Articles tagged with Transcriptomes
Researchers from Hiroshima University analyzed 839 collections of genetic material to identify common features of oxidative stress. They found two genes, CRIP1 and CRIP3, downregulated during oxidative stress, suggesting a relationship with zinc homeostasis. The study also identified shared biological processes between the two types of...
The NIH BRAIN Initiative Cell Census Network has published an atlas of cell types and neuronal wiring diagram for the mammalian primary motor cortex, derived from detailed studies of mice, monkeys, and humans. This comprehensive resource provides a foundation for further study of cell types in the rest of the brain.
Researchers at OIST and Tokyo University of Marine Science and Technology have developed a genetic resource for the kuruma shrimp, a species prone to white spot disease. The genome sequence has identified genes related to disease resistance, which could be used to establish a disease-resistant line of shrimp.
Researchers found that viral fossils in Australian marsupials are used to make non-coding RNAs that protect against outside infection. The study suggests that these viral fossils may be helping to immunize animals, potentially providing a mechanism similar to vaccination.
A study by the Center for Cell-Based Therapy in São Paulo, Brazil, has discovered a set of biomarkers that can be used to predict which patients with glioblastoma may have tumors resistant to radiation therapy. The genetic signature helps doctors choose the best treatment option for these patients.
A machine learning analysis has identified 50 genes strongly associated with neurological aging in both Drosophila fruit flies and humans. The study suggests that fruit flies could be used as a model organism to further investigate aging-related processes.
This study suggests exploiting urine RNAs as diagnostic markers for bladder cancer, identifying novel marker candidates and validated amplicons. Deep transcriptome analysis of urine RNA revealed coding sequences, non-coding sequences, and circular RNAs, providing promising insights into bladder cancer diagnosis.
Researchers have built a comprehensive catalogue of human non-coding RNAs using three sequencing methods. The project uncovered thousands of novel non-coding RNA genes and found correlations between RNA abundance and regulatory functions.
Researchers from Hiroshima University used a meta-analysis of publicly available transcriptome databases to identify four new genes associated with hypoxia. By combining transcriptomic and bibliometric analyses, they found previously unknown genes that were not well studied in relation to hypoxia.
Researchers have developed a novel AI technology, Swarm Learning, to analyze big data in decentralized fashion, enabling private and collaborative analysis of scientific data. The approach combines machine learning with blockchain technology, allowing for secure information exchange and optimized parameters.
Research finds that age-related changes in RNA levels alter gene function in human egg cells, leading to impaired maturation and reduced fertility. The study suggests that age may influence an oocyte's ability to process critical genes, with potential implications for reproductive medicine.
A new study has identified the transcriptome and proteome of Scrobiculariaplana, a bivalve used as a bioindicator for pollution. The database provides insights into molecular functions related to stress response mechanisms under pollution, helping to better gauge the effects on marine ecosystems.
Researchers developed an 'aging clock' that directly measures biological age from gene expression in Caenorhabditis elegans. The new BiT age clock uses a mathematical trick to minimize gene activity variation, allowing accurate predictions of biological age and its effects.
Researchers identified five molecular phenotypes of COVID-19, each with unique gene activity patterns, and found potential drug candidates for therapy. The study's results may lead to more effective treatments by tailoring therapies to individual patients.
The study found that polychlorinated biphenyls and dichlorodiphenyltrichloroethane impact salmon's lipid metabolism and environmental stress response. The transcriptome profiles suggest that OHC levels, rather than salmon origin, have a significant effect on the liver's gene expression.
A study on the Orobanchaceae parasitic plant Phtheirospermum japonicum reveals that β-1,4-glucanase enzyme is crucial for both plant parasitism and cross-species grafting. The enzyme facilitates cell-cell adhesion and transport of water and nutrients between the parasite and host plants.
Two studies published in Genome Research provide new insights into the core regulatory networks governing cell types across different vertebrate species. The research highlights the importance of understanding RNA expression in establishing cell function, morphology, and behavior. Long non-coding RNAs were found to affect cell growth a...
