bluuebunny/crossref_metadata_2025 huggingface dataset:
Mapping spatially-resolved transcriptomes in systemic sclerosis
Authors: Li Zhijian , Rigau Aleix Rius , Xie Wenjie , Huang Linlin , Shao Xiaohang , Li Yi-Nan , Matei Alexandru-Emil , Ye Wenjing , Zou Hejian , Pinello Luca , Distler Jörg H.W. , He Rui , Liang Minrui
Published: January 2025

Systemic sclerosis (SSc) is a prototypical fibrotic disease with high mortality and limited treatment options. Despite advances in single-cell RNA sequencing (scRNA-seq), the comprehensive understanding of cellular heterogeneity and cell-cell interaction within the fibrogenesis microenvironment remains limited. We generated spatially resolved transcriptome maps from healthy and SSc skin and built a scRNA-seq atlas to map the single-cell data to spatial space. This enabled us to identify a fibrotic niche, enriched with fibroblasts and macrophages, which is significantly expanded in SSc and correlated with clinical outcome. We revealed disease-specific cell states of fibroblasts and macrophages, and evaluated their spatial dependency on other cell types. We identified selective expression of ACKR3 in fibroblast progenitors that diminishes with SSc progression, which may serve to regulate CXCL12/CXCR4-mediated macrophage recruitment and fibrotic remodeling. Together, we provided an in-depth description at cellular and spatial levels of fine-tuned regulatory events occurring in SSc, offering spatiotemporal insights.

One Sentence Summary

Integrated spatial omics provide insight into the cellular and transcriptional landscape in spatially distinct microenvironments, which may drive fibrosis progression in SSc.
Targeting histone acetylation enables epigenetic modulation of inflammatory pathways – a novel therapeutic strategy for rheumatoid arthritis
Authors: Brinkmann Marie , Tosevska Anela , Luckerbauer Bianca , Madern Moritz , Göschl Lisa , Ellmeier Wilfried , Aletaha Daniel , Preglej Teresa , Bonelli Michael
Published: January 2025

Autoimmune diseases like rheumatoid arthritis (RA) are characterized by a systemic inflammation caused by autoreactive immune cells. Epigenomic modulation of these cells offers a strategy to reprogram pathogenic pathways without altering the genome, potentially restoring immune balance. Epigenetic inhibitors are already utilized in oncology but often exhibit adverse effects due to lack of selectivity and cytotoxic concentrations. Applying these drugs to treat autoimmune diseases necessitates more selective inhibitors and the use of tolerable concentrations. In this study, we screened a library of 25 compounds with varying degrees of target selectivity and different concentrations. Spectral cytometry enabled the analysis of cell-subset distribution and activation, followed by bulk RNA-sequencing for transcriptomic profiling.

We could demonstrate cell-subset specific and concentration-dependent immune modulation in PBMCs. Transcriptomic analysis showed that inhibitors of histone acetylation-modulating enzymes significantly altered gene expression, particularly in immune regulation pathways relevant to autoimmune diseases. Comparative analysis betweenin-vitrotreated healthy controls and RA patients demonstrated both shared and selective drug effects, with some inhibitors like Ricolinostat overlapping with established RA drug pathways.

Our findings highlight the potential of epigenetic inhibitors, especially those targeting histone acetylation, to modulate immune responses in a target-selective manner.

Graphical abstract
A Paper-Droplet Hybrid System for Efficient Blood Plasma Separation in Multiplex Diagnostics
Authors: Dash Amaan , Medicharla Rajeev Srikar , DasGupta Sunando
Published: January 2025

Single μPAD-based lateral flow blood plasma separation techniques suffer from low sensitivity, inconsistent performance, and extended turnaround times, hindering point- of-care whole blood multiplexing. Integrating multifunctional microfluidic approach could offer a paradigm shift, providing rapid, high-throughput blood testing with reduced sample alongside streamlined downstream automation. Herein we report a novel low-cost sessile-drop and paper hybrid blood plasma separation technique that achieves efficient (≥ 98 %) separation within seconds (∼70 s). Evaporation-driven natural convection within a sessile blood droplet facilitates effective mixing, while capillary forces prevalent in the paper structure selectively transport plasma to the detection zones, all without any externally applied motive force. The separated plasma is successfully analysed for simultaneous glucose and albumin detection using colorimetric assay. This method demonstrates high accuracy in predicting glucose and albumin levels in healthy and diseased samples when benchmarked against an Automated Biochemistry Analyzer. A 3D foldable all-in-one paper microfluidic device, complemented by a MATLAB based application (GPS App.) has been developed for quantitative assessment during on-field diagnostics. This study presents a rapid, efficient, and user-friendly alternative to traditional flow-based separation, providing reliable detection in resource-limited settings.
Clustering of Tandem Inverse Duplications in Centromeric and Subtelomeric Chromosomal Regions ofAspergillus flavus
Authors: Cary Jeffrey W. , Malik Amna , Smith Alexie , Flemington Erik , Lustig Arthur J
Published: January 2025

