bluuebunny/crossref_metadata_2025 huggingface dataset:
Presence of phage-plasmids in multiple serovars of Salmonella enterica
Authors: Nair Satheesh , Barker Clare R. , Bird Matthew , Greig David R. , Collins Caitlin , Painset Anaïs , Chattaway Marie , Pickard Derek , Larkin Lesley , Gharbia Saheer , Didelot Xavier , Ribeca Paolo
Published: May 2024

Evidence is accumulating in the literature that the horizontal spread of antimicrobial resistance (AMR) genes mediated by bacteriophages and bacteriophage-like plasmid (phage-plasmid) elements is much more common than previously envisioned. For instance, we recently identified and characterized a circular P1-like phage-plasmid harbouring a bla
CTX-M-15 gene conferring extended-spectrum beta-lactamase (ESBL) resistance in Salmonella enterica serovar Typhi. As the prevalence and epidemiological relevance of such mechanisms has never been systematically assessed in Enterobacterales, in this study we carried out a follow-up retrospective analysis of UK Salmonella isolates previously sequenced as part of routine surveillance protocols between 2016 and 2021. Using a high-throughput bioinformatics pipeline we screened 47 784 isolates for the presence of the P1 lytic replication gene repL, identifying 226 positive isolates from 25 serovars and demonstrating that phage-plasmid elements are more frequent than previously thought. The affinity for phage-plasmids appears highly serovar-dependent, with several serovars being more likely hosts than others; most of the positive isolates (170/226) belonged to S. Typhimurium ST34 and ST19. The phage-plasmids ranged between 85.8 and 98.2 kb in size, with an average length of 92.1 kb; detailed analysis indicated a high amount of diversity in gene content and genomic architecture. In total, 132 phage-plasmids had the p0111 plasmid replication type, and 94 the IncY type; phylogenetic analysis indicated that both horizontal and vertical gene transmission mechanisms are likely to be involved in phage-plasmid propagation. Finally, phage-plasmids were present in isolates that were resistant and non-resistant to antimicrobials. In addition to providing a first comprehensive view of the presence of phage-plasmids in Salmonella, our work highlights the need for a better surveillance and understanding of phage-plasmids as AMR carriers, especially through their characterization with long-read sequencing.
A novel genetic mouse model of fatal aortic dissection reveals massive inflammatory cell infiltration in the thoracic aorta
Authors: Kimura Kenichi , Motoyama Eri , Kanki Sachiko , Asano Keiichi , Sheikh Md Al Amin , Clarin Maria Thea Rane Dela Cruz , Raja Erna , Takeda Mariko , Ishii Ryutaro , Murata Kazuya , Deleeuw Violette , Sips Patrick , Mosquera Laura Muiño , De Backer Julie , Mizuno Seiya , Sakai Lynn Y , Nakamura Tomoyuki , Yanagisawa Hiromi
Published: May 2024

Background

Aortic dissection (AD) is the separation of medial layers of the aorta and is a major cause of death in patients with connective tissue disorders such as Marfan syndrome. However, molecular triggers instigating AD, its temporospatial progression, and how vascular cells in each vessel layer interact and participate in the pathological process remain incompletely understood. To unravel the underlying molecular mechanism of AD, we generated a spontaneous AD mouse model.

Methods

We incorporated a novel missense variant (p.G234D) inFBN1, the gene for fibrillin-1, identified in a non-syndromic familial AD patient into mice using CRISPR/Cas9 system. We performed histopathological analyses of the aortic lesions by histology, immunofluorescence staining, electron microscopy, synchrotron-based imaging and single-cell (sc)RNA-sequencing. Biochemical analysis was performed to examine the binding capacity of mutant human FBN1G234D protein to latent Tgfβ binding proteins (LTBPs), and signaling pathways in the mutant aortic wall were examined by western blot analysis.

Results

50% of theFbn1G234D/G234Dmutant mice died within 5 weeks of age from multiple intimomedial tears that expanded longitudinally and progressed to aortic rupture accompanied by massive immune cell infiltration. scRNA-sequencing, validated by immunostaining, revealed a significant increase in MHC class II-positive pro-inflammatory macrophages and monocytes at the site of intima tears with upregulation of MMP2/9 and marked disruption of elastic lamina. Subendothelial matrices, such as type IV collagen and laminin, expanded into the medial layer, where fibronectin expression was highly upregulated.Fbn1G234D/G234Dendothelial cells exhibited altered mechanosensing with loss of parallel alignment to blood flow and upregulation of VCAM-1 and ICAM-1, all of which likely contributed to the infiltration of immune cells. Biochemically, FBN1G234D lost the ability to bind to latent TGFβ binding protein (LTBP)-1, -2, and -4, resulting in the downregulation of TGFβ signaling in the aortic wall.

Conclusions

We show that dynamic interactions involving endothelial cells (ECs) and macrophages/monocytes in the intima, where the ECM microenvironment is altered with the reduced TGFβ signaling, contributes to the initiation of AD. Our novel AD mouse model provides a unique opportunity to identify target molecules involved in the intimomedial tears that can be utilized for development of therapeutic strategies.
SLC13A2-transported citrate is a metabolic signal for PKM2 acetylation and degradation to suppress tumor growth
Authors: Qin Mengyao , Shi Li , Chen Hao , Liu Chan , Tang Zhiquan , An Donghao , Yu Wanting , He Dandan , Shao Chang , Yuan Shengtao , Yu Hong , Hao Haiping , Xiong Jing
Published: May 2024

Background and aims

Metabolic reprogramming represents as a pivotal hallmark for cancer, but TCA cycle in tumorigenesis and progression has long been neglected. Solute carrier (SLC) transporters mediate the transport of TCA cycle intermediates across membrane, but their functions in cancer pathogenesis remains unclear.

