bluuebunny/crossref_metadata_2025 huggingface dataset:
Effects of therapeutically approved individual bile acids on the development of metabolic dysfunction-associated steatohepatitis a low bile acid mouse model
Authors: Taylor Rulaiha , Basaly Veronia , Kong Bo , Yang Ill , Brinker Anita M , Capece Gina , Bhattacharya Anisha , Henry Zakiyah R , Otersen Katherine , Yang Zhenning , Meadows Vik , Mera Stephanie , Joseph Laurie B , Zhou Peihong , Aleksunes Lauren M , Roepke Troy , Buckley Brian , Guo Grace L
Published: September 2024

Bile acid (BA) signaling dysregulation is an important etiology for the development of metabolic dysfunction-associated steatotic liver disease (MASLD). As diverse signaling molecules synthesized in the liver by pathways initiated with CYP7A1 and CYP27A1, BAs are endogenous modulators of farnesoid x receptor (FXR). FXR activation is crucial in maintaining BA homeostasis, regulating lipid metabolism, and suppressing inflammation. Additionally, BAs interact with membrane receptors and gut microbiota to regulate energy expenditure and intestinal health. Complex modulation of BAs in vivo and the lack of suitable animal models impede our understanding of the functions of individual BAs, especially during MASLD development. Previously, we determined that acute feeding of individual BAs differentially affects lipid, inflammation, and oxidative stress pathways in a low-BA mouse model, Cyp7a1/Cyp27a1 double knockout (DKO) mice. Currently, we investigated to what degree cholic acid (CA), deoxycholic acid (DCA), or ursodeoxycholic acid (UDCA) at physiological concentrations impact MASLD development in DKO mice. The results showed that these 3 BAs varied in the ability to activate hepatic and intestinal FXR, disrupt lipid homeostasis, and modulate inflammation and fibrosis. Additionally, UDCA activated intestinal FXR in these low-BA mice. Significant alterations in lipid uptake and metabolism in DKO mice following CA and DCA feeding indicate differences in cholesterol and lipid handling across genotypes. Overall, the DKO were less susceptible to weight gain, but more susceptible to MASH diet induced inflammation and fibrosis on CA and DCA supplements, whereas WT mice were more vulnerable to CA-induced fibrosis on the control diet.
Comprehensive genotoxicity and carcinogenicity assessment of molnupiravir
Authors: Escobar Patricia A , Sobol Zhanna , Miller Randy R , Ferry-Martin Sandrine , Stermer Angela , Jacob Binod , Muniappa Nagaraja , Sanchez Rosa I , Blanchard Kerry T , Galijatovic-Idrizbegovic Alema , Amin Rupesh P , Troth Sean P
Published: September 2024

Molnupiravir is registered or authorized in several countries as a 5-d oral coronavirus disease 2019 treatment for adults. Molnupiravir is a prodrug of the antiviral ribonucleoside β-D-N4-hydroxycytidine (NHC) that distributes into cells, where it is phosphorylated to its pharmacologically active ribonucleoside triphosphate (NHC-TP) form. NHC-TP incorporates into severe acute respiratory syndrome coronavirus 2 RNA by the viral RNA-dependent RNA polymerase, resulting in an accumulation of errors in the viral genome, leading to inhibition of viral replication and loss of infectivity. The potential of molnupiravir to induce genomic mutations and DNA damage was comprehensively assessed in several in vitro and in vivo genotoxicity assays and a carcinogenicity study, in accordance with international guideline recommendations and expert opinion. Molnupiravir and NHC induced mutations in vitro in bacteria and mammalian cells but did not induce chromosome damage in in vitro or in vivo assays. The in vivo mutagenic and carcinogenic potential of molnupiravir was tested in a series of in vivo mutagenicity studies in somatic and germ cells (Pig-a Assay and Big Blue® TGR Mutation Assay) and in a carcinogenicity study (transgenic rasH2-Tg mouse), using durations of exposure and doses exceeding those used in clinical therapy. In vitro genotoxicity results are superseded by robustly conducted in vivo studies. Molnupiravir did not increase mutations in somatic or germ cells in the in vivo animal studies and was negative in the carcinogenicity study. The interpretation criteria for each study followed established regulatory guidelines. Taken together, these data indicate that molnupiravir use does not present a genotoxicity or carcinogenicity risk for patients.
Development of machine learning-based quantitative structure–activity relationship models for predicting plasma half-lives of drugs in six common food animal species
Authors: Wu Pei-Yu , Chou Wei-Chun , Wu Xue , Kamineni Venkata N , Kuchimanchi Yashas , Tell Lisa A , Maunsell Fiona P , Lin Zhoumeng
Published: September 2024