Rearrangements associated with gene amplification are frequently initiated by the formation of inverted repeats. Among these rearrangements are breakage-fusion-bridge cycles and tandem inverted duplications (TIDs), both of which can be mediated through palindromic sequences. We have investigated spontaneous rearrangements within the genome of the filamentous fungusAspergillus flavusby high-coverage third-generation sequencing of vegetatively cultured strains. Analysis of sequence data identified a class of rare and transient rearrangements having structures typical of TIDs. These putative TIDs (pTIDs) form both unprocessed and processed species and have a variably sized deletion at the junction between direct and inverted sequences. Most intact junctions contain the predicted palindromic sequences, supporting the TID model. However, palindrome-free junctions are also infrequently observed. pTIDs are highly enriched in heterochromatic centromeric and subtelomeric A+T rich regions, suggesting that this process is a source of genetic instability in these domains. Consistent with this finding, A+T rich regions contain elevated levels of direct, inverted, and perfect palindromic repeats. We propose a replication-based model in which palindromes and short inverted repeats, under condition of replication stress, are responsible for pTID structures.

TEASER

The dynamic formation of duplication/inversions clustered in fungal chromosomes reveals the genetic instability of centromeric and subtelomeric regions.
Growth but not corticosterone, oxidative stress or telomere length is negatively affected by microplastic exposure in a filter-feeding amphibian
Authors: Martin Colette , Ruthsatz Katharina , Gomez-Mestre Ivan , Burraco Pablo
Published: January 2025

Microplastics (MPs) are of increasing global concern for species inhabiting aquatic habitats. However, the mechanisms behind animal responses to MPs need comprehensive exploration. Amphibians are the most threatened vertebrate group with most species having a complex life cycle, commonly with an aquatic larval stage. Here, we investigated whether exposure to an environmentally-relevant concentration of MPs affects the growth of filter-feeding larvae of the African clawed frog (Xenopus laevis), and the consequences for their stress physiology (corticosterone (CORT) levels), or health and ageing physiology (oxidative stress and telomere length). We conducted a 3×2 experiment with three levels of fibre exposure (fibres absent -control-, and MP and cellulose fibre treatments), and two stress levels (CORT absent –control-, and CORT present simulating a stressful condition). We observed a negative impact of MP exposure on larval growth; however, this did not alter the CORT levels, oxidative stress or telomere length. Our study shows that realistic concentrations of MPs is not enough to induce major alterations on the stress or health and ageing physiology of a filter-feeding amphibian. Whether compensatory growth responses during the post-metamorphic stages could lead to detrimental effects later in life should be explored in amphibians and other organisms with complex-life cycles.
A Novel Optimized Silver Nitrate Staining Method for Visualizing the Osteocyte Lacuno-Canalicular System
Authors: Wu Jinlian , Xue Chunchun , Li Qiang , Wu Hongjin , Zhang Jie , Wang Chenglong , Dai Weiwei , Wang Libo
Published: January 2025

A 50% silver nitrate solution is commonly used to stain and characterize the osteocyte lacuno-canalicular system (LCS) in bone biology research. However, variability in reagent concentrations and types, along with inconsistent staining procedures, have limited the broader application of this method in osteocyte research. In this study, we present a novel optimized silver nitrate staining technique aimed at addressing these limitations. This new method utilizes a 1 mol/L silver nitrate solution in combination with a type-B gelatin-formic acid solution at various concentrations (0.05%-0.5% gelatin and 0.05%-5% formic acid, or 1%-2% gelatin and 0.1%-2% formic acid) in volume ratios of 4:1, 2:1, or 1:1, or a 0.5 mol/L silver nitrate solution at a 4:1 ratio. The staining process is carried out for 1 hour under ultraviolet light or 90 minutes under regular room light (or dark), followed by washing with Milli-Q water to terminate the reaction. We applied this new method to stain the osteocyte LCS in bone samples from different species and pathological bone models. The technique consistently produced clear, distinct staining patterns across all samples. Moreover, our novel method revealed a greater number of LCS compared to the traditional 50% silver nitrate solution. This suggests that the commonly used 50% silver nitrate method may disrupt or inadequately reveal the LCS in certain species, potentially leading to an underestimation of LCS density and number. In conclusion, our novel silver nitrate staining method provides a simpler and more cost-effective alternative to the traditional technique. By offering a more accurate and comprehensive analysis of the LCS across species, this approach has the potential to advance research on osteocyte morphogenesis, as well as the functional and evolutionary adaptations of the osteocyte LCS across different taxa.
Contact mode high-speed AFM of phase separated lipid bilayers to study Amyloid-β interactions
Authors: Robinson Morgan , Payton Oliver , Picco Loren , Beazely Michael , Miles Mervyn , Leonenko Zoya
Published: January 2025

The lipid bilayer membrane is an essential feature of life, the composition and structure of which is important in governing cellular processes, some of which are mediated by the changes induced by proteins. Of particular interest is the role that the lipid membrane plays in amyloidogenic diseases such as Alzheimer’s disease (AD), including the role of lipid composition and cholesterol in mediating amyloid-β (Aβ) toxicity. Atomic force microscopy (AFM) is a key tool in studying the structures of lipid membranes as nanoscale structure is important for function, unfortunately many of these dynamic processes occur on time scales where traditional AFM cannot operate fast enough. Recent advances in contact mode high-speed AFM (HS-AFM) have made it possible to capture processes at video rate. We used a unique custom-built contact mode HS-AFM to image model lipid membranes in liquid and compare this to standard and HS-AFM images. We demonstrate that this technique can be used to capture the dynamics of interactions of Aβ(1-42) monomers and oligomers with phase separated lipid bilayers composed of three and five lipid components to elucidate the role of nanoscale domains in amyloid-membrane interactions. Overall, we demonstrate the potential of the HS-AFM to image biological processes on biologically relevant soft samples and discuss tip-sample interactions at high-speed operation in contact mode on lipid membrane models in liquid environment.
Anionic lipid catalyzes the generation of cytotoxic insulin oligomers
Authors: Saha Jhinuk , Wolszczak Audrey , Kaur Navneet , Dickwella Widanage Malitha C. , McCalpin Samuel D , Fu Riqiang , Ali Jamel , Ramamoorthy Ayyalusamy
Published: January 2025

