bluuebunny/crossref_metadata_2025 huggingface dataset:
Atoms and Subtle matter: Henry Power’s observations on plants in
Experimental Philosophy
Authors: Matei Oana
Published: November 2024

This paper examines Henry Power’s
Experimental philosophy
and suggests that Power’s observations of and experiments with plants were not used to reconcile Cartesian corpuscularianism with different approaches that stress the subtle character of matter. Instead, their purpose was rather to determine the nature of seeds and their role in the process of plant generation, i.e. whether they are containers of the ultimate division of matter (atoms) or parts of matter endowed with formative power. My argument starts with a discussion of Power’s presentation on the role of seeds in the process of plant generation in his
Experimental philosophy
. I claim that Power compares plant seeds to atoms, and that he does not strictly interpret seeds/atoms in the Cartesian corpuscularian and mechanical fashion. Power’s ‘atoms’ are of two kinds—subtle and grosser—where the subtle has the property to trigger natural processes. Moreover, I interpret seeds as parts of matter endowed with creative properties as an addition to the preformist interpretation of Power’s position on plant generation.
Microbispora maris sp. nov., a novel actinobacterium isolated from the gill of the leopard coral grouper (Plectropomus leopardus)
Authors: Xie Huan , Xie Qing-Yi , Ma Qing-Yun , Yang Li , Dai Hao-Fu , Zhao You-Xing , Hao Yu-E
Published: November 2024

A novel actinomycete, designated strain ZYX-F-249T, was isolated from the gill of a leopard coral grouper in Yongxing Island, Hainan Province, China. Based on 16S rRNA gene sequence analysis, strain ZYX-F-249T belonged to the genus Microbispora, with high similarities to Microbispora rosea ATCC 12950T (98.7 %), Microbispora hainanensis 211020T (98.5 %), Microbispora clausenae CLES2T (98.4 %), Microbispora bryophytorum NEAU-TX2-2T (98.1 %) and Microbispora oryzae
RL4-1ST (98.0 %). Phylogenetic analysis of the 16S rRNA gene sequence of strain ZYX-F-249T showed that the strain formed a stable subclade with Microbispora rosea ATCC 12950T in the genus Microbispora. The cell wall of the novel isolate contained meso-diaminopimelic acid, while whole-cell sugars were madurose, glucose and ribose. The predominant menaquinones were MK-9(H6), MK-9(H4), MK-9(H2) and MK-9(H0). The characteristic phospholipids (PLs) were phosphatidylethanolamine, phosphatidylinositol, diphosphatidylglycerol, phosphatidylmethylethanolamine, phosphatidylinositol mannoside, glycophospholipids and an unknown PL. The major cellular fatty acids (>10%) were iso-C16 : 0 and iso-C18 : 0. Genome sequencing showed a DNA G+C content of 71.6%. The low average nucleotide identity, digital DNA–DNA hybridization and average amino acid identity values demonstrated that strain ZYX-F-249T could be readily distinguished from closely related species. Based on data from these phylogenetic, chemotaxonomic and physiological characteristics, strain ZYX-F-249T represents a novel species of the genus Microbispora, for which the name Microbispora maris sp. nov. is proposed. The type strain is ZYX-F-249T (=CCTCC AA 2023030T =JCM 36778T).
Nanomotion technology: an innovative method to study cell metabolism in Escherichia coli, as a potential indicator for tolerance
Authors: Aubry Christèle , Kebbi-Beghdadi Carole , Luraschi-Eggemann Amanda , Cathomen Gino , Cichocka Danuta , Sturm Alexander , Greub Gilbert ,   The ERADIAMR Consortium§
Published: November 2024

Introduction. Antibiotic tolerance corresponds to the bacterial ability to survive a transient exposure to antibiotics and is often associated with treatment failure. Current methods of identifying tolerance based on bacterial growth are time-consuming. This study explores the use of a growth-independent method utilizing nanomotion technology to detect antibiotic-tolerant bacteria.

Hypothesis. The nanomotion signal obtained from a nanomechanical sensor measures real-time metabolic activity and cellular processes and could provide valuable information about the tolerance of bacteria to antibiotics that cannot be detected by standard antibiotic susceptibility tests.

Aim. The aim of this study is to investigate the potential of nanomotion technology to record antibiotic-tolerant bacteria.

Methodology. We generated a slow-growing Escherichia coli strain by manipulating mazF expression levels and confirmed its viability by several standard methods. We subsequently measured its nanomotion and the nanomotion of the WT E. coli in the presence or absence of antibiotics. Supervised machine learning was employed to distinguish slow-growing from exponentially growing bacteria. Observations for bacterial nanomotions were confirmed by standard kill curves.

Results. We distinguished slow-growing from exponentially growing bacteria using specific features from the nanomotion signal. Furthermore, the exposition of both growth phenotypes to polymyxin decreased the nanomotion signal indicating cell death. Similarly, when exponentially growing cells were exposed to ampicillin, an antibiotic whose efficacy depends on the growth rate, the nanomotion signal also decreased. In contrast, the nanomotion signal remained unchanged for slow-growing bacteria upon exposure to ampicillin. In addition, antibiotic exposure can cause bacterial elongation, in which the biomass of a cell increases without cell division. By overexpressing sulA, we mimicked antibiotic-induced elongation. Differences in the nanomotion signal were observed when comparing elongating and non-elongating phenotypes.

