bluuebunny/crossref_metadata_2025 huggingface dataset:
Predicting Mouse Lifespan-Extending Chemical Compounds with Machine Learning
Authors: Belikov Aleksey V. , Ribeiro Caio , Farmer Christopher K. , de Magalhães João Pedro , Freitas Alex A.
Published: November 2024

Pharmacological interventions targeting the biological processes of ageing hold significant potential to extend healthspan and promote longevity. In this study, we employed machine learning to predict how likely it is for a given chemical compound to extend lifespan. We used murine lifespan data from the DrugAge database for training the models. Our most successful Random Forest classifiers were trained on the annotations of direct protein targets of compounds, such as Gene Ontology, UniProt Keywords, pathways (KEGG, Reactome, Wiki) and protein domains (InterPro), whereas models trained on gene expression (LINCS) and chemical substructures (PubChem) underperformed. Models trained on male datasets performed better than those trained on mixed-sex and female datasets, with the latter suffering from severe class imbalance due to much fewer positive-class instances. Notably, features related to G-protein coupled receptors, especially receptors for neurotransmitters, metabolic hormones and sex hormones, were identified as strong predictors of lifespan extension. We used ensemble classifiers comprised of top models to screen compounds from DrugBank, highlighting novel candidates for longevity studies. Major clusters of compounds with the highest predicted longevity-promoting effects appear to target IGF1 and insulin receptors, beta adrenergic receptors, carbonic anhydrases, dopamine and serotonin receptors, voltage-gated potassium and calcium channels, sodium-dependent dopamine, serotonin and noradrenalin transporters, muscarinic acetylcholine receptors and adenosine receptors. Our study provides an important contribution not only to the longevity pharmacology field but also informs research on the fundamental mechanisms of ageing.
De novo clustering of large long-read transcriptome datasets with isONclust3
Authors: Petri Alexander J. , Sahlin Kristoffer
Published: November 2024

Long-read sequencing techniques can sequence transcripts from end to end, greatly improving our ability to study the transcription process. Although there are several well-established tools for long-read transcriptome analysis, most are reference-based. This limits the analysis of organisms without high-quality reference genomes and samples or genes with high variability (e.g., cancer samples or some gene families). In such settings, analysis using a reference-free method is favorable. The computational problem of clustering long reads by region of common origin is well-established for reference-free transcriptome analysis pipelines. Such clustering enables large datasets to be split up roughly by gene family and, therefore, an independent analysis of each cluster. There exist tools for this. However, none of those tools can efficiently process the large amount of reads that are now generated by long-read sequencing technologies.

We present isONclust3, an improved algorithm over isONclust and isONclust2, to cluster massive long-read transcriptome datasets into gene families. Like isONclust, IsONclust3 represents each cluster with a set of minimizers. However, unlike other approaches, isONclust3 dynamically updates the cluster representation during clustering by adding high-confidence minimizers from new reads assigned to the cluster and employs an iterative cluster-merging step. We show that isONclust3 yields results with higher or comparable quality to state-of-the-art algorithms but is 10-100 times faster on large datasets. Also, using a 256Gb computing node, isONclust3 was the only tool that could cluster 37 million PacBio reads, which is a typical throughput of the recent PacBio Revio sequencing machine.

Availability

https://github.com/aljpetri/isONclust3

Contact

kristoffer.sahlin@math.su.se
Genomic divergence of sympatric lineages withinStichopuscf.horrens(Echinodermata: Stichopodidae): Insights on reproductive isolation inferred from SNP markers
Authors: Kim Kenneth M. , Lizano Apollo Marco D. , Toonen Robert J. , Ravago-Gotanco Rachel
Published: November 2024

How reproductive barriers arise in early stages of divergence among broadcast spawning organisms that exist in sympatry remains poorly understood. Reproductively isolated lineages (Clade A and B) ofStichopuscf.horrenswere previously reported across the western Pacific, with an additional putative cryptic species detected within Clade B lineage warranting further examination. The present study further examines the hypothesis that the two mitochondrial lineages (Clade A and Clade B) ofStichopuscf. horrensrepresent putative cryptic species and whether another cryptic species within the Clade B lineage exists using a reduced representation genomic approach. Using double-digest RAD (ddRAD) sequencing, a total of 9,788 single nucleotide polymorphism (SNP) markers were used to examine divergence amongStichopuscf. horrenslineages (n = 82). Individuals grouped into three SNP genotype clusters, broadly concordant with their mitochondrial lineages and microsatellite genotype clusters, with limited gene flow inferred among clusters. Outlier analysis recovered highly divergent SNP loci with significant homology to proteins related to rhodopsin and tachykinin receptor signaling, sperm motility, transmembrane transport and hormone response. This study confirms the existence of three reproductively isolated genotype clusters withinStichopuscf.horrensand highlights gene regions related to reproduction that may contribute to establishing reproductive barriers between broadcast spawning species at an early stage of divergence.
Identifying Prognostic Cell State Interactions in the Tumor Microenvironment of IDH-Mutant Gliomas Using CSI-TME
Authors: Singh Arashdeep , Mehani Bharati , Gopalan Vishaka , Aldape Kenneth , Hannenhalli Sridhar
Published: November 2024

