bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural and functional evidence supports re-defining mouse higher order visual areas into a single area V2
Authors: Rowley Declan P. , Sedigh-Sarvestani Madineh 
Published: October 2024

AbstractThe mouse has become one of the main organisms for studies of the visual system. As a result, there is increased effort to understand universal principles of visual processing by comparing the mouse visual system to that of other species. In primates and other well-studied species including cats and tree shrews, the visual cortex is parcellated into an area V1 and several higher order areas defined by structural and functional differences, and a near complete map of the visual field. In mice, the visual cortex beyond V1 is parcellated into several higher order areas, with less notable structural and functional differences, partial coverage of the visual field, and areal boundaries defined by reversals in progression of the visual field. Notably, recent work in tree shrews and primates has shown that reversals in progression of the visual field can be a hallmark of complex retinotopic mapping within a single visual area. This, and other lines of evidence discussed here, provides a compelling case that the apparent existence of multiple higher order visual areas in the mouse is related to the false assumption of simple retinotopy. Specifically, we use simulations to show that complex retinotopy within a single visual area can recapitulate the appearance of multiple areal borders beyond mouse V1. In addition, we show that many reported differences in functional properties between higher order visual areas can be better explained by retinotopic differences rather than areal identity. Our proposal to reclassify some of the higher order visual areas in the mouse into a single area V2 is not mere semantics because areal definitions influence experimental design and data analysis. Furthermore, such a reclassification would produce a common set of rules for defining areal boundaries among mammals and would bring the mouse visual system into agreement with evolutionary evidence for a single area V2 in related lineages.
CREB3gain of function variants protect against ALS
Authors: Megat Salim , Marques Christine , Hernan Godoy Marina , Sellier Chantal , Stuart-Lopez Geoffrey , Dirrig-Grosch Sylvie , Gorin Charlotte , Brunet Aurore , Fischer Mathieu , Keime Céline , Kessler Pascal , Mendoza-Parra Marco Antonio , Scholz Sonja , Ferrucci Luigi , Ludolph Albert , Traynor Bryan , Chio Adriano , Dupuis Luc , Rouaux Caroline 
Published: October 2024

AbstractAmyotrophic lateral sclerosis (ALS) is a fatal and rapidly evolving neurodegenerative disease that arises from the loss of glutamatergic corticospinal neurons (CSN) and cholinergic motoneurons (MN). The disease is mostly sporadic, but genetics is expected to highly contribute to disease onset and progression. Genome wide association studies identified a few genetic disease modifiers, mostly associated with a negative outcome, and demonstrated that ALS is primarily a disease of excitatory glutamatergic neurons. Here, we reasoned that at least a subpart of genetic disease modifiers may directly modulate the molecular pathways selectively activated in vulnerable neurons as the disease progresses, and concentrated on CSN for their selective vulnerability and glutamatergic identity. We implemented comparative cross-species transcriptomics using snRNAseq data from postmortem motor cortex of ALS patients and controls, and longitudinal RNAseq data from anatomically defined CSN purified from theSod1G86Rmouse model of ALS. We report that disease vulnerable neuronal populations undergo ER stress and altered mRNA translation, and identify the transcription factor CREB3 and its regulatory network as a resilience marker of neuronal dysfunction in ALS. Using genetic and epidemiologic analyses we further identify the rare variant CREB3R119G(rs11538707) as a new disease modifier in ALS. Through gain of function, CREB3R119Gdecreases both the risk of developing ALS and the progression rate of ALS patients. This study reveals novel genetic variants that protect against ALS and highlights the benefice of combining transcriptomics and genetics to identify new disease modifiers and therapeutic targets.
Circulating microRNAs as biomarkers of chronic kidney disease and its association with renal and cardiovascular outcomes in non-dialysis patients
Authors: Ramil-Gómez Olalla , Cerqueira Ana , Moura Sara Reis , Carvalho Eduarda , Paulo Núria , Brandão Isabel , Santos Janete , Quaranta Patricia , Sousa Maria João , Pinho Ana , Diniz Hugo , Almeida Maria Inês , Pestana Manuel , Alencastre Inês Soares 
Published: October 2024