Misfolding and aggregation of proteins into amyloidogenic assemblies are key features of several metabolic and neurodegenerative diseases. Human insulin has long been known to form amyloid fibrils under various conditions, which affects its bioavailability and function. Clinically, insulin aggregation at recurrent injection sites poses a challenge for diabetic patients who rely on insulin therapy. Furthermore, decreased responsiveness to insulin in type 2 diabetic (T2D) patients may lead to its overproduction and accumulation as aggregates. Earlier reports have reported that various factors such as pH, temperature, agitation, and the presence of lipids or other proteins influence insulin aggregation. Our present study aims to elucidate the effects of non-micellar anionic DMPG (1,2-dimyristoyl-sn-glycero-3-phosphoglycerol) lipids on insulin aggregation. Distinct pathways of insulin aggregation and intermediate formation were observed in the presence of DMPG using a ThT fluorescence assay. The formation of soluble intermediates, alongside large insulin fibrils, was observed in insulin incubated with DMPG via TEM, DLS and NMR, as opposed to insulin aggregates generated without lipids.13C magic angle spinning solid-state NMR and FTIR experiments indicated that lipids do not alter the conformation of insulin fibrils but do alter the time scale of motion of aromatic and aliphatic sidechains. Furthermore, the soluble intermediates were found to be more cytotoxic as compared to fibrils generated with or without lipids. Overall, our study elucidates the importance of anionic lipids in dictating the pathways and intermediates associated with insulin aggregation. These findings could be useful in determining various approaches to avoid toxicity and enhance the effectiveness of insulin in therapeutic applications.
Void spot assay visualization optimization for use of Void Whizzard in rats (Rattus norvegicus)
Authors: Ruetten Hannah , Bothe Jadyn , Lankford Shannon , Badlani Gopal , Williams James Koudy
Published: January 2025

Void spot assay (VSA) noninvasively evaluates urination. VSA is often not performed in rats due to difficulty analyzing larger papers compared with mouse. This study optimizes VSA for rats by comparing post-assay visualization techniques: bright field light (BF), ultraviolet light (UV), and ninhydrin spray (N). Male rats were placed in cages lined by filter paper for 4 hours. Water and food was provided ad lib. After the assay all papers were dried overnight. BF images were photographed (digital camera). UV images were captured after cutting papers in half using a Darkroom ultraviolet imaging cabinet. Papers were sprayed with ninhydrin and photographed (digital camera). All images were converted to black and white for analysis with Void Whizzard. UV vs. BF showed significant differences in area. All three groups had significant differences in overall spot count and in the smallest sized spots (0-0.1 cm2). UV vs. N and UV vs. BF showed significant differences in 0.1-0.25 cm2 spots, UV vs. N in 0.25-0.5 cm2, and N vs. BF in spots 0.5-1 cm2. Overall BF visualization proved difficult. N provided an ideal way to highlight urine and image with a digital camera. Human fingerprints from pre-assay handling of paper interfered with analysis of the smallest sized spots however there were no differences in detection of larger spots, spot distribution, or overall spot area. This study contributes to the development of a standardized VSA protocol for assessing bladder function in both mouse and rat models.
Altered relaxation and Mitochondria-Endoplasmic Reticulum Contacts Precede Major (Mal)adaptations in Aging Skeletal Muscle and are Prevented by Exercise
Authors: Allen Ryan J. , Kronemberger Ana , Shi Qian , Pope Marshall , Cuadra-Muñoz Elizabeth , Son Wangkuk , Song Long-Sheng , Anderson Ethan J. , Pereira Renata O. , Lira Vitor A.
Published: January 2025

Sarcopenia, or age-related muscle dysfunction, contributes to morbidity and mortality. Besides decreases in muscle force, sarcopenia is associated with atrophy and fast-to-slow fiber type switching, which is typically secondary to denervation in humans and rodents. However, very little is known about cellular changes preceding these important (mal)adaptations. To this matter, mitochondria and the sarcoplasmic reticulum are critical for tension generation in myofibers. They physically interact at the boundaries of sarcomeres forming subcellular hubs called mitochondria-endo/sarcoplasmic reticulum contacts (MERCs). Yet, whether changes at MERCs ultrastructure and proteome occur early in aging is unknown. Here, studying young adult and older mice we reveal that aging slows muscle relaxation leading to longer excitation-contraction-relaxation (ECR) cycles before maximal force decreases and fast-to-slow fiber switching takes place. We reveal that muscle MERC ultrastructure and mitochondria-associated ER membrane (MAM) protein composition are also affected early in aging and are closely associated with rate of muscle relaxation. Additionally, we demonstrate that regular exercise preserves muscle relaxation rate and MERC ultrastructure in early aging. Finally, we profile a set of muscle MAM proteins involved in energy metabolism, protein quality control, Ca2+homeostasis, cytoskeleton integrity and redox balance that are inversely regulated early in aging and by exercise. These may represent new targets to preserve muscle function in aging individuals.
Environmental effects on constructed wetland microbial diversity and function in the context of wastewater management
Authors: Grandmont-Lemire Sandrine , Gearheart Bob , Cuellar-Gempeler Catalina
Published: January 2025

