bluuebunny/crossref_metadata_2025 huggingface dataset:
Quantitative evaluation of the role of the microenvironment in the phenotype, metabolism, and drug resistance of PDAC tumor organoids
Authors: Sorzabal Ioritz , Morales Xabier , Cortés-Domínguez Iván , Esparza Maider , Grande Lucía , Castillo Pedro , Narayanan Shruthi , Ponz-Sarvise Mariano , Vicent Silvestre , Ortiz-de-Solórzano Carlos
Published: January 2025

Tumor organoids are powerful tools to study cancer. However, the clinical translation of organoid-based studies depends on how closely the organoid scaffolding material recapitulates the tumor extracellular matrix (ECM). We present a quantitative analysis of the effect of scaffold composition on the phenotype, tissue remodeling, metabolism, and drug resistance of pancreatic ductal adenocarcinoma (PDAC) organoids. We grew PDAC organoids within hydrogels made of Matrigel, collagen-I, or a mixture of collagen-I and Matrigel. Our results show that 1) PDAC organoids grown in Matrigel-only are phenotypically and metabolically similar to low-physiological two-dimensional PDAC cultures; 2) collagen-containing hydrogels, and especially so those grown in hydrogels of mixed collagen-Matrigel composition, accurately reproduce invasive tumors that underwent epithelial-to-mesenchymal transition (EMT) regarding phenotype, tissue remodeling, metabolic activity, and drug resistance. In summary, our work illustrates the importance of three-dimensional (3D) matrix composition for PDAC growth and postulates that organoids grown in collagen-Matrigel hydrogels are the most adequate for studying the biology of invasive PDAC tumors.
Mycobacterium abscessuspromotesPseudomonas aeruginosabiofilm formation and antibiotic tolerance
Authors: McDaniel Melissa S. , Edmonds Sara E. , Patel Evani N. , Baty Joshua J. , Scoffield Jessica A.
Published: January 2025

Modulator therapies have improved outcomes for people with Cystic Fibrosis (pwCF), and currently more than 50% of pwCF are over the age of 18. This has resulted in an increased prevalence of atypical pathogens, including non-tuberculous mycobacteria (NTM). CF-isolation rates of NTM andPseudomonas aeruginosa(Pa) are high, and those co-colonized have worse clinical outcomes. We therefore investigated the behavior of these two organisms in a dual-species biofilm. We found that coculture ofMycobacterium abscessus(MAB) promoted biofilm formation byPa. Confocal imaging revealed changes in biomass and structural organization of thePabiofilm during coculture with MAB. DNase treatment slightly decreased dual-species biofilm, but biofilm formation was completely abrogated in Pel- and Psl-deficient mutants ofPa. Moreover, dual-species cultures promoted tolerance ofPato tobramycin treatment. Overall, our findings highlight an interaction betweenP. aeruginosaandM. abscessusthat may result in bacterial persistence for pwCF during antibiotic therapy.
An open-sourced 3D printable microscope with a large CNC stage
Authors: Dégut Clément , Plevin Michael J
Published: January 2025

3D printed laboratory tools are a fast-developing field, and microscopes in particular have seen several high-quality projects reported in recent years. However, currently available projects for 3D printed microscopes have not been optimised for molecular biology applications. We present an open-source, 3D-printable optical microscope that has been specifically designed for affordability, ease of use, and versatility in molecular biology applications, particularly for fluorescence detection, time lapse imaging, and higher throughput scanning of microtitre plates. The microscope integrates a large computer numerically controlled (CNC) stage, allowing precise scanning of wells in standard microtiter plates, and is equipped with a Raspberry Pi HQ camera module and customizable optical components, including standard microscope objectives. The modular design allows for a range of illumination setups, such as a 3 W blue LED for basic epifluorescence, and supports additional modifications, including dark field or RGB matrix lighting. The design opens new possibilities for cheap home-built microscopes for bioscience applications that are modular and easily adaptable for specific user needs.
Lipidomics Reveals Cell Specific Changes During Pluripotent Differentiation to Neural and Mesodermal Lineages
Authors: Odenkirk Melanie T. , Jostes Haley C. , Francis Kevin , Baker Erin S.
Published: January 2025

Due to their self-renewal and differentiation capabilities, pluripotent stem cells hold immense potential for advancing our understanding of human disease and developing cell-based or pharmacological interventions. Realizing this potential, however, requires a thorough understanding of the basal cellular mechanisms which occur during differentiation. Lipids are critical molecules that define the morphological, biochemical, and functional role of cells. This, combined with emerging evidence linking lipids to neurodegeneration, cardiovascular health, and other diseases, makes lipids a critical class of analytes to assess normal and abnormal cellular processes. While previous work has examined the lipid composition of stem cells, uncertainties remain about which changes are conserved and which are unique across distinct cell types. In this study, we investigated lipid alterations of induced pluripotent stem cells (iPSCs) at critical stages of differentiation toward neural or mesodermal fates. Lipdiomic analyses of distinct differentiation stages were completed using a platform coupling liquid chromatography, ion mobility spectrometry, and mass spectrometry (LC-IMS-MS) separations. Results illustrated a shared triacylglyceride and free fatty acid accumulation in early iPSCs that were utilized at different stages of differentiation. Unique fluctuations through differentiation were also observed for certain phospholipid classes, sphingomyelins and ceramides. These insights into lipid fluctuations across iPSC differentiation enhance our fundamental understanding of lipid metabolism within pluripotent stem cells and during differentiation, while also paving the way for a more precise and effective application of pluripotent stem cells in human disease interventions.
Protein Barcoding and Next-Generation Protein Sequencing for Multiplexed Protein Selection, Analysis, and Tracking
Authors: Chinnaraj Mathivanan , Huang Haidong , Hutchinson Sebastian , Meyer Michael , Pike Douglas , Ribezzi Marco , Sultana Sharmin , Ocampo Derrek , Ding Fengling , Carpenter Meredith L. , Chorny Ilya , Vieceli John
Published: January 2025