Plasma half-life is a crucial pharmacokinetic parameter for estimating extralabel withdrawal intervals of drugs to ensure the safety of food products derived from animals. This study focuses on developing a quantitative structure–activity relationship (QSAR) model incorporating multiple machine learning and artificial intelligence algorithms, and aims to predict the plasma half-lives of drugs in 6 food animals, including cattle, chickens, goats, sheep, swine, and turkeys. By integrating 4 machine learning algorithms with 5 molecular descriptor types, 20 QSAR models were developed using data from the Food Animal Residue Avoidance Databank (FARAD) Comparative Pharmacokinetic Database. The deep neural network (DNN) algorithm demonstrated the best prediction ability of plasma half-lives. The DNN model with all descriptors achieved superior performance with a high coefficient of determination (R2) of 0.82 ± 0.19 in 5-fold cross-validation on the training sets and an R2 of 0.67 on the independent test set, indicating accurate predictions and good generalizability. The final model was converted to a user-friendly web dashboard to facilitate its wide application by the scientific community. This machine learning-based QSAR model serves as a valuable tool for predicting drug plasma half-lives and extralabel withdrawal intervals in 6 common food animals based on physicochemical properties. It also provides a foundation to develop more advanced models to predict the tissue half-life of drugs in food animals.
Ohio Farmworkers and Heat-Related Illness Prevention
Authors: Edgerly Ashley , Gillespie Gordon Lee , Bhattacharya Amit , Hittle Beverly M.
Published: September 2024

Objective

The aim of the study is to understand farmworkers’ knowledge of heat-related illness prevention and behavioral and cultural factors related to heat-related illness (HRI) prevention.

Methods

The theory of planned behavior and an ethnographic study design were used. Data collection consisted of observations and interviews. Recorded interviews were conducted with participants and transcribed verbatim. Transcribed interviews were analyzed using thematic analysis.

Results

Overall, 14 interviews were conducted, and four themes emerged: acquisition and interpretation, perception, interoception, and action. Other findings included an insufficiency of formal training and the absence of knowledge of a protocol for acclimatization.

Conclusions

Better education and training are needed in this occupation, especially regarding acclimatization. Occupational health professionals must lead efforts to develop HRI plans and measures to ensure acclimatization protocols are adopted in the workforce.
Founding a Professional Organization
Authors: Ramirez Elda , Davis Wesley D.
Published: September 2024

The creation of the American Academy of Emergency Nurse Practitioners (AAENP) marked a significant milestone in the professionalization of emergency nurse practitioners (ENPs). This interview with Dr. Elda Ramirez, the founder of AAENP, explores the critical moments and challenges that led to the establishment of the organization. Driven by the need for a dedicated body to advocate for the unique role of ENPs, AAENP was founded to address gaps in regulatory recognition and professional standards within the broader nursing profession. The manuscript delves into the origins of AAENP, highlighting the pivotal roles of co-founders Drs. Arlo Weltge and Kyle Kincaid, and discusses the organization’s early achievements, including the development of a specialized certification exam. AAENP’s journey underscores the importance of professional societies in advancing specialty practices and advocating for the interests of their members.
Historical Evolution of Emergency Nurse Practitioner Education
Authors: Wilbeck Jennifer , Tucker Paula , Davis Wesley D.
Published: September 2024

This manuscript explores the historical evolution of emergency nurse practitioner (ENP) education from its inception to its current state. It discusses key milestones, innovative leaders, curricular approaches and current program characteristics. The paper concludes with a review of the current state of ENP education, persistent challenges, and future directions. Professional organizations that have shaped both the ENP role and education over time are also considered. By examining the historical context, this review provides insights into the evolution of ENP education, contributing to a deeper understanding of the ENP role and education's significance in emergency care.
Topical Ophthalmic Administration of VIAN-c4551 Antiangiogenic Peptide for Diabetic Macular Edema: Preclinical Efficacy and Ocular Pharmacokinetics
Authors: Adán-Castro Elva , Zamora Magdalena , Granados-Carrasco Daniela , Siqueiros-Márquez Lourdes , García-Rodrigo Jose F. , Bertsch Thomas , Triebel Jakob , Martínez de la Escalera Gonzalo , Robles Juan Pablo , Clapp Carmen
Published: September 2024

VIAN-c4551 is a cyclic antiangiogenic peptide that stands as a potent and stable inhibitor of vascular endothelial cell growth factor (VEGF), the major vasopermeability and angiogenic factor in diabetic macular edema and diabetic retinopathy. Intravitreal injections of inhibitors of VEGF are a first-line therapy, but the invasiveness, risk, and low adherence of frequent intravitreal injections interfere with the needed long-term treatments and successful outcomes. Eye drops are non-invasive and favor compliance. Here, we evaluated the preclinical efficacy, permeability, and ocular pharmacokinetics of VIAN-c4551 delivered in eye drops. VIAN-c4551 demonstrated high potency (IC50= 137 pM) to inhibit the permeability of human umbilical vein endothelial cell monolayers induced by VEGF. VIAN-c4551 eye drops potently (0.005% minimum effective dose) prevented the retinal vascular leakage induced by VEGF injected intravitreally for up to 24 hours and reversed the increase in retinal vascular permeability due to streptozotocin-induced diabetes in rats and mice. VIAN-c4551 exhibited high permeability across MDCK epithelium and, after a single topical ocular instillation in rabbits, reached the retina-choroid in micromolar concentrations several orders of magnitude above its IC50(Cmax= 51 µM at 6 hours) that lasted at least 24 hours. In conclusion, VIAN-c4551 eye drops reach the back of the eye at therapeutic concentrations, providing a potential, once-a-day, non-invasive intervention for preventing and reversing retinal vascular leakage in diabetic macular edema, diabetic retinopathy, and other vascular retinopathies and preserving sight.
Spatial microenvironments tune immune response dynamics in theDrosophilalarval fat body
Authors: Schlomann Brandon H. , Pai Ting-Wei , Sandhu Jazmin , Imbert Genesis Ferrer , Graham Thomas G.W. , Garcia Hernan G.
Published: September 2024

