Articles tagged with Transcriptomes
Researchers identified two opposing patterns of brain gene activity in mice carrying autism-risk mutations, which vary by sex and respond differently to experimental drugs. The patterns, which are shared across multiple analyses, suggest that many different genetic mutations converge into a limited number of molecular brain states.
Researchers at Vanderbilt University Medical Center used spatial transcriptomics to characterize acute rejection and response to immunomodulatory therapies following heart transplantation. The study linked cell-specific gene expression patterns to the development of cardiac allograft vasculopathy, a form of chronic rejection that limit...
Hepatopulmonary syndrome is characterized by pulmonary angiogenesis and refractory hypoxemia, with agrimoniin treatment attenuating pathological changes by restoring mitochondrial respiration and reducing glycolytic activity. Activation of PGC-1α is essential for mediating improvements in vascular remodeling and metabolic balance.
A new study reveals that macrophages, a key immune cell type, age differently across tissues and between sexes. The researchers found that aging macrophages become more focused on responding to stress and cellular damage, but lose some molecular programs involved in maintaining healthy tissue structure.
Researchers have developed an algorithmic tool called CytoSignal that can analyze spatial transcriptomic data to infer cell-cell communication. The method can identify defective signaling interactions underlying diseases and potentially lead to new treatments by targeting specific receptor proteins.
Researchers have synthesized long noncoding RNA molecules with anti-inflammatory properties, demonstrating a new paradigm in drug discovery. The team identified three lncRNA sequences that regulate inflammation and used them to create nanoparticles that reduced inflammation in human cell cultures and mice.
Researchers have identified three distinct immunotypes in EPTB patients, revealing new insights into disease mechanisms. Additionally, gene expression-based biomarkers have been developed to reliably diagnose both pulmonary and extrapulmonary tuberculosis.
Researchers at University of Texas M. D. Anderson Cancer Center discover that inflammation is responsible for driving the earliest stages of lung cancer, identifying potential targets for early intervention and suggesting a promising approach to intercepting lung cancer development.
A new study found that alpha-synuclein triggers early gene expression changes in a Parkinson's disease model, revealing brain region-specific and systemic transcriptomic alterations. These changes may contribute to disease development and serve as potential biomarkers.
Researchers have discovered new layers of hidden genetic diversity in wheat, which could help improve crop resilience and adaptability. The study used RNA analysis and de novo annotation to reveal previously unknown gene expression patterns, providing valuable insights for plant breeding programs.
A recent study reveals that ORC2 subunit regulates epigenetics and gene expression by compacting chromatin and attracting repressive histone marks at some sites, but activating gene expression at others. This regulation also prevents CTCF binding at certain sites, leading to changes in chromatin structure and gene expression.
HTGAnalyzer is an automated tool simplifying complex transcriptomic workflows, enabling clinicians without bioinformatics expertise to perform essential analyses in precision medicine. The tool has been validated using multiple datasets and identified differentially expressed genes linked to cancer diagnosis, treatment, and prognosis.
Researchers investigated pipetting speed's effect on yeast growth and gene expression, finding it had little to no impact within a tested range. The study provides guidelines for increasing efficiency and reproducibility in robot-based experiments.
This study identifies three molecular classifications of T-follicular helper lymphoma based on genetic mutations, including C1, C2, and C3, which show different prognostic outcomes. The research also classifies tumor microenvironments into three types, with TME2 linked to poor outcomes.
Researchers at the University of Tsukuba investigated the developmental fate of shell-forming cells in limpets using single-cell transcriptome and gene expression analyses. They found that the developmental fate of these cells was specified independently of interactions with neighboring cell lineages, contradicting conventional hypothe...
Researchers discovered that aging causes inflammation, oxidative stress, and gene disruption in the retinal pigment epithelium, a vital layer of cells in the eye. This study provides a clearer understanding of why aging leads to eye disease and introduces a reliable laboratory model for testing new therapies.
A study published in Nature Aging used an AI-based computer model to analyze the aging process of immune cells. The researchers found that specific genes are involved in aging processes and can be used as markers for different immune cell types, revealing new insights into cellular aging.
Researchers at KAIST have developed a technology that can treat colon cancer by converting cancer cells into normal-like cells. The breakthrough involves creating a digital twin of the gene network associated with normal cell differentiation, leading to significant promise for reversible cancer therapies.
Researchers at Sanford Burnham Prebys used two sequencing methods to reveal new mRNAs associated with Alzheimer's disease, dementia with Lewy bodies, and Parkinson's disease. The study found vast mRNA isoform diversity in genes related to neurodegenerative diseases.
Researchers have created a comprehensive database of protein changes in mice tissues due to aging, providing new insights into age-related diseases. The study reveals proteins that increase with age and improve understanding of the molecular mechanisms underlying aging.