Considering temporal and spatial change in biodiversity-ecosystem function (BEF) relationships is critical to predict and manage ecosystem services, especially in human mediated and impacted ecosystems. We propose that species responses to seasonal change and spatial distributions can act as a laboratory to reveal diversity-function relationships with management implications. This study investigates the relationship between bacterial diversity and ammonia removal function in a wastewater secondary treatment constructed wetland system. We took 8 samples across a system of 6 interconnected ponds, from August 2019 to February 2020, at the Arcata Wastewater Treatment Facility (AWTF), in Coastal Humboldt County (California, USA). We used 16S rRNA gene amplicon sequencing to measure bacterial diversity and composition, and an ammonia electrode probe to measure NH4at the influx and efflux positions of each pond. We found a significant negative relationship between ASV richness and ammonia removal, suggesting that nitrifying and denitrifying bacteria are poor competitors, known a negative selection effect. Bacterial richness effect on ammonia removal was strongest, followed by direct effects of season on richness and location on function, based on structural equation modeling. We identify taxa associated with function that may influence management strategies, including Planktophila, Legionella, Sulfurimonadaceae and Sporichtyaceae that thrive in ponds located after chlorination steps. This result challenges the traditional wastewater treatment reactor paradigm to reveal negative BEF relationships that appear stronger than environmental influences. By expanding our views of BEF relationships, we can further unravel how community diversity and composition influence ecosystem processes in natural and humanized systems.

IMPORTANCE

This study sheds new light on how biodiversity impacts ecosystem functions in human-made environments, specifically wastewater treatment systems. By examining bacterial diversity and ammonia removal efficiency across interconnected ponds, we challenge the conventional assumption that more species always lead to better ecosystem performance. The surprising finding that higher bacterial diversity can reduce ammonia removal efficiency (due to competition among key bacteria) offers fresh insights into how microbial communities work. This understanding is critical for improving wastewater treatment and designing systems that maximize efficiency. Moreover, identifying specific bacteria linked to ammonia removal provides practical information for better managing and enhancing treatment processes. By broadening how we think about the relationship between biodiversity and ecosystem function, this study offers valuable tools for both scientists and environmental managers working to balance human impact with ecosystem health.
Functionally diversified BiP orthologs control body growth, reproduction, stress resistance, aging, and ER-Phagy inCaenorhabditis elegans
Authors: Urban Nicholas D. , Lacy Shannon M. , Van Pelt Kate M. , Abdon Benedict , Mattiola Zachary , Klaiss Adam , Tabler Sarah , Truttmann Matthias C.
Published: January 2025

Cellular systems that govern protein folding rely on a delicate balance of functional redundancy and diversification to maintain protein homeostasis (proteostasis). Here, we useCaenorhabditis elegansto demonstrate how both overlapping and divergent activities of two homologous endoplasmic reticulum (ER)-resident HSP70 family chaperones, HSP-3 and HSP-4, orchestrate ER proteostasis and contribute to organismal physiology. We identify tissue-, age-, and stress-specific protein expression patterns and find both redundant and distinct functions for HSP-3 and HSP-4 in ER stress resistance, reproduction, and body size regulation. We show that only HSP-3 overexpression is sufficient to improve longevity and that loss of HSP-3 or HSP-4 during distinct stages of the worm cycle or specific tissues have opposing effects on worm lifespan. Furthermore, we find that loss of HSP-4, but not HSP-3, improves tolerance to protein aggregation induced-stress by activating ER-Phagy through the engagement of IRE-1 and the putative ER-Phagy receptor, C18E9.2. Mechanistically, we show that de-repression of IRE-1 via HSP-4 dissociation allows for direct inhibition of C18E9.2- mediated ER-Phagy and demonstrate that a conserved orthologous mechanism involving the respective human orthologs, BiP, Sec-62, and IRE-1, contributes to ER proteostasis regulation in human cells. Taken as a whole, our study demonstrates that functional diversification of orthologous proteins within a single organelle is an efficient mechanism to maximize stress resilience while also defining a novel link between ER- phagy and proteostasis regulation.
Sequence-based Drug-Target Complex Pre-training Enhances Protein-Ligand Binding Process Predictions Tackling Crypticity
Authors: Zhang Shuo , Xie Li , Tiourine Daniel , Xie Lei
Published: January 2025