Approaches & Results

Using integrated analysis of solute carrier (SLC) transporters for TCA cycle intermediates, we found that SLC13A2 was consistently downregulated in hepatocellular carcinoma (HCC) cells and liver tissues from human patients and heterogeneous mouse models. Adeno-associated virus (AAV)-transduced liver-specific knockout or overexpression of SLC13A2 promoted or ameliorated HCC progression in the primary mouse model, demonstrating that SLC13A2 served as a protective factor during HCC pathogenesis. SLC13A2 inhibited HCC cell proliferation by decreasing mitochondrial function via suppressed oxygen consumption and ATP production. Combined with metabolic flux analysis, we found that SLC13A2 imported citrate, which secreted acetyl-CoA as a precursor for the acetylation of pyruvate kinase muscle isozyme M2 (PKM2), which led to its protein degradation. Decreased activity of pyruvate kinase depleted pyruvate for the TCA cycle, thus inhibiting amino acid synthesis and nucleotide metabolism. Additionally, a decrease in nuclear PKM2 protein transduced to reprogrammed gene transcription for cell proliferation and metabolism which is required for tumor growth.

Conclusions

This study revealed that citrate transported by SLC13A2 acts as a signal to disrupt metabolic homeostasis for tumor growth and suggests potential drug targets for HCC therapy.

graphic abstract
An Introductory Implementation of Breast Cancer Detection from Mammograms and Pixel Intensity with Efficient-Net Other Neural Nets
Authors: Banerjee Sheekar , Kabir Humayun
Published: May 2024

In the world of civilized medical scientific progression, cancer has become a very serious threat for the natural survival of human beings where breast cancer stays to be the second most dangerous type. Mostly women are embracing very pathetic death because of the delayed detection of the cancer cell in the certain period of their life. Machine Learning mechanism can definitely help at the stage of medical imaging which can escalate the diagnosis of the cancer cells at a very early age of its biological formation and development. We focused upon the deep learning approach to classify the normal and abnormal breast according to the medical imaging from the MIAS dataset of Mammograms and Pixel Intensity. The Convolution Neural Network (CNN) alongside ResNet, AmoebaNet and EfficientNet have been used for the detection with 330 mammograms in which 194 images are normal and 136 are having the identification of abnormal breasts. The accuracy of the entire experimental results was carrying the torch of potential legacy of deep learning in the medical imaging arena. The research is ongoing for the further development and optimization of CNN, AmoebaNet-C and EfficientNet architecture for the Pixel Intensity with higher accuracy, proper segmentation and masking. Source code of this research is available here:https://github.com/ac005sheekar/Breast-Cancer-Detection-with-Pixel-Intensity/
Evolutionary Systems Biology Identifies Genetic Trade-offs In Rice Defense Against Above- and Belowground Attackers
Authors: Dunivant Taryn S. , Godinez-Vidal Damaris , Perkins Craig , Lee Madelyn G. , Ta Matthew , Groen Simon C.
Published: May 2024

Like other plants, wild and domesticated rice species (Oryza nivara, O. rufipogon, andO. sativa) evolve in environments with various biotic and abiotic stresses that fluctuate in intensity through space and time. Microbial pathogens and invertebrate herbivores such as plant-parasitic nematodes and caterpillars show geographical and temporal variation in activity patterns and may respond differently to certain plant defensive mechanisms. As such, plant interactions with multiple community members may result in conflicting selection pressures on genetic polymorphisms. Here, through assays with different above- and belowground herbivores, the fall armyworm (Spodoptera frugiperda) and the southern root-knot nematode (Meloidogyne incognita), respectively, and comparison with rice responses to microbial pathogens, we identify potential genetic trade-offs at theKSL8andMG1loci on chromosome 11.KSL8encodes the first committed step towards biosynthesis of either stemarane- or stemodane-type diterpenoids through the japonica (KSL8-jap) or indica (KSL8-ind) allele. Knocking outKSL8-japandCPS4, encoding an enzyme that acts upstream in diterpenoid synthesis, in japonica rice cultivars increased resistance toS. frugiperdaand decreased resistance toM. incognita. Furthermore,MG1resides in a haplotype that provided resistance toM. incognita, while alternative haplotypes are involved in mediating resistance to the rice blast fungusMagnaporthe oryzaeand other pests and pathogens. Finally,KSL8andMG1alleles are located within trans-species haplotypes and may be evolving under long-term balancing selection. Our data are consistent with a hypothesis that polymorphisms atKSL8andMG1may be maintained through complex and diffuse community interactions.
Homologous recombination promotes mitotic death to suppress the innate immune response
Authors: Szmyd Radoslaw , Casolin Sienna , French Lucy , Manjon Anna Gonzalez , Dhawan Andrew , Nelson Christopher B. , Cavalli Léa , Page Scott G. , Hau Eric , Pickett Hilda A. , Gee Harriet E. , Cesare Anthony J.
Published: May 2024