Intercellular communication between distinct transcriptional states of various cell types in the tumor microenvironment (TME) influence the progression and clinical outcome of the tumors. Details of such clinically relevant cellular state interactions (CSIs) in IDH-mutant gliomas remain obscure. Here we developed CSI-TME, a computational pipeline that deconvolves cell type-specific gene expression from bulk transcriptomic data, identifies distinct cell states, and uncovers prognostic cell state interactions by modelling the clinical data based on the joint activity of cell state pairs. We found a significantly reproducible cell state interaction network (CSIN) that is (i) predominantly pro-tumor, (ii) likely mediated through the interaction between cell surface molecules, (iii) differentially activated in IDH-mut astrocytoma and oligodendroglioma, and (iv) significantly associated with response to immune checkpoint blockade therapy. The distinct malignant cell states involved in CSIs resembled neuronal lineages such as astrocyte-like and oligodendrocyte progenitor cells-like states and captured key interactions between glioma stem cells and immune cells. Integration of CSIN with somatic mutation data suggests the anti-tumor role of CSIs in the early stages that transitions towards pro-tumor role as glioma progresses. In summary, CSI-TME provides valuable insights into the physiology of the TME in IDH-mutant glioma and provides a framework to prioritize ligand-receptor interactions or patients stratification for therapeutic interventions.
A polyketide-based biosynthetic platform for diols, amino alcohols and hydroxyacids
Authors: Dan Qingyun , Chiu Yan , Lee Namil , Pereira Jose Henrique , Zhao Xixi , Zhan Chunjun , Rong Yiou , Chen Yan , Cheong Seokjung , Li Chenyi , Gin Jennifer W. , Rodrigues Andria , Backman Tyler W. H. , Baidoo Edward E. K. , Petzold Christopher J. , Adams Paul D. , Keasling Jay D.
Published: November 2024

Medium- and branched-chain diols and amino alcohols are important industrial solvents, polymer building blocks, cosmetics and pharmaceutical ingredients, yet biosynthetically challenging to produce. Here, we present a novel approach utilising a modular polyketide synthase (PKS) platform for the efficient production of these compounds. This platform takes advantage of a versatile loading module from the rimocidin PKS and NADPH-dependent terminal thioreductases (TRs), previously untapped in engineered PKSs. Reduction of the terminal aldehyde with specific alcohol dehydrogenases enables production of diols, oxidation enables production of hydroxy acids, and transamination with specific transaminases enables production of various amino alcohols. Furthermore, replacement of the malonyl-coenzyme A (CoA)–specific acyltransferase (AT) in the extension module with methyl- or ethylmalonyl- CoA–specific ATs enables production of branched-chain diols and amino alcohols. In total, we demonstrated production of nine 1,3-diols (including the difficult-to-produce insect repellent and cosmetic ingredient 2-ethyl-1,3-hexanediol), six amino alcohols, and two carboxylic acids using our PKS platform inStreptomyces albus. Finally, tuning production of the PKS acyl-CoA substrates enabled production of high titers of specific diols and amino alcohols (1 g/L diol titer in shake flasks), demonstrating high tunability and efficiency of the platform.
Discovery and isolation of novel capsaicinoids and their TRPV1-related activity
Authors: Smith Joshua David , Stillerová Vendula Tvrdoňová , Dračinský Martin , Gaustad Hannah Lovinda Angermeier , Lorenzi Quentin , Smrčková Helena , Reinhardt Jakob K. , Liénard Marjorie Anne , Bednárová Lucie , Šácha Pavel , Pluskal Tomáš
Published: November 2024

Chilis contain capsaicin, an acclaimed molecule in both science and culinary ventures. Capsaicin’s target protein, the transient receptor potential cation channel subfamily V member 1 (TRPV1), has been linked to many post-activation effects, including changes in metabolism and pain sensation. Beneficial effects of TRPV1 activation by capsaicin have been explored through clinical trials. Capsaicinoids other than capsaicin also bind to TRPV1, but current studies often disregard non-capsaicin interactions. To fill in these gaps, we screened 40 different chili varieties derived from fourCapsicumspecies by means of untargeted metabolomics and a rat TRPV1 (rTRPV1) calcium influx activation assay. The resulting capsaicinoid profiles were specific to each variety but only partially corresponded with species delimitations. Based on rTRPV1 activation elicited by crude chili extracts, capsaicinoids act in a synergistic manner and a capsaicinoid profile can serve as a gauge of this activation. In addition, we isolated eighteen capsaicinoids, including five previously unreported ones, and confirmed their structure by NMR and MS/MS. We then tested rTRPV1 activation by 23 capsaicinoids and three related compounds. This testing revealed that even slight deviations from the structure of capsaicin reduce the ability to activate the target, with a mere single hydroxylation on the acyl tail reducing potency towards rTRPV1 by more than 100-fold. In addition, we tested how rTRPV1 activity changes in the presence of capsaicin together with non-activating capsaicin analogs and weakly activating capsaicinoids and found both classes of molecules to positively modulate the effects of capsaicin. This demonstrates that even such compounds have measurable pharmacological effects, making a case for the use and study of natural chili extracts.
Robust fine-mapping in the presence of linkage disequilibrium mismatch
Authors: Zhang Wenmin , Lu Tianyuan , Sladek Robert , Dupuis Josée , Lettre Guillaume
Published: November 2024

