bluuebunny/crossref_metadata_2025 huggingface dataset:
Compartment coupling integrates patterning and morphogenetic information during development
Authors: Prakash Anubhav , Raman Sukanya , Kaushik Raman , Manchanda Pallavi , Iyer Anton S , Ladher Raj K
Published: February 2025

Morphogenetic information arises from a combination of genetically encoded cellular properties and emergent cellular behaviours. The spatio-temporal implementation of this information is critical to ensure robust, reproducible tissue shapes, yet the principles underlying its organisation remain unknown. We investigated this principle using the mouse auditory epithelium, the organ of Corti (OC). OC consists of a sensory domain, which transduces sound through polar mechanosensory hair cells (HC), part of a mosaic with supporting cells (SC). On either side of the sensory domain are non-sensory domains. These domains undergo cellular rearrangements, which, together, lead to a spiral cochlea that contains planar polarised HCs. This makes the mammalian cochlea a compelling system to understand coordination across spatial scales. Using genetic and ex-vivo approaches, we found patterning of OC into sensory and non-sensory domains is associated with a combinatorial expression of adhesion molecules, which underpins OC into spatially defined compartments, enabling planar cell polarity (PCP) cues to regulate compartment-specific organisation. Through compartment-specific knockouts of the PCP protein, Vangl2, we find evidence of compartment coupling, a non-linear influence on the organisation within one compartment when cellular organisation is disrupted in another. In the OC, compartment coupling originates from vinculin-dependent junctional mechanics, coordinating cellular dynamics across spatial scales.
Detection of PCR chimeras in adaptive immune receptor repertoire sequencing using hidden Markov models
Authors: Chernyshev Mark , Stalmarck Aron , Corcoran Martin , Karlsson Hedestam Gunilla B , Murrell Ben
Published: February 2025

Adaptive Immune Receptor Repertoire sequencing (AIRR-seq) has emerged as a central approach for studying T cell and B cell receptor populations, and is now an important component of studies of autoimmunity, immune responses to pathogens, vaccines, allergens, and cancers, and for antibody discovery. When amplifying the rearranged V(D)J genes encoding antigen receptors, each cycle of the Polymerase Chain Reaction (PCR) can produce spurious "chimeric" hybrids of two or more different template sequences. While the generation of chimeras is well understood in bacterial and viral sequencing, and there are dedicated tools to detect such sequences in bacterial and viral datasets, this is not the case for AIRR-seq. Further, the process that results in immune receptor sequences has domain-specific challenges, such as somatic hypermutation (SHM), and domain-specific opportunities, such as relatively well-known germline gene "reference" sequences. Here we describe CHMMAIRRa, a hidden Markov model for detecting chimeric sequences in AIRR-seq data, that specifically models SHM and incorporates germline reference sequences. We use simulations to characterize the performance of CHMMAIRRa and compare it to existing methods from other domains, we test the effect of PCR conditions on chimerism using IgM libraries generated in this study, and we apply CHMMAIRRa to four published AIRR-seq datasets to show the extent and impact of artifactual chimerism.
Sensitivity Analysis to Isolate the Effects of Proteases and Protease Inhibitors on Extracellular Matrix Turnover
Authors: Yeganegi Amirreza , Robels Karla , Richardson William J.
Published: February 2025

Matrix metalloproteinases (MMPs) are a family of proteases that drive degradation of extracellular matrix (ECM) across many tissues. MMP activity is antagonized by tissue inhibitors of metalloproteinases (TIMPs), resulting in a complex multivariate system with many MMP isoforms and TIMP isoforms interacting across a network of biochemical reactions, each with their own distinct kinetic rates. This system complexity makes it very difficult to identify which specific molecules are most responsible for driving ECM turnover in vivo and therefore the most promising therapeutic targets. To help elucidate the specific roles of various MMP and TIMP isoforms, we present a computational systems biology model of collagen turnover capturing all possible interactions between type I collagen, four different MMP isoforms (MMP1, 2, 8, and 9), and three different TIMP isoforms (TIMP1, 2, and 4). We used dye-quenched fluorescent collagen to monitor the degradation of collagen in the presence of various MMP+TIMP cocktails, and we then used these experimental data to fit hypothetical reaction system topologies in order to investigate their respective accuracies. We determined kinetic rate constants for this system and used post-myocardial infarct time courses of collagen, MMP, and TIMP levels to perform a parameter sensitivity analysis across the model reaction rates and predict which molecules and interactions are the important regulators of ECM in the infarcted heart. Notably, the model suggested that MMP degradation and inactivation terms were more important for driving collagen levels than TIMP interaction terms. In sum, this work highlights the need for systems level analyses to distinguish the roles of various biomolecules operating with a complex system, prioritizes therapeutic targets for post-infarct cardiac remodeling, and presents a computational framework that can be applied to many other collagen-rich tissues.
Rethinking intensity: Repetitive transcranial magnetic stimulation across ethnic populations
Authors: Zhang Bella B B , Lin Tim T Z , Qin Penny P , Jin Minxia , Xia Adam W L , Kan Rebecca L D , Zhu Frank F , Kranz Georg S
Published: February 2025