Researchers developed an algorithm to analyze high-resolution spatial data from Seq-Scope and other technologies, called FICTURE. This enables scientists to see how and where a gene is expressed at microscopic resolution, improving our understanding of gene expression.
Researchers found that single-housed adult fish exhibited a longer egg-laying period and slower aging process compared to group-housed counterparts. The study suggests that early-life social environment may influence life-long attributes beyond the typical relationship between growth rate and lifespan.
Scientists have mapped the global repertoire of genes that determine the male or female sexual fates in Plasmodium falciparum malaria parasites. This study reveals key regulators of gene expression during development and identifies novel candidate 'driver' genes, shedding light on the complex biology of malaria transmission.
Researchers predict that circular RNAs will play a crucial role in cancer diagnosis and treatment, enabling innovative diagnostic and therapeutic developments. The study highlights the potential of circRNAs as biomarkers, therapy targets, and even immune response inducers against cancer cells.
Scientists successfully mapped transcriptomes from 1.3 million brain cortex cells to gain molecular insights into Alzheimer's vulnerability and resilience. The resulting atlas holds promise for gene and molecular discovery across pathways affecting brain health.
A new biomarker has been discovered that can help predict which patients with clear cell renal cancer are at higher risk of recurrence. The 15-gene signature was found to be independently associated with worse disease-free survival and disease-specific survival in two large validation datasets.
The new 'scLENS' tool overcomes challenges in single-cell transcriptomics by automatically differentiating signals from noise using Random Matrix Theory and Signal robustness test. This innovation significantly improves analysis accuracy and efficiency, enabling researchers to extract biological signals conveniently and automatically.
Researchers found that ~60% of tissues exhibit a significant negative correlation between age and stemness score, indicating a pan-tissue decline in stemness. This study adds weight to the idea that stem cell deterioration contributes to human aging, with hematopoietic stem cells from older individuals showing higher stemness scores.
Researchers developed chronological age prediction models by analyzing gene expression changes in the prefrontal cortex, identifying genes associated with aging and potential mechanisms. The models showed high correlation with age and demonstrated female and male-specific differences.
A recent study published in the Journal of Investigative Dermatology has revealed that hemoglobin is present in the epidermis, the outermost layer of our skin. This discovery adds a new facet to understanding the skin's defense mechanisms against aging and cancer.
Researchers developed a sensitive method for single-cell transcriptome analysis from tissue sections, enabling precise examination of cells with histological characteristics. The study unveiled gene expression differences in granulosa cells and revealed growth retardation in oocyte gene expression profiles.
Researchers discovered that aging alters the pancreas's circadian rhythm by reorganizing its transcriptome. The study found that fibroblasts play a crucial role in regulating this reorganization, which affects the organ's resilience to aging-related pathologies.
The study validates a comprehensive genomic profiling assay, NeXT Dx, which detects single nucleotide variants, indels, copy number alterations, and gene fusions. The assay demonstrates high analytic sensitivities and specificity, providing personalized recommendations critical to clinical decision-making.
Researchers investigated premature senescence in biliary atresia and assessed senotherapies. They found that human allogenic liver-derived progenitor cells reduced early markers of senescence and improved liver disease in a preclinical model, providing encouraging results for pediatric biliary cirrhosis treatment.
Recent studies in the New Journal of Pharmaceutical Analysis feature novel diagnostic tools, RNA sequencing-based workflows, and mechanical property evaluations to enhance cancer and cardiovascular disease treatment outcomes. These innovations aim to improve the therapeutic effect of drugs and promote personalized medicine.
Researchers used a multiomics approach to analyze changes in transposable elements after influenza A virus infection, identifying transcription factors contributing to individual responses. The study provides insights into the variable severity of illness among individuals infected with the same virus.
Researchers have identified distinct senescence subpopulations and dynamic changes in the transcriptome of human cells undergoing senescence. The study provides new understanding of the heterogeneous nature of senescence and its impact on aging diseases.
A new study from Duke University identifies 1,500 genes essential for invasive cell behavior in C. elegans worms. The researchers created a 'parts list' of these genes and proteins, which may help identify effective ways to stop cancer's spread.
Scientists have successfully mapped the landscape of m6A modification in mouse embryos, revealing intriguing patterns of gene activity and distribution in transposable elements. This study fills a gap in the transcriptome field, providing new insights into the function of m6A during development.
Researchers at McGill University found that analyzing gene activity can classify brain diseases into five primary groups, improving diagnosis accuracy. The study identified previously unknown relationships among diseases, such as language development disorders and obsessive-compulsive disorder, which share common genes and cell types.