Protein barcoding has emerged as a powerful tool for the multiplexed identification and characterization of proteins, providing a mechanism for precise tracking of protein affinity, location, and expression. In this study, we describe the development of a protein barcoding workflow for use with single-molecule Next-Generation Protein Sequencing™ (NGPS™) on the benchtop Platinum®instrument. We present data on the validation of eight peptide barcodes, each designed to minimize detection bias and maximize sensitivity across various experimental conditions. We have also optimized the design of expression constructs to decrease both the hands-on time and input requirements of the workflow. In this workflow, affinity-tagged proteins are expressed with unique peptide barcodes. Following experimental selection or treatments, the proteins are purified, and the peptide barcodes are cleaved and sequenced on the Platinum instrument. We demonstrate that we can detect barcodes at 400 fmol of sample input concentration within the eight-plex mixture, and at 50 fmol of sample input for individual barcodes. We also show the capacity of this barcoding approach to achieve a ten-fold dynamic range, underscoring its sensitivity in recovering variants with low abundance. Through the combination of protein barcoding and NGPS, we lay the groundwork for future studies aimed at characterizing protein interactions and improving targeted drug delivery strategies.

Motivation

Protein barcoding is an emerging tool for the multiplexed selection, analysis, and tracking of proteins. The motivation for this study was to address the limitations of existing protein barcode detection tools, such as mass spectrometry, which can have drawbacks related to quantification, cost, and accessibility. By integrating a protein barcoding workflow with the benchtop Platinum®protein sequencer, this work offers a sensitive and accessible approach for protein barcoding in applications ranging from protein engineering to nucleic acid therapy development.
Structure of an LGR dimer – an evolutionary predecessor of glycoprotein hormone receptors
Authors: Gong Zhen , Chen Shuobing , Fu Ziao , Kloss Brian , Wang Chi , Clarke Oliver B. , Fan Qing R. , Hendrickson Wayne A.
Published: January 2025

The glycoprotein hormones of humans, produced in the pituitary and acting through receptors in the gonads to support reproduction and in the thyroid gland for metabolism, have co-evolved from invertebrate counterparts1,2. These hormones are heterodimeric cystine-knot proteins; and their receptors bind the cognate hormone at an extracellular domain and transmit the signal of this binding through a transmembrane domain that interacts with a heterotrimeric G protein. Structures determined for the human receptors as isolated for cryogenic electron microscopy (cryo-EM) are all monomeric3–6despite compelling evidence for their functioning as dimers7–10. Here we describe the cryo-EM structure of the homologous receptor from a neuroendocrine pathway that promotes growth in a nematode11. This structure is an asymmetric dimer that can be activated by the hormone from that worm12, and it shares features especially like those of the thyroid stimulating hormone receptor (TSHR). When studied in the context of the human homologs, this dimer provides a structural explanation for the transactivation evident from functional complementation of binding-deficient and signaling-deficient receptors7, for the negative cooperativity in hormone action that is manifest in the 1:2 asymmetry of primary TSH:TSHR complexes8,9, and for switches in G-protein usage that occur as 2:2 complexes form9,10.
Convergent Evolutionary Traces of Genomic Innovations and Depletions in Socially Parasitic Ants
Authors: Harrison Mark C , Séguret Alice , Finke Christopher , Jongepier Evelien , Grandchamp Anna , Stoldt Marah , Heinze Jürgen , Foitzik Susanne , Bornberg-Bauer Erich , Feldmeyer Barbara
Published: January 2025

Parasitism, a common strategy across life, often involves genomic reduction. Socially parasitic “slavemaking” ants provide an excellent model to study the evolution of this lifestyle. Here, we compared the genomes of four closely related, independently evolved parasite-host pairs and their outgroups to identify convergent patterns. While genome size and gene numbers remain relatively stable, parasites show increased positive and relaxed selection, more putativede novogenes which have recently emerged from previously non-coding regions, and a significant loss of chemical receptors, particularly those associated with the evolution of sociality. Hosts, however, retain many duplicated genes. Gene co-expression networks associated with nest-defence in hosts are rather conserved, while the network structure of raiding parasites is much more variable and reflects the independent evolutionary origin of social parasitism. Our findings suggest that while hosts primarily rely on existing molecular mechanisms for defence, parasite genome evolution is characterised by extensive, convergent gene loss, innovation, and network rewiring.
A framework integrating multiscale in-silico modeling and experimental data predicts CD33CAR-NK cytotoxicity across target cell types
Authors: Ahmad Saeed , Xing Kun , Rajakaruna Harshana , Stewart William C. , Beckwith Kyle A. , Nayak Indrani , Kararoudi Meisam Naeimi , Lee Dean A. , Das Jayajit
Published: January 2025