Immune responses in tissues display intricate patterns of gene expression that vary across space and time. While such patterns have been increasingly linked to disease outcomes, the mechanisms that generate them and the logic behind them remain poorly understood. As a tractable model of spatial immune responses, we investigated heterogeneous expression of antimicrobial peptides in the larval fly fat body, an organ functionally analogous to the liver. To capture the dynamics of immune response across the full tissue at single-cell resolution, we established live light sheet fluorescence microscopy of whole larvae. We discovered that expression of antimicrobial peptides occurs in a reproducible spatial pattern, with enhanced expression in the anterior and posterior lobes of the fat body. This pattern correlates with microbial localization via blood flow but is not caused by it: loss of heartbeat suppresses microbial transport but leaves the expression pattern unchanged. This result suggests that regions of the tissue most likely to encounter microbes via blood flow are primed to produce antimicrobials. Spatial transcriptomics revealed that these immune microenvironments are defined by genes spanning multiple biological processes, including lipid-binding proteins that regulate host cell death by the immune system. In sum, the larval fly fat body exhibits spatial compartmentalization of immune activity that resembles the strategic positioning of immune cells in mammals, such as in the liver, gut, and lymph nodes. This finding suggests that tissues may share a conserved spatial organization that optimizes immune responses for antimicrobial efficacy while preventing excessive self-damage.
Optimal transport reveals dynamic gene regulatory networks via gene velocity estimation
Authors: Zhao Wenjun , Larschan Erica , Sandstede Björn , Singh Ritambhara
Published: September 2024

Inferring gene regulatory networks from gene expression data is an important and challenging problem in the biology community. We propose OTVelo, a methodology that takes time-stamped single-cell gene expression data as input and predicts gene regulation across two time points. It is known that the rate of change of gene expression, which we will refer to as gene velocity, provides crucial information that enhances such inference; however, this information is not always available due to the limitations in sequencing depth. Our algorithm overcomes this limitation by estimating gene velocities using optimal transport. We then infer gene regulation using time-lagged correlation and Granger causality via regularized linear regression. Instead of providing an aggregated network across all time points, our method uncovers the underlying dynamical mechanism across time points. We validate our algorithm on 13 simulated datasets with both synthetic and curated networks and demonstrate its efficacy on 4 experimental data sets.

Author summary

Understanding how genes interact to regulate cellular functions is crucial for advancing our knowledge of biology and disease. We present OTVelo, a method that uses single-cell gene expression data collected at different time points to infer gene regulatory networks. OTVelo offers a dynamic view of how gene interactions change over time, providing deeper insights into cellular processes. Unlike traditional methods, OTVelo captures temporal information through ancestor-descendant transitions without assuming a specific underlying regulatory model. We validate our approach using both simulated and real-world data, demonstrating its effectiveness in revealing complex gene regulation patterns. This method could lead to new discoveries in understanding biological systems and developing disease treatments.
Comparative Analysis of Stain-Free Fourier Ptychographic Microscopy and Traditional Histopathological Light Microscopy in Renal Membranous Nephropathy
Authors: Valentino Marika , Bianco Vittorio , D’Ambrosio Gioacchino , Paulli Marco , Smaldone Giovanni , Brancato Valentina , Miccio Lisa , Salvatore Marco , Gambacorta Marcello , Ferraro Pietro
Published: September 2024

Background

Histology remains a cornerstone in the diagnosis and prognosis of renal diseases, with histopathological analysis of kidney tissue being crucial for understanding renal pathophysiology. The availability of multiple stained sections is essential for conducting a comprehensive histopathological analysis and achieving an accurate diagnosis. Recently, Fourier Ptychographic Microscopy (FPM) earned a spot among the most promising microscopy techniques. The ability to provide high-resolution, quantitative phase-contrast images over a wide area, particularly in a stain-free mode, makes FPM highly appealing to experts in histopathology. Since renal pathologies are characterized by subtle morphological changes encoded in tissue slides, phase maps obtained using FPM are well-suited for providing detailed, high-contrast images of tissue structures. Thus, FPM provides a quantitative imaging tool that can be descriptive of the sample and/or expressive of the disease.

Methods

In this study, we explore FPM capability to image pathological kidney tissue, enabling pathologists to select regions of interest within the intricate architecture of renal tissue and zoom in to observe minute submicron structures, ranging from overall tissue organization and glomeruli distribution to individual cell membranes. Attention is focused on membranous glomerulonephritis since it is a nephropathy highly dependent on histological examination.

Results

The comparative analysis between FPM and traditional light microscopy showed a difference in thickness of glomerular basal membranes between healthy kidney tissues and those affected by membranous glomerulonephritis (MG). Moreover, the results reported in our investigation revealed better glomerular membranes contrast in FPM images with respect to the H&E-stained images.