Double strand breaks (DSBs) can initiate mitotic catastrophe, a complex oncosuppressive phenomenon characterized by cell death during or after cell division. Through single-cell analysis of extended live imaging, we unveiled how cell cycle-regulated DSB repair guides disparate mitotic catastrophe outcomes. Our data reveal that toxic double Holliday junctions (dHjs) generated during homologous recombination (HR) promote non-immunogenic intrinsic apoptosis in the immediate mitosis after S or G2-phase DSB induction. Conversely, the combined activity of non-homologous end joining (NHEJ), microhomology mediated end joining (MMEJ), and single strand annealing (SSA) enable G1 phase cells to tolerate high DSB loads at the cost of aberrant cell division, innate immune response activation and delayed extrinsic lethality. Targeting NHEJ, MMEJ, or SSA promotes HR-dependent mitotic death, while suppressing mitotic death fosters a robust immunogenic response. Together the data indicate that a temporal repair hierarchy, coupled with cumulative DSB load, serves as a reliable predictor of mitotic catastrophe outcomes. In this pathway, HR suppress the innate immune response by promoting mitotic lethality.
Efficiently determining membrane-bound conformations of peripheral membrane proteins using replica exchange with hybrid tempering
Authors: Natarajan Chandramouli , Srivastava Anand
Published: May 2024

Accurately sampling the membrane-bound conformations of a peripheral membrane proteins (PMP) using classical all-atom molecular dynamics simulations (AAMD) is a formidable enterprise due to the rugged free energy landscape of the protein-membrane system. In general, AAMD-based extraction of binding geometry requires simulations of multiple systems with different initial user-defined binding poses that may not be exhaustive. As an alternative, advanced sampling methods are also applied to elucidate the membrane-binding mechanism of PMPs but these techniques are generally computationally expensive and often depend on choice of the collective variables (CV). In this work, we showcase the utility of CV-free replica exchange with hybrid tempering (REHT) method in capturing the membrane-bound conformations of PMPs by testing it on the Osh4 amphipathic lipid-packing sensor (ALPS) motif, a 27 amino-acid membrane binding peptide. We show that REHT samples all the membrane-bound conformations of the Osh4 ALPS peptide at their correct populations and does it in a highly efficient manner with minimum computational time. We clearly show that, out of the two significant conformations, the peptide prefers horizontal conformations over vertical ones. In both the conformations, REHT captures all the vital residue-wise membrane contacts. The transition between the two configuration is not uncommon as our calculations reveal a ∼ 2 kT free energy difference between the two conformations. Interestingly, from our simulations we also find that the transition from vertical to horizontal conformation involves limited unfolding the main helix’s last turn. From our findings, we conclude that REHT samples the membrane-bound conformations of Osh4 ALPS peptide very efficiently and also provides additional insights and information that are often not available with regular piece-wise AAMD simulations. The method can be used as an efficient tool to explore the membrane-binding mechanisms of PMPs.
Parkinson's Disease-Linked Kir4.2 Mutation R28C Leads to Loss of Ion Channel Function
Authors: Chen Xiaoyi , Finol-Urdaneta Rocio K. , Chen Mo , Sykes Alex , Gao Bingmiao , Adams David J. , Mellick George D. , Ma Linlin
Published: May 2024

Parkinson's disease (PD) is a complex, progressive neurodegenerative disorder driven by multiple pathogenetic factors, including oxidative stress, mitochondria dysfunction, neuroinflammation, and ion imbalance. Recent evidence highlights the significant role of potassium channels in the pathophysiology of PD. We recently identified a PD-linked genetic mutation in the KCNJ15 gene (KCNJ15p.R28C), encoding the inwardly rectifying potassium channel Kir4.2, within a four-generation family with familial PD. However, the role of the Kir4.2 channel in neurodegenerative diseases remains largely unexplored. This study aimed to elucidate the impact of the KCNJ15p.R28C (Kir4.2R28C) mutation on the biophysical and biochemical properties of Kir4.2. Employing Kir4.2-overexpressing HEK293T cells as a model, we investigated how the mutation affects the channel's functional properties, total protein expression, intracellular processing in the endoplasmic reticulum and lysosomes, and plasma membrane trafficking. Patch clamp studies revealed that the Kir4.2R28C mutation results in loss of channel function with significant dominant-negative effects. This dysfunction is partially attributed to the substantial reduction in overall mutant channel protein expression compared to the wild-type (Kir4.2WT). We observed that both Kir4.2WT and Kir4.2R28C proteins undergo glycosylation during the post-translational modification process, albeit with differing protein turnover efficiencies. Furthermore, the Kir4.2R28C mutant exhibits reduced stability and compromised plasma membrane trafficking capacity compared to Kir4.2WT. These findings suggest that the Kir4.2R28C mutant has unique biomolecular and biophysical characteristics distinct from the Kir4.2WT channel, which potentially elucidates its role in the pathogenesis of PD.
Data-driven fine-grained region discovery in the mouse brain with transformers
Authors: Lee Alex Jihun , Dubuc Alma , Kunst Michael , Yao Shenqin , Lusk Nicholas , Ng Lydia , Zeng Hongkui , Tasic Bosiljka , Abbasi-Asl Reza
Published: May 2024