Conclusion. This work shows that nanomotion signals entail information about the reaction to antibiotics that standard MIC-based antibiotic susceptibility tests cannot detect. In the future, nanomotion-based antibiotic tolerance tests could be developed for clinical use in chronic or relapsing infections.
Identifying gene-level mechanisms of successful dispersal of Vibrio parahaemolyticus during El Niño events
Authors: Campbell Amy Marie , Gavilan Ronnie G. , Hauton Chris , van Aerle Ronny , Martinez-Urtaza Jaime
Published: November 2024

El Niño events, the warm phase of the El Niño Southern Oscillation, facilitate the movement of warm surface waters eastwards across the Pacific Ocean. Marine organisms transported by these waters can act as biological corridors for water-borne bacteria with attachment abilities. El Niño events have been hypothesized as driving the recent emergence of Vibrio parahaemolyticus (Vp) variants, marine bacterium causing gastroenteritis, in South America, but the lack of a robust methodological framework limited any further exploration. Here, we introduce two new analysis approaches to explore Vp dynamics in South America, which will be central to uncovering Vp dynamics in the future. Distributed non-linear lag models found that strong El Niño events increase the relative probability of Vp detection in Peru, with a 3–4-month lag time. Machine learning found that the presence of a specific gene (vopZ) involved in attachment to plankton in a pandemic Vp clone in South America was temporally associated with strong El Niño events, offering a possible strategy for survival over long-range dispersal, such as that offered by El Niño events. Robust surveillance of marine pathogens and methodological development are necessary to produce resolute conclusions on the effect of El Niño events on water-borne diseases.
A unified central thalamus mechanism underlying diverse recoveries in disorders of consciousness
Authors: Zhang Haoran , Ge Qianqian , Liu Xiao , Dang Yuanyuan , Xu Long , Zhuang Yutong , Wu Si , Laureys Steven , He Jianghong , Yu Shan
Published: November 2024

Disorders of consciousness (DoC) encompass a range of states characterized by prolonged altered awareness due to heterogeneous brain damage and are associated with highly diverse prognoses. However, the neural mechanisms underlying such diverse recoveries in DoC remain unclear. To address this issue, we analysed neuronal spiking activities recorded from the central thalamus (CT), a key hub in arousal regulation, in a cohort of 23 DoC patients receiving deep brain stimulation treatment. Using machine learning techniques, we identified a core set of electrophysiological features of the CT, particularly the theta rhythm, that could account for individual recovery outcomes across highly varied etiologies (trauma, brainstem hemorrhage, and anoxia), clinical baselines and patient ages. These features also correctly identified one subgroup of patients who exhibited poor initial clinical manifestations but recovered unexpectedly. Simulating a conductance-based model further revealed the neurodynamics of the theta rhythm in the CT during different stages of consciousness recovery. Taken together, these findings uncover a previously unknown, unified CT mechanism that governs the recoveries in DoC.
Enemy release of introduced parasitoids does not affect their establishment or success
Authors: Kishinevsky Miriam , Ferrer-Suay Mar , Ives Anthony R.
Published: November 2024

The enemy release hypothesis, that the success of invading species is due to release from natural enemies that occur in their home range but not in the new range, can be an important explanation for successful invasions. Testing this hypothesis is difficult, however, because testing requires documented cases of not only successful, but also unsuccessful invasions. Therefore, observational data on after-the-fact establishment following unintentional introductions is insufficient, because they only include successful invasions. Here, we investigate the role of enemy release for parasitoid biological control agents and their hyperparasitoid natural enemies. We created a dataset of all aphid parasitoid wasp species introduced into North America, including data on their hyperparasitoid species in the native and new range. In total, information on 29 species of primary parasitoids and 54 species of hyperparasitoids was obtained, combining to create 259 parasitoid-hyperparasitoid species associations. Results show that introduced parasitoids experience partial enemy release, but the degree of enemy release does not affect the chance of successful establishment or successful control. This lack of effect of enemy release might be due to the broad geographical range of the hyperparasitoids (perhaps from unintentional introductions) which reduces the degree of enemy release. In addition, the life-history traits of the hyperparasitoid communities in the new range were different from the native range, with relatively more generalist hyperparasitoid species in the new range. These results show that introduced natural enemies can experience enemy release, but that this does not necessarily help to predict their successful establishment.
PDBe tools for an in-depth analysis of small molecules in the Protein Data Bank
Authors: Choudhary Preeti , Kunnakkattu Ibrahim Roshan , Nair Sreenath , Lawal Dare Kayode , Pidruchna Ivanna , Afonso Marcelo Querino Lima , Fleming Jennifer R. , Velankar Sameer
Published: November 2024