Conclusions

Our study shows the broad potential of FPM in characterizing hallmarks of MG disease even in stain-free tissue slides.
Stabilization of fluctuating population dynamics via the evolution of dormancy
Authors: Miller Zachary R. , Vasseur David , Hull Pincelli M.
Published: September 2024

Dormancy is usually understood as a strategy for coping with extrinsically variable environments, but intrinsic population fluctuations also create conditions where dormancy is adaptive. By analyzing simple population models, we show that, very generally, population fluctuations favor the evolution of dormancy, but dormancy stabilizes population dynamics. This sets up a feedback loop that can enable the coexistence of alternative dormancy strategies. Over longer timescales, we show that evolution of dormancy to an evolutionary stable state can drive populations to the edge of stability, where dynamics are only weakly stabilized. We briefly consider how these conclusions are likely to apply in more complex community contexts. Our results suggest that chaos and high-amplitude population cycles are highly vulnerable to invasion and subsequent stabilization by dormancy, potentially explaining their rarity. At the same time, the propensity of ecological dynamics to fluctuate may be an underappreciated driver of the evolution of dormancy.
De novoRNA base editing in plant organelles with engineered synthetic P-type PPR editing factors
Authors: Mathieu Sébastien , Lesch Elena , Garcia Shahinez , Stéfanie Graindorge , Schallenberg-Rüdinger Mareike , Hammani Kamel
Published: September 2024

In plant mitochondria and chloroplasts, cytidine-to-uridine RNA editing plays a crucial role in regulating gene expression. While natural PLS-type PPR proteins are specialized in this process, synthetic PPR proteins offer significant potential for targeted RNA editing. In this study, we engineered chimeric editing factors by fusing synthetic P-type PPR guides with the DYW cytidine deaminase domain of a moss mitochondrial editing factor, PPR56. These designer PPR editors (dPPRe) elicited efficient and precisede novoRNA editing inEscherichia coli, and inNicotiana benthamianachloroplasts and mitochondria. Chloroplast transcriptome-wide analysis of the most efficient dPPRe revealed minimal off-target effects, with only three non-target C sites edited due to sequence similarity with the intended target. This study introduces a novel and precise method for RNA base editing in plant organelles, paving the way for new approaches in gene regulation applicable to plants and potentially other organisms.
Coexistence of bacteria with a competition-colonization tradeoff on a dynamic coral host
Authors: Gibbs Theo L. , Dahlin Kyle J.-M. , Brennan Joe , Silveira Cynthia B. , McManus Lisa C.
Published: September 2024

Many macroscopic organisms enter into tightly linked symbiosis with microbial communities. Although experimental work has demonstrated the importance of these symbioses, a theoretical understanding of stable, multi-scale coexistence remains underdeveloped. Here, we explored how the competition-colonization tradeoff, a classic coexistence mechanism, operates when bacterial species compete for a dynamic biological host. Specifically, we introduce a model where corals are colonized by fast-growing mutualists and slow-growing pathogens. We found that the vital rates of the host coral influenced coexistence outcomes between bacterial types. Notably, pathogen-induced host death expanded the region of parameter space where coexistence was stable for all three species and mutualistic bacteria enabled coexistence in systems that would have otherwise collapsed. These findings provide new insights into the interplay between microbial interactions and macroscopic processes. Our work illustrates how host-microbe interactions can shape ecosystem stability, providing a theoretical framework applicable to a wide range of symbiotic systems.
Dynamics of microcompartment formation at the mitosis-to-G1 transition
Authors: Goel Viraat Y. , Aboreden Nicholas G. , Jusuf James M. , Zhang Haoyue , Mori Luisa P. , Mirny Leonid A. , Blobel Gerd A. , Banigan Edward J. , Hansen Anders S.
Published: September 2024

As cells exit mitosis and enter G1, mitotic chromosomes decompact and transcription is reestablished. Previously, Hi-C studies showed that essentially all interphase 3D genome features including A/B-compartments, TADs, and CTCF loops, are lost during mitosis. However, Hi-C remains insensitive to features such as microcompartments, nested focal interactions betweencis-regulatory elements (CREs). We therefore applied Region Capture Micro-C to cells from mitosis to G1. Unexpectedly, we observe microcompartments in prometaphase, which further strengthen in ana/telophase before gradually weakening in G1. Loss of loop extrusion through condensin depletion differentially impacts microcompartments and large A/B-compartments, suggesting that they are partially distinct. Using polymer modeling, we show that microcompartment formation is favored by chromatin compaction and disfavored by loop extrusion activity, explaining why ana/telophase likely provides a particularly favorable environment. Our results suggest that CREs exhibit intrinsic homotypic affinity leading to microcompartment formation, which may explain transient transcriptional spiking observed upon mitotic exit.
Accurate and Rapid Prediction of Protein pKa: Protein Language Models Reveal the Sequence-pKa Relationship
Authors: Xu Shijie , Onoda Akira
Published: September 2024