Fine-mapping methods based on summary statistics from genome-wide association studies (GWAS) and linkage disequilibrium (LD) information are widely used to identify potential causal variants. However, LD mismatch between the external LD reference panel and the GWAS population is common and can lead to compromised accuracy of fine-mapping. We developed RSparsePro, a probabilistic graphical model with an efficient variational inference algorithm, to perform robust fine-mapping in the presence of LD mismatch. In simulation studies with a varying degree of LD mismatch, RSparsePro identified credible sets with a consistently higher power and coverage than SuSiE. In fine-mapping cis-protein quantitative trait loci, RSparsePro identified credible sets with a consistently higher enrichment of variants with functional impacts and cross-study replication rates. In fine-mapping risk loci for low-density lipoprotein cholesterol in ancestry-specific GWAS, RSparsePro identified biologically relevant variants in drug target genes and implicated potential regulatory mechanisms. RSparsePro is openly available athttps://github.com/zhwm/RSparsePro_LD.
Tunable differentiation of human CD4+ and CD8+ T cells from pluripotent stem cells
Authors: Jones Ross D. , Salim Kevin , Stankiewicz Laura N. , Edgar John M. , Leon Lorna , Gillies Jana K. , Murtaza Ali , Durland Lauren J. , Raval Divy , Taberna Thristan P. , Hsu Han Hsuan , Zimmerman Carla , Michales Yale S. , Rossi Fabio M. V. , Levings Megan K. , Zandstra Peter W.
Published: November 2024

Allogeneic T cell therapies are a highly desirable option to circumvent the cost and complexity of using autologous T cells to treat diseases. Allogeneic CD8+ T cells can be made from pluripotent stem cells (PSCs), but deriving CD4+ T cells from PSCs remained a significant challenge. Using feeder- and serum-free conditions, we found that CD4+ versus CD8+ T cell commitment from PSCs can be controlled by fine-tuning the dynamics of Notch and T cell receptor signaling delivered to CD4+CD8+ double positive T cells. Notch signaling negatively impacts CD4+ T cell commitment, and its timed removal allows generation of clonally-diverse and expandable CD4+ T cells from PSCs. The resulting CD4+ T cells respond to cytokine-mediated polarization by differentiating into Th1, Th2, or Th17 cells, recapitulating canonical helper cell function. These findings represent a significant step towards using PSC-derived CD4+ T cells as a low cost, off-the-shelf, cell therapy.
Transcriptomic analysis reveals lipid metabolism and macrophage involvement associated with nintedanib treatment in a rat bleomycin model
Authors: Bonatti Martina , Pitozzi Vanessa , Caruso Paola , Pontis Silvia , Pittelli Maria Gloria , Frati Caterina , Madeddu Denise , Quaini Federico , Lagrasta Costanza Anna Maria , Minato Ilaria , Bocchi Emanuela , Civelli Maurizio , Villetti Gino , Trevisani Marcello , Montanini Barbara
Published: November 2024

INTRODUCTION

Idiopathic pulmonary fibrosis (IPF) is a progressive and irreversible lung disease with a poor prognosis. While pirfenidone and nintedanib offer some benefits, they cannot cure IPF. Nintedanib inhibits various proliferative pathways and has antifibrotic effects, but its molecular mechanisms and impact on the lung transcriptome in vivo remain unclear. This study aims to evaluate nintedanib’s transcriptomic profile in a rat model of bleomycin-induced lung fibrosis.

METHODOLOGY/PRINCIPAL FINDINGS

Lung fibrosis was induced by two intratracheal administrations of bleomycin. Nintedanib protocol included three weeks of daily oral treatments beginning seven days after the first bleomycin dose. Left lungs were processed for histological evaluation using an automated fibrosis quantification system and the Ashcroft Score, while the right lungs were used for RNA sequencing to conduct differential expression and correlation network analysis (WGCNA). WGCNA modules were examined by cell and pathway enrichment analysis. Lipid peroxidation was assessed through the measurement of malondialdehyde in right lung lysates.

Bleomycin induced significant fibrotic lesions, as confirmed by the histological evaluations. Nintedanib reduced fibrotic lesion size by about 15% and decreased severe Ashcroft scores. When compared to controls, the number of differentially expressed genes decreased from over 2000 to barely more than 400 after nintedanib treatment. WGCNA identified two gene clusters correlated to histological parameters, with nintedanib-treated animals showing gene expression levels similar to control animals. One cluster was associated with mesenchymal cells and extracellular matrix-related pathways, in line with the known anti-fibrotic effect of nintedanib. The second cluster, involving principally macrophages, was related to lipid metabolism, potentially uncovering a new mechanistic role of nintedanib in modulating lung fibrosis.

