bluuebunny/crossref_metadata_2025_split huggingface dataset:
A parent-of-origin effect on embryonic telomere elongation determines telomere length inheritance
Authors: Jeon Hyuk-Joon , Levine Mia T. , Lampson Michael A. 
Published: January 2025

SummaryTelomere length is inherited directly as a DNA sequence and as a classic quantitative trait controlled by many genes across the genome. Here, we show that neither paradigm fully accounts for telomere length inheritance, which also depends on a parent-of-origin effect on telomere elongation in the early embryo. By reciprocally crossing mouse strains with different telomere lengths, we find that telomeres elongate in hybrid embryos only when maternal telomeres are short and paternal telomeres are long. In the reciprocal cross, telomeres shorten. These differences in embryonic telomere elongation, which emerge before zygotic genome activation, predict adult telomere length. Moreover, when telomeres do elongate, we find molecular signatures of a recombination-based mechanism of telomere elongation, called the Alternative Lengthening of Telomeres (ALT) pathway, previously suggested to elongate telomeres in the pre-implantation embryo. We propose that ALT is triggered by a combination of genetic asymmetry in telomere length and epigenetic asymmetry between maternal and paternal chromosomes in the zygote. Our findings offer new insight into the complex interaction of genetic and epigenetic determinants of telomere length inheritance.
The application of metagenomics in the detection of arboviruses in mosquitoes (Diptera: Culicidade). A systematic review
Authors: David Everson dos Santos , Komninakis Shirley Vasconcelos , da Costa Fonseca Erique , da Silva Soledade Anne Caroline , Carmo dos Santos Karen , Picanço Souto Raimundo Nonato 
Published: January 2025

ABSTRACTAdvances in deforestation and climate change directly imply changes in habits and the distribution of Culicidae across the globe, especially mosquitoes of medical importance and the main vectors of arboviruses. The viral metagenomics technique can be an important tool in characterizing the viral diversity present in mosquitoes. Thus, the aim was to identify evidence of the effectiveness of the viral metagenomics technique in detecting arboviruses in mosquitoes. This is a systematic review based on the PRISMA 2020 protocol. The research was carried out in five electronic databases: LILACS, PubMed, SciELO, Scopus and Web of Science, chosen to include studies published in health and interdisciplinary areas, as well as a complementary research on Google Scholar. Studies that used the viral metagenomics approach for the genomic evaluation of arboviruses found in mosquito samples were included, where the results demonstrated the presence of viral diversity and the identification of the genome of probable pathogenic viruses. The protocol was registered on the PROSPERO platform under the number CRD42024484713. 238 studies published in recent years were identified in the electronic databases. According to the inclusion/exclusion criteria, only 20 studies met the objectives for the systematic review. In all the studies, the viral metagenomics technique of genomic sequencing was applied to detect viruses, mainly those related to specific insect viruses, arboviruses, pathogenic viruses, animal viruses and plant viruses belonging to various viral families. Despite the challenges to be overcome in terms of the absence of reference sequences in genomic databases, the effectiveness of the metagenomics technique in characterizing the mosquito virome is clear from the studies, which broadens the understanding of viral diversity.
Single-cell transcriptional profiling reveals a novel RAB13+endothelial subpopulation and profibrotic mesenchymal cells in the aged human bone marrow
Authors: Cenzano Itziar , Cócera Miguel , Lopez-Perez Ana Rosa , Campos-Dopazo Lorea , Ruiz Javier , Sancho Ignacio , Martin-Uriz Patxi San , Sarvide Sarai , Aguirre-Ruiz Paula , Vilas-Zornoza Amaia , Ripalda-Cemborain Purificacion , Alignani Diego , Lopez Aitziber , Barrios Marta Miñana , Agreda Delia Quilez , Ye Jin , Lehmann Robert , Sudupe Laura , Abengozar-Muela Marta , Tamariz-Amador Luis-Esteban , Muiños-López Emma , Saez Borja , Tegner Jesper , Calvo Isabel A. , Gomez-Cabrero David , Prosper Felipe 
Published: January 2025