Uncovering mechanisms and predicting tumor cell responses to CAR-NK cytotoxicity is essential for improving therapeutic efficacy. Currently, the complexity of these effector-target interactions and the donor-to-donor variations in NK cell receptor (NKR) repertoire require functional assays to be performed experimentally for each manufactured CAR-NK cell product and target combination. Here, we developed a computational mechanistic multiscale model which considers heterogenous expression of CARs, NKRs, adhesion receptors and their cognate ligands, signal transduction, and NK cell-target cell population kinetics. The model trained with quantitative flow cytometry and in vitro cytotoxicity data accurately predicts the short- and long- term cytotoxicity of CD33CAR-NK cells against leukemia cell lines across multiple CAR designs. Furthermore, using Pareto optimization we explored the effect of CAR proportion and NK cell signaling on the differential cytotoxicity of CD33CAR-NK cells to cancer and healthy cells. This model can be extended to predict CAR-NK cytotoxicity across many antigens and tumor targets.
Structural conservation and divergence across the Receptor Tyrosine Kinase superfamily
Authors: Fassler Bakhman Anna , Kolodny Rachel , Kosloff Mickey
Published: January 2025

Members of the Receptor Tyrosine Kinase (RTK) superfamily are regulators of cellular signaling, playing essential roles in cellular growth, differentiation, and survival. Dysregulation of RTKs leads to diseases such as cancer, diabetes, and inflammatory disorders, making them important therapeutic targets. Despite extensive research on RTKs, the structural diversity and evolutionary relationships across the superfamily are not fully understood. Here, we systematically compared structural conservation and divergence among 245 extracellular domains from 54 RTKs, across 18 RTK families. Using experimentally-resolved structures and AlphaFold2 models, we conducted an all-versus-all structural alignment to explore domain architecture and quantify significant structural similarities within the RTK superfamily. We curated a comprehensive database encompassing PDB structures, 3D folds, ligand-binding properties, and sequence information of all RTK domains analyzed (https://fasslero.github.io/RTK-domains). Our analysis revealed numerous inter-family similarities and remote evolutionary connections, in particular among ligand-binding domains (LBDs), and distinct structural domain types and unexpected dissimilarities among domains previously classified as related. Our work highlights the intricate balance between structural conservation and divergence in RTKs and sheds light on the evolutionary mechanisms shaping this critical superfamily.
Terrestrial Organic Matter Amplifies Methane Emissions Across Sediments of the Mississippi River Headwaters
Authors: Sauer Hailey M. , Day Leslie A. , Hamilton Trinity L.
Published: January 2025

Terrestrial organic matter (tOM) plays a critical role in aquatic ecosystems, influencing carbon processes and greenhouse gas emissions. Here, we investigate the impact of tOM on methane production in littoral and pelagic sediments from the Mississippi River headwaters using a microcosm approach. Contrary to our expectations, tOM addition universally increased methane production across lentic sediments, with no significant difference between littoral and pelagic zones. Methane production was influenced by select sediment microorganisms, primarily methanogens and lignocellulose degrading bacteria, which responded similarly across different sediment habitats. The study highlights the role of cytochrome-containing methanogens and their syntrophic relationships with fermentative bacteria, emphasizing the significance of microbial community structure in sediment methane dynamics. Our findings suggest that increasing tOM loads to freshwater systems could have broader implications for methane emissions, driven by specific microbial interactions.

Author Contribution Statement

HMS and TLH conceived the study and obtained the funds. HMS led fieldwork and microcosm set-up. HMS and LAD analyzed gas samples and HMS performed the data analysis and graphical representation of the results. HMS wrote the first draft of the manuscript, and all authors contributed significantly to the preparation of the final draft.

Scientific Significance Statement

As human activities and climate change increase the amount of organic material entering lakes and rivers, understanding the effects this has on greenhouse gas emissions is crucial. Our study reveals that adding terrestrial organic matter to freshwater sediments universally boosts methane production, a potent greenhouse gas. Through the exploration of microbial communities responsible for this process, our research highlights how changes in terrestrial organic matter export to aquatic systems could increase methane emissions from sediments.

Data Availability Statement

Additional Supporting Information can be found in the online version of this article, including an extended version of methods and supplementary tables. Sequencing data associated with this paper is available on NCBI, BioProject PRJNA1164797.
Single-base m6A epitranscriptomics reveals novel HIV-1 host interaction targets in primary CD4+T cells
Authors: Huang Siyu , Zhao Yutao , Phillips Stacia , Wilms Bethany , He Chuan , Wu Li
Published: January 2025

