bluuebunny/crossref_metadata_2025_split huggingface dataset:
Chromosome evolution in Lepidoptera
Authors: Wright Charlotte J. , Stevens Lewis , Mackintosh Alexander , Lawniczak Mara , Blaxter Mark 
Published: May 2023

AbstractChromosomes are a central unit of genome organisation. One tenth of all described species on Earth are Lepidoptera, butterflies and moths, and these generally possess 31 holocentric chromosomes. However, a subset of lepidopteran species display dramatic variation in chromosome counts. By analysing 210 chromosomally-complete lepidopteran genomes, the largest analysis of eukaryotic chromosomal-level reference genomes to date, we show that the diverse karyotypes of extant species are derived from 32 ancestral linkage groups, which we term Merian elements. Merian elements have remained largely intact across 250 million years of evolution and diversification. Against this stable background, we identify eight independent lineages that have evaded constraint and undergone extensive reorganisation - either by numerous fissions or a combination of fusion and fission events. Outside these lineages, fusions are rare and fissions are rarer still. Fusions tend to involve small, repeat-rich Merian elements and/or the Z chromosome. Together, our results reveal the constraints on genome architecture in Lepidoptera and enable a deeper understanding of the importance of chromosomal rearrangements in shaping the evolution of eukaryotic genomes.
Transcriptomic profiling reveals host-specific evolutionary pathways promoting enhanced fitness in the plant pathogenRalstonia pseudosolanacearum
Authors: Gopalan-Nair Rekha , Jardinaud Marie-Françoise , Legrand Ludovic , Lopez-Roques Céline , Bouchez Olivier , Genin Stéphane , Guidot Alice 
Published: May 2023

AbstractThe impact of host diversity on the genotypic and phenotypic evolution of broad-spectrum pathogens is a remaining issue. Here, we used populations of the plant pathogenRalstonia pseudosolanacearumthat were experimentally evolved on five types of host plants, either belonging to different botanical families or differing in their susceptibility or resistance to the pathogen. We investigated whether changes in transcriptomic profiles dissociated from genetic changes could occur during the process of host adaptation, and whether transcriptomic reprogramming was dependent on host type. Genomic and transcriptomic variations were established for 31 evolved clones that showed a better fitness in their experimental host than the ancestral clone. Few genomic polymorphisms were detected in these clones, but significant transcriptomic variations were observed, with a high number of differentially expressed genes (DEGs). In a very clear way, a group of genes belonging to the network of regulation of the bacterial virulence such asefpR, efpHorhrpB, among others, were deregulated in several independent evolutionary lineages and appeared to play a key role in the transcriptomic rewiring observed in evolved clones. A double hierarchical clustering based on the 400 top DEGs for each clone revealed two major patterns of gene deregulation that depend on host genotype, but not on host susceptibility or resistance to the pathogen. This work therefore highlights the existence of two major evolutionary paths that result in a significant reorganization of gene expression during adaptive evolution and underscore clusters of co-regulated genes associated to bacterial adaptation on different host lines.Data summaryThe authors confirm all supporting data, code and protocols have been provided within the article or through supplementary data files.
Giants among Cnidaria: large nuclear genomes and rearranged mitochondrial genomes in siphonophores
Authors: Ahuja Namrata , Cao Xuwen , Schultz Darrin T. , Picciani Natasha , Lord Arianna , Shao Shengyuan , Burdick David R. , Haddock Steven H.D. , Li Yuanning , Dunn Casey W 
Published: May 2023