CONCLUSIONS/SIGNIFICANCE

The mechanisms involving macrophages and lipid metabolism, influenced by nintedanib in this study, may open new research directions to better inquire the role of this cellular type in tissue repair and pathological lung fibrosis.
Pangenome biology and evolution in harmful algal-bloom-forming pelagophyte algae
Authors: Sibbald Shannon J. , Lawton Maggie , Maclean Charlotte , Roger Andrew J. , Archibald John M.
Published: November 2024

In prokaryotes lateral gene transfer (LGT) is a key mechanism leading to intra-species variability in gene content and the phenomenon of pangenomes. In microbial eukaryotes, however, the extent to which LGT-driven pangenomes exist is unclear. Pelagophytes are ecologically important marine algae that includeAureococcus anophagefferens– a species notorious for causing harmful algal blooms. To investigate genome evolution across Pelagophyceae and withinAureococcus anophagefferens, we used long-read sequencing to produce high-quality genome assemblies for five strains ofAc. anophagefferens(52-54 megabase-pairs; Mbp), a telomere-to-telomere assembly forPelagomonas calceolata(32 Mbp), and the first reference genome forAureoumbra lagunensis(41 Mbp). Using comparative genomics and phylogenetics, we show remarkable strain level genetic variation inAc. anophagefferenswith a pangenome (23,356 orthogroups) that is 81.1% core and 18.9% accessory. Although gene content variation withinAc. anophagefferensdoes not appear to be largely driven by recent prokaryotic LGTs (2.6% of accessory orthogroups), 368 orthogroups were acquired from bacteria in a common ancestor of all analyzed strains and are not found inP. calceolataorAu. lagunensis. 1,077 recent LGTs from prokaryotes and viruses were identified within Pelagophyceae overall, constituting 3.5-4.0% of the orthogroups in each species. This includes genes likely contributing to the ecological success of pelagophytes globally and in long-lasting harmful blooms.
Inflammatory molecules in the glomerular endothelium in mild IgA-Nephropathy identified by single-cell and spatial transcriptome
Authors: Hasegawa Kumi , Kawashima Nagako , Kawabata Ayako , Sakakura Megumi , Onoda Naoki , Sano Takashi , Urakawa Itaru , Matsubara Masahiro , Naito Shokichi
Published: November 2024

Immunoglobulin A nephropathy (IgA-N) is a primary glomerulonephritis characterized by mesangial cell proliferation and expansion. It still leads to end-stage renal disease over the long course of the disease in many patients. Although glomerular endothelial cells (GE) have been implicated in the pathogenesis of IgA-N, their role remains poorly understood. We conducted single-cell and spatial transcriptomic analysis using human specimens with mild IgA-N compared with normal. We observed the significantly higher expression of several inflammation-associated molecules which have been reported and not reported to be involved in IgA-N pathogenesis, respectively. Furthermore, we show that several important molecules were also highly expressed in GE of IgA-N at protein level by tissue immunostaining. Our analysis suggests that the characteristic pathways identified in GE that involve these molecules are associated with the progression of IgA-N. These findings offer important insights on both the pathogenesis of IgA-N and its treatment at an early stage.
Breaking barriers: the fungal toxin candidalysin disrupts epithelial integrity and induces inflammation in a gut-on-chip model
Authors: Morelli Moran , Queiroz Karla
Published: November 2024

Candida albicansis an opportunistic pathogenic yeast commonly found in the gastrointestinal tract, vagina, and mouth of healthy humans. Under certain conditions, it can become invasive, causing mucosal or life-threatening systemic infections. One mechanism used byC.albicansto breach the epithelial barrier is the secretion of candidalysin, a cytolytic peptide toxin. Candidalysin damages epithelial membranes and activates the innate epithelial immune response, making it key toC.albicans’pathogenicity and a promising therapeutic target. Although candidalysin mediatesC. albicanstranslocation through intestinal layers, its impact on epithelial responses is not fully understood.

This study aims to characterize this response and develop scalable, quantitative methodologies to assess candidalysin’s toxicological effects using gut-on-chip models.

We used the OrganoPlate®, a microfluidic platform to culture up to 64 perfused, membrane-free intestinal epithelial tubes. We exposed Caco-2 tubes to candidalysin and evaluated their response with trans-epithelial electrical resistance (TEER), protein detection, and immunostaining. We then validated our findings in a proof-of-concept experiment using human intestinal organoid tubules.

Candidalysin impaired barrier integrity, as indicated by decreased TEER and increased permeability in a fluorescent dye assay. It also induced actin remodeling and DRAQ7™ dye uptake, a marker of cell permeability. This disruption was associated with the release of LDH, cytokines, and the antimicrobial peptide LL37, suggesting cellular damage, inflammation, and antimicrobial activity.

This study strengthens our understanding of candidalysin’s role inC. albicanspathogenesis and suggests new therapeutic strategies targeting this toxin. Moreover, the use of patient-derived organoids shows promise for capturing patient heterogeneity and developing personalized treatments.

Graphical Abstract
The impacts of climate variability on the niche concept and distributions of species
Authors: Berti Emilio , Rosenbaum Benjamin , Reuman Daniel C.
Published: November 2024

1

Inter-annual climate variability affects the long-term growth rate and thus the viability of populations. Despite the importance of climate variability, niche models and species distribution models (SDMs) typically do not account for it. This causes systematic biases in the projected distributions of species and can mislead conservation measures. Here, we use ideas from stochastic demography to quantify the effects of inter-annual climate variability on population performance and distributions of species, developing a new SDM framework which we call XSDM. The new framework expands the traditional deterministic notion of the fundamental niche, re-conceptualizing the niche to account for stochasticity. XSDM can be applied widely, requiring only occurrence data, e.g. from GBIF, and it shows superior performance to commonly-used SDMs in simulation studies. Using XSDM, we assessed the impacts of inter-annual climate variability on 10 North-American species chosen as illustrative examples. We found that climate variability reduces the potential distribution of the species on average by 26% and up to 57%. SDMs and niche concepts that do not incorporate variability cannot account for this reduction and can thus be strongly biased. Because climate change is altering not only average conditions, but also the frequency and intensity of extreme events, which are aspects of variability, it is paramount to better understand how climate variability influences the distributions of species in order to help mitigate future biodiversity losses due to climate change. Our new XSDM approach provides a new foundation for such a research program by helping re-orient niche theory to include stochastic effects.