N6-methyladenosine (m6A) is the most prevalent cellular mRNA modification and plays a critical role in regulating RNA stability, localization, and gene expression. m6A modification plays a vital role in modulating the expression of viral and cellular genes during HIV-1 infection. HIV-1 infection increases cellular RNA m6A levels in many cell types, which facilitates HIV-1 replication and infectivity in target cells. However, the function of m6A modification in regulating HIV-1 infection of primary CD4+T cells remains unclear. Here, we demonstrate that HIV-1 infection of Jurkat CD4+T cells and primary CD4+T cells promotes the interaction between the m6A writer complex subunits methyltransferase-like 3 and 14 (METTL3/METTL14). Using single-base m6A-specific RNA sequencing, we identified several differentially m6A-modified cellular mRNAs, includingperilipin 3(PLIN3), during HIV-1 infection in primary CD4+T cells. Interestingly, HIV-1 infection increasedPLIN3mRNA level by enhancing its stability, but PLIN3 protein level was decreased. Knocking down PLIN3 in primary CD4+T cells reduced HIV-1 production but enhanced virion infectivity. In contrast, in Jurkat cells,PLIN3mRNA and protein expression levels were unaffected by HIV-1 infection, and knocking out PLIN3 did not impact HIV-1 production or infectivity. These results indicate that the interplay between HIV-1 and PLIN3 is cell-type specific and only observed in primary CD4+T cells. Overall, our results highlight the importance of m6A RNA modification in HIV-1-infected primary CD4+T cells and suggest its significance as a regulatory mechanism in HIV-1 infection.

Author Summary

N6-methyladenosine (m6A) is a common chemical modification on mRNA that helps control RNA stability, localization, and gene expression. m6A modification of viral and cellular RNA is important for HIV-1 infection. In this study, we found that HIV-1 infection of CD4+T cells enhanced the interaction between two proteins, METTL3 and METTL14, which are responsible for adding m6A modifications to RNA. Using m6A-specific RNA sequencing, we identified several mRNAs with altered m6A modifications during HIV-1 infection, including one calledPLIN3. Interestingly, HIV-1 infection stabilized and increasedPLIN3mRNA levels, but reduced PLIN3 protein expression in primary CD4+T cells. When we knocked down PLIN3 in primary CD4+T cells, it decreased HIV-1 production but made the HIV-1 particles more infectious. In contrast, in the Jurkat CD4+T cell line, HIV-1 infection did not affect PLIN3 expression and knockout of PLIN3 did not alter HIV-1 production or infectivity, suggesting that the effect is specific to primary CD4+T cells. Our findings show the importance of m6A RNA modification in HIV-1 infection by regulating host genes likePLIN3and suggest a unique regulatory mechanism in HIV-1 infected primary CD4+T cells.
Precise calcium-to-spike inference using biophysical generative models
Authors: Broussard Gerard Joey , Diana Giovanni , Urra Quiroz Francisco J. , Sermet B. Semihcan , Rebola Nelson , Lynch Laura A. , DiGregorio David A. , Wang Samuel S.-H.
Published: January 2025

The intramolecular dynamics of fluorescent indicators of neural activity can distort the accurate estimate of action potential (“spike”) times. In order to develop a more accurate spike inference algorithm we characterized the kinetic responses to calcium of three popular indicator proteins, GCaMP6f, jGCaMP7f, and jGCaMP8f, using in vitro stopped-flow and brain slice recordings. jGCaMP8f showed a use-dependent slowing of fluorescence responses that caused existing inference methods to generate numerous false positives. From these data we developed a multistate model of GCaMP and used it to create Bayesian Sequential Monte Carlo (BiophysSMC) and machine learning (BiophysML) inference methods that reduced false positives substantially. This biophysical method dramatically improved spike time accuracy, detecting individual spikes with a median uncertainty of 4 milliseconds, a performance level that reached the theoretical limit and is twice as accurate as any previous method. Our framework thus highlights advantages of physical model-based approaches over model-free algorithms.
A comprehensive analysis of the inherited lncRNA and circRNA repertoire of zebrafish
Authors: Joshi Dheeraj Chandra , Kadam Aakanksha , Sachidanandan Chetana , Pillai Beena
Published: January 2025

Inherited non-coding RNAs can be the third major component of epigenetic information transfer from one generation to the next. Here, we present a comprehensive resource of lncRNAs and circular RNAs that are inherited, compiled from meta-analysis of zebrafish transcriptomics data and comparative genomics with mouse and human. Maternal and paternal inheritance of mRNA into the zygote is accepted to be an important regulator of embryonic development as well as adult characteristics. Although inheritance of certain specific miRNAs is known, other non-coding RNA inheritance remains less explored. We performed a comprehensive analysis of the inherited lncRNAs and circRNAs in zebrafish. We discovered that nearly 20% of all known lncRNA and 7% of circRNAs are inherited. Many of these lncRNAs are conserved in mammals, and are expressed widely in adult tissues of zebrafish. The male and female gametes carry a highly similar pool of inherited lncRNAs, with only a few sperm/ oocyte specific transcripts. The majority of inherited circRNAs originate from genes important for fertilization and can potentially regulate translational processes. Contrary to general belief, the inherited lncRNAs and circRNAs do not undergo degradation en masse coincidental to zygotic genomic activation, suggesting that these RNAs may have more sustained roles in development.
Auditory tract maturation in early infancy: Links to speech production
Authors: Liu Feihong , Wang Yaoxuan , Gu Jinchen , Liu Jiameng , Cai Xinyi , Zhang Han , Feng Jun , Wang Zhaoyan , Wu Hao , Shen Dinggang
Published: January 2025