Protein pKa prediction is a key challenge in computational biology. In this study, we present pKALM, a novel deep learning-based method for high-throughput protein pKa prediction. pKALM uses a protein language model (PLM) to capture the complex sequence-structure relationship of proteins. While traditionally considered a structure-based problem, our results show that a PLM pre-trained on large-scale protein sequence databases can effectively learn this relationship and achieve state-of-the-art performance. pKALM accurately predicts the pKa values of six residues (Asp, Glu, His, Lys, Cys, and Tyr) and two termini with high precision and efficiency. It excels at predicting both exposed and buried residues, which often deviate from standard pKa values measured in solvent. We demonstrate a novel finding that predicted protein isoelectric points (pI) can be used to improve the accuracy of pKa prediction. High-throughput pKa prediction of the human proteome using pKALM achieves a speed of 4,965 pKa predictions per second, which is several orders of magnitude faster than existing state-of-the-art methods. The case studies illustrate the efficacy of pKALM in estimating pKa values and the constraints of the method. pKALM will thus be a valuable tool for researchers in the fields of biochemistry, biophysics, and drug design.
Rapid adaptation to a globally introduced virulent pathogen in a keystone species
Authors: Cassin-Sackett Loren , Tsuchiya Mirian TN , Dikow Rebecca B.
Published: September 2024

Emerging infectious diseases are one of the foremost contemporary threats to biodiversity conservation. Outbreaks of novel pathogens can lead to extinction of host populations, loss of gene flow due to extirpation, and bottlenecks in host populations with surviving individuals. In outbreaks with survivors, pathogens can exert strong selection on hosts, in some cases leading to the evolution of resistance or tolerance in the host population. The pathogen causing sylvatic plague,Yersinia pestis, was introduced to North America in the early 20thcentury and caused rapid population declines in prairie dogs (genusCynomys), which experience >95% mortality during epizootics. Recently, survival from plague has been documented in a small number of black-tailed prairie dogs (C. ludovicianus) in natural populations in Colorado (USA). We performed whole-genome sequencing on 7 individuals from 3 colonies that survived infection with plague and 7 individuals from the same colonies that likely died during a plague epizootic. Using genome-wide association tests, FSToutlier tests, and other inferences of selection, we detected SNPs on 5 scaffolds that were strongly associated with survivorship from plague in the wild. Some genes associated with these scaffolds also differ in humans that survived versus died in the plague pandemic in London, UK, suggesting conservation of gene function across taxonomically diverse lineages. Understanding the genetic basis of immunity can enable genetically-informed management actions such as targeted relocation to protect prairie dogs and the species that rely on them. More generally, understanding how rapid adaptation to pathogens occurs can help us predict the time frame and spatial scale at which adaptation may occur, during which other interventions are needed.

Significance Statement

Emerging infectious diseases are one of the foremost threats to global biodiversity, causing extinctions and population crashes on all continents. Introduced pathogens can exert strong selection on hosts for the evolution of tolerance or resistance, yet these evolutionary events are rare and it remains challenging to identify and sample both immune and susceptible individuals during an epizootic. This study leverages one of the only documented examples of prairie dogs surviving infection from introduced sylvatic plague in nature and compares their genomes to those of individuals that perished. We find strong signatures of selection in a small number of immune and non-immune genes, one of which has been implicated in survival from plague in humans. These findings suggest that adaptation to novel pathogens may occur via a combination of conserved genes and the co-opting of genes outside of classical immune pathways. Finally, it provides evidence that in native species with sufficient standing genetic variation, there is potential for adaptation to introduced pathogens.
Real-space heterogeneous reconstruction, refinement, and disentanglement of CryoEM conformational states with HetSIREN
Authors: Herreros D. , Mata C.P. , Noddings C. , Irene D. , Krieger J. , Agard D.A. , Tsai M.-D. , Sorzano C.O.S. , Carazo J.M.
Published: September 2024

Single-particle analysis by Cryo-electron microscopy (CryoEM) provides direct access to the conformation of each macromolecule. However, the image’s signal-to-noise ratio is low, and some form of classification is usually performed at the image processing level to allow structural modeling. Classical classification methods imply the existence of a discrete number of structural conformations. However, new heterogeneity algorithms introduce a novel reconstruction paradigm, where every state is represented by a lower number of particles, potentially just one, allowing the estimation of conformational landscapes representing the different structural states a biomolecule explores. In this work, we present a novel deep learning-based method called HetSIREN. HetSIREN can fully reconstruct or refine a CryoEM volume in real space based on the structural information summarized in a conformational latent space. The unique characteristics that set HetSIREN apart start with the definition of the approach as a real space-based only method, a fact that allows spatially focused analysis, but also the introduction of a novel network architecture specifically designed to make use of meta-sinusoidal activations, with proven high analytics capacities. Continuing with innovations, HetSIREN can also refine the pose parameters of the images at the same time that it conditions the network with prior information/constraints on the maps, such as Total Variation andL1denoising, ultimately yielding cleaner volumes with high-quality structural features. Finally, but very importantly, HetSIREN addresses one of the most confusing issues in heterogeneity analysis, as it is the fact that real structural heterogeneity estimation is entangled with pose estimation (and to a lesser extent with CTF estimation), in this way, HetSIREN introduces a novel encoding architecture able to decouple pose and CTF information from the conformational landscape, resulting in more accurate and interpretable conformational latent spaces. We present results on computer-simulated data, public data from EMPIAR, and data from experimental systems currently being studied in our laboratories. An important finding is the sensitivity of the structure and dynamics of the SARS-CoV-2 Spike protein on the storage temperature.
Successful stimulation of myocardial ganglionic plexuses by TAU 20 in the absence of cardiac damage
Authors: Li Shengzhe , Kay Jamie A , Agha-Jaffar Danya , Gao Cindy S Y , Perkins Justin , Koutsoftidis Simos , Drakakis Emm Mic , Cantwell Chris , Wang Liliang , Kanagaratnam Prapa , Chowdhury Rasheda A
Published: September 2024