Spatial transcriptomics offers unique opportunities to define the spatial organization of tissues and organs, such as the mouse brain. We address a key bottleneck in analysis of organ-scale spatial transcriptomic data by establishing a workflow for self-supervised spatial domain detection that is scalable to multimillion cell datasets. This workflow uses a self-supervised framework for learning latent representations of tissue spatial domains or niches. We use a novel encoder-decoder architecture, which we named CellTransformer, to hierarchically learn higher-order tissue features from lower-level cellular and molecular statistical patterns. Coupling our representation learning workflow with minibatched GPU-accelerated clustering algorithms allows us to scale to multi-million cell MERFISH datasets where other methods cannot. CellTransformer is effective at integrating cells across tissue sections, identifying domains highly similar to ones in existing ontologies such as Allen Mouse Brain Common Coordinate Framework (CCF) while allowing discovery of hundreds of uncataloged areas with minimal loss of domain spatial coherence. CellTransformer domains recapitulate previous neuroanatomical studies of areas in the subiculum and superior colliculus, and characterize putatively uncataloged subregions in subcortical areas which currently lack subregion annotation. CellTransformer is also capable of domain discovery in whole-brain Slide-seqV2 datasets. Our workflows enable complex multi-animal analyses, achieving nearly perfect consistency of up to 100 spatial domains in a dataset of four individual mice with nine million cells across more than 200 tissue sections. CellTransformer advances the state of the art for spatial transcriptomics, by providing a performant solution for detection of fine-grained tissue domains from spatial transcriptomics data.
Advancing microRNA Target Site Prediction with Transformer and Base-Pairing Patterns
Authors: Bi Yue , Li Fuyi , Wang Cong , Pan Tong , Davidovich Chen , Webb Geoffrey I. , Song Jiangning
Published: May 2024

Micro RNAs (miRNAs) are short non-coding RNAs involved in various cellular processes, playing a crucial role in gene regulation. Identifying miRNA targets remains a central challenge and is pivotal for elucidating the complex gene regulatory networks. Traditional computational approaches have predominantly focused on identifying miRNA targets through perfect Watson-Crick base pairings within the seed region, referred to as canonical sites. However, emerging evidence suggests that perfect seed matches are not a prerequisite for miRNA-mediated regulation, underscoring the importance of also recognizing imperfect, or non-canonical, sites. To address this challenge, we propose Mimosa, a new computational approach that employs the Transformer framework to enhance the prediction of miRNA targets. Mimosa distinguishes itself by integrating contextual, positional, and base-pairing information to capture in-depth attributes, thereby improving its predictive capabilities. Its unique ability to identify non-canonical base-pairing patterns makes Mimosa a standout model, reducing the reliance on pre-selecting candidate targets. Mimosa achieves superior performance in gene-level predictions and also shows impressive performance in site-level predictions across various non-human species through extensive benchmarking tests. To facilitate research efforts in miRNA targeting, we have developed an easy-to-use web server for comprehensive end-to-end predictions, which is publicly available athttp://monash.bioweb.cloud.edu.au/Mimosa/.
TACTILE EDGES AND MOTION VIA PATTERNED MICROSTIMULATION OF THE HUMAN CORTEX
Authors: Valle Giacomo , Alamari Ali H. , Lienkämper Robin , Downey John E. , Sobinov Anton R. , Endsley Linnea J. , Prasad Dillan , Boninger Michael L. , Collinger Jennifer L. , Warnke Peter C. , Hatsopoulos Nicholas G. , Miller Lee E. , Gaunt Robert A. , Greenspon Charles M. , Bensmaia Sliman J.
Published: May 2024

Intracortical microstimulation (ICMS) of somatosensory cortex evokes tactile sensations whose location and properties can be systematically manipulated by varying the electrode and stimulation parameters1–3. This phenomenon can be used to convey feedback from a brain-controlled bionic hand about object interactions. However, ICMS currently provides an impoverished sense of touch, limiting dexterous object manipulation and conscious experience of neuroprosthetic systems. Leveraging our understanding of how these sensory features are encoded in S14,5, we sought to expand the repertoire of ICMS-based artificial touch to provide information about the local geometry and motion of objects in individuals with paralysis. First, we simultaneously delivered ICMS through multiple, spatially patterned electrodes, adopting specific arrangements of aligned projected fields (PFs). Unprompted, the participants reported the sensation of an edge. Next, we created more complex PFs and found that participants could intuitively perceive arbitrary tactile shapes and skin indentation patterns. By delivering patterned ICMS sequentially through electrodes with spatially discontinuous PFs, we could even evoke sensations of motion across the skin, the direction and speed of which we were able to systematically manipulate. We conclude that appropriate spatiotemporal patterning of ICMS inspired by our understanding of tactile coding in S1 can evoke complex sensations. Our findings serve to push the boundaries of artificial touch, thereby enriching participants’ conscious sensory experience from simple artificial percepts to highly informative sensations that mimic natural touch.
Identifying weather patterns affecting household date palm sap consumption in Bangladesh, 2013-2016
Authors: Jackson Jules , Shanta Ireen Sultana , McKee Clifton , Luby Stephen P , Haider Najmul , Sharker Yushuf , Plowright Raina , Hudson Peter , Gurley Emily
Published: May 2024