2

Significance statement

Inter-annual climate variability influences populations’ long-term viability and, therefore, species’ distributional ranges. However, existing niche concepts and species distribution models (SDMs) typically do not account for such variability and therefore cannot accurately predict species’ distributions. Here, we developed the new SDM framework “XSDM” that accounts for climate variability when assessing the ecological niche of a species and predicting its distribution. We tested XSDM using simulations, where it performs better than traditional SDMs. By applying XSDM to 10 example species, we found that climate variability impacts their distribution, reducing potential range by up to half. As global change alters climate variability, e.g., through increased frequency and intensity of extreme events, our new paradigm provides better tools for countering future biodiversity losses.
Beyond size dimorphism: the past, present, and future of Rensch’s Rule
Authors: Toyama Ken S.
Published: November 2024

‘Rensch’s Rule’ is known as a pattern of allometry in which the degree of male-biased sexual size dimorphism (SSD) increases with species body size. Over the last decades, a growing amount of Rensch’s Rule studies has advanced our understanding of SSD, its prevalence in nature, and the mechanisms underlying its evolution. However, Bernhard Rensch, when describing the pattern for the first time, considered the allometry of SSD only as a special case of a more general pattern in which dimorphism in any relative sexual difference increased with body size. In this perspective I revisit the history of Rensch’s Rule, starting with its popularization in recent decades, then diving into the original works by Rensch to rediscover his original observations, and finally discussing the implications of studying Rensch’s pattern beyond its applications to SSD. The strong bias towards body size in the study of Rensch’s Rule has proven valuable regarding our understanding of the evolution of SSD. Using empirical examples I propose, however, that expanding the study of the pattern to other traits might prove insightful for the general study of sexual dimorphism and phenotypic diversity.
An integrative RNA spliceosomic landscape of pancreatic neuroendocrine tumors unveils novel clinicomolecular associations
Authors: Blázquez-Encinas Ricardo , García-Vioque Víctor , Mafficini Andrea , Landoni Luca , Moreno-Montilla María Trinidad , Alcala Nicolas , Ventura Sebastián , Eyras Eduardo , Paiella Salvatore , Salvia Roberto , Rovite Vita , Foll Matthieu , Luchini Claudio , Fernandez-Cuesta Lynnette , Lawlor Rita T. , Scarpa Aldo , Ibáñez-Costa Alejandro , Pedraza-Arevalo Sergio , Castaño Justo P.
Published: November 2024

Alterations in alternative splicing are emerging as a novel hallmark in cancer biology, offering new insights. However, integrative analyses of splicing are still scarce, particularly in rare cancers such as pancreatic neuroendocrine tumors (PanNETs). These tumors are highly heterogeneous, complicating diagnosis and treatment. This study is the first to comprehensively investigate the RNA splicing landscape in PanNETs, identifying distinct spliceosomic profiles correlated with unique clinical and molecular characteristics. We analyzed RNA-seq data from 174 samples, identifying three distinct spliceosomic groups (SPN1, SPN2, SPN3) with unique clinical and molecular characteristics. SPN1 exhibited intermediate clinical features and specific splicing machinery profile, SPN2 was associated with frequent mutations inMEN1andDAXX/ATRXgenes, and SPN3 showed a prevalence of well-differentiated tumors with distinct splicing patterns. These groups were linked to different clinical outcomes and activated key biological processes like mTOR signaling and hormone secretion pathways. Our findings underscore the significant impact of RNA splicing on PanNET heterogeneity and suggest that detailed splicing profiles could serve as valuable tools for identifying novel biomarkers and therapeutic targets. This study provides crucial insights into PanNET molecular biology and paves the way for personalized therapies based on splicing features.
Reaction norm fitness peak tracking applied on sparse time series in the fossil record
Authors: Ergon Rolf
Published: November 2024

Species that have existed over millions of years have done so because of sufficient mean fitness for survival through the ages, such that the mean phenotypic traits continuously have been tracking the optimal phenotypic values that maximize fitness. These optimal values are predominantly functions of the environment, for example the sea temperature. The mean phenotypic traits over time will thus predominantly be determined by the environment over time, and the trait history may be found in the fossil record. Here, I simulate such a tracking system by use of a univariate intercept-slope reaction norm model and show how both linear and nonlinear mean phenotype vs. environment functions can be found also from quite sparse and short time series from the fossil record, and I also discuss how this methodology can be extended to multivariate systems. The simulations also include cases with a constraint on the individual trait values and with other factors than environment influencing the optimal phenotypic values. The methodology is finally applied on two time-varying mean traits in a record of bryozoanMicroporella agonistesfossils spanning 2.3 million years, using the∂18Omeasure as environmental variable. From few irregular samples of phenotypic mean traits found in the fossil record, it was possible to identify linear mean phenotype vs. environment functions, and thus to predict the continuous mean phenotypic traits as functions of time.
Immunologic comparisons of strain and induction method in an improved mouse model of intrauterine fibrosis
Authors: Hernandez Jamie L. , Daniel Jonathan , Stelzel Jessica L. , Prasad Neeti R. , Soares Vance V. , Doloff Joshua C.
Published: November 2024