Atrial fibrillation (AF) is a major healthcare burden worldwide. For AF that is resistant to pharmacological intervention, the standard invasive treatment is a pulmonary vein isolation (PVI) procedure. Ganglionated plexuses (GP) ablation can be used as an adjunctive therapy to PVIs, together reducing the likelihood of AF recurrence. High-frequency stimulation (HFS) is a technique used to identify ectopy-triggering GP sites. However, to locate GP sites, sequential HFS must be delivered over the whole atria. Therefore, ensuring the safety of HFS delivery is integral to avoid causing irreversible damage from excessive pacing. We tested Tau-20 version 2 neural simulator, a prototype of a novel electrophysiological pacing and recording system that has the potential to guide intracardiac AF treatments. Using anex vivoporcine Langendorff model that closely resembles the anatomy and physiology of a human heart, we confirmed that HFS can successfully trigger AF, indicating that HFS-positive locations contain GP sites. Additionally, we found that the HFS delivered via Tau-20 version 2 did not cause any damage to the heart. These findings evidence that once fully optimised, the Tau-20 system could be suitable for use in clinical settings.
Structural Repetition Detector: multi-scale quantitative mapping of molecular complexes through microscopy
Authors: Mendes Afonso , Saraiva Bruno M. , Jacquemet Guillaume , Mamede João I. , Leterrier Christophe , Henriques Ricardo
Published: September 2024

From molecules to organelles, cells exhibit recurring structural motifs across multiple scales. Understanding these structures provides insights into their functional roles. While super-resolution microscopy can visualise such patterns, manual detection in large datasets is challenging and biased. We present the Structural Repetition Detector (SReD), an unsupervised computational framework that identifies repetitive biological structures by exploiting local texture repetition. SReD formulates structure detection as a similarity-matching problem between local image regions. It detects recurring patterns without prior knowledge or constraints on the imaging modality. We demonstrate SReD’s capabilities on various fluorescence microscopy images. Quantitative analyses of three datasets highlight SReD’s utility: estimating the periodicity of spectrin rings in neurons, detecting HIV-1 viral assembly, and evaluating microtubule dynamics modulated by EB3. Our open-source ImageJ and Fiji plugin enables unbiased analysis of repetitive structures across imaging modalities in diverse biological contexts.
Humatch - fast, gene-specific joint humanisation of antibody heavy and light chains
Authors: Chinery Lewis , Jeliazkov Jeliazko R. , Deane Charlotte M.
Published: September 2024

1

Antibodies are a popular and powerful class of therapeutic due to their ability to exhibit high affinity and specificity to target proteins. However, the majority of antibody therapeutics are not genetically human, with initial therapeutic designs typically obtained from animal models. Humanisation of these precursors is essential to reduce immunogenic risks when administered to humans.

Here, we present Humatch, a computational tool designed to offer experimental-like joint humanisation of heavy and light chains in seconds. Humatch consists of three lightweight Convolutional Neural Networks (CNNs) trained to identify human heavy V-genes, light V-genes, and well-paired antibody sequences with near-perfect accuracy. We show that these CNNs, alongside germline similarity, can be used for fast humanisation that aligns well with known experimental data. Throughout the humanisation process, a sequence is guided towards a specific target gene and away from others via multiclass CNN outputs and gene-specific germline data. This guidance ensures final humanised designs do not sit ‘between’ genes, a trait that is not naturally observed. Humatch’s optimisation towards specific genes and good VH/VL pairing increases the chances that final designs will be stable and express well and reduces the chances of immunogenic epitopes forming between the two chains. Humatch’s training data and source code are provided open-source.

Availability

Source code is freely available at github.com/oxpig/Humatch. Data can be found at doi.org/10.5281/zenodo.13764770

Contact

deane@stats.ox.ac.uk

Supplementary information

Supplementary data are available atbioRxivonline.
A PROXIMITY LIGATION SCREEN IDENTIFIES SNAT2 AS A NOVEL TARGET OF THE MARCH1 E3 UBIQUITIN LIGASE
Authors: Balthazard Renaud , Mitchell William , Raymond Maxime , Vidal Arnau Ballestero , Roy Dominic G. , Zambrano Libia Cecilia Palma , Moulefera Mohamed Abdelwafi , Faubert Denis , Pasquin Sarah , Gauchat Jean-François , Thibodeau Jacques
Published: September 2024