Infants exhibit remarkable language acquisition abilities, supported by highly plastic neural substrates that dynamically interact with early speech experiences. However, the developmental mechanisms of these neural substrates and their specific role in speech acquisition remain incompletely understood. Here, we present NeoAudi Tract (NAT), a robust automated toolbox for extracting the full set of auditory tracts in infants from birth to 24 months using3T diffusion MRI data. By characterizing the microstructural changes in these tracts, we demonstrate a gradual and continuous maturation process of the auditory system. Additionally, we identify significant correlations between auditory tract maturation and bothfine-motor skillsandexpressive languaget-scores from the Mullen Scales of Early Learning tests. Our findings highlight the role of the auditory system in speech production and indicate the intertwined development of auditory and motor systems that underlies speech acquisition, particularly during perceptual reorganization.
Hypoxia-Induced Active Dynamics Promotes Early Tumorigenesis
Authors: Wang Zhengduo , Tian Li , Li Bo
Published: January 2025

Abstract

Understanding early tumor formation offers critical insights for cancer prevention at the earliest stages. However, mostin vivostudies focus on later stages, providing limited information on initial tumorigenesis. Hypoxia, a common physiological condition, is a primary microenvironmental factor in cancer. While molecular studies indicate significant yet sometimes conflicting roles of hypoxia in cancer progression, experimental data on hypoxia’s impact on tumor formation from a single cell, especially regarding cellular dynamics, remain scarce. To address this gap, we developed an integrated platform for live-cell imaging under hypoxic conditions, enabling, for the first time, observation of 3D tumor spheroid development from a single cell. Our results show that tumorigenesis is markedly accelerated under hypoxia. Beyond linear growth, we demonstrate that directional movement enhances fusion events, leading to larger spheroids that, in turn, stimulate further proliferation — a positive feedback loop between spheroid dynamics and growth. Actin polymerization and cell-cell adhesion are optimized to promote spheroid fusion. Additionally, hypoxia induces cells with outreaching F-actin co-localized with smaller nuclei to bridge gaps between spheroids, facilitating fusion, while the appearance of tiny nuclei suggests genetic instability. These findings provide direct insights into hypoxia’s role in early tumorigenesis, highlighting the potential of modulating dynamic, mechanical, and physiological factors for cancer prevention.
Receptor dimerization enables ligand discrimination through tunable response heterogeneity
Authors: Biran Assaf , Antebi Yaron E.
Published: January 2025

Signaling pathways enable cells to coordinate collective behaviors by exchanging specific information. Many pathways utilize multiple ligand variants to activate the same intracellular signaling cascade, raising the question of how cells discriminate between these seemingly redundant signals. It has been shown that individual cells can discriminate between signals based on their induced level of activity, temporal dynamics or combinatorial effect. Here, we demonstrate that ligand discrimination could also emerge at the population level. Using mathematical models of ligand-receptor interactions, we examine how response heterogeneity at the population level can encode ligand identity. We introduce a local scaling metric to quantify how variation in pathway components affects the cellular response. Our results reveal that for pathways with dimeric receptors, and more significantly for heterodimeric receptors, biochemical parameters of the ligands control the resulting heterogeneity in the response of a population of cells. Furthermore, we show that the population-level heterogeneity encodes the enzymatic activity of the resulting receptor complex. This suggests a functional advantage for utilizing heterodimeric receptor complexes in pathways acting across a population of cells, such as the type I interferon pathway, which shows several of the characteristics of our model. This contrasts to juxtacrine pathways, such as Notch, that do not act at the population level and use a single component receptor. Overall, our findings highlight a novel mechanism by which receptor architecture enables cells to encode ligand-specific information through population-level heterogeneity, offering insights into immune regulation, tissue development, and synthetic biology.

Significance Statement

Cells often communicate using distinct molecular signals (ligands) that activate the same pathway. Yet, how cells distinguish between these signals remains unclear. This study reveals that ligand discrimination can emerge at the level of entire cell populations, not just individual cells. By analyzing mathematical models, we show that certain receptor architectures, especially those involving heterodimeric receptors, allow signals to control the heterogeneity of the response level across a population. This mechanism enables cell populations to decode specific information about their environment, impacting processes like immune responses and tissue development. Our findings provide new insights into how signals coordinate collective behaviors and suggest strategies for designing synthetic systems to precisely control biological responses.
LCORLandSTC2variants increase body size and growth rate in cattle and other animals
Authors: Bai Fengting , Cai Yudong , Qiu Min , Liang Chen , Pan Linqian , Liu Yayi , Feng Yanshuai , Cao Xuesha , Yang Qimeng , Ren Gang , Jiao Shaohua , Gao Siqi , Lu Meixuan , Wang Xihong , Heller Rasmus , Lenstra Johannes A. , Jiang Yu
Published: January 2025

