenfold lower compared to maize ADKs. Two monomeric structures in a ternary complex highlight the characteristic transition from an open to a closed state upon substrate binding. This suggests that the oligomeric state switch can modulate the activity of moss ADKs and likely other plant ADKs. Moreover, dimer association represents a novel negative feedback mechanism, helping to maintain steady levels of adenosine and AMP.
Chasing non-existent “microRNAs” in cancer
Authors: Orang Ayla , Warnock Nicholas I , Migault Melodie , Dredge B Kate , Bert Andrew G , Bracken Julie M , Gregory Philip A , Pillman Katherine A , Goodall Gregory J , Bracken Cameron P
Published: December 2024

MicroRNAs (miRNAs) are important regulators of gene expression whose dysregulation is widely linked to tumourigenesis, tumour progression and Epithelial-Mesenchymal Transition (EMT), a developmental process that promotes metastasis when inappropriately activated. However, controversy has emerged regarding how many functional miRNAs are encoded in the genome, and to what extent non-regulatory products of RNA degradation have been mis-identified as miRNAs. Central to miRNA function is their capacity to associate with an Argonaute (AGO) protein and form an RNA-Induced Silencing Complex (RISC), which mediates target mRNA suppression. We report that numerous “miRNAs” previously reported in EMT and cancer contexts, are not incorporated into RISC and are not capable of endogenously silencing target genes, despite the fact that hundreds of publications in the cancer field describe their roles. Apparent function can be driven through the expression of artificial miRNA mimics which is not necessarily reflective of any endogenous gene regulatory function. We present biochemical and bioinformatic criteria that can be used to distinguish functional miRNAs from mistakenly annotated RNA fragments.
Gfa2bin enables graph-based GWAS by converting genome graphs to pan-genomic genotypes
Authors: Vorbrugg Sebastian , Bezrukov Ilja , Bao Zhigui , Xian Wenfei , Weigel Detlef
Published: December 2024

Variation graphs offer superior representation of genomic diversity compared to traditional linear reference genomes, capturing complex features that are otherwise inaccessible to analysis. It seems self-evident that integrating these graphs with genome-wide association studies (GWAS) should enable more comprehensive understanding of genetic landscapes, potentially uncovering novel associations between genetic variations and traits. This approach takes full advantage of rich genomic information, thereby providing deeper insights into the genetic base of complex traits. Our tool, gfa2bin, offers multiple methods to (i) genotype variation graphs and (ii) convert the genotypes to well-established data formats for genome-wide association studies (GWAS). We demonstrate that variation graphs are feasible alternatives to traditional linear references for GWAS. Our case study using Arabidopsis thaliana and 1,695 traits shows that our approach complements SNP-based approaches, often identifying additional associations, with all associations having on average higher significance compared to SNP-based approaches. gfa2bin is implemented in Rust. Commented source code is available under MIT license at https://github.com/MoinSebi/gfa2bin. Examples of how to run gfa2bin are provided in the documentation. We added several Python scripts and a Snakemake pipeline for easy processing of our tool using larger data sets. In addition, we recommend using packing (https://github.com/MoinSebi/packing) for reduced storage and preprocessing (normalization) of sequence-to-graph alignments coverage.
Impact of Mycotoxins and Glyphosate residue on the Gut Microbiome and Resistome of European Fallow Deer
Authors: Tóth Adrienn Gréta , Nagy Sára Ágnes , Lakatos István , Solymosi Norbert , Stágel Anikó , Paholcsek Melinda , Posta Katalin , Ferenczi Szilamér , Szőke Zsuzsanna
Published: December 2024

Mycotoxins and herbicides residue significant threats to animal health. This study investigated the impact of these toxins on the gut microbiome of the fallow deer, a valuable game species. We analyzed the intestinal contents of deer exposed to varying levels of zearalenone (ZEA) and other mycotoxins and toxic compounds such as aflatoxins, deoxynivalenol, fumonisin B1 and glyphosate residues. Metagenomic analysis revealed significant alterations in the bacterial community composition, particularly in the abundance of specific taxa. Higher ZEA levels were associated with decreased alpha diversity, whereas higher aflatoxin levels had the opposite effect. We also observed changes in the abundance of antibiotic resistance genes (ARGs), suggesting a potential link between mycotoxin exposure and antimicrobial resistance. Furthermore, five complete bacterial genomes were assembled from the metagenomic data. These findings highlight the complex interplay between environmental toxins, the gut microbiota, and animal health. Understanding these interactions is crucial for developing strategies to mitigate the negative effects of toxin exposure on wildlife populations.
Structural, genetic, and adaptive basis of superhydrophobicity in rice leaves
Authors: Hiraiwa Asuka , Aiga Saori , Zhu Tian , Mimura Manaki , Yoshikawa Takanori , Sato Yutaka , Itoh Jun-ichi
Published: December 2024