ABSTRACTThe bone marrow (BM) microenvironment plays a crucial role in regulating hematopoiesis, yet the molecular and functional changes associated with aging in humans remain poorly understood. Using single-cell RNA sequencing (scRNA-seq), we uncovered transcriptional shifts in BM endothelial cells (EC) and mesenchymal stem cells (MSC) during aging. Our analysis revealed that aged sinusoidal EC adopt a prothrombotic, exhibit mitochondrial dysfunction, and have compromised vascular function. Additionally, we identified a unique arterial EC subset, present only in aged individuals, associated with transcriptional elongation and senescence processes and characterized byRAB13expression. MSC from aged subjects displayed an impaired matrix remodeling and epithelial-mesenchymal transition, driven partly by a subpopulation of THY1+profibrotic stromal cells absent in young subjects. Aged MSC were also characterized by an increased ATP-oxidative metabolism and reduced protein folding capacity. Finally, using immunofluorescent imaging and spatial transcriptomics, we confirmed the presence of RAB13+senescent EC in aged samples and revealed significant age-related changes in cell-cell communication within the BM niche. In summary, this work provides a comprehensive view of the molecular diversity, cellular interactions, and spatial organization of aged EC and MSC, offering novel insights and potential targets that could be exploited for preventing aged-associated changes in humans.
Morphology and distribution of a new scale mechanoreceptor type in olive-headed sea snakes (Hydrophis major)
Authors: Wagner Alizée , Johnson Chad , Ha Myoung Hoon , Sanders Kate L. , Collin Shaun P. , Crowe-Riddell Jenna M. 
Published: January 2025

ABSTRACTSnakes are known for their superb sensory specialisations but are not widely appreciated for their sense of touch despite emerging evidence of tactile specialisation among sea snakes. This is partly due to the challenges in quantifying such small and numerous scale mechanoreceptors or ‘scale sensilla’ across individuals. By using a novel application of gel-based 3D profilometry (GelSight scanner) in combination with scanning electron-and light microscopy, we comprehensively quantified the morphology and distribution of scale mechanoreceptors in a sea snake,Hydrophis major(Hydrophiinae), for the first time. We discovered a new type of scale mechanoreceptor distinguished by its larger size (43.65 ± 22.57 μm height) and asymmetrical peak shape, created by a thickening in the cornified outer layers of the epidermis. Asymmetrical peaks contain a dermal papilla with central cells, indicative of meissner-like corpuscles that underlie smooth dome-shaped mechanoreceptors (31.88 ± 19.03 μm height) typically found in both sea snakes, but is positioned slightly off centre from the tallest point of the asymmetrical peak. Smooth domes are concentrated anterior-posteriorly on the head with the highest densities on the rostrum and nasal scales (9.83 ± 1.88 and 5.24 ± 2.85 per mm², respectively). Asymmetrical peaks are rarer; detected only on the dorsal and lateral sides of the head and most common on the postocular scale (mean density 1.26 ± 0.72 per mm²). We suggest functional differences in mechanosensory capabilities: asymmetrical peaks may serve primarily proprioceptive purposes whereas smooth domes are used for hydrodynamic reception.
ScaleSC: A superfast and scalable single cell RNA-seq data analysis pipeline powered by GPU
Authors: Hu Wenxing , Zhang Haotian , Sun Yu H. , Cao Shaolong , Gagnon Jake , Ouyang Zhengyu , Moroishi Yuka , Zhang Baohong 
Published: January 2025

AbstractThe rise of large-scale single-cell RNA-seq data has introduced challenges in data processing due to its slow speed. Leveraging advancements in GPU computing ecosystems, such as CuPy, and building on Scanpy and rapids-singlecell package, we developed ScaleSC, a GPU-accelerated solution for single-cell data processing. ScaleSC delivers over a 20x speedup through GPU computing and significantly improves scalability, handling datasets of 10–40 million cells with over 1000 batches by overcoming the memory bottleneck on a single A100 card- far surpassing rapids-singlecell’s capacity of processing only 1 million cells without multi-GPU support. We also resolved discrepancies between GPU and CPU algorithm implementations to ensure consistency. In addition to core optimizations, we developed new advanced tools for marker gene identification, cluster merging, and more, with GPU-optimized implementations seamlessly integrated. Designed for ease of use, the ScaleSC package is compatible with Scanpy workflows, requiring minimal adaptation from users. The ScaleSC package (https://github.com/interactivereport/ScaleSC) promises significant benefits for the single-cell RNA-seq computational community.
Towards Multi-Brain Decoding in Autism: A Self-Supervised Learning Approach
Authors: Ranjabaran Ghazaleh , Moreau Quentin , Dubois Adrien , Dumas Guillaume 
Published: January 2025