E3 ubiquitin ligases are part of various families of proteins and include hundreds of members, which play key roles in all aspects of cell biology. They generally regulate the half-life of other proteins but can also modulate their cellular localization and functions. The MARCH family of ubiquitin ligases is composed of 11 members and two closely related proteins, MARCH1 and MARCH8, share similar targets, while being active in different cell types. Although they appear to target principally immune cell components, such as MHC class II molecules and the co-stimulatory molecule CD86, the repertory of their targets remains to be fully documented. Here, to further define the MARCH1’s interactome, we adapted a proximity-dependent biotin identification (BioID)-based screening approach in live HEK293 cells. We transfected a fusion protein consisting of mouse MARCH1 linked to YFP at its N-terminus and to the biotin ligase ofAquifex aeolicusat its C-terminus. Upon transient overexpression of this construct in the presence of exogenous biotin, we could recover biotinylated proteins that are presumably found within 10nm of MARCH1. To help in the identification ofbona fidedown-regulated specific targets, we compared MARCH1’s interactome with the one obtained using a ubiquitination-deficient MARCH1 mutant (MARCH1W104A). CD98 and CD71, two previously described targets of MARCH1, were identified in this screen. Of 16 other biotinylated proteins identified by semi-quantitative mass spectrometry, 10 were tested directly by flow cytometry to monitor their expression in the presence or absence of transfected MARCH1. The protein levels of five of these endogenous targets, CD29, CD112, NKCC1, CD147 and SNAT2, confirmed their negative regulation by MARCH1 in this system. SNAT2 was particularly sensitive to the presence of MARCH1 and was found to be ubiquitinated on Western blots following immunoprecipitation. Thus, BioID2 is an effective mean of characterizing the interactome of MARCH1 and the identification of SNAT2 suggests a role of this ubiquitin ligase in cellular metabolism.
Structure-guided assembly of an influenza spike nanobicelle vaccine provides pan H1 intranasal protection
Authors: Myers Mallory L. , Gallagher John R. , Woolfork De’Marcus D. , Khorrami Noah D. , Park William B. , Maldonado-Puga Samantha , Bohrnsen Eric , Schwarz Benjamin H. , Alves Derron A. , Bock Kevin W. , Dearborn Altaira D. , Harris Audray K.
Published: September 2024

Development of intranasal vaccines for respiratory viruses has gained popularity. However, currently only a live-attenuated influenza vaccine is FDA-approved for intranasal administration. Here, we focused on influenza virus as it circulates seasonally, has pandemic potential, and has vaccine formulations that present hemagglutinin (HA) in different structural arrangements. These display differences have not been correlated with induction of pan-H1 antibodies or shown to provide intranasal protection. Using electron microscopy, biochemistry and animal studies, we identified HA complexes arranged as lipid discs with multiple trimeric HAs displayed along the perimeter, termed spike nanobicelles (SNB). We utilized a structure-guided approach to synthesize in vitro assembled spiked nanobicelles (IA-SNB) from a classical 1934 H1N1 influenza virus. IA-SNBs elicited pan-H1 antibodies and provided protection against antigenically divergent H1N1 viruses via intranasal immunizations. Viral glycoprotein spikes displayed as SNBs could aid in combating antigenic variation and provide innovative intranasal vaccines to aid universal influenza vaccine development.
From the Ground Up: Stakeholder Perspectives on Housing Interventions to Reduce Environmentally Mediated Infections
Authors: Acklin Matthias , Graham Jay P. , Benjamin-Chung Jade
Published: September 2024

Background

Housing conditions are intrinsically linked to human health, with inadequate housing potentially increasing exposure to environmentally mediated pathogens. Housing interventions that aim to improve housing and reduce environmentally mediated infections, such as finished floors and housing upgrades for vector-borne diseases, remain relatively under-explored as health interventions. This study explored facilitators of and barriers to funding, implementing, and scaling up housing improvements as health interventions to reduce environmentally mediated infectious diseases.

Methods

Sixteen key informants (KIs) with direct experience in implementing or working within housing interventions and environmentally mediated infectious diseases in low- and middle-income countries were interviewed using a semi-structured interview format. KIs had diverse backgrounds, including academics researching housing interventions, housing policy advisors, and practitioners implementing housing interventions. A thematic analysis approach was used to identify key themes in interview transcripts, highlighting patterns, commonalities, and variations in participants’ responses.

Results

KIs emphasized the multi-dimensional impacts of housing interventions that are intrinsically linked to Sustainable Development Goals (SDGs), including physical and mental health, as well as environmental, social, and economic dimensions. Moreover, a pronounced shortage of funding and financial systems to address housing interventions was highlighted, alongside the urgent need for more rigorous evidence and cost-benefit analyses. Furthermore, the imperative to raise awareness of the significance of housing and the critical importance of strong collaboration across sectors and stakeholders were stressed. Emphasizing the necessity for project-based and context-specific housing policies, the interviews revealed that contextualizing interventions to their specific setting and fostering community involvement are essential for successful implementation and scale-up.