AbstractSiphonophores (Cnidaria:Hydrozoa) are abundant predators found throughout the ocean and are important components in worldwide zooplankton. They range in length from a few centimeters to tens of meters. They are gelatinous, fragile, and difficult to collect, so many aspects of the biology of these 190 species remain poorly understood. To survey siphonophore genome diversity, we performed Illumina sequencing of 32 species sampled broadly across the phylogeny. Sequencing depth was sufficient to estimate nuclear genome size from k-mer spectra in 8 specimens, ranging from 0.7-4.8Gb. In 6 specimens we got heterozygosity estimates between 0.7-5.3%. Rarefaction analyses indicate k-mer peaks can be absent with as much as 30x read coverage, suggesting minimum genome sizes range from 1.0-3.8Gb in the remaining 27 samples without k-mer peaks. This work confirms most siphonophore nuclear genomes are large, but also identifies several with reduced size that are tractable targets for future siphonophore nuclear genome assembly projects. We also assembled mitochondrial genomes for 32 specimens from these new data, indicating a conserved gene order among Hydrozoa, Cystonectae and some Physonectae, also revealing the ancestral gene organization of siphonophores. There then was extensive rearrangement of mitochondrial genomes within other physonects and in Calycophorae, including the repeated loss of atp8. Though siphonophores comprise a small fraction of cnidarian species, this survey greatly expands our understanding of cnidarian genome diversity. This study further illustrates both the importance of deep phylogenetic sampling and the utility of Illumina genome skimming in understanding genomic diversity of a clade.SignificanceDescriptions of basic genome features, such as nuclear genome size and mitochondrial genome sequences, remain sparse across many clades in the tree of life, leading to over generalizations from very small sample sizes and often limiting selection of optimal species for genome assembly efforts. Here we use Illumina genome skimming to assess a variety of genome features across 35 siphonophores (Cnidaria). This deep dive within a single clade identifies six species that are optimal candidates of future genomic work, and reveals greater range in nuclear genome size and diversity of mitochondrial genome orders within siphonophores than had been described across all Cnidaria.
Identification of Region-Specific Gene Isoforms in the Human Brain Using Long-Read Transcriptome Sequencing and Their Correlation with DNA Methylation
Authors: Shimada Mihoko , Omae Yosuke , Kakita Akiyoshi , Gabdulkhaev Ramil , Miyagawa Taku , Honda Makoto , Fujimoto Akihiro , Tokunaga Katsushi 
Published: May 2023

AbstractBackgroundSite specificity is known in neuropsychiatric disorders, and differences in gene expression patterns could potentially explain this mechanism. However, studies using long-read transcriptome sequencing to analyze gene expression in different regions of the human brain have been limited, and none have focused on the hypothalamus, which plays a crucial role in regulating autonomic functions.ResultsWe performed long-read RNA sequencing on 12 samples derived from three different brain regions of the same individuals; the cerebellum, hypothalamus, and temporal cortex. We found that, compared to other regions, many genes with higher expression levels in the cerebellum and temporal cortex were associated with neuronal pathways, whereas those with higher expression levels in the hypothalamus were primarily linked to immune pathways. In addition, we investigated genes with different major isoforms in each brain region, even with similar overall expression levels among regions, and identified several genes, such asGAS7, that express different major isoforms in different regions. Many of these genes are involved in “actin filament-based process” and “cell projection organization” pathways, suggesting that region-dependent isoforms may have distinct roles in dendritic spine and neuronal formation in each region. Furthermore, we investigated the involvement of DNA methylation in these isoforms and found that DNA methylation may be associated with isoforms that have different first exons.ConclusionsOur results provide potentially valuable findings for future research on brain disorders and shed light on the mechanisms underlying isoform diversity in the human brain.
REPIC — an ensemble learning methodology for cryo-EM particle picking
Authors: Cameron Christopher JF , Seager Sebastian JH , Sigworth Fred J , Tagare Hemant D , Gerstein Mark B 
Published: May 2023

Cryo-EM (cryogenic electron microscopy) particle identification from micrographs (i.e., picking) is challenging due to the low signal-to-noise ratio and lack of ground truth for particle locations. Moreover, current computational methods (“pickers”) identify different particle sets, complicating the selection of the best-suited picker for a protein of interest. Here, we present REPIC, an ensemble learning methodology that uses multiple pickers to find consensus particles. REPIC identifies consensus particles by framing its task as a graph problem and using integer linear programming to select particles. REPIC picks high-quality particles when the best picker is not known a priori and for known difficult-to-pick particles (e.g., TRPV1). Reconstructions using consensus particles achieve resolutions comparable to those from particles picked by experts, without the need for downstream particle filtering. Overall, our results show REPIC requires minimal (often no) manual picking and significantly reduces the burden on cryo-EM users for picker selection and particle picking.Availabilityhttps://github.com/ccameron/REPIC
Non-invasive optical synthetization of hearing sensation in non-genetically modified animal
Authors: Tamai Yuta , Uenaka Miku , Okamoto Aya , Hosokawa Keito , Ito Yuki , Toda Koji , Hiryu Shizuko , Kobayasi Kohta I. 
Published: May 2023