The Protein Data Bank (PDB) is the primary global repository for experimentally determined 3D structures of biological macromolecules and their complexes with ligands, proteins, and nucleic acids. PDB contains over 47,000 unique small molecules bound to the macromolecules. Despite the extensive data available, the complexity of small molecule data in the PDB necessitates specialised tools for effective analysis and visualisation. PDBe has developed a number of tools, including PDBe CCDUtils (https://github.com/PDBeurope/ccdutils) for accessing and enriching ligand data, PDBe Arpeggio (https://github.com/PDBeurope/arpeggio) for analysing interactions between ligands and macromolecules, and PDBe RelLig (https://github.com/PDBeurope/rellig) for identifying the functional roles of ligands (such as reactants, cofactors, or drug-like molecules) within protein-ligand complexes. Furthermore, the enhanced ligand annotations and data generated by these tools are presented in a comprehensive view on the novel PDBe-KB ligand pages, providing a holistic view of small molecules that enables the establishment of their biological contexts (Example page for Imatinib:https://wwwdev.ebi.ac.uk/pdbe-srv/pdbechem/chemicalCompound/show/STI). By improving the standardisation of ligand identification, adding various annotations, and offering advanced visualisation capabilities, these tools help researchers navigate the complexities of small molecules and their roles in biological systems, facilitating mechanistic understanding of biological functions. The ongoing enhancements to these resources are designed to support the scientific community in gaining valuable insights into ligands and their applications across various fields, including drug discovery, molecular biology, systems biology, structural biology, and pharmacology.
Examining Changes in Gramicidin Current Induced by Endocannabinoids
Authors: Mayar Sultan , Cyr-Athis Audrey , D’Avanzo Nazzareno
Published: November 2024

Endocannabinoids are a diverse family of lipid molecules, which circulate in the human body, impacting the cardiovascular and the nervous systems. Endocannabinoids can influence pain perception, appetite, stress responses, mood, memory and learning. Regulation of these lipids present a promising therapeutic avenue for numerous neurological disorders. In addition to acting as agonists to cannabinoid receptors (CBRs), endocannabinoids can also modulate the function of various ion channels and receptors independently of CBRs. This modulation of function can arise from direct binding to the channel proteins, or via changes to the lipid properties such as membrane elasticity/stiffness, curvature, or hydrophobic thickness. Here, we assess the effects of endocannabinoids on membrane properties by examining changes in gramicidin (gA) currents inXenopusoocytes. Endocannabinoids from both classes (Fatty acid ethanolamides (FAEs) and 2-monoacylglycerols (2-MGs)) are studied and current-voltage relationships are assessed. Employing gramicidin channels as molecular force probes can enable both predictive and quantitative studies on the impact of bilayer-mediated regulation on membrane protein function by endocannabinoids.
Parallel in-depth analysis of repeat expansions: an updated Clin-CATS workflow for nanopore R10 flow cells
Authors: Scholz Veronika , Schönrock Veronika , Erdmann Hannes , Prokosch Vitus , Schoedel Maria , Almus Manuela , Sauer Mayra , Mayer Veronika , Breithausen Eva , van Buren Inga , Dineiger Christine , Heintz Caroline , Hallermayr Ariane , Neuhann Teresa , Holinski-Feder Elke , Abicht Angela , Benet-Pagès Anna , Lucas Morghan C
Published: November 2024

Hereditary ataxias, caused by expansions of short tandem repeats, are difficult to diagnose using traditional PCR and Southern blot methods, which struggle to detect complex repeat expansions and cannot assess repeat interruptions or methylation. We present an updated Clinical Nanopore Cas9-Targeted Sequencing (Clin-CATS) workflow for analyzing repeat expansions, now compatible with the Oxford Nanopore Technologies R10 flow cell. The workflow incorporates the ONT wf-human-variation Epi2Me workflow, including the Straglr tool to analyze basecalled reads, ensuring compatibility with past, current, and future sequencing chemistries. It expands the number of genes analyzed from 10 to 27 within the ataxia panel and introduces new gene panels for myopathy, neurodegeneration, and ALS/motor neuron disease. Validated with Coriell reference and clinical samples, this method improves the analysis of pathogenic repeat expansions, providing deeper insights into repeat structures while addressing the limitations of traditional approaches.
Whole-genome sequencing across space and time reveals impact of population decline and reduced gene flow in Florida Scrub-Jays
Authors: Nguyen Tram N. , Cosgrove Elissa J. , Chen Nancy , Lehr Natasha , Lokey Mitchell G. , Beaudry Felix E. G. , Fitzpatrick Sarah W. , Bowman Reed , Miller Karl E. , Fitzpatrick John W. , Clark Andrew G.
Published: November 2024

Whole-genome sequence data is proving to be highly informative about the past demography of free-living populations, and in the context of endangered species, it can provide a quantification of the genetic risk posed by reduced genetic diversity and inbreeding. Prior to 1920, the Florida scrub-jay (Aphelocoma coerulescens) had been widespread across Florida, but with the expansion of agriculture and human habitation, its population has declined by 95%, resulting in fragmentation into semi-isolated subpopulations. By sequencing 241 individuals sampled from five different regions and across two time points, this study quantifies a greater magnitude of loss of genetic diversity and greater levels of inbreeding in smaller and more isolated subpopulations. Consistent with population genetics theory, reduction in population size results in a dramatic loss of rare alleles, skewing the site frequency spectrum far from the expected equilibrium. Increased inbreeding in the smaller, more remote subpopulations is especially evident in the increased size and number of runs of homozygosity. The Florida scrub-jay displays limited dispersal, and habitat fragmentation has greatly reduced the magnitude of gene flow in the past 30 years, resulting in further decline of genetic diversity, especially in the peripheral populations. Analysis of these data is informative in guiding conservation efforts to retain genetic diversity and minimize the consequences of inbreeding in the Florida scrub-jay.