In most plants, leaf surfaces exhibit water-repellent properties, which protect against pathogens and weather. Plants such as lotus and rice have evolved outstanding water-repellent properties, so-called superhydrophobicity. However, the structural and genetic basis of these properties in crop plants remains unclear. In this study, we identified the genes and microstructures responsible for superhydrophobicity by analyzing water repellence in rice mutants and cultivars, as well as wildOryzaspecies. Analysis of the surface structure of mutant leaves revealed that the degree of water repellency in rice largely depends on the accumulation of cuticular wax. Meanwhile, although papillae differentiation contributes minorly to water repellency, it is suggested to play a crucial role in achieving superhydrophobicity. These morphological characteristics are regulated by at least five previously characterized genes. We also found that superhydrophobicity is present in ancestral species, is retained by most cultivated rice, and appears to have evolved independently of rice domestication. Understanding the mechanisms of water repellence and their applications should provide important insight into the natural design of water repellence, as well as a basis for future innovation.
Multi-scale parameterization of neural rhythmicity with lagged Hilbert autocoherence
Authors: Zhang Siqi , Szul Maciej J , Papadopoulos Sotirios , Massera Alice , Rayson Holly , Bonaiuto James J
Published: December 2024

Analysis of neural activity in different frequency bands is ubiquitous in systems and cognitive neuroscience. Recent analytical breakthroughs and theoretical developments rely on phase maintenance of oscillatory signals without considering whether or not this assumption is met. Lagged (auto)coherence, the coherence between a signal and itself at increasing temporal delays, has been proposed as a way to quantify the rhythmicity, or periodicity, of a signal. However, current Fourier-based lagged autocoherence algorithms suffer from poor spectral accuracy and resolution, aliasing effects that become more pronounced at higher frequencies, and conflation with amplitude covariation, especially in frequency ranges in which the signal power is low. We introduce a continuous lagged autocoherence metric, lagged Hilbert autocoherence, that addresses these shortcomings by using multiplication in the frequency domain for precise bandpass filtering, instantaneous analytic signals via the Hilbert transform, and thresholding using the amplitude covariation of surrogate data generated by an autoregressive model. We show that this version of lagged coherence yields vastly higher spectral accuracy and resolution than lagged Fourier autocoherence, and that this unlocks additional, increasingly fine-grained applications. This includes examination of: 1) frequency-specific differences in rhythmicity between conditions, 2) changes in signal rhythmicity during learning, and 3) the relationship between frequency-specific rhythmicity and behavior, trial-by-trial. Lagged Hilbert autocoherence thus offers a significant toolset advancement for analysis of neurophysiological rhythmicity.
Cholinergic waves have a modest influence on the transcriptome of retinal ganglion cells
Authors: Somaiya Rachana Deven , Po Matthew A. , Feller Marla B. , Shekhar Karthik
Published: December 2024

In the early stages of development, correlated activity known as retinal waves causes periodic depolarizations of retinal ganglion cells (RGCs). The β2KO mouse, which lacks the β2 subunit of the nicotinic acetylcholine receptor, serves as a model for understanding the role of these cholinergic waves. β2KO mice have disruptions in several developmental processes of the visual system, including reduced retinotopic and eye-specific refinement of RGC axonal projections to their primary brain targets and an impact on the retinal circuits underlying direction selectivity. However, the effects of this mutation on gene expression in individual functional RGC types remain unclear. Here, we performed single-cell RNA sequencing on RGCs isolated at the end of the first postnatal week from wild-type and β2KO mice. We found that in β2KO mice, the molecular programs governing RGC differentiation were not impacted and the magnitude of transcriptional changes was modest compared to those observed during two days of normal postnatal maturation. This contrasts with the substantial transcriptomic changes seen in downstream visual system areas under wave disruption in recent studies. However, we identified ∼238 genes whose expression was altered in a type-specific manner. We confirmed this result viain situhybridization and whole-cell recording by focusing on one of the downregulated genes in aRGCs,Kcnk9, which encodes the two-pore domain leak potassium channel TASK3. Our study reveals a limited transcriptomic impact of cholinergic signaling in the retina and instead of affecting all RGCs uniformly, these waves show subtle modulation of molecular programs in a type-specific manner.