Repetitive transcranial magnetic stimulation (rTMS) targeting the left dorsolateral prefrontal cortex is a widely used adjunctive therapy for various neurological and psychiatric disorders. Traditionally, the standard practice for dosing rTMS has involved adjusting the intensity to a defined percentage of the motor threshold. However, we perceive anatomical differences among ‘White’, ‘Han Chinese’ and ‘Black or African American’ethnic groups that result in unequal doses of stimulation at the left dorsolateral prefrontal cortex, a prime target for therapeutic rTMS. Therefore, we hypothesize that diverse ethnic populations experience different therapeutic effects with FDA-approved rTMS protocols that have been adopted globally. This also raises concerns about varying therapeutic effects and potential biases in existing research comparing efficacy across ethnicities. More importantly, our hypothesis emphasizes the need to tailor rTMS safety guideline for diverse ethnic populations. We call for well-powered clinical trials to systematically examine the effects of rTMS intensity in diverse ethnic groups.
Warmer climate threatens the occurrence of giant trees in the Amazon basin
Authors: de Lima Robson Borges , de Oliveira Cinthia Pereira , S. da Silva Diego Armando , de Souza Daniela Granato , Gonçalves Lorraine Aparecida , Vasconcelos Caroline da Cruz , Batista Anderson Pedro B. , de Matos Filho João R. , da Silva Joselane P. Gomes , Lopes Iran Jorge Correa , de Abreu Jadson Coelho , Aparício Perseu da Silva , de Souza Carla S. Campelo , Ometto Jean Pierre , Görgens Eric Bastos
Published: February 2025

Giant trees in the Amazon play crucial ecological roles by acting as substantial carbon sinks and supporting diverse forest ecosystems. However, these emergent trees are increasingly vulnerable to climatic changes, and recent research suggests that the distribution and niche of many emergent species are severely threatened. This study employs ecological niche modeling using data LiDAR and forest inventory, global repository data, and bioclimatic variables to project the potential larger tree distributions under past, current, and future climate scenarios (SSP1-2.6 and SSP5-8.5) in different biogeographic provinces in the Amazon basin. We used algorithms MARS, RandomForest, MaxEnt, and GAM to assess the impact of critical climatic factors, including isothermality, maximum temperatures, and precipitation patterns, on the habitat suitability of these larger trees and speciesDinizia excelsaandGoupia glabra. Our results show that the tall trees dataset,Dinizia excelsaandGoupia glabraexhibit congruent distinct responses to climate variables, withDinizia excelsabeing more sensitive to increased temperature extremes, particularly in the Guiana Shield and Roraima Provinces. In contrast,Goupia glabradisplays a broader tolerance to precipitation variability. Under the high-emission scenario (SSP5-8.5), both species are projected to lose up to 45% of their suitable habitats by 2080, primarily in southern Amazon provinces like Xingu-Tapajós, where increased drought frequency and temperature extremes are expected. Conversely, the low-emission scenario (SSP1-2.6) suggests potential habitat stability or even slight expansions in the northern Amazon regions due to moderate temperature and rainfall conditions. These findings highlight the urgent need for conservation strategies to protect critical refugia and enhance ecosystem resilience. By integrating niche modeling with climate projections, our study provides vital insights into managing Amazonian giant trees, emphasizing their potential role in mitigating global climate change impacts.
Estimating gene conversion rates from population data using multi-individual identity by descent
Authors: Browning Sharon R , Browning Brian L
Published: February 2025

In humans, homologous gene conversions occur at a higher rate than crossovers, however gene conversion tracts are small and often unobservable. As a result, estimating gene conversion rates is more difficult than estimating crossover rates. We present a method for multi-individual identity-by-descent (IBD) inference that allows for mismatches due to genotype error and gene conversion. We use the inferred IBD to detect alleles that have changed due to gene conversion in the recent past. We analyze data from the TOPMed and UK Biobank studies to estimate autosome-wide maps of gene conversion rates. For 10 kb, 100kb, and 1 Mb windows, the correlation between our TOPMed gene conversion map and the deCODE sex-averaged crossover map ranges from 0.56 to 0.67. We find that the strongest gene conversion hotspots typically die back to the baseline gene conversion rate within 1 kb. In 100 kb and 1 Mb windows, our estimated gene conversion map has higher correlation than the deCODE sex-averaged crossover map with PRDM9 binding enrichment (0.34 vs 0.29 for 100 kb windows and 0.52 vs 0.34 for 1 Mb windows), suggesting that the effect of PRDM9 is greater on gene conversion than on crossover recombination. Our TOPMed gene conversion maps are constructed from 55-fold more observed allele conversions than the recently published deCODE gene conversion maps. Our map provides sex-averaged estimates for 10 kb, 100 kb, and 1 Mb windows, whereas the deCODE gene conversion maps provide sex-specific estimates for 3 Mb windows.
Cryptic variation fuels plant phenotypic change through hierarchical epistasis
Authors: Zebell Sophia G. , Martí-Gómez Carlos , Fitzgerald Blaine , Pinto Da Cunha Camila , Lach Michael , Seman Brooke M. , Hendelman Anat , Sretenovic Simon , Qi Yiping , Bartlett Madelaine , Eshed Yuval , McCandlish David M. , Lippman Zachary B.
Published: February 2025