Predicting protein-ligand binding processes, such as affinity and kinetics, is critical for accelerating drug discovery. However, many existing computational methods face key limitations, including insufficient integration of comprehensive databases, inadequate representation of protein structural dynamics, and incomplete modeling of microscale protein-ligand interactions. To address these challenges, we introduce ProMoNet, a sequence-based pre-training and fine-tuning framework to enhance protein-ligand binding process prediction. ProMoNet connects protein and molecular foundation models to expand data coverage and enhance diversity, and it integrates large-scale binding site pre-training with efficient fine-tuning for affinity and kinetics prediction. During pre-training, it effectively models microscale protein-ligand interactions and captures the dynamic nature of proteins, including binding site crypticity, without relying on 3-dimensional structural inputs. Notably, ProMoNet’s pre-training module surpasses or matches state-of-the-art structure-based methods in identifying exposed and cryptic binding sites. In the fine-tuning stage, it transfers pre-trained knowledge, achieving superior performance in affinity and kinetics prediction tasks with high computational efficiency. The combination of ProMoNet’s powerful modeling capabilities and demonstrated success across multiple tasks highlight its potential for broad applications in drug discovery.
Use of cellular FAD autofluorescence as a label-free cellular attribute for the production of chimeric antigen receptor-T cells
Authors: Cheung Ka-Wai , Kairi Faris , Lin Teo Denise Bei , Sin Wei-Xiang , Lee Yie Hou , Birnbaum Michael E.
Published: January 2025

Chimeric antigen receptor T (CAR-T) cell therapy has become an attractive approach for treating hematological malignancies. However, the accessibility of this therapy is limited by factors such as complex manufacturing process, limited capacity of manufacturing facilities and the requirement of highly skilled workforce for the manual steps of CAR-T cell production. To minimize the manual processes, CAR-T cell manufacturing field is shifting towards closed and automated systems, including analytical tools that offer intermittent monitoring of cells in production. Therefore, label-free technologies for closely monitoring CAR-T cells in closed systems are needed. Here, we evaluate the use of a flow cytometer equipped with a 405nm violet laser for investigating the NADH and FAD autofluorescence in T cells. Our results revealed the increase of NADH and FAD autofluorescence were significantly correlated with the upregulation of T cell activation marker, CD25 and the increase of extracellular lactate in spent media in the first three days after T cell activation. We demonstrate the potential use of FAD for determining the endpoint of CAR-T cell manufacture by establishing a relationship between the rate of change in the mean fluorescence intensity (MFI) of FAD in CAR-T cells and the rate of change in T cell proliferation using a G-Rex bioreactor. Collectively, these findings suggest that autofluorescence, particularly FAD autofluorescence, can serve as a label-free biomarker (cellular attribute) for monitoring T cell activation and expansion during CAR-T cell production. The use of 405nm visible light to substitute the genotoxic UV wavelengths for assessing the NADH and FAD autofluorescence, paves the way to incorporate autofluorescence measurements into closed and automated systems for in-process monitoring of CAR-T cell manufacturing.
Leveraging AI to Explore Structural Contexts of Post-Translational Modifications in Drug Binding
Authors: Medvedev Kirill E. , Schaeffer R. Dustin , Grishin Nick V.
Published: January 2025

Post-translational modifications (PTMs) play a crucial role in allowing cells to expand the functionality of their proteins and adaptively regulate their signaling pathways. Defects in PTMs have been linked to numerous developmental disorders and human diseases, including cancer, diabetes, heart, neurodegenerative and metabolic diseases. PTMs are important targets in drug discovery, as they can significantly influence various aspects of drug interactions including binding affinity. The structural consequences of PTMs, such as phosphorylation-induced conformational changes or their effects on ligand binding affinity, have historically been challenging to study on a large scale, primarily due to reliance on experimental methods. Recent advancements in computational power and artificial intelligence, particularly in deep learning algorithms and protein structure prediction tools like AlphaFold3, have opened new possibilities for exploring the structural context of interactions between PTMs and drugs. These AI-driven methods enable accurate modeling of protein structures including prediction of PTM-modified regions and simulation of ligand-binding dynamics on a large scale. In this work, we identified small molecule binding-associated PTMs that can influence drug binding across all human proteins listed as small molecule targets in the DrugDomain database, which we developed recently. 6,131 identified PTMs were mapped to structural domains from Evolutionary Classification of Protein Domains (ECOD) database. Using recent AI-based approaches for protein structure prediction (AlphaFold3, RoseTTAFold All-Atom, Chai-1), we generated 14,178 models of PTM-modified human proteins with docked ligands. Our results demonstrate that these methods can predict PTM effects on small molecule binding, but precise evaluation of their accuracy requires a much larger benchmarking set. We also found that phosphorylation of NADPH-Cytochrome P450 Reductase, observed in cervical and lung cancer, causes significant structural disruption in the binding pocket, potentially impairing protein function. All data and generated models are available from DrugDomain database v1.1 (http://prodata.swmed.edu/DrugDomain/) and GitHub (https://github.com/kirmedvedev/DrugDomain). This resource is the first to our knowledge in offering structural context for small molecule binding-associated PTMs on a large scale.
MetaLigand: A database for predicting non-peptide ligand mediated cell-cell communication
Authors: Xin Ying , Jin Yang , Qian Cheng , Blackshaw Seth , Qian Jiang
Published: January 2025