Nipah virus spillovers via consumption of date palm sap in Bangladesh vary substantially between years and have been associated with lower winter temperatures and precipitation. However, the mechanisms driving the interannual variation and the influence of weather remain unexplained. Here we investigated the hypothesis that weather patterns change human sap consumption and explain interannual variation in observed spillovers. We analyzed responses from a nationally representative survey conducted among 10,000 households in Bangladesh in 2013-2016 on household date palm sap consumption and weather data for each division of Bangladesh, using logistic regression to examine whether sap consumption is associated with weather variability. We found significant associations of lower minimum temperatures and precipitation with increased household sap consumption during the sap harvesting season. This relationship was largely similar within all months and divisions, and strong associations of temperature (χ2(1, n =5,027) = 7.74,p< 0.01) and, independently, precipitation (χ2= 8.00,p< 0.01) remained strong after accounting for month, location, and annual sap season. Interannual variation in date palm sap consumption in Bangladesh is likely best explained by temperature and precipitation patterns, where colder, drier winter days pose a higher risk for Nipah virus spillover. The synthesis of approaches to determine the driving forces of seasonality in our study may be a valuable method for investigating seasonality in other zoonotic pathogens.
United States Life Expectancy Increased in 2023
Authors: Wetzler Harry
Published: May 2024

From 2019 to 2021 life expectancy at birth in the United States (US) declined by approximately 2.45 years to values not seen since 1996. Although life expectancy increased in 2022, the 2019 levels were not regained. Abridged life tables for 2019 to 2023 were constructed for the total US population, females, and males using mortality data from the CDC WONDER Multiple Cause of Death database and Census Bureau Vintage population estimates. Life expectancy at birth in 2023 increased approximately 1 year compared to 2022. The increase at age 65 was about 0.6 years. The increases in 2022 and 2023 replaced approximately 76% of the pandemic-era declines.
Metabolic enzymes moonlight as selective autophagy receptors to protect plants against viral-induced cellular damage
Authors: Clavel Marion , Bianchi Anita , Kobylinska Roksolana , Groh Roan , Ma Juncai , Papareddy Ranjith K. , Grujic Nenad , Picchianti Lorenzo , Stewart Ethan , Schutzbier Michael , Stejskal Karel , de la Concepcion Juan Carlos , de Medina Hernandez Victor Sanchez , Voichek Yoav , Clauw Pieter , Gunis Joanna , Durnberger Gerhard , Muelders Jens Christian , Grimm Annett , Sedivy Arthur , Erhardt Mathieu , Vyboishchikov Victoria , Gao Peng , Lechner Esther , Vantard Emilie , Jez Jakub , Roitinger Elisabeth , Genschik Pascal , Kang Byung-Ho , Dagdas Yasin
Published: May 2024

Abstract

RNA viruses co-opt the host endomembrane system and organelles to build replication complexes for infection. How the host responds to these membrane perturbations is poorly understood. Here, we explore the autophagic response ofArabidopsis thalianato three viruses that hijack different cellular compartments. Autophagy is significantly induced within systemically infected tissues, its disruption rendering plants highly sensitive to infection. Contrary to being an antiviral defense mechanism as previously suggested, quantitative analyses of the viral loads established autophagy as a tolerance pathway. Further analysis of one of these viruses, the Turnip Crinkle Virus (TCV) that hijack mitochondria, showed that despite perturbing mitochondrial integrity, TCV does not trigger a typical mitophagy response. Instead, TCV and Turnip yellow mosaic virus (TYMV) infection activates a distinct selective autophagy mechanism, where oligomeric metabolic enzymes moonlight as selective autophagy receptors and degrade key executors of defense and cell death such as EDS1. Altogether, our study reveals an autophagy-regulated metabolic rheostat that gauges cellular integrity during viral infection and degrades cell death executors to avoid catastrophic amplification of immune signaling.
Evolutionary analysis of paired box gene family and biological function exploration ofLr.Pax7in lamprey(Lethenteron reissneri)
Authors: Nurmamat Ayqeqan , Yan Zihao , Jiang Yao , Guan Haoran , Zhuang Ruyu , Zhang Shuyuan , Zhou Yuesi , Xiu Min , Pang Ya , Li Ding , Zhao Liang , Liu Xin , Han Yinglun
Published: May 2024

ThePax(paired box)gene family comprises highly conserved transcription factors that play a crucial regulatory role in embryonic development, tissue morphogenesis, and cell differentiation. The gene family comprises of nine members, namelyPax1toPax9, each exhibiting distinct functionalities and expression patterns. Among the members of the Pax family,Pax7is particularly involved in key regulatory functions related to skeletal muscle development and satellite cell biology in vertebrates. However, the precise role ofPax7and its downstream targets in jawless vertebrates such as lamprey remains relatively understudied. Therefore, investigating the expression and function of lamprey’sPaxgenes holds significant value as a model organism for understanding developmental processes, evolution, and interactions with other vertebrates. In this study, we identifiedPax7inLethentero reissneriand multiple bioinformatics analyses suggested that it may represent the ancestral gene of thePax7shared among higher vertebrates. To further elucidate the function and regulatory mechanism ofPax7, we performed transcriptome sequencing analysis after silencingLr.Pax7expression which revealed alterations in metabolic processes along with associated genes(Plcy,Jagged2,Hes,Myod,Frizzled2,etc) involved in various immune pathways(Notch, Wnt, IL-17, TNF, etc), myogenesis process, adipocyte formation process consistent with those observed in higher vertebrates. Comparative studies between lamprey and high vertebrates could provide valuable insight into understanding the functional role ofPax7and its downstream targets across diverse biological process as well as disease states.
GenomicLinks: Deep learning predictions of 3D chromatin loops in the maize genome
Authors: Schlegel Luca , Bhardwaj Rohan , Shahryary Yadollah , Demirtürk Defne , Marand Alexandre P. , Schmitz Robert J. , Johannes Frank
Published: May 2024