Highlights

Five regional populations show distinct degrees of population isolation and decline.

There has been commensurate loss of genetic diversity, skewed site frequency spectra, reduced migration, and increased inbreeding (FROH).

As many state-wide populations decline, the smaller, more remote populations provide a glimpse into the future and a testbed for remediation approaches.
Generative AI for Patient Communication in Radiology and Nuclear Medicine: A Pilot Study in Thai
Authors: Badawy Mohamed K , Carrion Daniel , Khamwan Kitiwat
Published: November 2024

Purpose: Effective patient communication in procedures involving radiation is crucial, especially for patients facing literacy or language barriers. Generative Artificial Intelligence offers innovative solutions for creating personalised, multilingual patient education materials. This pilot study assesses the effectiveness of GenAI, specifically using HeyGen, in generating personalised patient information videos in the Thai language. Methods: An avatar of a medical physicist was created using HeyGen. Two English health information scripts on nuclear medicine and radiology were translated into Thai with HeyGen's translation tool, and videos were generated featuring the avatar delivering the content in Thai. Native Thai-speaking medical physicists and postgraduate students (n = 13) evaluated the videos using a 5-point Likert scale on criteria such as translation accuracy, naturalness of delivery, and usefulness as a patient education tool. Objective translation quality was assessed using the Bilingual Evaluation Understudy scoring system. Results: Both videos received high median scores for translation accuracy (median = 4.0), with BLEU scores of 0.57 and 0.66, indicating good translation quality. Participants noted minor issues with formal language and unnatural phrasing but generally found the videos understandable and valuable. Feedback suggested improvements in the naturalness of the avatar's delivery to enhance relatability. Conclusions: This pilot study shows that GenAI can effectively create personalised patient information videos and translate them into Thai, helping to bridge communication gaps in procedures involving radiation. While minor issues remain, the findings suggest that tools like HeyGen could significantly support patient communication with further refinement, especially for those facing language barriers.
Guidance for the design and analysis of cell-type specific epigenetic epidemiology studies
Authors: Walker Emma M , Dempster Emma L , Franklin Alice , Klokkaris Anthony , Chioza Barry , Davies Jonathan P , Blake Georgina ET , Burrage Joe , Policicchio Stefania , Bamford Rosemary A , Schalkwyk Leonard C , Mill Jonathan , Hannon Eilis
Published: November 2024

Recent studies on the role of epigenetics in disease have focused on DNA methylation profiled in bulk tissues limiting the detection of the cell-type affected by disease related changes. Advances in isolating homogeneous populations of cells now make it possible to identify DNA methylation differences associated with disease in specific cell-types. Critically, these datasets will require a bespoke analytical framework that can characterise whether the difference affects multiple or is specific to a particular cell-type. We take advantage of a large set of DNA methylation profiles (n = 751) obtained from five different purified cell populations isolated from human prefrontal cortex samples and evaluate the effects on study design, data preprocessing and statistical analysis for cell-specific studies, particularly for scenarios where multiple cell types are included. We describe novel quality control metrics that confirm successful isolation of purified cell populations, which when included in standard preprocessing pipelines provide confidence in the dataset. Our power calculations show substantial gains in detecting differentially methylated positions for some purified cell populations compared to bulk tissue analyses, countering concerns regarding the feasibility of generating large enough sample sizes for informative epidemiological studies. In a simulation study, we evaluated different regression models finding that this choice impacts on the robustness of the results. These findings informed our proposed two-stage framework for association analyses. Overall, our results provide guidance for cell-specific EWAS, establishing standards for study design and analysis, while showcasing the potential of cell-specific DNA methylation analyses to reveal links between epigenetic dysregulation and disease.
Hope for Others: Research Results from the University of Pittsburgh Rapid Autopsy Program for Breast Cancer
Authors: Chang Alexander CC , Balic Marija , Bartholow Tanner , Bhargava Rohit , Brown Daniel D. , Brown Lauren , Brufsky Adam , Cao Ye , Carleton Neil , Clark Amanda M. , Cody Morgan , Ding Kai , Deible Christopher , Elangovan Ashuvinee , Foldi Julia , Geisler Daniel , Hodgdon Christine , Howard Naomi , Li Zheqi , Lopez-Nunez Jie Bin Liu Oscar , Mary Sheeba John , McGinn Olivia , Miller Lori , Mori Kanako , Pecar Geoffrey , Priedigkeit Nolan , Puhalla Shannon , Rosenzweig Margaret Q. , Roy Partha , Savariau Laura , Walker Stephanie , Waltermire Hunter , Wedn Abdalla M , Wells Alan , Yates Megan E. , Xavier Jennifer , Lee Adrian V , Oesterreich Steffi
Published: November 2024

Breast cancer affects 1/8 of women throughout their lifetimes, with 90% of cancer deaths being caused by metastasis. However, metastasis poses unique challenges to research, as complex changes in the microenvironment in different metastatic sites and difficulty obtaining tissue for study hinder the ability to examine in depth the changes that occur during metastasis. Rapid autopsy programs thus fill a unique need in advancing metastasis research. Here, we describe our protocol and processes for establishing and improving the US-based Hope for OTHERS (Our Tissue Helping Enhance Research and Science) program for organ donation in metastatic breast cancer. Our results reveal key logistical and protocol improvements that are uniquely beneficial to certain programs based on identifiable features, such as working closely with patient advocates, methods to rescue RNA quality in cases where tissue quality may degrade due to time delays, as well as guidelines and future expansions of our program with new research and novel research findings in patient outcomes, metastatic phylogeny, living model development and more.