Non-peptide ligands (NPLs), including lipids, amino acids, carbohydrates, and non-peptide neurotransmitters and hormones, play a critical role in ligand-receptor-mediated cell-cell communication, driving diverse physiological and pathological processes. To facilitate the study of NPL-dependent intercellular interactions, we introduce MetaLigand, an R-based and web-accessible tool designed to infer NPL production and predict NPL-receptor interactions using transcriptomic data. MetaLigand compiles data for 233 NPLs, including their biosynthetic enzymes, transporter genes, and receptor genes, through a combination of automated pipelines and manual curation from comprehensive databases. The tool integrates both de novo and salvage synthesis pathways, incorporating multiple biosynthetic steps and transport mechanisms to improve prediction accuracy. Comparisons with existing tools demonstrate MetaLigand’s superior ability to account for complex biogenesis pathways and model NPL abundance across diverse tissues and cell types. Furthermore, analysis of single-nucleus RNA-seq datasets from age-related macular degeneration samples revealed that distinct retinal cell types exhibit unique NPL profiles and participate in specific NPL-mediated pathological cell-cell interactions. Finally, MetaLigand supports single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics data, enabling the visualization of predicted NPL production levels and heterogeneity at single-cell resolution.
Stone Age anthropogenic impacts to forest development in the interior Scandinavian Peninsula
Authors: Bertheussen Anastasia , Wright David K. , Dahl Svein Olaf , Birk Jago J. , Bergman Jonas , Buckby Joseph , Fiedler Sabine , Mjærum Axel
Published: January 2025

Forest growth and development is a highly studied phenomenon in which humans have proven to be influential in shaping structure and composition. Delineating the long-term processes of human-environment interactions is crucial for understanding the history and trajectory of landscape formation and vegetation development. Yet, extensive knowledge of the ecological impacts of Stone Age anthropogenic activity is still lacking, particularly from Fennoscandian sites. A sediment core from South Mesna lake from the interior Scandinavian Peninsula was extracted to investigate the long-term evolutionary effects of human-environment interactions following deglaciation (c. 10,500 cal. BP) and initial colonization of the region. Analysis of the core involved microscopic/trace analytical methods, including geochemical analysis, stable isotope analysis, fecal biomarker analysis, and pollen analysis. The combined evidence demonstrates that anthropogenic impacts are prominent shapers of the ecological trajectory and landscape development of the region since the Early Neolithic (c. 5900 cal. BP), which has left a footprint on modern-day land cover.

Significance

Anthropogenic impacts on the environment have been observed to have had notable consequences on global and regional ecological trajectories and environmental development. Yet, how coupled human-environment interactions affect the long-term ecological complexion of boreal landscapes, such as those of the interior Scandinavian Peninsula, is not widely studied. This article presents evidence of early anthropogenic impacts to a forest’s ecology during the Holocene. Fecal biomarker and pollen analyses make it possible to provide micro-archaeological evidence of human activity and correlate it with noteworthy changes in forest structure. Our data points to a specific co-evolutionary forest development trajectory which is connected to millennial-scale human settlement patterns.
Patagonian fjords/channels vs. open ocean: phytoplankton molecular diversity in Southern Chilean coast
Authors: Fuenzalida Gonzalo , Sanchez Roland , Silva Andrea , Figueroa Alvaro , Artal Osvaldo , Jorquera Milko , Trefault Nicole , Espinoza Oscar , Guzman Leonardo
Published: January 2025

Environmental filtering hypothesis studies have revealed immense diversity of microorganisms across oceans; however, these studies are scarce along the Southeast Pacific coast. In this work, we describe the molecular diversity of phytoplankton communities from two biogeographic areas with contrasting oceanographic characteristics, namely fjords and channels versus the open Pacific Ocean (36°S to 53°S). Both areas have seen an increase in the frequency and intensity of Harmful Algal Bloom events (HABs). Using a molecular approach based on metabarcoding of the SSU ribosomal gene, we retrieve micro-phytoplankton diversity, community composition, and biogeographical patterns. The ASVs assigned to Dinophyceae and Bacillariophyta classes show differences in richness and dominance between both studied areas. The diversity pattern described in this work shows a higher harmful potential in fjord/channel areas versus the open ocean, which provides grounds for future studies about the factors triggering temporal variations in phytoplankton communities within these two contrasting environments.
Comparing the Seasonal Diets of Buff-tailed Bumblebees and Honey Bees in a Forest Landscape: A Metabarcoding Approach
Authors: Gay Claire , Cochard Précillia , Thouin Julien , Morin Elie , Moreau Fabienne , Poirot Benjamin
Published: January 2025

The declining diversity of pollinating insects is a major threat to ecosystem conservation, pollination services, and global food security. Honeybees dominate managed pollination, but their dominance can affect other pollinators. Competition for resources can lead to decreased foraging success and survival rates for wild bees, especially bumblebees. This study explores the dietary composition of honeybees and bumblebees using molecular metabarcoding techniques with three primers (ITS2, TrnLgh, and TrnLch) in an agricultural and forest land, Avensan, France. It aims to characterize pollen diversity within their diets, allowing for the inference of floral diversity in the study site. The primers detected pools of different species, indicating a high diversity of floral species in the plants visited by both species. The “primer” effect was more important than the “pollinator” effect in segregating plants found. The Schoener index revealed a slight diet overlap in plant species used by honeybees and bumblebees, depending on the primer. Correspondence analyses showed a high segregation between species associated with honeybees and species associated with bumblebees, regardless of the primer. However, the metabarcoding technique was found to be accurate in separating different pollinator food niches, and did not find a significant overlap in the diet of these two insects. The study provides a good approach to study their floral resources sharing in the same geographical area and time scale, but it is not powerful enough to infer floral diversity.
Negative frequency-dependent selection contributes to modular structure of effector repertoires inPseudomonas syringae
Authors: Li Shuanger , Laderman Eric , Märkle Hanna , Yang Yunze , Bergelson Joy , Pascual Mercedes
Published: January 2025