Using ancestral recombination graphs, we investigated recent selection signatures in European beef cattle breeds, pinpointing sweep-driving variants in theLCORLandSTC2loci with notable effects on body size and growth rate. The ACT-to-A frameshift mutation inLCORLoccurs mainly in central-European cattle, and stimulates growth. Remarkably, similar truncating mutations were found in seven of the other most important domesticated species, but not in most populations of wild relatives. In theSTC2locus, we identified a missense C-to-G mutation located within the conserved region across vertebrates. We validated the two natural mutations in gene-edited mouse models, where both variants in homozygous carriers increase the average weight by 11%. Our findings provide insights into a seemingly recurring gene target of body size enhancing truncating mutations across domesticated species, and offer valuable targets for gene editing-based breeding in animals.
Scrutinization on Docking Against Individually Generated Target Pockets for Each Ligand
Authors: Zhan Rui , Zhang Wenyi , Huang Jing
Published: January 2025

The longstanding challenge of limited exploration in protein receptor conformational space continues to constrain the precision of molecular docking. Ensemble docking, which employs methods such as molecular dynamics simulations to generate multiple receptor conformations for docking, has improved accuracy but remains limited by incomplete sampling and an inability to fully account for ligand-induced fit. To address these limitations, we introduce the concept of individual docking, a novel approach that involves docking against receptor conformations generated individually for each ligand in the docking library. This approach has only very recently become feasible due to advances in protein structure prediction, in particular end-to-end protein-ligand complex prediction technologies exemplified by AlphaFold3 and NeuralPLexer. In this study, we performed individual docking on 27 targets from the DUD-E dataset, using a two-step protocol that integrates NeuralPLexer’s inference as the receptor sampling step with subsequent physics-based docking. Our results reveal that individual docking leads to approximately 24% reduction in the enrichment factors compared with standard docking, yet it recovers different sets of active ligands. Detailed analyses of pocket and ligand conformations suggest several potential incompatibilities between deep learning-based and physics-based virtual screening tools.
Paratransgenesis: The dynamics of engineeredEnterobactersymbionts and Cry1Ac-producingEnterobacterfor biocontrol ofHelicoverpainsect pests in crop production
Authors: Ojha Abhishek
Published: January 2025

The potential application of insect gut microorganisms in paratransgenic crop pest management techniques is being investigated. TheHelicoverpagut is known to harbor the symbiontEnterobacter. However, little is known about the dynamics ofEnterobacterin theHelicoverpagut, its interaction with the phyllosphere, and the mechanisms by which it is delivered to this Lepidopteran species. To evaluate the insecticidal activity of Cry1Ac and its capacity to colonize theHelicoverpagut and the tomato phyllosphere, the symbiontEnterobacter, which was isolated from theHelicoverpagut, was transformed with constructs 2 (cry1Ac-KmR-pUC18) and 3 (KmR-pGFP). Within 48 hours and 24 hours, respectively, theHelicoverpagut and tomato phyllosphere were effectively colonized by the GFP-producing construct 3-Enterobacter. In insect bioassays, Cry1Ac-producing constructs 2-E. coli(K12) and 2-Enterobacterwere used for diet and leaf-dip testing.Helicoverpaneonates died 86-100% when fed diets supplemented with 10 -10 cells of Cry1Ac-producing construct 2-E. coli(K12), whereas 79–100% died when fed diets supplemented with 10 -10 cells of Cry1Ac-producing construct 2-Enterobacter. Furthermore, when the Cry1Ac-producing construct 2-Enterobacter(0.10 x 109cells) was applied to the tomato phyllosphere, it caused 100% mortality of neonates within 192 hours. The successful vector modification, genetic transformation, and establishment of recombinantEnterobactercells in the guts ofHelicoverpalarvae and on tomato leaves lay the foundation for advancing a paratransgenic strategy. This engineered bacterium could potentially replace synthetic insecticides for managing lepidopteran pests in crops.
The role of STN beta oscillations on lower extremity muscle activity in Parkinsonian stepping
Authors: Simpson Thomas G. , He Shenghong , Pogosyan Alek , Plazas Fernando Rodriguez , Hart Michael G. , Shah Rahul , Hasegawa Harutomo , Wiest Christoph , Wehmeyer Laura , Yassine Sahar , Guo Xuanjun , Merla Anca , Perera Andrea , Raslan Ahmed , O’Keeffe Andrew , Welter Marie-Laure , Ashkan Keyoumars , Morgante Francesca , Andrade Pablo , Visser-Vandewalle Veerle , Pereira Erlick A. , Tan Huiling
Published: January 2025

Freezing of gait (FOG) is a devastating symptom of Parkinson’s disease (PD) often resulting in disabling falls and loss of independence. It affects half of patients, yet current therapeutic strategies are insufficient, and the underlying neural mechanisms remain poorly understood. This study investigated beta oscillation dynamics in the STN during different locomotor states, while examining the effects of levodopa. In particular, it aimed to identify pathological activity by analysing the relationship between the STN and lower limb muscles during stepping. Local field potentials (LFP) in the STN and muscle activity (EMG) of the gastrocnemius and peroneus longus were recorded in 14 PD patients during standing and stepping, ON and OFF levodopa. Levodopa reduced stepping variability, implying improved stepping abilities. Distinct STN beta patterns were observed between stepping and standing, with lower high-beta and higher low-beta during stepping compared to standing, suggesting a distinct role of these frequency bands in motor control during postural and movement states. Levodopa reduced low-beta but increased high-beta activity, highlighting a potential physiological function of high-beta in the STN during standing and stepping. In addition, step-phase specific effects of levodopa included reduced broad-beta band activity in the STN and lower limb muscles during the late-stance and pushing-off phase of the contralateral leg when ON medication. Further analyses suggest that pathological STN activity amplifies muscle activation around movement initiation, potentially reducing the ability of the patient to move freely. These findings offer insight for developing phase-specific stimulation strategies targeting STN beta oscillations during gait.
VGluT3 BNST neurons transmit GABA and restrict feeding without affecting rewarding or aversive processing
Authors: Ly Annie , Karnosky Rachel , Prévost Emily D. , Hotchkiss Hayden , Pelletier Julianne , Spencer Robert L. , Ford Christopher P. , Root David H.
Published: January 2025