Gene regulation in eukaryotes is partly shaped by the 3D organization of chro]matin within the cell nucleus. Distal interactions betweencis-regulatory elements and their target genes are widespread and many causal loci underlying heritable agricultural traits have been mapped to distal non-coding elements. The biology underlying chromatin loop formation in plants is poorly understood. Dissecting the sequence features that mediate distal interactions is an important step toward identifying putative molecular mechanisms. Here, we trained GenomicLinks, a deep learning model, to identify DNA sequence features predictive of 3D chromatin interactions in maize. We found that the presence of binding motifs of specific Transcription Factor classes, especially bHLH, are predictive of chromatin interaction specificities. Using anin silicomutagenesis approach we show the removal of these motifs from loop anchors leads to reduced interaction probabilities. We were able to validate these predictions with single-cell co-accessibility data from different maize genotypes that harbor natural substitutions in these TF binding motifs. GenomicLinks is currently implemented as an open-source web tool, which should facilitate its wider use in the plant research community.
TRPγ regulates lipid metabolism throughDh44neuroendocrine cells
Authors: Nath Dharmendra Kumar , Dhakal Subash , Lee Youngseok
Published: May 2024

Understanding how the brain controls nutrient storage is pivotal. Transient receptor potential (TRP) channels are conserved from insects to humans. They serve in detecting environmental shifts and in acting as internal sensors. Here, we found that a TRPγ mutant exhibited inDrosophila melanogasterare required for maintaining normal lipid and protein levels. In animals, lipogenesis and lipolysis control lipid levels in response to food availability. Lipids are mostly stored as triacylglycerol in the fat bodies (FBs) ofD. melanogaster. Interestingly,trpγdeficient mutants exhibited elevated TAG levels and our genetic data indicated thatDh44neurons are indispensable for normal lipid storage but not protein storage. Thetrpγmutants also exhibited reduced starvation resistance, which was attributed to insufficient lipolysis in the FBs. This could be mitigated by administering lipase or metformin orally, indicating a potential treatment pathway. Gene expression analysis indicated thattrpγknockout downregulatedbrummer, a key lipolytic gene, resulting in chronic lipolytic deficits in the gut and other fat tissues. The study also highlighted the role of specific proteins, including neuropeptide DH44 and its receptor DH44R2 in lipid regulation. Our findings provide insight into the broader question of how the brain and gut regulates nutrient storage.
Phenomics demonstrates cytokines additive induction of epithelial to mesenchymal transition
Authors: Boché Alphonse , Morel Mathieu , Kellouche Sabrina , Carreiras Franck , Lambert Ambroise
Published: May 2024

Epithelial to Mesenchymal Transition (EMT) is highly plastic with a program where cells lose adhesion and become more motile. EMT heterogeneity is one of the factors for disease progression and chemoresistance in cancer. Omics characterizations are costly and challenging to use. We developed single cell phenomics with easy to use wide-field fluorescence microscopy. We analyse over 70000 cells and combined 51 features. Our simplistic pipeline allows efficient tracking of EMT plasticity, with a single statistical metric. We discriminate four high EMT plasticity cancer cell lines along the EMT spectrum. We test two cytokines, inducing EMT in all cell lines, alone or in combination. The single cell EMT metrics demonstrate the additive effect of cytokines combination on EMT independently of cell line EMT spectrum. Single cell phenomics is uniquely suited to characterize the cellular heterogeneity in response to complex microenvironment, and show potential for drug testing assays.
PS Poly: A chain tracing algorithm to determine persistence length and categorize complex polymers by shape
Authors: Conley Elizabeth A. , Schaefer Katherine G. , Davison Harrison C. , King Gavin M.
Published: May 2024

The fundamental molecules of life are polymers. Prominent examples include nucleic acids and proteins, both of which assume a vast array of mechanical properties and three-dimensional shapes. The persistence length represents a numerical value to classify the bending rigidity of individual polymers. The shape of a polymer, dictated by the topology of the polymer backbone - a line trace through the center of the polymer along the contour path – is also a critical metric. Common architectures include linear, ring-like or cyclic, and branched; combinations of these can also exist, as in complex polymer networks. Determination of persistence length and shape are largely informative to polymer function and stability in biological environments. Here we demonstrate PS Poly, a near-fully automated algorithm to obtain polymer persistence length and shape from single molecule images obtained in physiologically relevant fluid conditions via atomic force microscopy. The algorithm, which involves image reduction via skeletonization followed by end point and branch point detection via filtering, is capable of rapidly analyzing thousands of polymers with subpixel precision. Algorithm outputs were verified by analysis of deoxyribose nucleic acid, a very well characterized macromolecule. The utility of method was further demonstrated by application to a recently discovered polypeptide chain named candidalysin. This toxic protein segment polymerizes in solution and represents the first human fungal pathogen yet discovered. PS poly is a robust and general algorithm. It can be used to extract fundamental information about polymer backbone stiffness, shape, and more generally, polymerization mechanisms.
BinBencher: Fast, flexible and meaningful benchmarking suite for metagenomic binning
Authors: Nissen Jakob Nybo , Lindéz Pau Piera , Rasmussen Simon
Published: May 2024