AbstractBrain-machine interfaces are emerging devices that act as a medium for communication between the neural system and external software and hardware. Over the last decade, there has been a discussion on applying infrared laser stimulation to the brain-machine interfaces, including cochlear implants. Infrared lasers can selectively activate neural populations without introducing exogenous agents to tissues. This study presents the first demonstration that laser irradiation of the cochlea, a peripheral sensory organ, can elicit a clear behavioral auditory response. Mongolian gerbils (Meriones unguiculatus) were divided into two groups, each subjected to classical conditioning where a reward water delivery was predicted by either cochlear laser stimulation or sound stimulus. Laser-conditioned animals successfully learned licking behavior, with conditioned responses and behavioral properties comparable to auditory-conditioned animals. The laser-evoked response was significantly inhibited by auditory masking, and auditory-conditioned animals demonstrated stimulus generalization to laser stimulation. In a subsequent experiment, simultaneous presentation of auditory and laser stimulation induced nonlinear amplification in both auditory cortical and behavioral responses, suggesting that combining auditory and laser stimulation can enhance auditory perception beyond the effects of each stimulus alone. These findings indicate that infrared laser irradiation of the cochlea can potentially evoke and enhance auditory perception, making it a promising candidate for implementation in auditory prostheses.
Sleep-insomnia superposition: opposing brain signatures of sleep in task-based and resting-state conditions
Authors: Abdelhack Mohamed , Zhukovsky Peter , Milic Milos , Harita Shreyas , Wainberg Michael , Tripathy Shreejoy J , Griffiths John D , Hill Sean L , Felsky Daniel 
Published: May 2023

AbstractSleep and depression have a complex, bidirectional relationship, with sleep-associated alterations in brain dynamics and structure impacting a range of symptoms and cognitive abilities. Previous work describing these relationships has provided an incomplete picture by investigating only one or two types of sleep measures, depression, or neuroimaging modalities in parallel. We analyzed the correlations between task and resting-state brain-wide signatures of sleep, cognition, and depression in over 30,000 individuals. Neural signatures of insomnia and depression were negatively correlated with neural signatures of sleep duration in the task condition but positively correlated in the resting-state condition, showing that resting-state neural signatures of insomnia and depression resemble that of rested wakefulness. This was further supported by our finding of hypoconnectivity in task but hyperconnectivity in resting-state data in association with insomnia and depression This information disputes conventional assumptions about the neurofunctional manifestations of hyper– and hypo-somnia, and may explain inconsistent findings in the literature.
Skp1 proteins are structural components of the synaptonemal complex inC. elegans
Authors: Blundon Joshua , Cesar Brenda , Bae Jung Woo , Čavka Ivana , Haversat Jocelyn , Ries Jonas , Köhler Simone , Kim Yumi 
Published: May 2023

SummaryThe synaptonemal complex (SC) is a hallmark of meiotic prophase that plays a crucial role in regulating crossovers between homologous chromosomes. Here, we demonstrate that two Skp1-related proteins inC. elegans, SKR-1 and SKR-2, serve as structural components of the SC, independent of their canonical functions within the Skp1-Cul1-F-box (SCF) ubiquitin ligase complex. SKR-1 and SKR-2 localize to the central region of the SC, and synapsis requires their dimerization through a hydrophobic interface that overlaps with the binding sites for CUL-1 and F-box proteins. Usingin vitroreconstitution andin vivoanalysis of mutant proteins, we show that SKR proteins interact with the other SC proteins using their C-terminal helices to form a soluble complex, which likely represents a basic building block for SC assembly. Our findings demonstrate how conserved Skp1 proteins are repurposed as part of the SC and may provide insight into how synapsis is coupled to cell cycle progression.
The androgen receptor does not directly regulate the transcription of DNA damage response genes
Authors: Hasterok Sylwia , Scott Thomas G. , Roller Devin G. , Spencer Adam , Dutta Arun B. , Sathyan Kizhakke M , Frigo Daniel E. , Guertin Michael J. , Gioeli Daniel 
Published: May 2023