Intrauterine adhesions are growths of fibrotic tissue within the uterine cavity and can arise from a variety of tissue-damaging stimuli. Immune cells are known to mediate fibrotic responses, but specific mechanisms require further elucidation. Here, we compared intrauterine fibrosis development and immune responses across different mouse strains and induction methods. We aimed to identify a consistent and more clinically relevant mouse model of intrauterine fibrosis, whether immune responses differ in response to different stimuli, and which potential key immune cell populations are responsible for intrauterine fibrosis susceptibility. Intrauterine fibrosis induction methods were compared using surgical curettage or transcervically administered chemical (quinacrine) models. Measurements of tissue morphology and collagen gene expression indicate BALB/c mice are more susceptible than C57BL/6 mice to intrauterine fibrosis. In chemically induced BALB/c uterine tissues, gene expression and flow cytometry data show greater pro-inflammatory macrophage responses, implicating a possible role in fibrogenesis consistent with human intrauterine adhesion data. Findings from this study demonstrate the importance of mouse strain selection in studies of intrauterine adhesions. Furthermore, we show that a new hormone-synchronized, chemically induced mouse model can more uniformly and reliably provoke fibrotic tissue response. This model may allow for greater elucidation of mechanisms involved in intrauterine adhesion development, and exploratory therapeutic studies for treatment intervention.
Conditional activation of NK cell function using chemically synthetic constrained bicyclic peptides directed against NKp46 and tumor-expressed antigens
Authors: Dufort Fay J. , Leitheiser Christopher J. , Rezvaya Alexandra , Ezell Tucker R. , Ho Kathleen Q.W. , Bezerra Gustavo A. , Blakeman Ben J. F. , Uhlenbroich Sandra , Zammit William H. , Stanczuk Lukas , Brown Peter N. , Mudd Gemma E. , McDonnell Kevin , Keen Nicholas , Brandish Philip E.
Published: November 2024

Natural killer (NK) cells have the unique potential to recognize and kill tumor cells independently of MHC-I presentation of antigens, as well as to secrete cytokines that engage adaptive anti-tumor immunity and the function of cytolytic T cells. We have discovered and characterized chemically synthetic, constrained bicyclic peptides that bind with high affinity and specificity to NKp46, an activating receptor expressed selectively on NK cells in the tumor microenvironment. Chemical coupling to other bicyclic peptides specific for the tumor antigens EphA2 or MT-1 created NKp46 agonists whose function was completely conditional on binding to the tumor antigen. These chemical conjugates effectively convert the tumor antigen into a “kill me” signal for NK cells. Not only did these newly created tumor-immune cell agonists (TICAs) direct potent and efficient killing of human tumor cells by primary human NK cells in vitro, but they also caused secretion of the pro-inflammatory cytokines TNFα and IFNγ. Importantly, the TICAs directed production of FLT3 ligand, an essential mitogen for conventional dendritic cells which are central to the development of anti-tumor immunity in cancer. We illustrate the TICA-directed interaction of NK cells with tumor cells using confocal microscopy and we show that TICAs enable sustained function over multiple rounds of killing. These novel tools are well positioned to harness the potential of NK cells in the treatment of cancer.
How partial phenotyping to reduce generation intervals can help to increase annual genetic gain in selected honeybee populations
Authors: Kistler Tristan , Brascamp Evert W. , Basso Benjamin , Phocas Florence , Bijma Piter
Published: November 2024

Honeybee breeding is organized around annual cycles, following seasonal change. Generation intervals are thus commonly multiples of whole years. Most queens are generally raised during spring or early summer in temperate climates. A generation interval of 1 year limits phenotyping to early recordable traits, before the spring following queens’ births. Some traits, however, can only be recorded later, as is typically the case for total honey yield. Their recording on selection candidates thus increases the generation interval to at least 2 years, a common interval on the dam path. Using stochastic simulation, we investigated the impact of halving the dam generation interval and therefore recording only early traits on candidate dams. The generation interval on the sire path remained at 2 years with complete phenotyping. Breeding goals with varying weights on early and late traits were considered, as well as different genetic correlations between traits, from negative to positive. The acceleration of the breeding scheme generally resulted in an increased genetic gain for the two-trait breeding goals, from 0% up to +47% after 20 years of selection. Although inbreeding rates per generation were slightly lower in the accelerated breeding scheme, associate inbreeding levels were about 20-30% higher after 20 years of selection due to the 33% increased generation turnover. To avoid too high inbreeding, shortening the generation interval should thus be accompanied by strategies to limit inbreeding while still retaining most of the genetic gain, such as increasing the breeding nucleus size by relaxing selection intensity.
Genetic Diversity Analysis for Heat Stress Tolerance in Chili (Capsicum annumL.)
Authors: Usmani Saad Farid , Saddique Muhammad Abu Bakar , Tahir Muhammad Hammad Nadeem , Faried Hafiz Nazar
Published: November 2024