New methods for metagenomic binning are typically evaluated using benchmarking software, and become tuned to maximize whatever criterion is measured by the benchmark. Subtleties in benchmarking procedures can cause misleading evaluations, derailing method development. Differences between procedures used to evaluate binning tools make them hard to compare, which slows progress in the field. We introduce BinBencher, a free software suite for benchmarking, and show how BinBencher produces evaluations that are more biologically meaningful than alternative benchmarking approaches.
ELONGATED HYPOCOTYL 5 (HY5) and POPEYE (PYE) Regulate Intercellular Iron Transport in Plants
Authors: Mankotia Samriti , Dubey Abhishek , Jakhar Pooja , Satbhai Santosh B.
Published: May 2024

Plants maintain iron (Fe) homeostasis under varying environmental conditions by balancing processes such as Fe uptake, transport, and storage. In Arabidopsis, POPEYE (PYE), a basic helix-loop-helix (bHLH) transcription factor (TF), has been shown to play a crucial role in regulating this balance. In recent years, the mechanisms regulating Fe uptake have been well established but the upstream transcriptional regulators of Fe transport and storage are still poorly understood. In this study, we report that ELONGATED HYPOCOTYL5 (HY5), a basic leucine zipper (bZIP) TF which has recently been shown to play a crucial role in Fe homeostasis, interacts with PYE. Molecular, genetic and biochemical approaches revealed that PYE and HY5 have overlapping as well as some distinct roles in regulation of Fe deficiency response. We found that HY5 and PYE both act as a repressor of Fe transport genes such asYSL3, FRD3 NPF5.9, YSL2, NAS4,andOPT3. HY5 was found to directly bind on the promoter of these genes and regulate intercellular Fe transport. Further analysis revealed that HY5 and PYE directly interact at the same region onPYEandNAS4promoter. Overall, this study revealed that HY5 regulates Fe homeostasis by physically interacting with PYE as well as independently.
Communicating mass spectrometry quality information in mzQC with Python, R, and Java
Authors: Bielow Chris , Hoffmann Nils , Jimenez-Morales David , Van Den Bossche Tim , Vizcaíno Juan Antonio , Tabb David L. , Bittremieux Wout , Walzer Mathias
Published: May 2024

Mass spectrometry is a powerful technique for analyzing molecules in complex biological samples. However, inter- and intra-laboratory variability and bias can affect the data due to various factors, including sample handling and preparation, instrument calibration and performance, and data acquisition and processing. To address this issue, the Quality Control (QC) working group of the Human Proteome Organization’s Proteomics Standards Initiative has established the standard mzQC file format for reporting and exchanging information relating to data quality. mzQC is based on the JavaScript Object Notation (JSON) format and provides a lightweight yet versatile file format that can be easily implemented in software. Here, we present open-source software libraries to process mzQC data in three programming languages: Python, using pymzqc; R, using rmzqc; and Java, using jmzqc. The libraries follow a common data model and provide shared functionality to operate on mzQC files, including the (de)serialization and validation of mzQC files. We demonstrate use of the software libraries for extracting, analyzing, and visualizing QC metrics from different sources and show how these libraries can be integrated with each other, with existing software tools, and in automated workflows for the QC of mass spectrometry data. All software libraries are available as open source under the MS-Quality-Hub organization on GitHub (https://github.com/MS-Quality-Hub).
The Mycobacterium lipid transporter MmpL3 is dimeric in detergent solution, SMALPs and reconstituted nanodiscs
Authors: Cioccolo Sara , Barritt Joseph D. , Pollock Naomi , Hall Zoe , Babuta Julia , Sridhar Pooja , Just Alicia , Morgner Nina , Dafforn Tim , Gould Ian , Byrne Bernadette
Published: May 2024

The mycobacterial membrane protein large 3 (MmpL3) transports key precursor lipids to the outer membrane of Mycobacterium species. Multiple structures of MmpL3 from bothM. tuberculosisandM. smegmatisin various conformational states indicate that the protein is both structurally and functionally monomeric. However, most other resistance, nodulation and cell division (RND) transporters structurally characterised to date are either dimeric or trimeric. Here we present an in depth biophysical and computational analysis revealing that MmpL3 fromM. smegmatisexists as a dimer in a variety of membrane mimetic systems (SMALPs, detergent-based solution and nanodiscs). Sucrose gradient separation of MmpL3 populations fromM. smegmatis,reconstituted into nanodiscs, identified monomeric and dimeric populations of the protein using laser induced liquid bead ion desorption (LILBID), a native mass spectrometry technique. Preliminary cryo-EM analysis confirmed that MmpL3 forms physiological dimers. Untargeted lipidomics experiments on membrane protein co-purified lipids revealed PE and PG lipid classes were predominant. Molecular dynamics simulations, in the presence of physiologically-relevant lipid compositions revealed the likely dimer interface.
MicroRNA Tae-miR1130p targets wheat ferroportin1 (TaFPN1) in the absence of iron-responsive element/iron-regulatory protein1 module
Authors: Sharma Shivani , Joon Riya , Singh Ajit Pal , Tyagi Deekshikha , Kaur Gazaldeep , Pandey Ajay Kumar
Published: May 2024