AbstractChronic kidney disease (CKD) affects over 10% of the population worldwide and entails a significant risk for cardiovascular disease (CVD), leading to a 500-fold increase in cardiovascular mortality in advanced stages. Still, the pathophysiological mechanisms underlying kidney-heart intercommunication remain largely unknown. In recent years, microRNAs (miRNAs) emerged as important key regulators of gene expression that may serve as biomarkers for several diseases, however, their role in kidney-heart crosstalk in CKD remains underexplored. In this study, we evaluated the expression of a miRNA panel in plasma samples from non-dialysis CKD patients and explored their association with main comorbidities and significant outcomes in a 5-year follow-up. Results show that miR-30c-5p and miR-132-3p were downregulated in CKD patients presenting a significant power to discriminate the disease state. Importantly, only miR-30c-5p was downregulated in early glomerular filtration rate (GFR) categories, being able to discriminate these CKD patients from non-diseased individuals. Concerning cardiovascular outcomes, miR-199a-5p was found to be associated with an increased frequency of CVD. When analyzing the major disease outcomes in a 5-year time, miR-199a-5p upregulation at baseline was associated with increased mortality, while miR-324-3p was downregulated in patients who progressed to more advanced stages of the disease. These findings highlight the involvement of novel circulating miRNAs in CKD onset and progression, and identify, for the first time, the enrollment of miR-199a-5p in kidney-heart pathophysiological crosstalk, paving the way for the establishment of new biomarkers and therapeutic targets for CKD and its outcomes.
HighALPS: Ultra-High-Throughput Marker-Gene Amplicon Library Preparation and Sequencing on the Illumina NextSeq and NovaSeq Platforms
Authors: Flörl Lena , Cabrera Paula Momo , Moccia Maria Domenica , Plüss Serafina , Bokulich Nicholas A. 
Published: October 2024

AbstractMicrobiome research using amplicon sequencing of microbial marker genes has surged over the past decade, propelled by protocols for highly multiplexed sequencing with barcoded primer constructs. Newer Illumina platforms like the NovaSeq and NextSeq series significantly outperform older sequencers in terms of reads, output, and runtime. However these platforms are more prone to index-hopping, which limits the application of protocols designed for older platforms such as the Earth Microbiome Project (EMP) protocols, hence there is a need to adapt these established protocols. Here, we present an ultra-High-throughputAmpliconLibraryPreparation andSequencing protocol (HighALPS) incorporating the capabilities of these newer sequencing platforms, designed for both 16S rRNA gene and fungal internal transcribed spacer (ITS) domain sequencing. Our results demonstrate good run performance across different sequencing platforms and flow cells, with successful sequencing of mock communities, validating the protocol’s effectiveness. The new HighALPS library preparation method offers a robust, cost effective, and ultra-high-throughput solution for microbiome research, compatible with the latest sequencing technologies. This protocol allows multiplexing thousands of samples in a single run at a read depth of tens of millions of sequences per sample.
A collection of split-Gal4 drivers targeting conserved signaling ligands inDrosophila
Authors: Ewen-Campen Ben , Joshi Neha , Hermon Ashley Suraj , Thakkar Tanuj , Zirin Jonathan , Perrimon Norbert 
Published: October 2024

AbstractCommunication between cells in metazoan organisms is mediated by a remarkably small number of highly conserved signaling pathways. Given the relatively small number of signaling pathways, the existence of multiple related ligands for many of these pathways is thought to represent a key evolutionary innovation for encoding complexity into cell-cell signaling. Relatedly, crosstalk and other interactions between pathways is another critical feature which allows a modest number pathways to ultimately generate an enormously diverse range of outcomes. It would thus be useful to have genetic tools to identify and manipulate not only those cells which express a given signaling ligand, but also those cells that specifically co-express pairs of signaling ligands. Here, we present a collection of split-Gal4 knock-in lines targeting many of the ligands for highly conserved signaling pathways inDrosophila(Notch, Hedgehog, FGF, EGF, TGFβ, JAK/STAT, JNK, and PVR). We demonstrate that these lines faithfully recapitulate the endogenous expression pattern of their targets, and that they can be used to specifically identify the cells and tissues that co-express pairs of signaling ligands. As a proof of principle, we demonstrate that the 4th chromosome TGFβligandsmyoglianinandmaverickare broadly co-expressed in muscles and other tissues of both larva and adults, and that the JAK/STAT ligandsupd2andupd3are partially co-expressed from cells of the midgut following gut damage. Together with our previously collection of split-Gal4 lines targeting the seven Wnt ligands, this resource allowsDrosophilaresearchers to identify and genetically manipulate cells that specifically express pairs of conserved ligands from nearly all the major intercellular signaling pathways.
Escherichia coligrowth under low pH, low temperature, and high osmotic stress conditions requires thewzxEflippase for the enterobacterial common antigen intermediate
Authors: Yamaguchi Saki , Ishikawa Kazuya , Furuta Kazuyuki , Kaito Chikara 
Published: October 2024