SIGNIFICANCE STATEMENT

Spontaneous retinal waves are critical for the development of the mammalian visual system. However, their role in transcriptional regulation in the retina across the diverse retinal ganglion cell (RGC) types that underpin the detection and transmission of visual features is unclear. Using single-cell RNA sequencing, we analyzed RGC transcriptome from wild-type mice and mice with disrupted retinal waves. We identified several genes that show RGC-type-specific regulation in their expression, including multiple neuropeptides and ion channels. However, wave-dependent changes in the transcriptome were more subtle than developmental changes, indicating that spontaneous activity-dependent molecular changes in retinal ganglion cells are not primarily manifested at the transcriptomic level.
An all-atom view into the disordered interaction interface of the TRIM5αPRYSPRY domain and the HIV capsid
Authors: Haas-Neill Liam , Meneksedag-Erol Deniz , Andeejani Ibraheem , Rauscher Sarah
Published: December 2024

Tripartite motif-containing protein 5, alpha isoform (TRIM5α) is an innate immune factor that provides rhesus macaques with immunity to HIV. Despite high sequence similarity to rhesus TRIM5α, human TRIM5αdoes not restrict HIV without the introduction of mutations. The structural underpinnings of this functional difference are poorly understood because the interaction interface between the HIV capsid and TRIM5αinvolves intrinsically disordered regions. Here, we use all-atom molecular dynamics simulations to study several TRIM5αvariants: rhesus TRIM5α, human TRIM5α, and human TRIM5αwith the R332P mutation (a mutation known to enhance HIV restriction). Our data reveal differences in the conformational ensembles of wild-type and R332P human TRIM5α, including a significant increase in the formation of a turn that includes the mutation site residue. We also carried out simulations of rhesus TRIM5αin complex with the HIV capsid protein. Our results indicate that the variable loops of TRIM5αare highly flexible, both in solution and in the complex with the capsid protein, indicative of a fuzzy interaction interface. Simulations of the complex suggest a plausible mechanism for HIV restriction by TRIM5αwith the R332P mutation; replacing the positively charged arginine with a neutral residue enhances electrostatic interactions with residue R82 of the capsid protein. Overall, our simulations provide a first view of the atomistic details of the HIV capsid-TRIM5αbinding interface, providing a potential molecular mechanism for the observed functional differences between variants of the TRIM5αprotein.
Conceptualizing Ribosomal mRNA Unwinding Utilizing DMS MaP-Seq
Authors: Kellenberger Preston A. , Cornish Peter V.
Published: December 2024

Examining the dynamicity of RNA structure has deepened our understanding of its vast biological functions. Perhaps the protein complex that encounters the most diverse landscape of RNA structure is the ribosome. In translation, the ribosome must linearize countless mRNA conformations for proper protein production. Some RNA structures, however, reliably make up sequences which hinder the ability of the ribosome to maintain its reading frame. Arguably, the most well-studied of these structures is the RNA pseudoknot. Here, we present an approach utilizing dimethyl sulfate probing with mutational profiling and sequencing (DMS MaP-Seq) to precisely examine RNA unwinding. DMS MaP-Seq is a method typically used in predicting RNA secondary structure. Instead, we employ the method to understand the unfolding of the Sugarcane Yellow Leaf Virus pseudoknot (ScYLVPK). We demonstrate that the unwinding of ScYLVPKis inherently different with regards to the ribosome and temperature. Additionally, we find that minor-groove triplex interactions support coaxial stacking, providing a major source of stability to ScYLVPKin ribosomal unwinding.
Elevated levels of intracellular RNA lariats suppress the antiviral response
Authors: Duan Chaorui , Buerer Luke , Bowers Cory , Taggart Allison J , OBrien Mara H , Gunasekera Sarah , Lin Chien-Ling , Wang Jing , Staley Jonathan P , Fredericks Alger M , Monaghan Sean F , Welch Anastasia , Clark Nathaniel E , Gao Daxing , Marr Nico , Zhang Shen-Ying , Casanova Jean-Laurent , Fairbrother William G
Published: December 2024

Recent studies report the genetic loss of the lariat debranching enzyme (DBR1) activity increases susceptibility to viral infection. Here, we show that more than 25% of human introns contain large hairpin structures created by the folding of two Alu elements inserted in opposite orientation. In wildtype cells, this large reservoir of endogenous dsRNA is efficiently degraded. In DBR1-null cells, lariats accumulate in the cytosol and dsRNA becomes enriched. We demonstrate how the chronic exposure to these lariats attenuates the dsRNA sensors, reducing the response of the MDA5, RIG-I, RNase L and PKR sensing pathways. We observe evidence for both attenuation and endogenous dsRNA in anti-viral response and viral evasion. Lariats are transiently elevated during infection (e.g. HSV-1, influenza, KSHV). The HSV-1 genome expresses multiple, stable lariats that may attenuate dsRNA sensors during latency.
Efficacy and Best Practices of Health-care worker Smoking Cessation Treatment in Sub-Saharan Africa
Authors: Davison W. , Sime M. , Khan W. , Yamoah E. , Bhurji K. , Surti R.
Published: December 2024

Background

Tobacco smoking causes over 8 million deaths annually worldwide and is expected to increase by 148% in sub-Saharan Africa by 2030. This puts significant strain on already heavily burdened healthcare systems. Healthcare workers (HCWs) are at the forefront of patient care and play a crucial role in smoking cessation (SC) efforts.