Cryptic genetic variants exert minimal or no phenotypic effects alone but have long been hypothesized to form a vast, hidden reservoir of genetic diversity that drives trait evolvability through epistatic interactions. This classical theory has been reinvigorated by pan-genome sequencing, which has revealed pervasive variation within gene families and regulatory networks, including extensive cis-regulatory changes, gene duplication, and divergence between paralogs. Nevertheless, empirical testing of cryptic variation’s capacity to fuel phenotypic diversification has been hindered by intractable genetics, limited allelic diversity, and inadequate phenotypic resolution. Here, guided by natural and engineered cis-regulatory cryptic variants in a recently evolved paralogous gene pair, we identified an additional pair of redundant trans regulators, establishing a regulatory network that controls tomato inflorescence architecture. By combining coding mutations with a cis-regulatory allelic series in populations segregating for all four network genes, we systematically constructed a collection of 216 genotypes spanning the full spectrum of inflorescence complexity and quantified branching in over 27,000 inflorescences. Analysis of the resulting high-resolution genotype-phenotype map revealed a layer of dose-dependent interactions within paralog pairs that enhances branching, culminating in strong, synergistic effects. However, we also uncovered an unexpected layer of antagonism between paralog pairs, where accumulating mutations in one pair progressively diminished the effects of mutations in the other. Our results demonstrate how gene regulatory network architecture and complex dosage effects from paralog diversification converge to shape phenotypic space under a hierarchical model of epistatic interactions. Given the prevalence of paralog evolution in genomes, we propose that paralogous cryptic variation within regulatory networks elicits hierarchies of epistatic interactions, catalyzing bursts of phenotypic change.

Keyword:cryptic mutations, paralogs, redundancy, cis-regulatory, tomato, inflorescence, gene regulatory network, modeling, epistasis
A Multistage Mixed Methods Methodology to Develop a Toolkit to Reduce Infections Following Durable LVAD Implantation
Authors: Chandanabhumma P. Paul , Swaminathan Sriram , Cabrera Lourdes , Zhou Shiwei , Chenoweth Carol E. , Hou Hechuan , Comstock Sarah , Malani Preeti N. , Aaronson Keith D. , Pagani Francis D. , Likosky Donald S.
Published: February 2025

Background

Infections following durable left ventricular assist device (dLVAD) implantation are common and associated with increased morbidity and mortality. Despite documented interhospital variability, few studies have identified strategies to mitigate their occurrence. This national study uses a multistage mixed methods design to develop a customizable and deployable toolkit of expert-guided recommendations to reduce infections post-dLVAD.

Methods

Representatives from low, medium, and high-performance hospitals across the U.S. were interviewed to assess factors contributing to post-dLVAD infections. Draft toolkit recommendations were iteratively developed after integrating thematically analyzed qualitative and quantitative data. A national advisory team of ventricular assist device (VAD) subject matter experts provided mixed methods input to refine the toolkit’s content and structure.

Results

Seventy-three clinical and operational VAD team members were interviewed, and 14 subject matter experts provided stakeholder feedback to refine the toolkit. The resulting toolkit contains 39 infection prevention recommendations that address VAD program care processes (e.g., real-time provider communication), clinicians (e.g., multidisciplinary protocol development), patients & caregivers (e.g., engaging patient advisors in patient education), and VAD leadership (e.g., unit and service level data reporting). Accompanying resources (e.g., team-based exercises, data collection worksheets) support implementing and evaluating site-specific strategies. Input from clinical and research experts provided preliminary evidence of the toolkit’s acceptability and considerations for enhancing the toolkit’s adoption and implementation.

Conclusions

Using mixed methods approaches, an infection prevention toolkit was developed to enhance care coordination among VAD team members and mitigate post-dLVAD infections. Future work should evaluate the effectiveness of implementing this infection prevention toolkit within the dLVAD setting.

What is Known

Six out of every 10 patients develop an infection within 2 years of durable left ventricular assist device (dLVAD) implantation.

Infections contribute to an increased risk of major morbidity and mortality.

Post-dLVAD infection rates vary across hospitals, even after risk adjustment.

What the Study Adds

A customizable toolkit of infection prevention recommendations was developed and pilot tested using mixed methods approaches.

Recommendations focus on modifiable aspects of organizational structure, patient care, patient education, quality reporting.
Squash flowers as microhabitats: the effects of floral temperature and humidity on pollen viability and visitor behavior
Authors: Dahake Ajinkya , Coates Charlotte , Obregon Diana , Chai Jonathan , Nunes-Silva Patricia , Kevan Peter , Raguso Robert A.
Published: February 2025

Flowers represent intricate microcosms shaped by their chemical and micrometeorological properties. Notable examples include thermogenic flowers that create a warm microclimate for visitors and residents. We document a distinct microclimate within the large flowers of both wild and domesticated squashes (Cucurbita spp.). Unlike thermogenic flowers, squash flower temperatures remain near ambient, but their humidity consistently exceeds ambient levels from bud to senescence, resulting from stomatal and petal transpiration rather than nectar evaporation. Experimentally reducing humidity in greenhouse-grown male squash flowers results in significant pollen tube rupture, directly impacting plant fitness. To explore the role of floral humidity within a broader ecological context, we performed similar humidity manipulations on squash farms to assess impacts on the behavior of their specialist squash bee pollinator (Xenoglossa pruinosa), generalist pollinators (bumblebees, honeybees), and specialist herbivores (cucurbit beetles). Experimentally reduced floral humidity lower visitation frequency by squash bees but have no effect on generalist pollinators. Manipulation of floral humidity did not influence the foraging duration of any pollinators but impacted the residence of male squash bees in wilted flowers compared with unmanipulated flowers. Finally, there was a positive correlation between the dryness of the ambient air and the abundance of squash bees and cucurbit beetles residing in the humid wilted floral chambers. In conclusion, our findings showcase squash flowers as a humid microhabitat that influences reproductive success directly by affecting pollen viability and indirectly by altering interactions with squash bees, their specialist pollinators.
Divergent granulopoiesis at extramedullary sites safeguards host defense
Authors: Silvestre-Roig Carlos , Chevre Raphael , Bender Alexander , Vöcking Lina M. , Hageb Ali , Richter Mathis , Farjia Merieme , Braster Quinte , Guzman Mauricio , Sintes Jordi , Sharma Samriti , Lemnitzer Patricia , Ahern David , Osei-Sarpong Collins , Engel Daniel R. , Monaco Claudia , Dersch Petra , Kibler Artur , Cerutti Andrea , Chavakis Triantafyllos , Jablonska Jadwiga , Soehnlein Oliver
Published: February 2025