Statement of Significance

Rapid autopsy programs are unique research settings with huge potential for studying metastatic cancer, however, they have complex research challenges. Our work provides a valuable resource in advancing this field of research.
Comprehensive protease specificity profiling
Authors: Zhu Bo , Lane Michael D. , Baller Joshua A. , Jagtap Pratik D. , Griffin Timothy J. , Seelig Burckhard
Published: November 2024

Protease enzymes are of great importance in medicine, industry, and as research tools. Despite the crucial need for detailed knowledge of their proteolytic cleavage specificity, many proteases are poorly characterized. We present a method for fully characterizing the cleavage specificity of proteases through the comprehensive profiling of all possible permutations of octamer peptide substrates in a single experiment. The powerful combination of in vitro selection with high-throughput sequencing, mass spectrometry, and automated motif mining enabled the screening of mixtures of >1012unique peptides. We developed freely available software that easily integrates the massive amounts of cleavage data into user-friendly specificity information. We applied this method to three different proteases that had either narrow (factor Xa) or broad specificity (ADAM17 and streptopain). The resulting specificity maps revealed motifs that corroborate canonical known cleavage sites, yet step further into extended spectrum preferences and yield insights into the function of broad specificity proteases.
Sonoran Desertex situconservation gap analysis: charting the path towards conservation
Authors: Chávez-Hernández María Guadalupe , Gómez-Barreiro Pablo , White Joseph Douglas Mandla , Way Michael
Published: November 2024

Plant biodiversity is under threat. With two out of five plants at risk of extinction, preserving taxa throughex situconservation approaches must be considered a priority. The Sonoran Desert (SD), a highly biodiverse ecoregion shared between Mexico and the United States is home to over 4000 native plant taxa. A method to determine conservation priorities was developed in collaboration with institutions from both countries. Herbaria records and data from nine seed banks were analysed to identify gaps in previous conservation efforts. The SD native taxa were prioritised based on a Priority Score (PS) and their potential distribution was modelled to identify priority regions. 4029 native taxa were reported. 1441 have accessions preserved in seed banks, but only 412 have been collected inside the SD. The PS considers some potentially endemic (126) and threatened taxa (112) as the most urgent to preserve. It also includes information about the storage behaviour (3236 orthodox), useful plants (1406), and taxa without populations in protected areas (230) to categorise the species. Although most of the SD flora is not represented in seed banks, at least 80% is predicted to produce desiccation-tolerant seeds and thus can be cost-effectively stored. Spatial analysis shows that the central region of the Baja California Peninsula stands out for its species richness and endemism. Our study presents the firstex situconservation gap analysis of the SD flora and provides a replicable methodology for identifying priority species and potential areas forex situcollection.
A type-specific B cell epitope at the apex of Outer surface protein C (OspC) of the Lyme disease spirochete,Borreliella burgdorferi
Authors: Vance David J. , Freeman-Gallant Grace , McCarthy Kathleen , Piazza Carol Lyn , Chen Yang , Vorauer Clint , Muriuki Beatrice , Rudolph Michael J. , Cavacini Lisa , Guttman Miklos , Mantis Nicholas J.
Published: November 2024

Broadly protective immunity to the Lyme disease spirochete,Borreliella burgdorferi, is constrained by an overwhelming antibody response against type-specific epitopes on Outer surface protein C (OspC), a homodimeric helix-rich lipoprotein essential for early stages of spirochete dissemination in vertebrate hosts. However, the molecular basis for type-specific immunity has not been fully elucidated. In this report, we produced and characterized an OspC mouse monoclonal antibody, 8C1, that recognizes native and recombinant OspC type A (OspCA) but not OspC types B or K, and arrestsB. burgdorferimotility independent of complement. Epitope mapping by HDX-MS localized 8C1’s epitope to a protruding ridge on the apex of OspCAα-helix 3 (residues 130-150) previously known to be an immunodominant region of the molecule. Alanine scanning pinpointed 8C1’s core binding motif to a solvent exposed patch consisting of residues K141H142T143D144. In parallel, analysis of 26 Lyme disease positive serum samples confirmed antibody reactivity with this region of OspCA, with residues E140and D144as being most consequential. Our results underscore the importance of α-helix 3 as a target of type-specific epitopes on OspCAacross mice and humans that should be taken into consideration in Lyme disease vaccine design.
An extended and improved CCFv3 annotation and Nissl atlas of the entire mouse brain
Authors: Piluso Sébastien , Verasztó Csaba , Carey Harry , Delattre Émilie , L’Yvonnet Thibaud , Colnot Éloïse , Romani Armando , Bjaalie Jan G. , Markram Henry , Keller Daniel
Published: November 2024