Objectives

To assesses the effectiveness and identify barriers to smoking cessation provision by HCWs in sub-Saharan Africa.

Method

A systematic review was conducted in accordance with PRISMA guidelines to retrieve studies relevant to the implementation of SC strategies in sub-Saharan Africa and research on the barriers and facilitators of the adoption of SC practices. Studies were retrieved from PubMed, Medline, Ovid, Cochrane Library and Scopus; all included literature was published in English after 2014. Risk of bias and methodological quality were evaluated through the Critical Appraisal Skills Programme (CASP) tool.

Results

Twelve studies met the inclusion criteria. HCWs in sub-Saharan with formal training were more likely to offer SC interventions, with lack of training and resources identified as key barriers. Greater HCW engagement with patients also facilitated SC efforts. Inadequate resources, cultural differences and structural failures were further barriers. Socioeconomic and educational differences also influenced quit attempts, with wealthier and better-educated individuals more likely to quit.

Discussion

HCW competency and training significantly impacts SC efforts, suggesting the need for comprehensive programs to boost HCW skills and knowledge. Socioeconomic and cultural factors also affected SC outcomes, highlighting the need for tailored health campaigns.

However, the heterogenicity of the evidence base makes it challenging to compare SC interventions and determine if identified barriers are only region specific or generalisable.

Conclusion

HCW training and support is crucial for SC provision across sub-Saharan Africa, but structural barriers and sociocultural challenges must be addressed for these programs to succeed. Interventions should therefore both empower HCWs and be tailored to the local area.
Structure and Cl-Conductance Properties of the Open State of Human CFTR
Authors: Zeng Zhi-Wei , Ing Christopher E. , Pomès Régis
Published: December 2024

The cystic fibrosis transmembrane conductance regulator (CFTR) is an anion channel that plays a vital role in water and ion secretion on epithelial surfaces. Loss of function in CFTR causes the life-threatening disease cystic fibrosis (CF). The functionally open state of CFTR has so far eluded detailed structural characterization. Although multiple near-atomic resolution structures of CFTR have been solved under conditions that promote channel opening, they all lack a continuous ion conduction pathway. In recent molecular dynamics (MD) simulations, structural fluctuations of human CFTR in a hydrated lipid bilayer led to the observation of transient Cl-conducting states, but the stability and conduction properties of these putative open states were not established. Here, we conduct massively repeated simulations initiated from these Cl-permeable conformations. Reproducible structural relaxation of the pore leads to a stable open conformation featuring five symmetrically arranged pore-lining helices. Unlike previously reported structures, this novel penta-helical arrangement reproduces experimentally determined properties of the open pore, including a Cl-conductance close to that measured at physiological voltages. Together, our results support the validity of this newly identified pore conformation as a model of the fully open channel. Detailed analysis highlights the role of cationic pore-lining residues in the Cl-permeation mechanism and suggests that the kinks observed in several transmembrane helices play a role in channel gating.
Naturally ornate RNA-only complexes revealed by cryo-EM
Authors: Kretsch Rachael C. , Wu Yuan , Shabalina Svetlana A. , Lee Hyunbin , Nye Grace , Koonin Eugene V. , Gao Alex , Chiu Wah , Das Rhiju
Published: December 2024

Myriad families of natural RNAs have been proposed, but not yet experimentally shown, to form biologically important structures. Here we report three-dimensional structures of three large ornate bacterial RNAs using cryogenic electron microscopy at resolutions of 2.9-3.1 Å. Without precedent among previously characterized natural RNA molecules, Giant, Ornate, Lake- and Lactobacillales-Derived (GOLLD), Rumen-Originating, Ornate, Large (ROOL), and Ornate Large Extremophilic (OLE) RNAs form homo-oligomeric complexes whose stoichiometries are retained at concentrations lower than expected in the cell. OLE RNA forms a dimeric complex with long co-axial pipes spanning two monomers. Both GOLLD and ROOL form distinct RNA-only multimeric nanocages with diameters larger than the ribosome. Extensive intra- and intermolecular A-minor interactions, kissing loops, an unusual A-A helix, and other interactions stabilize the three complexes. Sequence covariation analysis of these large RNAs reveals evolutionary conservation of intermolecular interactions, supporting the biological importance of large, ornate RNA quaternary structures that can assemble without any involvement of proteins.