A global collaboration of scientists has examined the diversification of plant species, genes and genomes across 1 billion years. The study, published in Nature, involved 200 researchers from over 30 countries, including University of Tennessee faculty members C. Neal Stewart Jr. and Ed Schilling.
A study published in PLOS Biology analyzed RNA transcripts from a 14,300-year-old canid preserved in Siberian permafrost, providing evidence that RNA from ancient animals may be well-preserved. The analysis revealed tissue-specific transcriptomes in the ancient wolf, with many liver-specific transcripts matching modern samples.
Researchers at Karolinska Institutet developed a new method to identify compounds that prevent aging by analyzing the transcriptome of human cells. This approach identified several candidate substances, including Hsp90 inhibitors, which have been shown to extend lifespan and improve health in C. elegans.
Researchers at the University of Córdoba have sequenced the Holm oak transcriptome, providing insights into the tree's reactions to stress and other biological aspects. The study has generated over 34,000 annotated transcriptions, offering a first approximation of the genome and potential for future research projects.
Researchers have made a major breakthrough in understanding how brain circuits control behavior by identifying two types of intermingled nerve cells with distinct roles. The study used extensive analyses of neurons' shapes, gene activity, and function to tease out which cells are responsible for planning and initiating movements.
Researchers have developed an assay that concurrently profiles the epigenome and transcriptome of each cell type, revealing how different cells interpret their genetic code. The study provides insights into the relationship between epigenome and transcriptome, as well as the regulation of gene expression across various cell types.
Researchers found that naked mole-rat breeders have changed aging rates, living longer than non-breeders due to higher resistance to muscle loss during aging. The study suggests that genetic mechanisms underlying social suppression of sexual maturation may contribute to their exceptional lifespan.
Research suggests that night shift work can disrupt human circadian rhythms, leading to gene expression changes and immune system dysregulation. The study's findings highlight the potential risks of long-term night shift work on human health, particularly in relation to medical disorders such as diabetes and cancer.
Endocrine-disrupting chemicals like DES can cause developmental effects in mouse seminal vesicles, affecting gene expression and DNA methylation. The study also reveals that estrogen receptor alpha plays a key role in mediating these effects.
Scientists have detailed the normal human blood-nerve barrier transcriptome for the first time, revealing 12,881 RNA transcripts that define its structure and function. This comprehensive guide will help physicians understand how to keep nerves healthy and design targeted treatments for peripheral nerve disease.
Researchers analyzed RNA from transplanted hearts to discover new risk factors for dilated cardiomyopathy and other heart conditions. The study identified 228 genes that are expressed differently in DCM patients and healthy subjects, including 60 new genes linked to the disease.
A new technique called CITE-seq enables simultaneous measurement of transcriptomes and proteins on thousands of single cells, offering a major breakthrough in cell typing and disease research. The tool has the potential to characterize tumor heterogeneity and develop new immunotherapeutic approaches.
A new genomic tool for salamander biology has been developed, providing a comprehensive resource for researchers studying limb regeneration. The tool offers insights into the molecular mechanisms underlying this process and may hold potential for repairing human tissues damaged by injury or disease.
A new study reveals that no single model or common molecular toolkit exists behind the diverse array of mollusk shells. Instead, each species has evolved its own 'shell secretome' through a combination of co-opting existing genes and rapid evolution of novel genes.
Researchers developed a resource of over 5 million microsatellites for use in various plant species, making genetic research cheaper and easier. The study also provides guidelines for researchers using microsatellites.
Researchers have identified 39 generic biomarkers for human neuronal maturation using single cell transcriptome profiling. The study found that certain genes are consistently elevated when neurons mature, highlighting the importance of calcium signaling, mitochondrial function, and ubiquitination-related processes.
A new approach has been devised to map the transcriptome, revealing RNA variants that were largely invisible to previous techniques. The study identified complex splice variants in mammals, which are strikingly common and likely have roles in gene regulation across tissues and human diseases.