Extramedullary organs such as the spleen can assume granulopoiesis as a supportive mechanism to cope with the demands during persistent inflammation. However, the quantitative output of extramedullary granulopoiesis is limited, thus raising the question if the spleen in fact provides neutrophils of a qualitative difference rather than merely contributing to neutrophil numbers. Here we report splenic stress granulopoiesis with distinct production and differentiation trajectories. Myeloid progenitors in the spleen engage in accelerated production of neutrophils with an immature phenotype. Yet, neutrophils generated during persistent stress granulopoiesis are fully competent to exert antimicrobial functions and are necessary to contain bacterial invasion. Activation of type I interferon signaling in the spleen is required for splenic neutrophil production and its loss impairs host defense. Thus, the spleen provides an immunological environment for stress-induced rapid production and priming of highly active neutrophils to meet the demands during infection.
Apoptotic caspases silence spontaneous innate immune signals by specifically cleaving activated mitochondrial antiviral signalling protein (MAVS)
Authors: Gradzka-Boberda Sylwia , Parui Ishita , Chakraborty Pallab , Anthony Danielle Paige , Puthussery Bhagya K. , Weber Arnim , Brokatzky Dominik , Giansanti Piero , Mergner Julia , Öllinger Rupert , Rad Roland , Kirschnek Susanne , Gentle Ian E. , Häcker Georg
Published: February 2025

Caspases-9, -3 and -7 are activated in the mitochondrial apoptosis pathway and lead to the apoptotic phenotype. Caspases also function to limit inflammation upon apoptotic mitochondrial permeabilization through degradation of the signalling proteins cGAS, MAVS and IRF3. Cells and mice lacking caspases have higher interferon levels and are resistant to viral infection. We report that in unstimulated, non-apoptotic cells caspase-3 functions to cleave specifically activated MAVS and very likely cGAS. In unstimulated HeLa cells, constitutive caspase-9- and -3-but not 7-dependent proteolytic events were observed. Inhibition of the mitochondrial apoptosis pathway in various healthy cells induced type I interferon (IFN I) through increased cGAS activity in the absence of changes to cGAS levels. We observed enhanced MAVS-dependent signals upon RIG-I-like helicase stimulation in the absence of BAX, caspase-9 or caspase-3 or upon caspase-inhibition. During activation, MAVS forms complexes, and blockade of mitochondrial apoptosis signalling increased complex abundance in unstimulated and stimulated cells. MAVS complexes were more sensitive to caspase-degradation than the monomer, and mutation of caspase-3-cleavage sites in MAVS spontaneously increased complex formation. Inhibition of voltage-dependent anion channel 1 (VDAC1) oligomerization blocked BAX/BAK- and caspase-regulated IFN induction, suggesting a stimulating role of leakage of mitochondrial DNA. We propose that low level, spontaneous activity of the mitochondrial apoptosis pathway, through specific caspase-3-mediated cleavage of only active signaling proteins, counteracts mitochondrial release of nucleic acids to reduce inflammation in the absence of infection. Caspase-3 therefore has a novel function in conformation- and activation-specific cleavage of substrates.
In vivo anti-FAP CAR T therapy reduces fibrosis and restores liver homeostasis in metabolic dysfunction-associated steatohepatitis
Authors: Yashaswini Chittampalli N. , Cogliati Bruno , Qin Tianyue , To Tran , Williamson Thomas , Papp Tyler E. , Li Kenneth , Rasul Raisa , Chen Li , Lightstone Adi , Aghajanian Haig , Parhiz Hamideh , Wang Shuang , Rurik Joel G. , Epstein Jonathan A. , Friedman Scott L.
Published: February 2025

In this study, we aimed to determine the efficacy of in vivo chimeric antigen receptor (CAR) T cell therapy, generated by targeted lipid nanoparticles (t-LNPs), as an anti-fibrotic in metabolic dysfunction-associated steatotic liver disease. Hepatic fibrosis is a key predictor of mortality in liver disease, driven by fibrogenic hepatic stellate cells (HSCs). In heart, chimeric antigen receptor (CAR) T cells targeting fibroblast activation protein alpha (FAP) reduce murine cardiac fibrosis. However, the value of this approach in liver is unknown. We explored the anti-fibrotic potential of in vivo-generated anti-FAP CAR T cells in metabolic dysfunction-associated steatohepatitis (MASH), a highly prevalent disease with no approved anti-fibrotic therapies. We first established that FAP expression in both human and murine MASH is specific to HSCs. We then used flow cytometry, Sirius Red morphometry, digital pathology analysis, and single nuclear RNA-sequencing to assess the impact of anti-FAP CAR T cell therapy on murine MASH. Anti-CD5 targeted-LNPs carrying anti-FAPCAR mRNA generate activated, transient anti-FAP CAR T cells, which significantly reduced fibrosis by depleting pro-fibrogenic HSCs, and by modulating immune cells, endothelial cells and hepatocytes in a non-cell autonomous manner to mitigate inflammation and restore hepatic homeostasis. These findings reinforce the potential of in vivo CAR T therapy to attenuate a highly morbid and pervasive liver disease through integrated, multicellular salutary effects.