AbstractThe clinical success of combined androgen deprivation therapy (ADT) and radiation therapy (RT) in prostate cancer (PCa) created interest in understanding the mechanistic links between androgen receptor (AR) signaling and the DNA damage response (DDR). Convergent data have led to a model where AR both regulates, and is regulated by, the DDR. Integral to this model is that the AR regulates the transcription of DDR genes both at steady state and in response to ionizing radiation (IR). In this study, we sought to determine which immediate transcriptional changes are induced by IR in an AR-dependent manner. Using PRO-seq to quantify changes in nascent RNA transcription in response to IR, the AR antagonist enzalutamide, or the combination of the two, we find that enzalutamide treatment significantly decreased expression of canonical AR target genes but had no effect on DDR gene sets in PCa cells. Surprisingly, we also found that the AR is not a primary regulator of DDR genes either in response to IR or at steady state in asynchronously growing PCa cells. Our data indicate that the clinical benefit of ADT and RT is not due to the direct regulation of DDR gene transcription by AR.
Spatial Tracking Across Time (STAT): Tracking Neurons Across In-Vivo Imaging Sessions through Optimizing Local Neighborhood Motion Consistency
Authors: Gu Shijie , Mackevicius Emily L. , Fee Michale S. , Zhou Pengcheng 
Published: May 2023

Chronic calcium imaging has become a powerful and indispensable tool for analyzing the long-term stability and plasticity of neuronal activity. One crucial step of the data processing pipeline is to register individual neurons across imaging sessions, which usually extend over a few days or even months, and show various levels of spatial deformation of the imaged field of view (FOV). Previous solutions align FOVs of all sessions first and then register the same neurons according to their shapes and locations [1, 2]. However, the FOV registration is computational intensive, especially in the case of nonrigid case.Here we propose a cell tracking method that does not require FOV image registration. Specifically, the algorithmSTAT(short forStayTogether,AlignTogether, and forSpatialTrackingAcrossTime) represents neurons from two sessions as two sets of neuronal centroids, uses point set registration (PSR) to find a spatially smooth transformation to align them while assigning correspondences. The optimization method iteratively updates between the general motion and individual neuron identity tracking, an idea seen in the computer vision literatures [3, 4]. Our method can be thought of as a specialization and simplification of these more general methods to calcium imaging neuron tracking.We validate STAT on datasets with simulated nonrigid motion that is hard to motion correct without extensive manual intervention. Next, we test STAT on experimental data from singing birds collected on three different days, and observe stable song-locked activity across days. An example use case of this package is reference [5].
Hyperphosphorylated tau Inflicts Intracellular Stress Responses That Are Mitigated by Apomorphine
Authors: Song Zhenfeng , Wang Kuang-Wei , Hagar Hsiao-Tien Chien , Chen Hong-Ru , Kuan Chia-Yi , Zhang Kezhong , Kuo Min-Hao 
Published: May 2023

BackgroundAbnormal phosphorylation of the microtubule-binding protein tau in the brain is a key pathological marker for Alzheimer’s disease and additional neurodegenerative tauopathies. However, how hyperphosphorylated tau causes cellular dysfunction or death that underlie neurodegeneration remains an unsolved question critical for the understanding of disease mechanism and the design of efficacious drugs.MethodsUsing a recombinant hyperphosphorylated tau protein (p-tau) synthesized by the PIMAX approach, we examined how cells responded to the cytotoxic tau and explored means to enhance cellular resistance to tau attack.ResultsUpon p-tau uptake, the intracellular calcium levels rose promptly. Gene expression analyses revealed that p-tau potently triggered endoplasmic reticulum (ER) stress, Unfolded Protein Response (UPR), ER stress-associated apoptosis, and pro-inflammation in cells. Proteomics studies showed that p-tau diminished heme oxygenase-1 (HO-1), an ER stress associated anti-inflammation and anti-oxidative stress regulator, while stimulated the accumulation of MIOS and other proteins. P-tau-induced ER stress-associated apoptosis and pro-inflammation are ameliorated by apomorphine, a brain-permeable prescription drug widely used to treat Parkinson’s disease symptoms, and by overexpression of HO-1.ConclusionOur results reveal probable cellular functions targeted by hyperphosphorylated tau. Some of these dysfunctions and stress responses have been linked to neurodegeneration in Alzheimer’s disease. The observations that the ill effects of p-tau can be mitigated by a small compound and by overexpressing HO-1 that is otherwise diminished in the treated cells inform new directions of Alzheimer’s disease drug discovery.
Hi-Fi fMRI: High-resolution, fast-sampled and sub-second whole-brain functional MRI at 3T in humans
Authors: Franceschiello Benedetta , Rumac Simone , Hilbert Tom , Nau Matthias , Dziadosz Martyna , Degano Giulio , Roy Christopher W. , Gaglianese Anna , Petri Giovanni , Yerly Jérôme , Stuber Matthias , Kober Tobias , van Heeswijk Ruud B. , Murray Micah M. , Fornari Eleonora 
Published: May 2023