The evolutionary fate of multi-strain pathogens is shaped by host-pathogen ecological interactions. In bacterial pathogens of plants, enhanced strain characterization and advances in our understanding of molecular mechanisms underlying defense pathways open the door for revisiting the role of negative frequency-dependent selection (NFDS) in strain structure, including its interplay with genetic exchange. NFDS arising from specific defense is one potential mechanism for generating, maintaining, and structuring pathogen diversity. In plants, specific protection against microbial pathogens involves Resistance proteins (R-proteins) that recognize virulence factors (effectors) secreted by pathogens, typically to subvert the initial line of host defense. Here we formulate a stochastic computational co-evolution model that explicitly incorporates variable length R-gene and effector repertoires, and migration from their regional pools. We use this model to understand potential mechanisms shaping effector repertoire structure and associated strain coexistence in the generalist plant pathogenP. syringae. The demonstration of a modular structure in our numerical simulations motivates the analysis of genome sequences from 76 strains collected in the Midwestern US and 1104 strains from global sources. We find that effector repertories both locally and globally exhibit a modular structure, with higher similarity within than between clusters. The observed modules are consistent with the core genome phylogeny and are unexplained by plant host species, location of isolation, and genetic linkage between effectors. An extension of the model is needed to take into account the evidence for genetic exchange and the phylogenetic congruence of effector modules. We initialize the system with a phylogenetically congruent modular structure and include recombination rates decreasing as a function of phylogenetic distance. We show that NFDS can counter-balance the effects of mixing due to recombination and in so doing, contributes to the maintenance of strain structure. These findings indicate that the observed similarity clusters may constitute, in part, emergent niches arising from eco-evolutionary dynamics that contribute to strain coexistence.
KILDA: identifying KIV-2 repeats from kmers
Authors: Corentin Molitor , Timothy Labidi , Antoine Rimbert , Bertrand Cariou , Mathilde Di Filippo , Claire Bardel
Published: January 2025

Motivation

High concentration of lipoprotein(a), a lipoprotein with proatherogenic properties, is an important risk factor for cardiovascular disease. This concentration is mostly genetically determined by a complex interplay between the number of Kringle-IV type 2 repeats and Lipoprotein(a)-affecting variants. Besides lipoprotein(a) plasma concentration, there is an unmet need to identify individuals most at risk based on theirLPAgenotype.

Results

We developed KILDA, a Nextflow pipeline, to identify the number of Kringle-IV type 2 repeats and Lp(a)-affecting variants directly from kmers generated from FASTQ files. The pipeline was tested on the 1000 Genomes Project (n=2459) and results were equivalent to DRAGEN-LPA (R2=0.93).In-silicodatasets proved the robustness of KILDA’s predictions under different scenarios of sequencing coverage and quality.

Conclusion

KILDA is an open-source and free-to-use pipeline to identify the number of Kringle-IV type 2 repeats and lipoprotein(a)-associated variants. Its results are equivalent to DRAGEN-LPA, offering a free and robust tool for determining theLPAkringle number even when inputting low coverage libraries.

Availability

KILDA is publicly available athttps://github.com/HCL-HUBL/KILDAalong with a recipe to build an Apptainer image containing all the required dependencies.

Contact:corentin.molitor@chu-lyon.fr

Supplementary information

Supplementary data are available atBioinformaticsonline.
Disease-associated Kv1.3 variants are energy compromised with impaired nascent chain folding
Authors: Sykes Aaron , Caruth Lannawill , Setia Verma Shefali , Hoshi Toshinori , Deutsch Carol
Published: January 2025

Human Kv1.3, encoded byKCNA3, is expressed in neuronal and immune cells. Its impaired expression or function produces chronic inflammatory disease and autoimmune disorders, the severity of which correlates with Kv1.3 protein expression. The intersubunit recognition domain, T1, at the cytosolic N-terminus of Kv1.3, acquires secondary, tertiary, and quaternary structures during early biogenesis while the nascent protein is attached to the ribosome and/or the ER membrane. In this study, we ask whether nativeKCNA3gene variants in T1 are associated with human disease and whether they manifest early-stage folding defects, energetic instabilities, and conformational distortion of subunits. We use three approaches: first, the unbiased “genome-first” approach to determine phenotype associations of specificKCNA3rare variants. Second, we use biochemical assays to assess early-stage tertiary and quaternary folding and membrane association of these variants during early biogenesis. Third, we use all-atom molecular dynamics simulations of the T1 tetramer to assess structural macroscopic and energetic stability differences between wildtype (WT) Kv1.3 and a single-point variant, R114G. Measured folding probabilities and membrane associations are dramatically reduced in several of the native variants compared to WT. Simulations strikingly show that the R114G variant produces more energetically unstable and dynamic T1 domains, concomitant with tertiary unwinding and impaired formation of symmetrical tetramers. Our findings identify molecular mechanisms by which rare variants influence channel assembly, potentially contributing to diverse clinical phenotypes underlying human disease.
Allometric spreading and focal adhesion collective organization are coordinated by cell-scale geometrical constraints
Authors: Bimbard Célian , Wahhod Ali-Alhadi , Mitrossilis Démosthène , Vermeil Joseph , Bousquet Rémi , Richert Alain , Pereira David , Durand Pauline , Asnacios Sophie , Étienne Jocelyn , Asnacios Atef , Fouchard Jonathan
Published: January 2025