One Sentence Summary

RNA-based treatment transiently reprograms immune cells to target scar-forming cells in fatty liver disease, thus improving liver health overall.
Metagenomics reveals potential interactions between CPR bacteria and their phages in groundwater ecosystems
Authors: Hu Bingxin , An Liyun , Wu Mengdi , Xu Jinbo , Nie Yong , Wu Xiao-Lei
Published: February 2025

Candidate phyla radiation (CPR) is a vast lineage composed of bacteria with ultra-small size, streamlined genomes, notable defects in core metabolic potential and symbiotic lifestyle, which are widely detected in groundwater ecosystems. Increasing attention has focused on the physiological and ecological significance of CPR bacteria, while the potential interactions between CPR bacteria and their phages still need more exploration. Here, we collected 82 groundwater metagenomic datasets and further derived 1,162 phages with the potential to infect 2,439 groundwater CPR metagenome-assembled genomes (MAGs). Notably, the groundwater CPR MAGs were predominantly infected by temperate phages, and the abundance profiles of phage-CPR interactions in groundwater ecosystems supported the ‘Piggybacking the Winner’ (PtW) hypothesis, suggesting that lysogenic infection was a strategy co-evolved by CPR bacteria and their phages in groundwater ecosystems. Intriguingly, the groundwater CPR phages encoded various auxiliary metabolic genes (AMGs) that might promote symbiotic lifestyle and metabolic potential of host CPR MAGs. These included AMGs associated with concanavalin A-like lectin/glucanases superfamily and O-Antigen nucleotide sugar biosynthesis, which could enhance surface adhesion of host CPR MAGs. Moreover, AMGs related to ABC transport system and P-type transporter could strengthen metabolic exchange and uptake of essential nutrients from surroundings. Additionally, AMGs involved in various metabolic pathways might alleviate metabolic deficiencies in host CPR MAGs. This study elucidated the mechanisms of phage-CPR interactions and the potential roles of phages in modulating the physiology and ecology of CPR bacteria within groundwater ecosystems.
Experimental and theoretical approaches reveal that antimicrobial blue light killing efficiency decreases with biofilm growth in a Pseudomonas aeruginosa model.
Authors: Insero Giacomo , Maldonado Carmona Nidia , Panier Thomas , Romano Giovanni , HENRY Nelly
Published: February 2025

Recently, the use of antimicrobial blue light (aBL) has gained interest across various applications. However, a comprehensive framework that addresses the key factors driving bacterial photoinhibition remains lacking, particularly concerning biofilms, the predominant bacterial lifestyle. The goal of this work was to evaluate the potential of photokilling in this wide-spread microbial adherent community type, and to decipher the specific mechanisms at stake. To investigate aBL killing efficiency, we conducted experiments in a Pseudomonas aeruginosa biofilm model using a well-defined millifluidic device that allows real-time microscopy and quantitative analysis of a living biofilm under local irradiation at a defined light dose. In addition, we developed a theoretical model for light-biofilm interaction that accounts for the three-dimensional nature of the bacterial biofilm. To inform our model, we examined the light dose-response in isolated cells and found a profile indicative of a multi-target mechanism of lethality. By comparing the experimental and theoretical results, we identified a loss in killing efficiency as the biofilm grows, due in part to the increase in thickness of the living material inherent to this mode of development. Our findings also highlight a reduction in the intrinsic bacterial sensitivity to blue light as biofilm development progresses, which we attribute to the low oxygen levels typical of densely populated bacterial environments. These findings reveal new features of the photokilling mechanism and redefine the approach to designing effective antimicrobial photoinactivation strategies by integrating the key physical characteristics of bacterial biofilms.
A monophyletic origin of domesticated barley
Authors: Tan Cong , Ye Lingzhen , Chen Jing , Zhang Chenyang , Zhou Ping , Tong Cen , Chen Zhonghua , Waugh Robbie , Li Chengdao , He Tianhua
Published: February 2025

The origin of domesticated barley has been debated extensively over the past century. Early botanical and comparative morphological research and recent genetic research supported a polyphyletic origin. A monophyletic origin was proposed after the discovery that a single genetic locus controls the presence of hull-less grains in all domesticated barley. Interpreting the origin of domesticated barley is further complicated by the archaeological record showing that the first domesticates had two rows of grain on the inflorescence, as does its wild progenitor. However, these two-rowed types effectively disappeared from the record for thousands of years, and they were replaced by derived six-rowed types that dominated barley’s cultivation history and only reappeared in the record around one thousand years ago. Here, we used two independent datasets with large sample sizes and genome-wide genetic markers to re-evaluate barley cultivation history. We unequivocally demonstrate that modern domesticated barley has a monophyletic origin. Phylogenetic reconstruction and examination of current archaeological records suggests that the west Fertile Crescent was most likely where barley was first domesticated. Modern two-rowed types were likely derived from six-rowed domesticated types not earlier than 3,500 years ago in modern Türkiye and Iran. We conclude that the two distinct non-brittle rachis haplotypes, coinciding with distinct row types in cultivated barley, are likely the results of two chronological events along the same evolutionary line. Our results provide a reconcilable framework for explaining genetic and phytogeographic patterns and pave the way for a consensus on the origin of barley domestication.
Diffeomorphic Independent Contrasts for Ancestral Reconstruction of Shapes
Authors: Severinsen Michael Lind , Akhøj Morten , Nielsen Rasmus , Sommer Stefan , Hipsley Christy Anna
Published: February 2025