ABSTRACTFunctional magnetic resonance imaging (fMRI) is a methodological cornerstone of neuroscience. Most studies measure blood-oxygen-level-dependent (BOLD) signal using echo-planar imaging (EPI), Cartesian sampling, and image reconstruction with a one-to-one correspondence between the number of acquired volumes and reconstructed images. However, EPI schemes are subject to trade-offs between spatial and temporal resolutions. We overcome these limitations by measuring BOLD with a gradient recalled echo (GRE) with 3D radial-spiral phyllotaxis trajectory at a high sampling rate (28.24ms) on standard 3T field-strength. The framework enables the reconstruction of 3D signal time courses with whole-brain coverage at simultaneously higher spatial (1mm3) and temporal (up to 250ms) resolutions, as compared to optimized EPI schemes. Additionally, artifacts are corrected before image reconstruction; the desired temporal resolution is chosen after scanning and without assumptions on the shape of the hemodynamic response. By showing activation in the calcarine sulcus of 20 participants performing an ON-OFF visual paradigm, we demonstrate the reliability of our method for cognitive neuroscience research.
Paneth and Paneth-like cells undergoing necroptosis fuel intestinal epithelial cell proliferation following IFN-γ stimulation
Authors: Encarnacion-Garcia Maria R. , De la Torre-Baez Raul , Hernandez-Cueto Maria A. , Velázquez-Villegas Laura A. , Candelario-Martinez Aurora , Horta-López Perla H. , Montoya-García Armando , Jaimes-Ortega Gustavo Alberto , Lopez-Bailon Luis , Piedra-Quintero Zayda , Carrasco-Torres Gabriela , De Ita Marlon , del Pilar Figueroa-Corona Maria , Muñoz-Medina José Esteban , Sánchez-Uribe Magdalena , Meraz-Ríos Marco Antonio , Villa-Treviño Saúl , Garcia-Sierra Francisco , Cisneros Bulmaro , Schnoor Michael , Ortíz-Navarrete Vianney F. , Villegas-Sepúlveda Nicolás , Valle-Rios Ricardo , Medina-Contreras Oscar , Noriega Lilia G. , Nava Porfirio 
Published: May 2023

ABSTRACTThe quality of life in patients with inflammatory bowel diseases (IBD) is strongly impaired. Alterations of intestinal epithelial homeostasis contribute to the development and establishment of IBD. Intestinal Paneth and Paneth-like cells produce and secrete luminal proteins sustaining epithelial homeostasis. Here we show that IFN-γ stimulates Paneth and Paneth-like cells degranulation that triggers the proliferation of intestinal epithelial cells (IEC) in a Wnt/β-catenin independent manner. Degranulation in Paneth and Paneth-like cells was mTORC1 and necroptosis dependent. Remarkably, lack of IFN-γ, inhibition of mTORC1, or impeding necroptosis reduces IEC proliferation cytokine-mediated. Our findings identify a new role for IFN-γ in stimulating IEC proliferation through inducing degranulation of Paneth and Paneth-like cells which is mTORC1 and necroptosis- dependent. In a mouse model of colitis, mTORC1 activation and necroptosis regulate Paneth and Paneth-like cell secretion. Furthermore, the colitogenic environment triggers PC metaplasia in the distal region of the large intestine to simulate cell proliferation.Highlights:IFN-γ stimulates proliferation,β-catenin independent.IFN-γ enhances mitochondrial activity and proliferationIFN-γ regulates PC biogenesis.mTORC1-dependent necroptosis mediates secretion in Paneth and Paneth-like cells.