Chili (Capsicum annuum L.) also known as hot pepper and red pepper is a valuable condiment all around the world. It holds significant importance in the global economy and is used in a variety of products such as sauces, pickles, medicines, and insect-repellent sprays. Pakistan is 4thlargest chili producer worldwide. Global warming a is an important issue around the globe that causes losses to global agricultural productivity. In this study, chili germplasm was screened to identify heat-tolerant genotypes. The experiment was carried out following factorial under RCBD (randomized complete block design) having 785 with two treatments and three repeats. The genotypes were sown in nursery trays in November 2023 and transplanted in the field in February 2024. The data recording was performed twice. The data collected in March-April was considered as data from controlled treatment while data recorded during June-July was considered as heat-stressed treatment. The data was recorded for Days to flowering, NDVI value, plant height (cm), number of primary branches per plant, fruit length (cm), fruit diameter (cm), individual fruit weight (g), number of fruits per plant, fruit yield per plant, and pollen viability. Heat susceptibility indices for all traits were calculated. The data was subjected to analysis of variance, path coefficient, and biplot analysis. Genotypes D1, D4, D7, D12, 12, 42, 75, 76, 118, 172, 217, 229, 424, 497, 514, 532, and 772 are selected as heat tolerant genotypes because the yield of these genotypes was unaffected or slightly affected due to heat stress during the experiment, while on the other hand, the genotypes 41, 44, 57, 63, 94, 123, 141, 154, 285, 347, 516, 540, 601 and 663 are selected as heat susceptible because these genotypes have high heat susceptibility index and there was a huge decrease in the yield in heat-stressed condition as compared to non-stressed condition.
Multiplexed Ultrasound Imaging of Gene Expression
Authors: Nyström Nivin N. , Jin Zhiyang , Bennett Marisa E. , Zhang Ruby , Swift Margaret B. , Shapiro Mikhail G.
Published: November 2024

Acoustic reporter genes (ARGs) have enabled the imaging of gene expression with ultrasound, which provides high-resolution access to deep, optically opaque living tissues. However, unlike their fluorescent counterparts, ARGs have so far been limited to a single “color,” preventing multiplexed imaging of cellular states or populations. Here, we use rational protein design and directed evolution to develop two novel ARGs that can be distinguished from each other based on their acoustic pressure response profiles, enabling “two-color” ultrasound imaging of gene expression. We demonstrate the utility of multiplexed ARGs for delineating bacterial cell species and cell statesin vitro, and then apply them towards imaging distinct subpopulations of probiotics in the mouse gastrointestinal tract and in tumor-colonizing bacterial agentsin vivo. Just as the first wavelength-shifted derivatives of fluorescent proteins opened a vivid world for optical microscopy, our next-generation acoustic proteins set the stage for a richer symphony of ultrasound signals from living subjects.
GeneCover: A Combinatorial Approach for Label-free Marker Gene Selection
Authors: Wang An , Hicks Stephanie , Geman Donald , Younes Laurent
Published: November 2024

The selection of marker gene panels is critical for capturing the cellular and spatial hetero-geneity in the expanding atlases of single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics data. Most current approaches to marker gene selection operate in a label-based framework, which is inherently limited by its dependency on predefined cell type labels or clustering results. In contrast, existing label-free methods often struggle to identify genes that characterize rare cell types or subtle spatial patterns, and they frequently fail to scale efficiently with large datasets. Here, we introduce geneCover, a label-free combinatorial method that selects an optimal panel of minimally redundant marker genes based on gene-gene correlations. Our method demonstrates excellent scalability to large datasets and identifies marker gene panels that capture distinct correlation structures across the transcriptome. This allows geneCover to distinguish cell states in various tissues of living organisms effectively, including those associated with rare or otherwise difficult-to-identify cell types. We evaluate the performance of geneCover across various scRNA-seq and spatial transcriptomics datasets, comparing it to other label-free algorithms to highlight its utility and potential in diverse biological contexts.
Multiomics reveals age-dependent metabolic reprogramming of macrophages by wound bed niche secreted signals
Authors: Forni Maria Fernanda , Pizzurro Gabriela A. , Krause Will , Alexander Amanda F. , Bridges Kate , Xu Yiting , Justynski Olivia , Gabry Anthony , Camara Niels Olsen Saraiva , Miller-Jensen Kathryn , Horsley Valerie
Published: November 2024

The cellular metabolism of macrophages depends on tissue niches and can control macrophage inflammatory or resolving phenotypes. Yet, the identity of signals within tissue niches that control macrophage metabolism is not well understood. Here, using single-cell RNA sequencing of macrophages in early mouse wounds, we find that, rather than gene expression of canonical inflammatory or resolving polarization markers, metabolic gene expression defines distinct populations of early wound macrophages. Single-cell secretomics and transcriptomics identify inflammatory and resolving cytokines expressed by early wound macrophages, and we show that these signals drive metabolic inputs and mitochondrial metabolism in an age-dependent manner. We show that aging alters the metabolome of early wound macrophages and rewires their metabolism from mitochondria to glycolysis. We further show that macrophage-derived Chi3l3 and IGF-1 can induce metabolic inputs and mitochondrial mass/metabolism in aged and bone marrow-derived macrophages. Together, these findings reveal that macrophage-derived signals drive the mitochondrial metabolism of macrophages within early wounds in an age-dependent manner and have implications for inflammatory diseases, chronic injuries, and age-related inflammatory diseases.