AbstractColanic acid and enterobacterial common antigen (ECA) are cell surface polysaccharides that are produced by manyE. coliisolates. Colanic acid is induced under low pH, low temperature, and hyperosmotic conditions and is important inE. coliresistance to these stresses; however, the role of the ECA is unclear. In this study, we observed that knockout of the flippasewzxE, which converts ECA intermediates from the cytoplasmic side of the inner membrane to the periplasmic side, resulted in low pH sensitivity inE. coli. ThewzxE-knockout mutant showed reduced growth potential and viable counts in the extracts of several vegetables (cherry tomatoes, carrots, celery, lettuce, and spinach), which are known to be low pH environments. A double knockout strain ofwzxEandwecF, which encodes an enzyme that synthesizes an ECA intermediate, did not show sensitivity to low pH, nor did a double knockout mutant ofwzxEandwcaJ, which encodes a colanic acid synthase. ThewzxE-knockout mutant was sensitive to low temperature or hyperosmotic conditions, which induced colanic acid synthesis, and these sensitivities were abolished by the additional knockout ofwcaJ. These results suggest that ECA intermediates causeE. colisusceptibility to low pH, low temperature, and high osmotic pressure in a colanic acid-dependent manner, and thatwzxEsuppresses this negative effect.ImportancePolysaccharides covering bacterial cell surfaces, such as colanic acid, confer resistance to various stresses, such as low pH. However, the role of enterobacterial common antigens, carbohydrate antigens that are conserved throughout enterobacteria, in stress resistance is unclear. Our results suggest that lipid III enterobacterial common antigen, a substrate of flippase, causes sensitivity ofEscherichia colito low pH, low temperature, and high osmolarity in dependence on colanic acid synthesis, whilewzxEinhibits this negative effect. ThewzxE-knockout mutant was sensitive to crude vegetable extracts, suggesting that the creation of WzxE inhibitors could lead to new food poisoning prevention agents.
Sex-specific effects of intensity and dose of physical activity on BOLD-fMRI cerebrovascular reactivity and cerebral pulsatility
Authors: Potvin-Jutras Zacharie , Intzandt Brittany , Mohammadi Hanieh , Liu Peiying , Chen Jean J. , Gauthier Claudine J. 
Published: October 2024

AbstractCerebrovascular reactivity (CVR) and cerebral pulsatility (CP) are important indicators of cerebrovascular health and have been shown to be associated with physical activity (PA). Sex differences have been shown to influence the impact of PA on cerebrovascular health. However, the sex-specific effects of PA on CP and CVR, particularly in relation to intensity and dosage of PA, remains unknown. Thus, this cross-sectional study aimed to evaluate the sex-specific effects of different intensities and doses of PA on CVR and CP. The Human Connectome - Aging dataset was used, including 626 participants (350 females, 276 males) aged 36-85 (mean age: 58.8 ± 14.1 years). Females were stratified into premenopausal and postmenopausal groups to assess the potential influence of menopausal status. Novel tools based solely on resting state fMRI data were used to estimate both CVR and CP. The International Physical Activity Questionnaire was used to quantify weekly self-reported PA as metabolic equivalent of task. Results indicated that both sexes and menopausal subgroups revealed negative linear relationships between relative CVR and PA. Furthermore, females presented a unique non-linear relationship between relative CVR and total PA in the cerebral cortex. In females, there were also relationships with total and walking PA in occipital and cingulate regions. In males, we observed relationships between total or vigorous PA and CVR in parietal and cingulate regions. Sex-specific effects were also observed with CP, whereby females benefited across a greater number of regions and intensities than males, especially in the postmenopause group. Overall, males and females appear to benefit from different amounts and intensities of PA, with menopause status significantly influencing the effect of PA on cerebrovascular outcomes, underscoring the need for sex-specific recommendations in promoting cerebrovascular health.
The genetic basis of replicated bullseye pattern reduction across the Trionum Complex
Authors: Yeo May T. S. , Fairnie Alice L. M. , Travaglia Valentina , Walker Joseph F. , Riglet Lucie , Zeyrek Selin , Moyroud Edwige 
Published: October 2024