Brain atlases are essential for quantifying cellular composition in mouse brain regions. The Allen Institute’s Common Coordinate Framework version 3 (CCFv3) is widely used, delineating over 600 anatomical regions, but it lacks coverage for the most rostral and caudal brain parts, including the main olfactory bulb, cerebellum, and medulla. Additionally, the CCFv3 omits key cerebellar layers, and its corresponding Nissl-stained reference volume is not precisely aligned, limiting its utilisability. To address these issues, we developed an extended atlas, the Blue Brain Project CCFv3 augmented (CCFv3aBBP), which includes a fully annotated mouse brain and an improved Nissl reference aligned in the CCFv3. This enhanced atlas also features the central nervous system annotation (CCFv3cBBP). Using this resource, we aligned 734 Nissl-stained brains to produce an average Nissl template, enabling an updated distribution of neuronal soma positions. These data are available as an open-source resource, broadening applications such as improved alignment precision, cell type mapping, and multimodal data integration.
Relative Effects of Habitat Amount and FragmentationPer Seon the Genetic Diversity of The Glanville Fritillary Butterfly
Authors: Fernandez Multigner Lola , Bras Audrey , DiLeo Michelle , Saastamoinen Marjo
Published: November 2024

Habitat loss and fragmentation are considered the key drivers of biodiversity loss. Understanding their relative roles is difficult as habitat loss and fragmentation tend to co-occur. It has been proposed that the total habitat amount available in the local landscape mainly drives species richness while fragmentationper se– the breaking apart of habitat independent of habitat amount - has negligible or even a positive effect on biodiversity. Several studies support this at the species richness level. Yet, the potential effects of fragmentationper seon genetic diversity at the landscape scale are understudied. Using the Glanville fritillary butterfly metapopulation in the Åland islands, we tested the effects of fragmentationper seon genetic diversity using a landscape-based approach and 2,610 individuals genotyped at 40 neutral SNP markers. We assessed the independent effect of habitat amount and fragmentation (i.e. number of patches) within the local landscape on the focal patch genetic diversity. The amount of habitat in the local landscape had a positive effect on genetic diversity, while fragmentationper sehad a more negligible impact on the genetic diversity. Our results thus highlight that all fragments, even the small ones, likely contribute to the maintenance of genetic diversity of the focal population.
Denoising Reveals Low-Occupancy Populations in Protein Crystals
Authors: Fadini Alisia , Apostolopoulou Virginia , Lane Thomas J. , van Thor Jasper J.
Published: November 2024

Advances in structural biology increasingly focus on uncovering protein dynamics and transient or weak macromolecular complexes. Such studies require modeling of low-occupancy species, for instance time-evolving intermediates and bound ligands. In protein crystallography, difference maps that compare paired perturbed and reference datasets are a powerful way to identify and aid modeling of low-occupancy species. Current methods to generate difference maps, however, rely on manually tuned parameters and, in cases of weak signal due to low occupancy, can fail to extract clear, chemically interpretable signals.

We address these issues, first by showing negentropy is an effective metric to assess difference map quality and can therefore be used to automatically determine parameters needed during difference map calculation. Leveraging this, we apply total variation denoising, an image restoration technique that requires a choice of regularization parameter, to crystallographic difference maps. We show that total variation denoising improves map signal-to-noise and enables us to estimate the latent phase contribution of low-occupancy states. This technology opens new possibilities for time-resolved and ligand-screening crystallography in particular, allowing the detection of states that previously could not be resolved due to their inherently low occupancy.
BaNDyT: Bayesian Network modeling of molecular Dynamics Trajectories
Authors: Mukhaleva Elizaveta , Manookian Babgen , Chen Hanyu , Ma Ning , Wei Wenyuan , Urbaniak Konstancja , Gogoshin Grigoriy , Bhattacharya Supriyo , Vaidehi Nagarajan , RODIN ANDREI S , Branciamore Sergio
Published: November 2024

Bayesian network modeling (BN modeling, or BNM) is an interpretable machine learning method for constructing probabilistic graphical models from the data. In recent years, it has been extensively applied to diverse types of biomedical datasets. Concurrently, our ability to perform long-timescale molecular dynamics (MD) simulations on proteins and other materials has increased exponentially. However, the analysis of MD simulation trajectories has not been data-driven but rather dependent on the user's prior knowledge of the systems, thus limiting the scope and utility of the MD simulations. Recently, we pioneered using BNM for analyzing the MD trajectories of protein complexes. The resulting BN models yield novel fully data-driven insights into the functional importance of the amino acid residues that modulate proteins' function. In this report, we describe the BaNDyT software package that implements the BNM specifically attuned to the MD simulation trajectories data. We believe that BaNDyT is the first software package to include specialized and advanced features for analyzing MD simulation trajectories using a probabilistic graphical network model. We describe here the software's uses, the methods associated with it, and a comprehensive Python interface to the underlying generalist BNM code. This provides a powerful and versatile mechanism for users to control the workflow. As an application example, we have utilized this methodology and associated software to study how membrane proteins, specifically the G protein-coupled receptors, selectively couple to G proteins. The software can be used for analyzing MD trajectories of any protein as well as polymeric materials.
Co-Therapy with S1P and Heparan Sulfate Derivatives to Restore Endothelial Glycocalyx and Combat Pro-Atherosclerotic Endothelial Dysfunction
Authors: Mitra Ronodeep , Pentland Kaleigh , Kolev Svilen , Eden Matthew , Levine Erel , Oakes Jessica M. , Ebong Eno E.
Published: November 2024