AbstractThis study introduces a self-supervised learning (SSL) approach to hyperscanning electroencephalography (EEG) data, targeting the identification of autism spectrum condition (ASC) during social interactions. Hyperscanning enables simultaneous recording of neural activity across interacting individuals, offering a novel path for studying brain-to-brain synchrony in ASC. Leveraging a large-scale, single-brain EEG dataset for SSL pretraining, we developed a multi-brain classification model fine-tuned with hyperscanning data from dyadic interactions involving ASC and neurotypical participants. The SSL model demonstrated superior performance (78.13% accuracy) compared to supervised baselines and logistic regression using spectral EEG biomarkers. These results underscore the efficacy of SSL in addressing the challenges of limited labeled data, enhancing EEG-based diagnostic tools for ASC, and advancing research in social neuroscience.
The heritability of migration behaviours in a wide-ranging ungulate
Authors: Bonar Maegwin , Wootton Eric , Anderson Charles R. , Wittemyer George , Northrup Joseph M. , Shafer Aaron B. A. 
Published: January 2025

AbstractMigration behaviour is thought to be declining globally in the face of rapid human-mediated environmental change. While many species exhibit individual plasticity in their migratory behaviour, not all species demonstrate the level of plasticity necessary to adjust to novel conditions. Selection on heritable behaviours might therefore play an important role in the maintenance of migratory phenotypes for some species. Using GPS and genomic data from 242 individuals (256 animal-years) in a pedigree-free quantitative genetic approach, we estimated heritability, repeatability, and sources of environmental variation for migration traits in migrating mule deer (Odocoileus hemionus). We also estimated heritability of body size to ensure validity of our results. Heritability estimates of body size traits were comparable to the current estimates for ungulate body size. We found low heritability for broad patterns of migration timing, distance, and duration, but high heritability for movement rate along the migratory route. Our findings suggest that wild mule deer populations have the potential to respond to selection pressure generated by human activity or global environmental changes through microevolutionary changes in migration behaviours.Significance StatementMigration behaviour is critical for the reproduction and survival of a wide variety of taxa, yet there have been global declines in migrations in the face of rapid human-mediated environmental change. Despite our understanding that variation in migration behaviour has both genetic and environmental components, studies quantifying the sources of genetic variation contributing to migration phenotypes are lacking. Our study provides, to our knowledge, the first empirical evidence of heritability in a migration behaviour in ungulates. These results have implications for the evolution and maintenance of migration behaviours in natural populations.
Identity-by-descent mapping using multi-individual IBD with genome-wide multiple testing adjustment
Authors: Cai Ruoyi , Browning Sharon R. 
Published: January 2025

AbstractWe present an identity-by-descent mapping approach to test the association between genome-wide loci and complex traits. Our method evaluates whether levels of genetic similarities at specific genomic locations, captured by local relatedness matrices derived from multi-individual IBD sharing, are associated with phenotypic variation in complex traits. In addition, we propose an approach to adjust for multiple testing in genome-wide IBD mapping scans based on the correlation structure between test statistics across the genome. Through simulation studies, we demonstrate that our test has a well-controlled genome-wide type-I error rate and superior power to detect rare and untyped variants compared to standard single-variant tests. We applied our method to systolic blood pressure data from White British individuals in the UK Biobank.
Platelet mitochondrial transfer via extracellular vesicles modulates neutrophil phenotype and function
Authors: Allan Harriet E. , Dark Nicola , Vulliamy Paul , Crescente Marilena , Armstrong Paul C. , Ferreira Plinio , Warner Timothy D. 
Published: January 2025

