Articles tagged with Transcriptomics
Researchers have created the first spatial map of malaria infection in the mouse liver using Spatial Transcriptomics and single-cell RNA-sequencing. This discovery sheds light on the parasite's lifecycle, revealing changes in host cell gene expression near infected areas.
A new open-source platform, Nova-ST, is transforming gene expression profiling in tissue samples by offering affordable and high-resolution spatial analysis. This approach allows scientists to map gene expression across a tissue section with a spatial context, enabling the study of complex biological processes.
Researchers developed more resilient varieties of cotton by analyzing its genes and physical traits. They found two key regulatory genes that help cotton plants manage water stress while maintaining fiber production.
Researchers have developed ENGRAM, a method that records cell signals and biological states as they occur inside living cells. This approach offers a novel way to capture biological information in living systems, potentially helping answer questions about cellular pasts and futures.
Researchers found that the frequency of activated TREG cells remained elevated during treatment and continued to be high even after the virus was eliminated. Inflammatory features, such as increased TNF signaling, were sustained in TREG cells, indicating long-term immune system changes induced by the chronic infection.
A team of researchers has completed the diploid genome assembly of the Malbec grapevine, revealing the genetic factors that contribute to its exceptional wine quality. The study identifies polymorphic regions and gene expression differences among clones, shedding light on the molecular mechanisms driving clonal variation.
A recent study found that oleacein increases BDNF expression in human neuronal cells and reduces depressive behavior in mouse models. Gene expression analysis reveals the activation of cell cycle and neurogenesis processes, as well as a decrease in inflammatory response.
A platform called Open-ST enables scientists to reconstruct gene expression in cells within a tissue in three dimensions, capturing molecular and (sub)cellular structures. The platform was used to study cell types at subcellular resolution in tissues from mice brains, tumor tissue, and healthy lymph nodes, providing insights into cance...
A study by researchers at the Center for Genomic Regulation found that changes in mRNA content between germline and somatic cells are the primary source of variation in lifespan. Knocking down specific genes increased life expectancy, suggesting randomness in gene activity affects ageing.
A new atlas provides a detailed map of how cells and tissues age in roundworms, shedding light on the aging process and potential treatments. The study reveals unique aging features of different tissues and identifies key mechanisms underlying cellular aging.
Researchers used machine learning to integrate high-throughput transcriptomic, proteomic, metabolomic, and lipidomic profiles to identify four distinct molecular profiles of Alzheimer's Disease. These profiles were associated with varying levels of cognitive function and neuropathological features.
Researchers from Tokyo Medical and Dental University used long-read RNA sequencing to decode genetic intricacies and disease links. The study identified novel isoforms, cell-type-specific splicing patterns, and disease-linked transcripts associated with immune-related diseases.
A comprehensive, user-friendly repository has been created to help study Alzheimer's disease. The ssREAD database encompasses 277 integrated datasets from 67 scRNA-seq & snRNA-seq studies, totaling 7,332,202 cells, and includes interactive visualizations for comprehensive analysis interpretations.
A research team has successfully assembled a nearly gap-free, telomere-to-telomere genome of P. ussuriensis, filling gaps present in the P. trichocarpa genome. The assembly's high collinearity with P. trichocarpa facilitates comparative genomics, epigenetic research, and reproductive biology studies.
A comprehensive study by McLean Hospital researchers reveals both shared and unique molecular changes across brain regions, genomic layers, cell types, and blood in individuals with posttraumatic stress disorder (PTSD) and major depressive disorder (MDD). The findings provide potential avenues for novel therapeutics and biomarkers.
Researchers analyzed genome of Oikopleura dioica, finding it has wildly different languages despite identical physical characteristics. The 'scrambling' phenomenon suggests genes are regulated differently, challenging assumptions about species identity.
Researchers have developed a modular epigenome editing platform to study the impact of chromatin modifications on transcription. The system allows for precise programming of nine biologically important chromatin marks, enabling the discovery of causal relationships between chromatin marks and gene regulation.
Researchers found associations between inflammatory and metabolic biomarkers and accelerated aging, with GlycA and GrimAge showing robust correlations. The study provides insight into the relationship between aging and cardiometabolic health, potentially informing vulnerable populations.
Researchers at Karolinska Institutet developed a Single Cell Atlas (SCA) platform to profile human biology through multi-omics technologies. The extensive collection of data provides unique insights into individual cell properties and tissue interactions.
Researchers have found that genetic mutations are not essential for cancer onset, and instead, epigenetic dysregulation plays a crucial role. Epigenetic changes can cause gene expression to be altered, leading to tumour formation even after the signal has been restored.