The bed nucleus of the stria terminalis (BNST) is involved in feeding, reward, aversion, and anxiety-like behavior. We identify BNST neurons defined by the expression of vesicular glutamate transporter 3, VGluT3. VGluT3 neurons were localized to anteromedial BNST, were molecularly distinct from accumbal VGluT3 neurons, and co-express vesicular GABA transporter (VGaT). Cell-type specific presynaptic processes were identified in arcuate nucleus (ARC) and the paraventricular nucleus of the hypothalamus (PVN), regions critical for feeding and homeostatic regulation. Whole-cell patch-clamp electrophysiology revealed that, while these neurons co-express VGluT3 and VGaT, they functionally transmit GABA to both ARC and PVN, with rare glutamate co-transmission to ARC. Neuronal recordings of VGluT3 BNST neurons showed greater calcium-dependent signaling in response to sucrose consumption while sated compared with fasted. When fasted, optogenetic stimulation of BNST VGluT3 neurons decreased sucrose consumption using several stimulation conditions but not when stimulation occurred prior to sucrose access, suggesting that BNST VGluT3 activation concurrent with consumption in the fasted state reduces feeding. BNST VGluT3 activation during anxiety-like paradigms (novelty-suppressed feeding, open field, and elevated zero maze) and real-time place conditioning resulted in no changes in anxiety-like or reward/aversion behavior. We interpret these data such that VGluT3 BNST neurons represent a unique cellular population within the BNST that provides inhibitory input to hypothalamic regions to decrease feeding without affecting anxiety-like or reward/aversion behavior.
The mechanosensory DEG/ENaC channel DEGT-1 is a proprioceptor ofC. elegansforegut movement
Authors: Bayer Emily A. , Mango Susan E. , Hobert Oliver , Schier Alexander F.
Published: January 2025

The gastrointestinal tract is subjected to extensive mechanosensory stimulation during food ingestion. However, the identities of mechanosensory receptors in the enteric nervous system are largely unknown. The pharynx ofC. elegansis a structurally and functionally homologous model of the vertebrate foregut, but is comprised of only 20 neurons that are embedded within the muscles and epithelial cells of the organ. Here we report that the DEG/ENaC family ion channel DEGT-1 is a proprioceptor of pharynx movement. DEGT-1 protein is expressed in 4 pharyngeal neurons (MI, M3, I4, and M5) and localized to their neuronal soma in direct contact with the collagenous pharyngeal basement membrane.degt-1mutants display abnormally rapid feeding in the presence of food, causing global changes in lipid accumulation.degt-1mutants also pump rapidly when pumping is induced by the presence of serotonin alone, suggesting thatdegt-1is required for proprioception of pharyngeal pumping itself, rather than sensing ingested food. DEGT-1 is required in only two pharyngeal neurons (I4 and M5) to control pumping rate. Taken together, these results suggest that DEGT-1 modulates pharyngeal pumping rate by relaying proprioceptive feedback generated by the shear force of the pharynx against its own basement membrane. Thus, mechanosensors in enteric nervous systems modulate organ function not only by detecting forces from ingested contents, but also the movements of the organ itself.
Differences in apple fruit shape are independent of fruit size
Authors: DeViller Kylie , Chitwood Daniel H. , Myles Sean , Li Mao , Migicovsky Zoë
Published: January 2025

Premise

Fruit quality is crucial in breeding new apple accessions. Before tasting, consumers assess freshness and flavour based on the physical appearance of fruit. Understanding how fruit quality traits such as shape and size vary across diverse apples provides a foundation for future breeding efforts.

Methods

We analyzed images of 5724 apples representing 743 different trees and 534 unique accessions from Canada’s Apple Biodiversity Collection to quantify variation in fruit shape and size. To achieve this, we used a pseudo-landmarking approach paired with traditional linear measurements including length, width, area, solidity, and aspect ratio. We also incorporated previously collected fruit weight measurements from the same trees.

Results

Using a comprehensive measure of shape, we determined that the primary source of variation in apple fruit shape was the width to length (aspect) ratio of the fruit. This variation was not significantly correlated with differences in fruit size from its area and harvest weight.