Endothelial cell (EC) glycocalyx (GCX) shedding due to disturbed blood flow and chemical factors leads to low-density lipoprotein infiltration and reduced nitric oxide synthesis, causing vascular dysfunction and atherosclerosis. This study evaluates a novel therapy combining sphingosine-1-phosphate (S1P) and heparin (heparan sulfate derivative). We hypothesized that heparin/S1P would repair mechanically damaged EC GCX in disturbed flow (DF) regions and restore anti-atherosclerotic mechanotransduction function, addressing cardiovascular disease. We used a parallel-plate flow chamber to simulate flow conditions in vitro and a partial carotid ligation mouse model to mimic DF in vivo. Heparin and albumin-bound S1P were administered to assess their reparative effects on the endothelial GCX. Immunocytochemistry, fluorescent staining, confocal microscopy, cellular alignment studies, and ultrasound were performed to evaluate EC function and endothelial-dependent vascular function. Barrier functionality was assessed via macrophage uptake. Heparin/S1P mechanism-of-action insights were gained through fluid dynamics simulations and staining of GCX synthesis enzyme as well as S1P receptor. Statistical analyses validated results. In vitro data showed that heparin/S1P therapy improves the function of DF-conditioned ECs by restoring EC GCX and promoting EC alignment and elevated vasodilator eNOS (endothelial-type nitric oxide synthase) expression. The in vivo studies confirmed GCX degradation, increased vessel inflammation and hyperpermeability, and vessel wall thickening in the partially ligated left carotid artery. Heparin/S1P treatment restored GCX in the left carotid artery, enhancing GCX thickness and coverage of the blood vessel wall. This work advances a new approach to regenerating the EC GCX and restoring its function in ECs under DF conditions.
Tear secretionviaa paracellular pathway in lacrimal gland is regulated by myosin-mediated modulation of tight junction permeability
Authors: Ohno Yuta , Hu Gaizun , Robak Dominik , Zheng W. Sharon , Ebrahim Seham
Published: November 2024

“Dry eye”, characterized by symptoms of ocular discomfort and visual disturbances due to decreased tear secretion, affects 16 million Americans. Yet, there is currently no cure for dry eye as the mechanistic details of water secretion in the tear-producing lacrimal gland have not been fully elucidated. While a transcellular water secretion pathwayviawater channels like AQP5 has been reported, the existence and function of a paracellular pathwayviatight junctions between epithelial cells remains controversial. The actomyosin cytoskeleton localizes to the apical junctions of epithelial cells across organs and regulates tight junction integrity. Here, we report that non-muscle myosin IIC (NMIIC) is enriched at apical junctions of ductal epithelial cells in the lacrimal gland, leading us to hypothesize that NMIIC regulates tear secretion through modulation of tight junction permeability. Consistent with this hypothesis, we found that tear volume after carbachol stimulation was significantly increased in mice lacking NMIIC, and levels of the tight junction protein ZO-1 were significantly reduced. Furthermore, pharmacological activation of NMIIC by 4-Hydroxyacetophenone in wildtype mice significantly inhibited tear secretion. In summary, our findings reveal a paracellular water secretion pathway in the lacrimal gland, which is regulated by NMIIC-mediated modulation of ductal cell tight junctional permeability, and can be targeted by small molecules.

Significance Statement

While dry eye affects more than 16 million Americans, there is currently no cure as the mechanisms underlying tear secretion are incompletely understood. Here, we report first evidence for the existence and function of a paracellular water pathway, in which water flows between cells, in the lacrimal gland. We also show that this pathway is directly regulated by the modulation of tight junction permeability by non-muscle myosin IIC (NMIIC). This study thus identifies a new mechanism for exocrine secretion, which can be targeted towards developing treatments for dry eye/mouth syndrome.
TomoScore: A Neural Network Approach for Quality Assessment of Cellular cryo-ET
Authors: Tan Xuqian , Boniuk Ethan , Abraham Anisha , Zhou Xueting , Yu Zhili , Ludtke Steven J. , Wang Zhao
Published: November 2024

Electron cryo-tomography (cryo-ET) is a powerful imaging tool that allows three-dimensional visualization of subcellular architecture. During morphological analysis, reliable tomogram segmentation can only be achieved through high-quality data. However, unlike single-particle analysis or subtomogram averaging, the field lacks a useful quantitative measurement of cellular tomogram quality. Currently, the most prevalent method to determine cellular tomogram resolvability is an empirical judgment by experts, which is time-consuming. Methods like FSC between split tilt series suffer from severe geometrical artifacts. We address this gap with a neural network model to predict per-slice resolvability that can apply to tomograms collected from various species and magnifications. We introduce a novel metric, “TomoScore”, providing a single-value evaluation of cellular tomogram quality, which is a powerful tool for pre-screening tomograms for subsequent automatic segmentation. We further explore the relationship between accumulated electron dose and resulting quality, suggesting an optimum dose range for cryo-ET data collection. Overall, our study streamlines data processing and reduces the need for human involvement during pre-selection for tomogram segmentation.
Genetic and Environmental Determinants of Streaming and Aggregation inMyxococcus xanthus
Authors: Khan Trosporsha T , Murphy Patrick , Zhang Jiangguo , Igoshin Oleg A , Welch Roy D
Published: November 2024