A consortium of scientists, including Brazilians, has successfully sequenced the reference genome of Arabica coffee. The study identified genes responsible for resistance to rust and other diseases, as well as those related to the aroma of Arabica coffee. By comparing a dihaploid-derived genome with a common tetraploid variety, researc...
A new study identifies the mechanism underlying N6-methyladenosine (m6A) RNA modification in mammals, revealing its role in regulating gene expression and promoting genome stability. The study found that DDX21 and METTL3 work together to facilitate m6A deposition co-transcriptionally.
Researchers have discovered a way to enhance the functionality of CD34-negative hematopoietic stem cells, which could lead to better treatments for blood-related diseases. The treated cells showed improved homing abilities and increased gene activity, suggesting they could be more effective as a treatment option.
Researchers have deciphered trabectedin's precise mechanism of action, revealing its ability to induce persistent DNA breaks in cancer cells. This disruption of the transcription-coupled nucleotide excision repair (TC-NER) pathway leads to long-lasting DNA breaks that ultimately kill cancer cells.
A recent study by Pusan National University scientists discovered the crucial role of PKM gene and EPHA2 pathway in HNSCC development. The research highlights the importance of HPV infection status in shaping the tumor microenvironment, enabling precision medicine for targeted treatment.
Scientists used new techniques to analyze gene activities during mouse prenatal development, revealing hundreds of cell types and their formation. The study showed that massive transcriptional changes occur at birth, potentially necessary for survival outside the womb.
A new study unveiled over a thousand protein-protein interactions during early embryonic development, highlighting the role of transcription factors like paired-like homeobox (PRDL) family. This research paves the way for understanding embryonic genome activation and advancing treatments for developmental disorders.
A new study reveals a larger number of transposable elements in the human genome than previously known, shedding light on their potential role in human diseases. The 'genomic time machine' approach allowed researchers to identify degenerate TEs that were missed in previous studies.
A new statistical model developed by UChicago researchers accurately identifies causal genes and variants for a disease. The tool reduces false positives and takes into account multiple genes and variants, leading to the discovery of 35 putative causal genes for LDL cholesterol levels.
Researchers mapped dental pulp and periodontal ligament stem cells' genomes, revealing significant differences in their differentiation potential. The study identifies the genetic composition and mechanisms of differentiation, paving the way for targeted regenerative therapies.
Researchers identified RBM5 as a key regulator of HOXA9 expression in leukemia cells, revealing its dual function in DNA and RNA handling. Removing RBM5 from cells significantly reduced HOXA9 mRNA levels, suggesting its potential as a therapeutic target for acute myeloid leukemia treatment.
Researchers discovered a previously unreported neuron type with vulnerability in Parkinson's disease, shedding light on the complexity of the disease and potential therapeutic targets. The study identified distinct transcriptomic signatures of this neuron type and found reduced RIT2 expression in Parkinson's disease patients.
Researchers created a single-cell atlas of the human placenta, revealing changes in gene expression patterns among cell types. The study found that cells most affected by labor were in chorioamniotic membranes and generated inflammatory signaling.
A multidisciplinary study has elucidated the structure of the machinery responsible for writing much of our 'dark genome', a 98% unknown biological function. This discovery may lead to novel treatments for autoimmune diseases, cancer and neurodegeneration.
The study maps over 32 million cells in the mouse brain, describing their type, location, and molecular information. This atlas paves the way for a greater understanding of the human brain and development of precision therapeutics for mental and neurological disorders.
Spatial transcriptomics reveals cellular heterogeneity, organizational patterns, and molecular communications foundational to tissue structure and dynamics. The technique has enhanced throughput and resolution, offering a synthesized perspective of biological entities across various levels of detail.
A team has successfully assembled the telomere-to-telomere gap-free reference genome of Vaccinium duclouxii, revealing insights into sugar and acid accumulation, anthocyanin biosynthesis and genetic improvement. The study provides a foundation for understanding the evolution of the Vaccinium genus.
Researchers discuss a new approach integrating genomic, epigenomic, transcriptomic, and machine learning methods to identify functional genetic variants and characterize their mode of action in regulating target genes. This method aims to improve understanding of disease etiology and prioritize causative inherited genetic variants.
Researchers created a comprehensive chromatin map to understand gene regulatory networks contributing to differences between pediatric acute lymphoblastic leukemia subtypes. The study identified key transcription factor footprints and chromatin accessibility patterns, which can predict leukemia subtype with 89% accuracy.
Researchers identified a promising dual-purpose target, KDM1A, using AI analysis of transcriptomic data from 16,740 healthy samples and 11,303 tumors. KDM1A was found to significantly extend lifespan in Caenorhabditis elegans and has anti-cancer activities established in preclinical and clinical studies.