A recent study reveals the first high-quality nuclear genome sequence and assembly of Babesia duncani, a neglected species until now. The parasite's evolution and mechanism of virulence have been identified, providing leads for the development of effective therapies.
Researchers at HKU use single-cell transcriptomic data and phylostratigraphy to estimate the evolutionary origin of different cells in C. elegans. They find significant variation in transcriptome age among cell types, revealing insights into adaptation and developmental patterns.
Researchers developed a novel machine-learning algorithm that analyzes a person's entire transcriptome to create an 'atlas' of pediatric cancer. The platform refines cancer diagnoses for 85% of pediatric cancer patients, identifying 455 subtypes of cancer and revealing subtle differences within subtypes.
Researchers identified 11,378 viroid-like cccRNAs in 4,409 species-level clusters, exceeding previously known elements. These findings reveal viroids are more common and abundant than thought, with distant relatives of human Hepatitis Delta Virus discovered.
Researchers at Children's Hospital of Philadelphia developed ESPRESSO, a new computational tool that can accurately discover and quantify RNA molecules from error-prone long-read RNA sequencing data. This will enable better diagnosis of rare genetic diseases and discovery of potential therapeutic targets in cancer.
Researchers discovered poly(A)-tail-mediated remodeling of maternal mRNA during the oocyte-to-embryo transition, involving partial degradation and re-polyadenylation. This process is essential for human embryo development, as blocked re-polyadenylation leads to failed first embryo cleavage.
Researchers at Okayama University discovered genes and proteins responsible for the rapid contraction of axopodia in Heliozoa, a group of eukaryotes. The study identified key players in microtubule disruption, including katanin p60, kinesin, and calcium signaling proteins.
A new toolkit enables researchers to map individual RNA data to a more diverse 'pantranscriptome', addressing reference bias and increasing the accuracy of gene expression mapping. This approach builds on pangenomics, allowing for the comparison of an individual's genome to genetically diverse cohorts of reference sequences.
A new study has identified distinct patterns of circular RNA expression in human ALS muscle tissue, which display disease-specific gradients and could inform about neuromuscular molecular programs in ALS. The research reveals that specific circRNAs are elevated in ALS muscle biopsies but reduced in spinal cord samples from ALS patients.
A study using spatial single-cell transcriptomics reveals the spatial organization of cancer cells in patient tissues across ages and locations. The research highlights age- and location-dependent differences in tumor biology, suggesting that kids and adults with diffuse midline gliomas may need different treatments.
Researchers discovered that krill oil protects dopaminergic neurons from age-related degeneration through temporal transcriptome rewiring and suppression of several hallmarks of aging. Krill oil increases neuronal resilience, promoting anti-oxidative stress and anti-inflammation, and abrogating multiple aging hallmarks.
Researchers at Leibniz-HKI discovered a yellow natural substance that regulates the multicellular stage of the amoeba <em>D. discoideum</em>. The polyketide, dictyoden, prevents premature hatching from spores, maintaining the development cycle. The study provides insights into the complex transition from single- to multicellularity.
Researchers have developed a new DNA nanotechnology-driven method called Light-Seq that enables the analysis of gene expression patterns in hard-to-access cells within intact tissues. This approach overcomes limitations of existing spatial transcriptomics methods, allowing for deeper understanding of disease mechanisms and biology.
A study by Osaka University researchers comprehensively analyzed mRNA and microRNA expression patterns in the blood of patients with severe COVID-19, revealing specific mRNAs and microRNAs associated with the immune response pathway. The findings suggest that interferon-β plays a crucial role in COVID-19 severity.
Researchers have mapped RNA diversity in human tissues at unprecedented depth, discovering tens of thousands of novel transcripts. The study used long read sequencing to catalog the genetic code's transcripts, shedding light on how genetic and environmental differences affect gene regulation.
Researchers have developed Fanflow4Insects, a functional annotation workflow that annotates gene functions in insects. The team has annotated the Japanese stick insect and silkworm, providing valuable information for entomological research and genome editing.
Researchers studied ant brains using single cell technology, revealing functional specialization and complementary brain cell composition differences among individuals. The study found specialized neurons for learning and memory in worker ants and optic lobe cells in male ants.
Researchers analyzed 139 patient blood samples to identify common mechanisms underlying COVID-19 recovery. They found that a gradual reduction in neutrophil counts and changes in molecular regulation of the immune system characterize the recovery process.
Researchers investigated physiological changes in Japanese Black cattle during feeding, uncovering metabolic and nutritional conditions. They found increased blood triglycerides, insulin levels, and fat metabolism during fattening phases.
The study highlights the need to analyze molecular markers, such as genetic sequences or brain proteins, to obtain more accurate assays, diagnoses and therapies. The results show changes in astrocytes attempting to adapt to toxic environments from the disease, worsening its progression.