Conclusions

Housing interventions play a pivotal role in mitigating environmentally mediated diseases. These interventions can complement existing strategies like water, sanitation, and hygiene (WASH) interventions, ensuring comprehensive approaches to healthy housing and sustainable development goals amidst climate change.
Autophagy acts as a brake on obesity-related fibrosis by controlling purine nucleoside signalling
Authors: Piletic Klara , Kayvanjoo Amir H. , Richter Felix Clemens , Borsa Mariana , Lechuga-Vieco Ana V. , Popp Oliver , Grenet Sacha , Long Ko Jacky Ka , Zec Kristina , Kyriazi Maria , Koneva Lada , Sansom Stephen , Mertins Philipp , Powrie Fiona , Alsaleh Ghada , Simon Anna Katharina
Published: September 2024

A hallmark of obesity is a pathological expansion of white adipose tissue (WAT), accompanied by marked tissue dysfunction and fibrosis. Autophagy promotes adipocyte differentiation and lipid homeostasis, but its role in obese adipocytes and adipose tissue dysfunction remains incompletely understood. Here, we demonstrate that autophagy is a key tissue-specific regulator of WAT remodelling in diet-induced obesity. Importantly, loss of adipocyte autophagy substantially exacerbates pericellular fibrosis in visceral WAT. Change in WAT architecture correlates with increased infiltration of macrophages with tissue-reparative, fibrotic features. We uncover that autophagy regulates purine nucleoside metabolism in obese adipocytes, preventing excessive release of the purine catabolites xanthine and hypoxanthine. Purines signal cell-extrinsically for fibrosis by driving macrophage polarisation towards a tissue reparative phenotype. Our findings reveal a novel role for adipocyte autophagy in regulating tissue purine nucleoside metabolism, thereby limiting obesity-associated fibrosis and maintaining the functional integrity of visceral WAT. Purine signals may serve as a critical balance checkpoint and therapeutic target in fibrotic diseases.
WITHDRAWN: Strand dependent bypass of DNA lesions during fork reversal by ATP-dependent translocases SMARCAL1, ZRANB3, and HLTF
Authors: Adolph Madison B. , Warren Garrett M. , Couch Frank B. , Greer Briana H. , Eichman Brandt F. , Cortez David
Published: September 2024

Withdrawal Statement

The authors have withdrawn this manuscript because they identified problems with how some figure panels were processed. Those experiments will be repeated before deposition of a new manuscript. Therefore, the authors do not wish this work to be cited as reference for the project. If you have any questions, please contact the corresponding authors.
A glyphosate-based herbicide selects for genetic changes while retaining within-species diversity in a freshwater bacterioplankton community
Authors: Derrick Emma , Barbosa da Costa Naíla , Barrett Rowan D. H. , Shapiro B. Jesse
Published: September 2024

Bacterial populations evolve rapidly in the lab when faced with experimentally-applied selective pressures. Yet how bacteria evolve in nature, in more complex multi-species communities, is both challenging to study and essential to our understanding of ecosystem responses to rapid anthropogenic change. It has been theorized that selection purges within-species diversity in genome-wide selective sweeps, but the prevalence of such sweeps in response to known selective pressures in nature remains unclear. To track bacterial evolution in a semi-natural context, we applied Roundup, a glyphosate-based herbicide (GBH) as a selective pressure to 1000 L ponds containing bacterioplankton communities from a pristine lake. Using metagenomic analyses, we found that GBH treatment substantially affected community diversity, reducing species richness twofold, but did not consistently purge within-species genetic diversity over the four weeks of the experiment. We identified several functional categories of genes targeted by GBH selection across 11 different species of bacteria. There was no evidence for selection on the enzyme targeted by glyphosate, which interferes with amino acid synthesis; however genes involved more broadly in amino acid transport and metabolism were more likely to experience changes in allele frequency, particularly in inferred GBH-sensitive species. Together, these results show how environmental change can rapidly affect bacterial community structure while leaving within-species diversity largely intact. Even without evident genome-wide selective sweeps, we identify consistent genetic targets of selection, pointing to alternative mechanisms of GBH resistance in nature, and suggesting a role for soft or gene-specific selective sweeps in adaptation.
Cryo-PRO facilitates whole blood cryopreservation for single-cell RNA sequencing of immune cells from clinical samples
Authors: DuBois Alyssa K. , Ankomah Pierre O. , Campbell Alexis C. , Hua Renee , Nelson Olivia K. , Zeuthen Christopher A. , Das M. Kartik , Mann Shira , Mauermann Abigail , Parry Blair A. , Shapiro Nathan I. , Filbin Michael R. , Bhattacharyya Roby P.
Published: September 2024

Single-cell RNA sequencing (scRNA-seq) of peripheral blood mononuclear cells (PBMCs) has enhanced our understanding of host immune mechanisms in small cohorts, particularly in diseases with complex and heterogeneous immune responses such as sepsis. However, PBMC isolation from blood requires technical expertise, training, and approximately two hours of onsite processing using Ficoll density gradient separation (‘Ficoll’) for scRNA-seq compatibility, precluding large-scale sample collection at most clinical sites. To minimize onsite processing, we developed Cryo-PRO (Cryopreservation with PBMC Recovery Offsite), a method of PBMC isolation from cryopreserved whole blood that allows immediate onsite sample cryopreservation and subsequent PBMC isolation in a central laboratory prior to sequencing. We compared scRNA-seq results from samples processed using Cryo-PRO versus standard onsite Ficoll separation in 23 patients with sepsis. Critical scRNA-seq outputs including cell substate fractions and marker genes were similar for each method across multiple cell types and substates, including an important monocyte substate enriched in patients with sepsis (Pearson correlation 0.78, p<0.001; 70% of top marker genes shared). Cryo-PRO reduced onsite sample processing time from >2 hours to <15 minutes and was reproducible across two enrollment sites, thus demonstrating potential for expanding scRNA-seq in multicenter studies of sepsis and other diseases.