Abstract

Ancestral reconstruction is a fundamental challenge in evolutionary biology, requiring methods that can capture complex morphological changes while accounting for phylogenetic relationships. Current approaches are based on linear assumptions that often oversimplify the spatial relationships between anatomical features and fail to account for landmark correlations within shapes. Here, we introduce a novel method that combines the ability of Large Deformation Diffeomorphic Metric Mapping (LDDMM) to model smooth, invertible transformations between shapes while preserving the relationships between landmarks with Felsenstein’s Independent Contrasts (IC) to iteratively reconstruct ancestral shapes along the branches of a phylogenetic tree. We call this method Diffeomorphic Independent Contrasts for Ancestral Reconstruction of Shapes (DICAROS). We validate DICAROS against two existing methods: (1) Linear predictors using Ordinary Least Squares and (2) Ancestral character estimation using maximum likelihood under Brownian Motion and apply DICAROS to a dataset of swallowtail butterfly species (Family Papilonidae, Order Lepiodetra) to reconstruct the ancestral shape and visualize evolutionary trajectories in a phylomorphospace from the contrasts. We conclude that DICAROS outperforms the existing methods in terms of accuracy and provides a more accurate reconstruction of the ancestral shape for non-symmetric phylogenetic trees. With DICAROS we show a transition between un-tailed and tailed papilinodae species while also illustrating how images of modern species would look under the DICAROS ancestral reconstruction
Identification of 4-Amino-2-Nitrophenol as a novel inducer of phenotypic antibiotic resistance inEscherichia coli: roles of Lon protease and its substrate MarA
Authors: Nandini Santhi Sanil , Jagdish Sirisha , Rana Subinoy , Nandi Dipankar
Published: February 2025

In prokaryotes, the energy-dependent protein degradation is controlled primarily by two ATP-dependent proteases, Lon and Clp. This study investigates the roles of the Lon protease in the metabolism of 2,4-dinitrophenol (2,4-DNP), a toxic industrial compound, inEscherichia coli(E. coli). During the study, an observation was made that the absence of Lon protease resulted in an enhanced conversion of yellow coloured 2,4-DNP to a reddish-brown product. This study aims to characterise the compound observed in the media with wild type (WT) and Δlonstrains, understand the mechanisms of 2,4-DNP conversion and decipher the roles of Lon protease in the conversion of 2,4-DNP. UV-visible and LC-MS analyses revealed differences in the conversion products between the WT and Δlonstrains. One of the substrates of Lon protease is MarA, a transcription factor. Growth studies with different mutants and trans-complemented strains demonstrated MarA-dependent conversion. The bathochromic shift of spectral peaks suggested a reduction process and possible involvement of nitroreductase enzymes. Indeed, the expression of two nitroreductases,nfsAandnfsB, increased with 2,4-DNP and was dependent on MarA. Importantly, the production of the reddish-brown product was lower in strains lackingnfsAornfsB. Finally, LC-MS analysis identified one of the conversion products of 2,4-DNP to be 4-Amino-2-nitrophenol (4,2-ANP). Dose studies with purified 4,2-ANP demonstrated that it did not lower the growth ofE. coli(unlike 2,4-DNP) but induced phenotypic antibiotic resistance (like 2,4-DNP). This study contributes to our understanding of biological treatment of nitroaromatics and may offer insights into environmental pollution mitigation strategies.

Importance

This study identifies the roles of Lon protease and its substrate MarA in inducing nitroreductases, NfsA and NfsB, in reducing toxic 2,4-DNP to less toxic 4,2-ANP, a novel inducer of phenotypic antibiotic resistance. This study contributes to understanding the biological treatment of nitroaromatics, offering insights into environmental pollution mitigation strategies and the development of efficient bioremediation techniques.
Mapping Animal Cultures: The Animal Culture Database (ACDB)
Authors: Basava Kiran , Alam Md Nafis Ul , Roberts Liam , Martinet Kristen , Cherry Paige , Garcia-Verdugo Hector , Román-Palacios Cristian
Published: February 2025

Socially transmitted behaviors are widespread across the animal kingdom, yet comprehensive datasets documenting their distribution and ecological significance remain scarce. Additionally, knowledge of animal behavioral traditions could be essential for understanding many species' responses to anthropogenic disturbances and further enhancing conservation efforts. Here, we introduce the first open-access database that synthesizes data on animal cultural behaviors and traditions. The Animal Culture Database (ACDB) summarizes culture-related features for a total of 56 species. The current release of the database contains descriptions of 112 behaviors including forms of vocal communication, migration, predator defense, foraging practices, habitat alteration, play, mating displays, and other social behaviors for 102 bird and mammal populations across six continents. In addition to offering an open-access resource for researchers, educators, and conservationists, the ACDB represents a critical step toward recognizing the role of social learning in animal populations.
RfaH is Essential for Virulence and Adaptive Responses in Yersinia pseudotuberculosis Infection
Authors: Waititu Joram Kiriga , Nilsson Kristina , Larrouy-Maumus Gerald , Costa Tiago R D , Avican Kemal
Published: February 2025