Conclusions

Our findings indicate that two critical aspects of morphological variation in apple—fruit shape and size—are independent, suggesting it is possible to select for a diverse range of fruit shapes while maintaining a consistent and marketable size.
IFN-γsignaling is required for the efficient replication of murine hepatitis virus (MHV) strain JHM in the brains of infected mice
Authors: Kerr Catherine M. , Proctor-Roser Macie A. , Parthasarathy Srivatsan , O’Connor Joseph J. , Pfannenstiel Jessica J. , Orozco Robin C. , Fehr Anthony R.
Published: January 2025

Neurotropic viruses are a major public health concern as they can cause encephalitis and other severe brain diseases. Many of these viruses, including flaviviruses, herpesviruses, rhabdoviruses and alphaviruses enter the brain through the olfactory neuroepithelium (ONE) in the olfactory bulbs (OB). Due to the low percentage of encephalitis that occurs following these infections, it’s thought that the OBs have specialized innate immune responses to eliminate viruses. Murine hepatitis virus strain JHM (JHMV) is a model coronavirus that causes severe encephalitis in mice and can access the brain through olfactory sensory neurons. We’ve shown that a JHMV Mac1-mutant virus, N1347A, has decreased replication and disease in the brains of mice. Here we further show that this virus replicates poorly in the OB. However, it is unknown which innate immune factors restrict N1347A replication in the OB. RNA seq analysis of infected olfactory bulbs showed that IFNγ was upregulated in the OB while IFN-βwas barely detectable at 5 days post-infection. To determine if IFN-γ restricts JHMV N1347A replication, we utilized IFN-γ and IFN-γ receptor (IFN-γR) knockout (KO) mice. Surprisingly we found that JHMV WT and N1347A replicated very poorly in the OB and whole brains of both IFN-γ and IFN-γR KO mice following intranasal infection, though survival and weight loss were unaltered. Furthermore, we determined that microglia were the primary cells producing IFN-γ during the early stages of this infection. We conclude that IFN-γ is required for the efficient replication of JHMV in the brains of infected mice.
A semi-empirical Bayes approach for calibrating weak instrumental bias in sex-specific Mendelian randomization studies
Authors: Huang Yu-Jyun , Kurniansyah Nuzulul , Levey Daniel F. , Gelernter Joel , Huffman Jennifer E. , Cho Kelly , Wilson Peter W.F. , Gottlieb Daniel J. , Rice Kenneth M. , Sofer Tamar
Published: January 2025

Strong sex differences exist in sleep phenotypes and also cardiovascular diseases (CVDs). However, sex-specific causal effects of sleep phenotypes on CVD-related outcomes have not been thoroughly examined. Mendelian randomization (MR) analysis is a useful approach for estimating the causal effect of a risk factor on an outcome of interest when interventional studies are not available. We first conducted sex-specific genome-wide association studies (GWASs) for suboptimal-sleep phenotypes (insomnia, obstructive sleep apnea (OSA), short and long sleep durations, and excessive daytime sleepiness) utilizing the Million Veteran Program (MVP) dataset. We then developed a semi-empirical Bayesian framework that (i) calibrates variant-phenotype effect estimates by leveraging information across sex groups, and (ii) applies shrinkage sex-specific effect estimates in MR analysis, to alleviate weak instrumental bias when sex groups are analyzed in isolation. Simulation studies demonstrate that the causal effect estimates derived from our framework are substantially more efficient than those obtained through conventional methods. We estimated the causal effects of sleep phenotypes on CVD-related outcomes using sex-specific GWAS data from the MVP and All of Us. Significant sex differences in causal effects were observed, particularly between OSA and chronic kidney disease, as well as long sleep duration on several CVD-related outcomes. By applying shrinkage estimates for instrumental variable selection, we identified multiple sex-specific significant causal relationships between OSA and CVD-related phenotypes.
Impact of Mydriasis on Image Gradability and Automated Diabetic Retinopathy Screening with a Handheld Camera in Real-World Settings
Authors: Diogenes Iago , Restrepo David , Ribeiro Lucas Zago , Aragaki Andre Kenzo , Malerbi Fernando Korn , Regatieri Caio Saito , Nakayama Luis Filipe
Published: January 2025

Purpose

Diabetic retinopathy (DR) screening in low- and middle-income countries (LMICs) faces challenges due to limited access to specialized care. Portable retinal cameras provide a practical alternative, but image quality, influenced by mydriasis, affects artificial intelligence (AI) model performance. This study examines the role of mydriasis in improving image quality and AI-based DR detection in resource-limited settings.

Methods

We compared the proportion of gradable images between mydriatic and non-mydriatic groups and used logistic regression to identify factors influencing image gradability, including age, gender, race, diabetes duration, and systemic hypertension. A ResNet-200d algorithm was trained on the mBRSET dataset and validated on mydriatic and non-mydriatic images. Performance metrics, such as accuracy, F1 score, and AUC, were evaluated.

Results

The mydriatic group had a higher proportion of gradable images (82.1% vs. 55.6%,P< 0.001). Factors such as systemic hypertension, older age, male gender, and longer diabetes duration were associated with lower image gradability in non-mydriatic images. Mydriatic images achieved better AI performance, with accuracy (82.91% vs. 79.23%), F1 score (0.83 vs. 0.79), and AUC (0.94 vs. 0.93). Among gradable images, the performance difference was not statistically significant.

Conclusion

Mydriasis improves image gradability and enhances AI model performance in DR screening. However, optimizing AI for non-mydriatic imaging is critical for LMICs where mydriatic agents may be unavailable. Refining AI models for consistent performance across imaging conditions is essential to support the broader implementation of AI-driven DR screening in resource-constrained settings.