AbstractAngiosperm flowers exhibit a wide diversity of colorful motifs on their petals. Such patterns fulfill both biotic and abiotic functions, mediating plant-pollinator communication and providing protection against damaging UV rays or desiccation. These motifs are often evolutionary labile, varying in size, shape and hue between closely related species and constitute excellent systems to illuminate the evolutionary processes that generate morphological diversity or instead lead to the repetitive emergence of similar forms.Hibiscus trionumflowers have a prominent bullseye pattern combining a purple center contrasting against a white margin.H. trionumbelongs to a small clade ofHibiscusknown as the Trionum Complex that displays a range of petal patterns within and between species. Here, we integrate phylogenomic approaches, molecular techniques and genetic manipulation to solve species relationships across the Trionum Complex, identify key genes involved in the production of bullseye pigmentation, and reveal molecular events underpinning pattern variation during the evolution of the group. We find that repetitive bullseye reduction events primarily occur through independent modifications of a single genetic locus encoding BERRY1, an R2R3 MYB that regulates anthocyanin pigment production in petals. Moreover, we demonstrate that buff-tailed bumblebees(Bombus terrestris)discriminate against flowers with smaller bullseye sizes suggesting that a reduction in bullseye proportions potentially impacts plant fitness and contributes to trait distribution across the group. Collectively, our results demonstrate how repeated mutations in a single locus led to morphological variation in petal patterning, a trait that contributes to angiosperm reproductive isolation and speciation.
Vibrioare a potential source of novel colistin-resistance genes in European coastal environments
Authors: Saad Jamal , Boulo Viviane , Goudenège David , Broquard Coralie , Andree Karl B. , Auguste Manon , Petton Bruno , Labreuche Yannick , Tris Pablo , Furones Dolors , Gil Augusti , Vezzulli Luigi , Corno Gianluca , Di Cesare Andrea , Koechlin Hugo , Labadie-Lafforgue Emilie , Courtay Gaelle , Romatif Océane , Pouzadoux Juliette , Escoubas Jean-Michel , Munaron Dominique , Charrière Guillaume M. , Toulza Eve , Travers Marie-Agnès , Montagnani Caroline , Wegner Mathias K. , Destoumieux-Garzón Delphine 
Published: October 2024

AbstractColistin is a widespread last resort antibiotic for treatment of multidrug-resistant bacteria. The recent worldwide emergence of colistin resistance (Col-R) conferred bymcr-1 in human pathogens has raised concern, but the putative sources and reservoirs of novelmcrgenes in the marine environment remain underexplored. We observed a high prevalence of Col-R, particularly inVibrioisolated from European coastal waters by using a unique stock of specific-pathogen-free (SPF) oysters as a bioaccumulator. The high sequence diversity found in themcr/eptA gene family was geographically structured, particularly for three noveleptAgene variants, which were restricted to the Mediterranean (France, Spain) and occurred as adgkA-eptA operon controlled by the RstA/RstB two component system. By analyzing 29427Vibrionaceaegenome assemblies, we showed that this mechanism of intrinsic resistance is prevalent and specific to the Harveyi clade, which includes strains ofVibrio parahaemolyticusandVibrio alginolyticuscausing infections in humans. The operon conferred colistin-resistance when transferred to sensitive non-Vibriostrains. Whilemcr-andarn-based Col-R mechanisms were also identified, the widespread presence ofeptA gene variants inVibriosuggests they play a key role in intrinsic resistance to colistin. Beyond these ancienteptA gene copies having evolved with theVibriolineage, we also identified mobileeptA paralogues that have been recently transferred between and withinVibrioclades. This highlightsVibrioas a potential source of Col-R mechanisms, emphasizing the need for enhanced surveillance to prevent colistin-resistant infections in coastal areas.
An approach for coherent periodogram averaging of tilt-series data for improved CTF estimation
Authors: Khavnekar Sagar , Wan William 
Published: October 2024