We previously demonstrated that increased expression of the gene encoding transcriptional antiterminator RfaH during Yersinia pseudotuberculosis transcriptional reprogramming necessary for adapting to persistent infection. RfaH is known to regulate expression of the O-antigen biosynthesis operon in Y. pseudotuberculosis. In this study, we examined the role of RfaH in virulence, bacterial physiology under infection-relevant stress conditions, and determined the RfaH regulon in Y. pseudotuberculosis. We employed a mouse infection model and phenotypic assays to test RfaH's role in virulence and physiology, as well as RNA sequencing, including O-antigen biosynthesis-deficient strains. Our findings demonstrate that loss of rfaH significantly attenuates virulence, reducing the capacity of Y. pseudotuberculosis to establish persistent infection. RfaH expression is increased during the stationary growth phase and under various stress conditions, such as high osmolarity and temperature. Functional assays revealed that the ΔrfaH strain displayed defects in swimming and increased clumping, indicating altered surface properties affecting motility. Transcriptomic analysis showed that the absence of rfaH led to downregulation of genes involved in virulence besides O-antigen biosynthesis operon, suggesting RfaH's critical role in virulence and host adaptation. Notably, we identified a hypothetical non-coding RNA encoded within the 5'-UTR of the O-antigen biosynthesis operon, which may regulate gene expression of the urease operon in Y. pseudotuberculosis. Collectively, our findings suggest that RfaH is essential for the virulence and adaptive capacity of Y. pseudotuberculosis to colonize the host. This study provides insights into regulatory mechanisms that facilitate bacterial survival in hostile environments and highlights the importance of RfaH and its regulatory targets in the pathogenesis of Y. pseudotuberculosis.
Activity of human-specific Interlaminar Astrocytes in a Chimeric Mouse Model of Fragile X Syndrome
Authors: Anding Alexandria , Ren Baiyan , Padmashri Ragunathan , Burkovetskaya Maria , Dunaevsky Anna
Published: February 2025

Astrocytes, a type of glial cells, have multiple roles in regulating neuronal development and homeostasis. In addition to the typical mammalian astrocytes, in the primate cortex interlaminar astrocytes are located in the superficial layer and project long processes traversing multiple layers of the cerebral cortex. Previously, we described a human stem cell based chimeric mouse model where interlaminar astrocytes develop. Here, we utilized this model to study the calcium signaling properties of interlaminar astrocytes. To determine how interlaminar astrocytes could contribute to neurodevelopmental disorders, we generated a chimeric mouse model for Fragile X syndrome. We report that FXS interlaminar astrocytes exhibit hyperexcitable calcium signaling and cause an increase in dendritic spine dynamics.
Eukaryotes’ closest relatives are internally simple syntrophic archaea
Authors: Imachi Hiroyuki , Nobu Masaru K. , Ishii Shun’ichi , Hirakata Yuga , Ikuta Tetsuro , Isaji Yuta , Miyata Makoto , Miyazaki Masayuki , Morono Yuki , Murata Kazuyoshi , Nakagawa Satoshi , Ogawara Miyuki , Okada Satoshi , Saito Yumi , Sakai Sanae , Shimamura Shigeru , Tahara Yuhei O. , Takaki Yoshihiro , Takano Yoshinori , Tasumi Eiji , Uematsu Katsuyuki , Yoshimura Toshihiro , Takai Ken
Published: February 2025

Eukaryotes are theorized to have originated from an archaeal phylumPromethearchaeota(formerly ‘Asgard’ archaea)1,2. The first cultured representatives revealed valuable insight3,4but are distantly related to the first eukaryotic common ancestor (FECA), leaving many unknowns regarding this archaeon’s biology. Here, we report isolation of two strains belonging to the order proposed as FECA’s closest relative, ‘Hodarchaeales’,5as members of a pure co- and tri-culture with methanogenic partners. Both are obligately anaerobic, syntrophic, peptide-degrading, and mesophilic archaea that have simple internal cell structure and produce protrusions and vesicles, likePromethearchaeales3,4. All strains demonstrate behavior focused on cell construction rather than division, unlike typical prokaryotes6. Strain HC1 possesses genes associated with aerobic lifestyles but lacks complete pathways for aerobic respiration and co-cultures cannot grow under (micro)aerobic conditions, suggesting the genes support oxygen detoxification rather than respiration. Reflecting this, HC1 can survive and grow under microaerobic conditions only when aerobic organisms are present. Phylogenetic analyses indicate FECA may have possessed these genes and thus some aerotolerance. Physiological, genomic, and phylogenetic observations indicate FECA was a simple-celled anaerobic syntrophic peptide-degrading archaeon with a non-growth-centric lifestyle and potential adaptations towards an oxygenated planet—the archaea-eukaryote transition was steep in both cell structure and aerobiosis.
Human Lung Alveolar Model with an Autologous Innate and Adaptive Immune Compartment
Authors: Cabon Lauriane , Steinacher Linda , Gjeta Bruno , Pimentel Mendes Marisa , Cremasco Floriana , Cubela Irineja , Bellavista Marina , Gaspa Toneu Laura , Lauer Luisa , Yu Qianhui , Okuda Ryo , Nabet Barzin Y. , Gayevskiy Velimir , Siegel Michel , Ducret Axel , Lassalle Evodie , Lazzaroni Giacomo , Nikoloff Jonas , Camacho Rufino Miguel , Zundel Christelle , Kunz Leo , Zimmermann Tamara , Stoll Bilgenaz , Roth Cyrill , Roth Adrian B , Mohindra Rajat , Stokar-Regenscheit Nadine , Gjorevski Nikolche , Braun Armin , Recaldin Timothy , Camp Gray
Published: February 2025