Researchers characterized changes in cognitive behaviors, neuronal morphology and gene expression in a tauopathy mouse model. The study found significant decreases in dendritic arborization and synaptic gene upregulation over time.
Researchers discovered BMAL1 is significantly upregulated in senescent cells and modulates the senescence program through AP-1. The study highlights a previously unappreciated role of BMAL1 in regulating cellular senescence and circadian clock components.
Researchers at Memorial Sloan Kettering Cancer Center developed an open-source computational method, Spectra, to analyze single-cell transcriptomic data. The algorithm identifies functionally relevant gene expression programs and is well-suited for studying large patient cohorts.
The study aims to identify genetic and molecular factors associated with susceptibility and progression of liver disease in Hispanics/Latinos. Researchers will collect data from 300 participants, including those with metabolic-associated fatty liver disease and healthy controls.
Researchers analyzed over 2 million cells from 400 postmortem brain samples to identify cellular pathways that could become new drug targets for Alzheimer's treatments. They found impairments in mitochondrial function, synaptic signaling, and protein complexes, as well as disrupted lipid metabolism.
The Keck School of Medicine of USC has launched a five-year, $50.3 million multi-omics study to better understand the causes and prevention of various diseases, including NAFLD, in underrepresented racial and ethnic groups.
Researchers identified four novel receptors potentially linking endometrial cancer with polycystic ovary syndrome, highlighting a major pathway involved in the increased EC risk in PCOS. The PI3K-AKT signaling pathway is consistent with a link between PCOS and EC.
Research finds that immune cells in older adults are similar to those in newborns and children, but less effective at recognizing infected cells. The study, published in Nature Immunology, suggests that tailored vaccines and therapies could be developed for different age groups based on the unique characteristics of killer T cells.
A study published in eBioMedicine identified 9 sets of biomarkers, both metagenomic and transcriptomic, associated with 30-day mortality in patients with severe community-acquired pneumonia. The biomarkers were validated with an accuracy of 85%, significantly higher than existing clinical prediction models.
SARS-CoV-2's nucleocapsid protein (N) uses human body temperature to replicate, binding to RNA motifs at specific spatial folds. The study reveals new functions and potential targets for antiviral drugs.
Researchers have identified a neoplastic fusion transcript RAD51AP1-DYRK4 in luminal B breast cancer, associated with higher ki67 expression and aggressive clinical characteristics. MEK inhibitor trametinib may be effective in blocking the MEK-ERK signaling driven by this fusion.
Researchers at Carnegie Mellon University have developed a new AI method that uses transformer models to analyze images of human cells. The technology, called subcellular spatial transcriptomics cell segmentation (SCS), accurately identifies individual cells and their constituent parts, revealing critical information about cellular org...
A team of scientists at Harvard Medical School has identified six chemical cocktails that can restore cellular aging and rejuvenate human cells. The study builds upon the discovery of Yamanaka factors, which can convert adult cells into induced pluripotent stem cells, raising hopes for treating age-related diseases and injuries. The im...
Researchers at Nara Institute of Science and Technology identified the WOX13 gene as a key negative regulator of shoot regeneration in plants. The study found that WOX13 inhibits a subset of shoot meristem regulators while directly activating cell wall modifier genes involved in cell expansion and differentiation.
A new study by CNIC researchers reveals that low-grade systemic inflammation triggered by subclinical atherosclerosis accelerates epigenetic aging in otherwise healthy young individuals. The study found a strong association between atherosclerosis progression and accelerated biological age, with potential reversibility through lifestyl...
Researchers developed Precious1GPT, a multimodal transformer-based approach for aging clock development and feature importance analysis. The model utilizes methylation and transcriptomic data to predict biological age and identify disease-related genes, providing a pathway for therapeutic drug discovery.
Researchers developed a non-invasive diagnostic method that analyzes sebum for biomarkers of early-onset atopic dermatitis in infants. The study revealed distinct gene expression profiles associated with AD, allowing for early detection and potential treatment monitoring.
Coral reef fish larvae undergo significant physiological changes as they transition from open ocean swimming to settling on the reef floor. The study found that gene activity changes play a crucial role in adapting to hypoxic environments at night, allowing the fish to survive and thrive.
SpaceMarkers, a new machine learning software, can identify molecular interactions among distinct cell types in and around tumors. By analyzing spatial transcriptomics data, it reveals genes overexpressed due to cell-to-cell interactions, providing new avenues for understanding cancer progression and treatment responses.
A new computer-modeling system, scDesign3, has been developed to generate realistic synthetic data for analyzing genetic makeup of cells. The system can help researchers evaluate and validate computational methods for tasks such as gene expression analysis and cell trajectory modeling.