AbstractPlatelet activation causes the release of extracellular vesicles, of which a small proportion contain respiratory competent mitochondria. Mitochondria are integral for energy production and in the regulation of apoptotic pathways. However, the existence of extracellular mitochondria highlights a potential new role in intercellular communication. We hypothesised that platelet extracellular vesicles could be taken up by circulatory cells and alter their function. In this work we demonstrate that platelet extracellular vesicles containing mitochondria interact with and are internalised by neutrophils. Flow cytometry revealed that this interaction promotes neutrophil surface receptor changes, indicative of enhanced neutrophil activation, adhesion and migration pathways. The internalisation of platelet mitochondria renders neutrophils unable to subsequently engulf bacteria, demonstrating reduced phagocytic capacity, but enhances the formation of neutrophil extracellular traps, both alone and in the presence of additional stimuli. Our findings show that platelet mitochondria released in extracellular vesicles can alter neutrophil activity and so may be important intercellular communicators and modulators of inflammatory and immune responses.
Phage defense and genome editing using novel retrons sourced from isolated environmental bacteria
Authors: Nakamura Kazuo L , Zhang Karen , Mestre Mario R , Rojas-Montero Matías , Shipman Seth L 
Published: January 2025

ABSTRACTRetrons are bacterial immune systems that protect a bacterial population against phages by killing infected hosts. Retrons typically comprise a reverse transcriptase, a template noncoding RNA that is partially reverse transcribed into RT-DNA, and a toxic effector. The reverse transcriptase, noncoding RNA, and RT-DNA complex sequester the toxic effector until triggered by phage infection, at which point the toxin is released to induce cell death. Due to their ability to produce single-stranded DNA in vivo, retrons have also been engineered to produce donor templates for genome editing in both prokaryotes and eukaryotes. However, the current repertoire of experimentally characterized retrons is limited, with most retrons sourced from clinical and laboratory strains of bacteria. To better understand retron biology and natural diversity, and to expand the current toolbox of retron-based genome editors, we developed a pipeline to isolate retrons and their bacterial hosts from a variety of environmental samples. Here, we present six of these novel retrons, each isolated from a different host bacterium. We characterize the full operon of these retrons and test their ability to defend against a panel ofE. coliphages. For two of these retrons, we further unravel their mechanism of defense by identifying the phage genes responsible for triggering abortive infection. Finally, we engineer these retrons for genome editing inE. coli, demonstrating their potential use in a biotechnological application.
An early surge of norepinephrine along brainstem pathways drives sensory-evoked awakening
Authors: Matosevich Noa , Regev Noa , Kimchy Uddi , Zelinger Noam , Kabaha Sina , Gabay Noam , Marmelshtein Amit , Nir Yuval 
Published: January 2025

SummaryThe locus coeruleus norepinephrine (LC-NE) system regulates arousal and awakening; however, it remains unclear whether the LC does this in a global or circuit specific manner. We hypothesized that sensory-evoked awakenings are predominantly regulated by specific LC-NE efferent pathways. Anatomical, physiological, and functional modularities of LC-NE pathways involving the mouse basal forebrain (BF) and pontine reticular nucleus (PRN) were tested. We found partial anatomical segregation between the LC->PRN and LC->BF circuits. Extracellular NE dynamics in BF and PRN exhibited distinct sound-evoked activation during sleep, including a fast sound-evoked NE peak specific to PRN. Causal optogenetic interrogation of LC efferent pathways, by retro-ChR2 activation or PdCO silencing of synapses in target regions, revealed a pivotal role for early LC->PRN activity in driving arousal and sound-evoked awakenings. Together, our results uncover a prominent role for early LC-NE PRN activity in connecting sensory and arousal pathways and establish LC heterogeneity in regulating arousal.Abstract Figure
The Expression ofPax6Genes in an Eyeless Arachnid Suggests Their Ancestral Role in Arachnid Head Development
Authors: Joyce Isabella , Barnett Austen A. 
Published: January 2025