Ferroportin (FPN) belongs to the Major Facilitator Superfamily of transporters and is a known iron (Fe) exporter in humans, with orthologues also present in plant species. Human FPN is subjected to multi-level regulation at transcriptional, post-transcriptional, and post-translational levels. How plant FPNs are regulated remains to be explored. In the current study, we have characterized wheat FPN1, a plasma-membrane localized protein, for its role in Fe homeostasis. A spatial-temporal expression analysis of wheat FPN1 suggested that its tissue-specific expression is differentially upregulated during Fe deficiency conditions. Unlike human FPN, plant FPN lacks the necessary sites for hepcidin binding, thereby emphasizing the need to explore the transcriptional/post-transcriptional mode of regulation. The lack of Iron Responsive Elements (IRE) inTaFPN1promoter suggests no direct regulation through the Iron Regulatory Protein (IRP) mechanism like in humans. Further, to explore the miRNA-mediated regulation, we identified Fe-regulatedtae-miR1130b-3pcapable of targetingTaFPN1underin-vivoconditions. Transcript expression oftae-miR1130b-3pnegatively correlates with theTaFPN1. This alternative regulation pathway suggests a complex network of interactions governing the expression of genes involved in iron homeostasis, highlighting the intricacies of cellular regulatory mechanisms. Altogether, the work will unravel the cellular and physiological role of wheat FPN and contribute to a comprehensive understanding of plant iron homeostasis.
Neuromechanical Phase Lags and Gait Adaptation in the NematodeC. elegans
Authors: Pierce Christopher J. , Ding Yang , Chong Baxi , Lu Hang , Goldman Daniel I.
Published: May 2024

Undulation is a locomotor strategy in which waves of bending propagate along the body.This form of locomotion is observed in organisms that span orders of magnitude in size and represent diverse habitats and species. Despite this diversity, common neuromechanical phenomena have been observed across biologically disparate undulators, due to common mechanics. For example, Neuromechanical Phase Lags (NPL), a phenomenon where waves of muscle contraction travel at different speeds than body bends, have been observed in fish, lamprey and lizards. Existing theoretical descriptions of this phenomenon implicate the role of physical body-environment interactions. However, systematic experimental variation of body-environment interactions and measurement of the corresponding phase lags has not been performed. Using the nematodeCaenorhabditis eleganswe measured muscle and body curvature dynamics simultaneously, performing calcium imaging in the body wall muscles while systematically varying the environmental rheology. A mechanical model demonstrates that the measured phase lags are controlled by the relative strength of elastic torques within the body and resistive forces within the medium. We further show that the phase lags correspond with a difference in the wavenumber of the muscle activity and curvature patterns. Hence, the environmental forces that create NPL also act as a filter that shapes and modulates the gait commanded by the nervous system. Beyond nematodes, the simplicity of our model further suggests that tuning body elasticity may serve as a general means of modulating the degree of mechanical control in other undulators.
The major nucleoid-associated protein WHIRLY1 promotes chloroplast development in barley
Authors: Krupinska Karin , Eirich Jürgen , Repnik Urska , Desel Christine , Nia Monireh Saeid , Schäfer Anke , Voigt Ulrike , Bennewitz Bationa , Bilger Wolfgang , Finkemeier Iris , Hensel Götz
Published: May 2024

WHIRLY1 is a DNA-binding protein of high abundance in chloroplast nucleoids, which have a complex proteome consisting of proteins involved in gene expression and unexpected proteins indicating links to energy production and biosynthetic activities of chloroplasts. In addition, WHIRLY1 has a second localization in the nucleus making it an excellent candidate for chloroplast-to-nucleus communication. To unravel the role of WHIRLY1 for structure and protein composition of nucleoids and its potential involvement in retrograde signaling during chloroplast development, knockout mutants ofHvWHIRLY1were prepared by site-directed mutagenesis using Cas9 endonuclease. In contrast to mutants of rice and maize, which die after the seedling stage, the barleywhy1mutants survive and produce grains. Leaves of the mutants are initially pale and get green with time (xantha-to-greenphenotype). However, the chlorophyll content of primary leaves stayed distinctly lower than that of the wild-type leaves, coinciding with a rather heterogeneous plastid population, whereby only 50% developed a rather normal thylakoid membrane system. For comparison, mature foliage leaves had almost normal levels of chlorophyll but a severely reduced photosynthetic capacity.

A proteome analysis of chloroplasts isolated from mature foliage leaves revealed that in the absence of WHIRLY1, the abundances of a considerable fraction of proteins were downregulated. The fraction included multiple nucleoid-associated proteins including components of the transcriptional apparatus. Furthermore, ribosomal proteins, subunits of pyruvate dehydrogenase, CLP protease, ATP synthase, Rubisco and chaperons/chaperonins were found to be downregulated.

In conclusion, the characterization of the barleywhy1mutant plants revealed that WHIRLY1 is not essential for chloroplast development. Rather, it ensures a fast and failure-free progression of chloroplast development by remodeling nucleoids, which serve as assembly platforms for a concerted workflow of the numerous processes required for chloroplast development. Gene expression analyses revealed that the disturbance of chloroplast development is signaled to the nucleus, indicating that WHIRLY1 is not part of the biogenic retrograde signaling of plastids.