Under starvation conditions, a spot of a few millionMyxococcus xanthuscells on agar will migrate inward to form aggregates that mature into dome-shaped fruiting bodies. This migration is thought to occur within structures called ‘streams,’ which are considered crucial for initiating aggregation. The prevailing traffic jam model hypothesizes that intersections of streams cause cell crowding and ‘jamming,’ thereby initiating the process of aggregate formation. However, this hypothesis has not been rigorously tested, in part due to the lack of a standardized, quantifiable definition of streams. To address this gap, we captured time-lapse movies and conducted fluorescent cell tracking experiments using wild-type and two motility-deficient mutantM. xanthusstrains. By quantitatively defining streams and developing a novel stream detection mask, we show that streams are not essential for nascent aggregate formation, though they may accelerate the process. Moreover, our results indicate that streaming has a genetic component: disrupting only one of the twoM. xanthusmotility systems hinders stream formation. Together, these findings challenge the idea that stream intersections are required to drive aggregate formation and suggest thatM. xanthusaggregation may be driven by mechanisms independent of streaming, highlighting the need for alternative models to fully explain aggregation dynamics.
Differential Equation Modeling of Cell Population Dynamics in Skeletal Muscle Regeneration from Single-Cell Transcriptomic Data
Authors: Al-Ghazawi Renad , Shao Xiaojian , Perkins Theodore J.
Published: November 2024

Skeletal muscle regeneration is a complex process orchestrated by diverse cell populations within a dynamic niche. In response to muscle damage and intercellular signaling, these cells undergo cell fate and migration decisions including quiescence, activation, proliferation, differentiation, infiltration, apoptosis, and exfiltration. The emergence of single-cell RNA sequencing (scRNA-seq) studies of muscle regeneration offers a significant opportunity to refine models of regeneration and enhance our understanding of cellular interactions. To better understand how crosstalk between cell types governs cell fate decisions and cell population dynamics, we developed a novel non-linear ordinary differential equation model guided by scRNA-seq data. Our model consists of 9 variables and 19 parameters, capturing the dynamics of key myogenic lineage and immune cell types. We calibrated time-series scRNA-seq data to units of cells per cubic millimeter of tissue and fit our model’s parameters to capture the observed dynamics, validating on an independent time series. The model successfully captures regeneration dynamics, particularly after incorporating a novel type of regulatory interaction between M2 macrophages and satellite cells that has been hypothesized in the literature. Our model lays a foundation for future computational explorations of muscle regeneration, modeling of disease conditions, and in silico testing of therapeutic strategies.
sCellST: a Multiple Instance Learning approach to predict single-cell gene expression from H&E images using spatial transcriptomics
Authors: Chadoutaud Loïc , Lerousseau Marvin , Herrero-Saboya Daniel , Ostermaier Julian , Fontugne Jacqueline , Barillot Emmanuel , Walter Thomas
Published: November 2024

Advancing our understanding of tissue organization and its disruptions in disease remains a key focus in biomedical research. Histological slides stained with Hematoxylin and Eosin (H&E) provide an abundant source of morphological information, while Spatial Transcriptomics (ST) enables detailed, spatiallyresolved gene expression (GE) analysis, though at a high cost and with limited clinical accessibility. Predicting GE directly from H&E images using ST as a reference has thus become an attractive objective; however, current patch-based approaches lack single-cell resolution. Here, we present sCellST, a multipleinstance learning model that predicts GE by leveraging cell morphology alone, achieving remarkable predictive accuracy. When tested on a pancreatic ductal adenocarcinoma dataset, sCellST outperformed traditional methods, underscoring the value of basing predictions on single-cell images rather than tissue patches. Additionally, we demonstrate that sCellST can detect subtle morphological differences among cell types by utilizing marker genes in ovarian cancer samples. Our findings suggest that this approach could enable single-cell level GE predictions across large cohorts of H&E-stained slides, providing an innovative means to valorize this abundant resource in biomedical research.
Salt-dependent non-catalytic allostery of human USP14-regulated 26S proteasome
Authors: Zou Shitao , Zhang Shuwen , Zhao Lihong , Mao Youdong
Published: November 2024

USP14, a deubiquitylating enzyme, regulates 26S proteasome function both catalytically and non-catalytically through multiple checkpoints. How USP14 non-catalytically regulates the proteasome activity remains elusive. Here, we combined genetic engineering and cryo-EM to disentangle how USP14 non-catalytically regulates proteasome activity in a salt-dependent manner. By solving 16 high-resolution cryo-EM structures of substrate-engaged human 26S proteasome complexed with a catalytically deficient mutant USP14, we demonstrate that USP14’s non-catalytic activity alone can induce parallel pathways of proteasome state transitions, leading to opposing substrate fates. The USP14 mutant allosterically reprograms the AAA-ATPase motor, inducing novel substrate-engaged conformations and filling major gaps in understanding asymmetric ATP-hydrolysis cycling around the ATPase ring. Time-resolved cryo-EM and functional analysis reveal that sodium or potassium promotes substrate-engaged pathways and suppresses USP14 activity for enhanced degradation, uncovering another layer of complexity in proteasome regulation.