AbstractCryo-electron microscopy (cryo-EM) has become an indispensable technique for determining three-dimensional structures of biological macromolecules. A critical aspect of achieving high-resolution cryo-EM reconstructions is accurately determining and correcting for the microscope’s contrast transfer function (CTF). The CTF introduces defocus-dependent distortions during imaging; if not properly accounted for, the CTF can distort features in and limit the resolution of 3D reconstructions. For tilt-series data used in cryo-electron tomography (cryo-ET), CTF estimation becomes even more challenging due to the tilt of the specimen, which introduces a defocus gradient across the field of view, as well as the low dose and signal in individual tilt images. Here, we describe a simple algorithm to improve the accuracy of CTF estimation of tilted images by leveraging the tilt-series alignment parameters determined for tomographic reconstruction to explicitly account for the tilted specimen geometry. In brief, each tilt image is divided into patches, each of which are then stretched according to their defocus shift. These are then summed to provide a coherent power spectra at the tilt axis, which can then be used in standard CTF estimation algorithms. This uses all the data in each image to enhance the visibility of Thon rings, thereby improving high-resolution CTF estimation and subsequent enhancements in the resolution of subtomogram averages.
The fire blight pathogenErwinia amylovoraenters apple leaves through naturally-occurring wounds from the abscission of trichomes
Authors: Millett Felicia , Standish James , Scanley Jules , Miller Katelyn , Inguagiato John , Zuverza-Mena Nubia , Abril Maritza , Robinson Victoria , Li Yan , Sundin George W. , Zeng Quan 
Published: October 2024

SUMMARYThe plant epidermis is a single layer of cells covering all plant organs. How pathogens overcome this barrier and enter plants is an important aspect of plant-pathogen interactions. For bacterial plant pathogens, known entry points include natural openings such as stomata, hydathodes, and mechanical injuries caused by insect feeding, wind damage or hailstorms.Here, we report that the fire blight pathogenErwinia amylovoraenters apple leaves through naturally-occurring wounds caused by the abscission of trichomes during the course of leaf development.Through macroscopic and microscopic observations, we depicted a clear invasion path forE. amylovoracells, from epiphytic growth on glandular trichomes (GT) and non-glandular trichomes (NT), to entry through wounds caused by abscised trichomes, into the epithem, and subsequent spread through xylem. We further observed that GT and NT undergo an abscission process, and that the amount of naturally-occurring wounds during abscission is associated with the increase inE. amylovorapopulation. Key genes important for the colonization of GT and NT were identified. Contribution of the type III secretion system and amylovoran biosynthesis during GT colonization was validated.Our findings propose a novel host entry mechanism of plant pathogenic bacteria through naturally-occurring wounds during abscission of plant surface structures.
Systematic, high-throughput characterization of bacteriophage gene essentiality on diverse hosts
Authors: Chen Jackie , Nilsen Erick D. , Chitboonthavisuk Chutikarn , Mo Charlie Y. , Raman Srivatsan 
Published: October 2024

AbstractUnderstanding core and conditional gene essentiality is crucial for decoding genotype-phenotype relationships in organisms. We present PhageMaP, a high-throughput method to create genome-scale phage knockout libraries for systematically assessing gene essentiality in bacteriophages. Using PhageMaP, we generate gene essentiality maps across hundreds of genes in the model phage T7 and the non-model phage Bas63, on diverse hosts. These maps provide fundamental insights into genome organization, gene function, and host-specific conditional essentiality. By applying PhageMaP to a collection of anti-phage defense systems, we uncover phage genes that either inhibit or activate eight defenses and offer novel mechanistic hypotheses. Furthermore, we engineer synthetic phages with enhanced infectivity by modular transfer of a PhageMaP-discovered defense inhibitor from Bas63 to T7. PhageMaP is generalizable, as it leverages homologous recombination, a universal cellular process, for locus-specific barcoding. This versatile tool advances bacteriophage functional genomics and accelerates rational phage design for therapy.