Focal adhesions are protein complexes that transmit actin cytoskeleton forces to the extracellular matrix and serve as signaling hubs that regulate cell physiology. While their growth is achieved through a local force-dependent process, the requirement of sustaining stress at the cell scale suggests a global regulation of the collective organization of focal adhesions. To investigate evidence of such large-scale regulation, we compared changes in cell shape and the organization of focal adhesion-like structures during the early spreading of fibroblasts either on a two-dimensional substrate or confined between two parallel plates, and for cells of different volumes. In this way, we reveal that the areal density of focal adhesions is conserved regardless of cell size or third-dimensional confinement, despite different absolute values of the surface covered by adhesion clusters. In particular, the width of the focal adhesions ring, which fills the flat lamella at the cell front, adapts to cell size and third-dimensional confinement and scales with cell-substrate contact radius. We find that this contact radius also adapts in the parallel-plate geometry so that the cumulated area of cellsubstrate contact is conserved at the cell scale. We suggest that this behavior is the result of 3D cell shape changes which govern spreading transitions. Indeed, because of volume conservation constraints, the evolution of cell-body contact angle adjusts according to cell size and confinement, whereas the rate of early spreading at the cell-substrate contact is not affected by thirddimensional geometry. Overall, our data suggest that a coordination between global and local scales mediates the adaptation of cell-substrate contacts and focal adhesions distribution to large scale geometrical constraints, which allows an invariant cell-substrate adhesive energy.
Evolutionary trajectories of immune escape across cancers
Authors: Chen Wenjie , Baker Toby , Zhang Zhihui , Ogilvie Huw A. , Van Loo Peter , Gu Shengqing (Stan)
Published: January 2025

Immune escape is a critical hallmark of cancer progression and underlies resistance to multiple immunotherapies. However, it remains unclear when the genetic events associated with immune escape occur during cancer development. Here, we integrate functional genomics studies of immunomodulatory genes with a tumor evolution reconstruction approach to infer the evolution of immune escape across 38 cancer types from the Pan-Cancer Analysis of Whole Genomes dataset. Different cancers favor mutations in different immunomodulatory pathways. For example, the antigen presentation machinery is highly mutated in colorectal adenocarcinoma, lung squamous cell carcinoma, and chromophobe renal cell carcinoma, and the protein methylation pathway is highly mutated in bladder transitional cell carcinoma and lung adenocarcinoma. We also observe different timing patterns in multiple immunomodulatory pathways. For instance, mutations impacting genes involved in cellular amino acid metabolism were more likely to happen late in pancreatic adenocarcinoma. Mutations in the glucocorticoid receptor regulatory network pathway tended to occur early, while mutations in the TNF pathways were more likely to occur late in B-cell non-Hodgkin lymphoma. Mutations in the NOD1/2 signaling pathway and DNA binding transcription factor activity tended to happen late in breast adenocarcinoma and ovarian adenocarcinoma. Together, these results delineate the evolutionary trajectories of immune escape in different cancer types and highlight opportunities for improved immunotherapy of cancer.

Significance

Despite its critical role in cancer progression, the evolution of immune escape is poorly understood. We integrate functional genomics and tumor evolution reconstruction and infer immune escape trajectories across cancer types. Our results have important implications for developing biomarkers for immunoprevention and treatment strategies for immune escape of cancer.
Genome diversity and phylogeny of the sectionAlataeof genusLemna(Lemnaceae), comprising the presumed speciesLemna aequinoctialis, Le. perpusillaandLe. aoukikusa
Authors: Stepanenko Anton , Braglia Luca , Fuchs Jörg , Schubert Veit , Hoang Phuong TN , Lee Yuri , Chen Guimin , Gianì Silvia , Morello Laura , Schubert Ingo
Published: January 2025

The SectionAlataeof genusLemnaof the monocotyledonous aquatic duckweed family (Lemnaceae) consists of rather diverse accessions with unknown phylogeny and unclear taxonomic assignment. In contrast to other duckweeds, someAlataeaccessions, in addition to mainly vegetative propagation, produce readily flowers and viable seeds. We analyzed the genomic diversity and phylogenetic relationship of 52Alataeaccessions.

For this purpose, we applied multiple molecular and cytogenetic approaches, including plastid and nuclear sequence polymorphisms, chromosome counting, genome size determination and genomicin situhybridization in combination with geographic distribution.

We uncovered ploidy variation, recurrent hybridization, and backcrosses between diploid species and their hybrids. The latter successfully spread over three continents.

The results elucidate the evolution ofAlataeaccessions (summarized in Fig. 7) and explain the difficult taxonomic assignment of distinct accessions. Our study might be an example for analogous studies to resolve the hitherto unclear relationships among accessions of the duckweed generaWolffiellaandWolffia.