Genomics holds key to understanding ecological and evolutionary processes as Next-Generation Sequencing (NGS) technique is underutilised in invasion biology. NGS can transform our understanding of why non-native species adapt and thrive in new environments.
Researchers developed modified protocols to extract high-quality RNA from diverse plant species, overcoming challenges caused by secondary metabolites. The methods combine TRIzol reagent, TURBO DNA-free kit, and sodium lauroyl sarcosinate (sarkosyl) for improved extraction success.
Researchers mapped RNA activity in 29 tissue types, cell lines, and environmental conditions to understand gene expression in the nervous system and response to stress. The study identified new genes and rare RNAs involved in stress response and complex brain function.
Researchers at the University of Hawaii are studying copepods to understand their response to global climate change. They have published a transcriptome for the key North Atlantic copepod Calanus finmarchicus, which provides insights into population changes and may help predict future declines.
A new RNA extraction protocol for land plants has been developed, allowing for the extraction of high-quality RNA from a wide variety of plant species and tissue types. This protocol will greatly facilitate RNA-based studies of non-model plant species and enable comparative analyses of transcriptomes across diverse lineages.
A new study reveals fewer differences in white shark gene products associated with metabolism compared to humans than zebrafish, sparking questions about the distinctiveness of this iconic species. The research also finds greater similarity between white sharks and humans in other aspects of their heart transcriptome.
Researchers at Worcester Polytechnic Institute have sequenced the genetic code of Panagrellus redivivus, a tiny nematode also known as the beer-mat worm. The study reveals nearly 24,000 putative genes and sheds light on animal biology, including differences between male and female organisms and unique adaptations of parasitic worms.
Scientists assembled the transcriptome and genome of the noxious weed Brachypodium sylvaticum, providing insights into its invasive capabilities and adaptation to new environments. The study offers a model for studying ecological and evolutionary aspects of invasion.
Researchers sequenced primitively eusocial wasps' transcriptomes, finding workers have an active genetic profile while queens have a restricted one. This discovery sheds light on the evolution of sociality and the origin of alternative phenotypes.
A new study on the Newt transcriptome has identified 826 proteins specific to urodeles and several newly discovered proteins that may play roles in regeneration. The data outline genes present only in regenerating tissues, which could be crucial for regenerative medicine research.
A comprehensive analysis of the Drosophila genome reveals new genes, alternative splicing forms, and complex chromatin organization. The findings provide a foundation for in-depth functional studies and apply to understanding genomes across all organisms.
Scientists have discovered that long non-protein-coding RNA (lncRNA) are involved in the host response to viral infection. The study found that lncRNAs were triggered by virus infection and regulated in response, suggesting a new paradigm shift in understanding of innate immunity.
Researchers developed a new method for transcriptome analysis using next-generation sequencing technology, enabling the discovery of protein-coding genes and genetic markers in corals. The study identified approximately 11,000 genes, over 30,000 markers of genetic variation, and novel candidate genes for stress-related processes.
The study found that 34% of polyadenylated transcripts mapped to non-annotated genomic regions, indicating a large number of novel gene candidates. Additionally, the researchers identified 94,241 splice junctions, with 4,096 novel variants, highlighting exon skipping as the most prevalent form of alternative splicing.
The Salivaomics Knowledge Base (SKB) is an in silico saliva diagnostic atlas mapping salivary proteome and transcriptome to human chromosomes. The database includes profiles from healthy individuals and oral cancer patients, allowing for comparisons between groups. Future expansions will include other cancers and diseases.
Scientists have identified salivary proteins and RNA sequences that are highly discriminatory for oral cancer and Sjögren's Syndrome. The use of saliva as a diagnostic tool is only a few years away, with the potential to revolutionize disease detection.
The study reveals that genes use a broad distribution of start sites, allowing for subtle differences in species control. This knowledge could help explain why complex organisms like humans have more genes than simple ones despite similar numbers.
The mammalian transcriptome has been completely mapped, showing a massive abundance of noncoding RNAs and antisense genes. This discovery has significant implications for our understanding of genetics, gene regulation, and cellular functions.