Lung-resident immune cells, spanning both innate and adaptive compartments, preserve the integrity of the respiratory barrier, but become pathogenic if dysregulated1. Current in vitro organoid models aim to replicate interactions between the alveolar epithelium and immune cells but have not yet incorporated lung-specific immune cells critical for tissue residency2. Here we address this shortcoming by describing human lung alveolar immuno-organoids (LIO) that contain an autologous tissue-resident lymphoid compartment, primarily composed of tissue-resident memory T cells (TRMs). Additionally, we introduce lung alveolar immuno-organoids with myeloid cells (LIOM), which include both TRMs and a macrophage-rich alveolar myeloid compartment. The resident immune cells formed a stable immune-epithelial system, frequently interacting with the epithelium and promoting a regenerative alveolar transcriptomic profile. To understand how dysregulated inflammation perturbed the respiratory barrier, we simulated T-cell-mediated inflammation in LIOs and LIOMs and used single-cell transcriptomic analyses to uncover the molecular mechanisms driving immune responses. The presence of innate cells induced a shift in T cell identity from cytotoxic to immunosuppressive, reducing epithelial cell killing and inflammation. Based on insights obtained with bulk RNA-seq data from the phase 3 IMpower150 trial, we tested whether LIOM cultures could model clinically-relevant but poorly understood pulmonary side effects caused by immunotherapies such as the checkpoint inhibitor atezolizumab3. We observed a decrease in immunosuppressive T cells and identified gene signatures that matched the transcriptomic profile of patients with drug-induced pneumonitis. Given its effectiveness in capturing outcomes and mechanisms associated with a prevalent pulmonary disease, this system unlocks opportunities for studying a wide range of immune-related pathologies in the lung.
Mitochondria serve as a Holdout Compartment for Aggregation-Prone Proteins hindering Efficient Ubiquitin-Dependent Degradation
Authors: Gierisch Maria E , Barchi Enrica , Marogna Mirco , Wallnoefer Moritz H , Ankarcrona Maria , Naia Luana , Salomons Florian , Dantuma Nico P
Published: February 2025

The accumulation of protein aggregates has been causatively linked to the pathogenesis of neurodegenerative diseases. In this study, we have conducted a genome-wide CRISPR-Cas9 screen to identify cellular factors that stimulate the degradation of an aggregation-prone reporter protein. Our findings revealed that genes encoding proteins involved in mitochondrial homeostasis, including the translation factor eIF5A, were highly enriched among suppressors of degradation of an aggregation-prone reporter. Conversely, endoplasmic reticulum (ER)-associated ubiquitin ligases facilitated degradation, indicating opposing roles for these cellular compartments in the clearance of aggregation-prone proteins. Genetic or chemical inhibition of eIF5A led to the dissociation of the aggregation-prone substrate from mitochondria, which was accompanied by enhanced degradation through ER-associated ubiquitination. The presence of an aggregation-prone, amphipathic helix that localized the reporter to mitochondria was crucial for the stimulatory effect of eIF5A inhibition. Additionally, the steady-state levels of α-synuclein, a disease-associated protein containing an amphipathic helix that mislocalizes to mitochondria, were reduced upon eIF5A inhibition. We propose that mitochondria behave as a holdout compartment for aggregation-prone proteins, keeping them out of reach of ubiquitin ligases that target them for proteasomal degradation. Therefore, preventing mitochondrial localization of aggregation-prone proteins may offer a viable therapeutic strategy for reducing their levels in neurodegenerative disorders.
Fatty acid uptake activates an AXL–CAV1–β-catenin axis to drive melanoma progression
Authors: Chocarro-Calvo Ana , Jociles-Ortega Miguel , García-Martinez José Manuel , Louphrasitthiphol Pakavarin , Carvalho-Marques Sofia , Vivas-García Yurena , Ramírez-Sánchez Ana , Chauhan Jagat , Fiuza M. Carmen , Druan Manuel , Sánchez-Danés Adriana , Goding Colin R. , García-Jiménez Custodia
Published: February 2025

Interaction between the tumor microenvironment and cancer cell plasticity drives intratumor phenotypic heterogeneity and underpins disease progression and nongenetic therapy resistance. Phenotype-specific expression of the AXL receptor tyrosine kinase is a pivotal player in dormancy, invasion, and resistance to treatment. However, although the AXL ligand GAS6 is present within tumors, how AXL is activated in metastasizing cells remains unclear. Here, using melanoma as a model, we reveal that AXL is activated by exposure to human adipocytes and to oleic acid, a monounsaturated fatty acid abundant in lymph and in adipocytes. AXL activation triggers SRC-dependent formation and nuclear translocation of a β-catenin–CAV1 complex required for melanoma invasiveness. Remarkably, only undifferentiated AXLHighmelanoma cells engage in symbiosis with human adipocytes, in part by triggering WNT5a-mediated lipolysis, leading to AXL-dependent, but FATP-independent, fatty acid uptake and nuclear localization of the β-catenin–CAV1 complex. Significantly, human melanomas in the vicinity of adipocytes exhibit high levels of nuclear CAV1. The results unveil an AXL- and CAV1-dependent mechanism through which a nutritional input drives phenotype-specific activation of a prometastasis program. Given the key role of AXL in a broad range of cancers, the results offer major insights into the mechanisms of cancer cell dormancy and therapy resistance.