AbstractBackgroundMany animal lineages utilizePax6transcription factors during eye development. Within Arthropoda, evidence suggests thatPax6genes are necessary for the specification of eyes in myriapods, crustaceans, and insects. However, recent data have argued thatPax6genes lack a role in the development of the eyes in Chelicerata (=arachnids, horseshoe crabs, and sea spiders). An alternative hypothesis argues that the absence ofPax6expression in developing chelicerate eyes could be explained by an earlier role for these genes in patterning eye precursor cells. The arachnid miteArchegozetes longisetosuslacks eyes, however it retains twoPax6paralogs in its genome. By leveraging these aspects ofA. longisetosus, we tested the hypothesis that ancestrally chelicerates did not usePax6genes to pattern their eyes but rather used them to pattern the central nervous system. We reasoned that if we observed comparable expression patterns ofPax6genes inA. longisetosusin comparison to those in arachnids that have retained eyes, then this would support the hypothesis thatPax6genes were not ancestrally used for eye specification in chelicerates.ResultsWe followed the expression of canonical arthropod retinal determination genes to confirm thatA. longisetosusdoes not develop vestigial eyes. We found that the expression of thePax6paralogs was consistent with their roles in the development of the ocular region and central nervous system. By co- staining for these genes simultaneously with the conserved head patterning geneorthodenticle, we also observed early expression patterns of these genes in the protocerebrum of earlyA. longisetosusembryos that are comparable to those arachnids with embryonic eyes.ConclusionsOur data provide support for the hypothesis thatPax6genes were not ancestrally used to pattern chelicerate eyes. The expression patterns ofPax6genes inA. longisetosuswere comparable to those of other arachnids that have eyes. This suggests that the retention ofPax6genes inA. longisetosusis due to their ancestral, non-eye patterning roles. Further supporting this hypothesis is our observation thatA. longisetosusdoes not pattern vestigial eyes. Lastly, our data suggests that thePax6genes, withorthodenticle, acted to specify the ancestral arachnid protocerebrum.
MITF regulates gene expression in middle tufted neurons and other projection neurons of the olfactory bulb
Authors: Mechmet Fatich , San José Alba Sabaté , Sigurðsson Snævar , Gautsson Ingvi , Steingrímsson Eiríkur , Petersen Pétur Henry 
Published: January 2025

AbstractThe microphthalmia-associated transcription factor (MITF) is a master transcription factor in melanocytes and plays equally important roles in mast cells. It is required for the generation, differentiation, and function of these cell types in vertebrates.Mitfis also expressed in the projection neurons of the olfactory bulb (OB), the mitral and tufted (M/T) cells. Loss ofMitfleads to neuronal hyperactivity in primary M/T cells but the general function ofMitfin neurons is unknown. Here, we identify putative MITF target genes in M/T cells, which show limited overlap with known targets in other cell types. These genes can be divided into two groups, those likely to inhibit neuronal activity and genes expressed specifically in a subclass of tufted cells, the middle tufted cells (mTCs). The mTCs are reduced in number in theMitfmutant OB, suggesting a role forMitfin the generation or survival of the mTCs and/or their function.Significance statementIdentifying MITF target genes in the OB offers insights into its role in olfaction and the regulation of neuronal activity as well as uncovering its role in mTCs. MITF may play a role in various other processes in neurons.
Capturing dynamic phage-pathogen coevolution by clinical surveillance
Authors: Mathur Yamini , Boyd Caroline M. , Farnham Jeannette E. , Monir Md Mamun , Islam Mohammad Tarequl , Sultana Marzia , Ahmed Tahmeed , Alam Munirul , Seed Kimberley D. 
Published: January 2025

AbstractBacteria harness diverse defense systems that protect against phage predation1, many of which are encoded on horizontally transmitted mobile genetic elements (MGEs)2. In turn, phages evolve counter-defenses3, driving a dynamic arms race that remains underexplored in human disease contexts. For the diarrheal pathogenVibrio cholerae, a higher burden of its lytic phage, ICP1, in patient stool correlates with reduced disease severity4. However, direct molecular evidence of phage-driven selection of epidemicV. choleraehas not been demonstrated. Here, through clinical surveillance in cholera-endemic Bangladesh, we capture the acquisition of a parasitic anti-phage MGE, PLE11, that initiated a selective sweep coinciding with the largest cholera outbreak in recent records. PLE11 exhibited potent anti-phage activity against co-circulating ICP1, explaining its rapid and dominating emergence. We identify PLE11-encoded Rta as the novel defense responsible and provide evidence that Rta restricts phage tail assembly. Using experimental evolution, we predict phage counteradaptations against PLE11 and document the eventual emergence and selection of ICP1 that achieves a convergent evolutionary outcome. By probing how PLEs hijack phage structural proteins to drive their horizontal transmission while simultaneously restricting phage tail assembly, we discover that PLEs manipulate tail assembly to construct chimeric tails comprised of MGE and phage-encoded proteins. Collectively, our findings reveal the molecular basis of the natural selection of a globally significant pathogen and its virus in a clinically relevant context.