In Brief

This study reveals that macrophage subsets in early inflammatory stages of skin wound healing are defined by their metabolic profiles rather than polarization phenotype. Using single-cell secretomics, we establish key macrophage cytokines that comprise thein vivowound niche and drive mitochondrial-based metabolism. Aging significantly alters macrophage heterogeneity and increases glycolytic metabolism, which can be restored to OxPHOS-based metabolism with young niche cytokines. These findings highlight the importance of the tissue niche in driving macrophage phenotypes, with implications for aging-related impairments in wound healing.

Highlights

Single cell transcriptional analysis reveals that reveals that metabolic gene expression identifies distinct macrophage populations in early skin wounds.

Single-cell secretomic data show that young macrophages contribute to the wound bed niche by secreting molecules such as IGF-1 and Chi3l3.

Old wound macrophages display altered metabolomics, elevated glycolytic metabolism and glucose uptake, and reduced lipid uptake and mitochondrial mass/metabolism.

Chi3l3 but not IGF-1 secretion is altered in macrophages in an age dependent manner.

Chi3l3 can restore mitochondrial mass/metabolism in aged macrophages.
H2S remodels mitochondrial ultrastructure and destabilizes respiratory supercomplexes
Authors: Hanna David A. , Chen Brandon , Shah Yatrik M. , Khalimonchuk Oleh , Cunniff Brian , Banerjee Ruma
Published: November 2024

Mitochondrial form and function are intimately interconnected, responding to cellular stresses and changes in energy demand. Hydrogen sulfide, a product of amino acid metabolism, has dual roles as an electron transport chain substrate and complex IV (CIV) inhibitor, leading to a reductive shift, which has pleiotropic metabolic consequences. Luminal sulfide concentration in colon is high due to microbial activity, and in this study, we demonstrate that chronic sulfide exposure of colonocyte-derived cells leads to lower Mic60 and Mic19 expression that is correlated with a profound loss of cristae and lower mitochondrial networking. Sulfide-induced depolarization of the inner mitochondrial membrane activates Oma1-dependent cleavage of Opa1 and is associated with a profound loss of CI and CIV activities associated with respirasomes. Our study reveals a potential role for sulfide as an endogenous modulator of mitochondrial dynamics and suggests that this regulation is corrupted in hereditary or acquired diseases associated with elevated sulfide.

Significance Statement

Hydrogen sulfide is a product of host as well as gut microbial metabolism and has the dual capacity for activating respiration as a substrate, and inhibiting it at the level of complex IV. In this study, we report that chronic albeit low-level sulfide exposure elicits profound changes in mitochondrial architecture in cultured human cells. Disruption of mitochondrial networks is reversed upon removal of sulfide from the growth chamber atmosphere. Sulfide-dependent depolarization of the inner mitochondrial membrane is associated with loss of cristae and respiratory supercomplexes. Our study reveals the potential for sulfide to be an endogenous regulator of mitochondrial ultrastructure and function via modulation of electron flux and for this process to be corrupted in sulfide dysregulated diseases.
The key role of cheaters in the persistence of cooperation
Authors: Babajanyan Sanasar G. , Wolf Yuri I. , Koonin Eugene V. , Rochman Nash D.
Published: November 2024

Evolution of cooperation is a major, extensively studied problem in evolutionary biology. Cooperation is beneficial for a population as a whole but costly for the bearers of social traits such that cheaters enjoy a selective advantage over cooperators. Here we focus on coevolution of cooperators and cheaters in a multi-level selection framework, by modeling competition among groups composed of cooperators and cheaters. Cheaters enjoy a reproductive advantage over cooperators at the individual level, independent of the presence of cooperators in the group. Cooperators carry a social trait that provides a fitness advantage to the respective groups. In the case of absolute fitness advantage, where the survival probability of a group is independent of the composition of other groups, the survival of cooperators does not correlate with the presence of cheaters. By contrast, in the case of relative fitness advantage, where the survival probability of a group depends on the composition of all groups, the survival of cooperators positively correlates with the presence of cheaters. Increasing the strength of the social trait alone fails to ensure survival of cooperators, and the increase of the reproduction advantage of the cheaters is necessary to avoid population extinction. We validate these theoretical results with an agent-based model of a bacterial biofilm where emergence of the cooperative trait is facilitated by the presence of cheaters, leading to evolution of spatial organization. This finding contrasts the classical view that spatial organization facilitates cooperation. Our results suggest that, counterintuitively, cheaters often promote, not destabilize, evolution of cooperation.

Significance

Cooperation is central to the evolution of life and the emergence of multicellularity. Social traits stabilize populations against environmental volatility and enable division of labor. However, evolution of cooperation is beset by cheaters that benefit from cooperation without paying the cost. Analysis of a multilevel selection model of population evolution shows that, counterintuitively, the presence of cheaters can be beneficial or even essential for the survival of cooperators. This unexpected effect comes from multilevel selection whereby cheaters at the individual level become altruists at the group level, enabling overall growth of the population that is essential for the persistence of cooperators. These findings have broad implications for understanding the emergence of cooperation and host-parasite coevolution throughout the history of life.