Articles tagged with Gene Clustering
Researchers found two new types of gene clusters capable of producing large volumes of hydrogen in marine bacteria. The study suggests that the diversity in these clusters is related to speciation and ecological niches, with some species producing higher levels of hydrogen than others.
Researchers developed FAST-NPS, a new automated method to discover and scale up bioactive natural products from Streptomyces. The method uses self-resistance genes as markers to prioritize biosynthetic gene clusters with bioactivity.
Researchers at Rice University have identified a protein responsible for the clustering of gas vesicles in bacteria, a discovery that could enable new biomedical applications. The team used genetic, biochemical, and imaging approaches to understand the patterning of these structures, which are found in certain microorganisms.
Researchers developed an AI framework that combines dimension reduction techniques with a new clustering algorithm to quickly identify groups of viral genomes at risk. This enables proactive response measures like tailored vaccine development, potentially eliminating emerging variants before they spread.
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 have sequenced 52 Psilocybe specimens, including 39 species previously unsequenced, to understand the evolution of psychoactive psilocybin production. The study reveals two distinct gene orders within the psilocybin-producing gene cluster, suggesting an ancient split in the genus.
Researchers developed an AI model using epigenetic factors to predict patient outcomes across multiple cancer types. The model successfully divided patients into two groups with different survival chances, and its genes were found to have a significant overlap with cluster-defining signature genes.
A new study analyzing lice genetic diversity found that head lice arrived in the Americas twice – once with early human migrants and again during European colonization. This discovery supports existing theories on human migration and provides insights into how lice have evolved alongside humans.
Researchers from University of Freiburg and University of Cambridge have observed dynamic molecular aggregates in cells for the first time. These condensates play a crucial role in controlling biochemical processes and are regulated by active biological mechanisms, not just physical forces.
A new algorithm has been created to search fungal genomes for clusters of genes likely to result in interesting biological compounds. The algorithm, trained on a newly described type of chemistry in fungi, has discovered over 1,300 fungal species with biosynthetic gene clusters centered on isocyanide chemistry.
A recent study confirmed which genes in the HiVir cluster are essential and which contribute partially to the disease. The toxin produced by Pantoea ananatis has broad-spectrum activity, potentially targeting conserved functions within plants.
The study uses AI-assisted methods to discover novel deaminase proteins with unique functions through structural prediction and classification, expanding the utility of base editors. New DNA base editors with remarkable features were developed, enabling tailor-made applications for various breeding efforts.
Researchers at MD Anderson Cancer Center have engineered a new model of aggressive renal cell carcinoma, highlighting molecular targets and genomic events that trigger chromosomal instability. The loss of interferon receptor genes plays a pivotal role in allowing cancer cells to become tolerant of chromosomal instability.
Researchers at the University of Illinois have identified a novel class of ribosomal peptides called daptides, which exhibit hemolytic activity. This discovery opens up new avenues for therapeutic development and highlights the vast potential of undiscovered RiPP classes.
A new study by Weill Cornell Medicine investigators found four distinct types of beta cells in the pancreas, with cluster 1 beta cells producing more insulin than others and appearing better able to metabolize sugar. The loss of these high-functioning beta cells may contribute to type 2 diabetes development.
Lichen-forming fungi have evolved unique gene clusters to produce orange 'sunscreen' pigments, allowing them to thrive in sunny environments. The discovery of a critical ABC transporter gene within the pigment gene cluster provides a potential hypothesis for toxicity avoidance in these organisms.
Researchers at Rice University have developed a multiplex base-editing platform that significantly improves the pace of new drug discovery by inducing fungi to produce more bioactive compounds. The technique has been deployed as a tool for mining fungal genomes for medically useful compounds, reducing research timeline by over 80%.
Researchers found that a gene mutation in mice resulted in increased plaque deposits and larger clumps, suggesting the gene plays a critical role in immune defenses. The study may lead to new therapies targeting this gene mutation to slow progression of Alzheimer's disease.
Researchers at Max-Planck Institute for Terrestrial Microbiology have deciphered the biosynthesis of benzobactins, a class of natural compounds with special biological activity. The study reveals that these compounds are widespread in diverse bacteria and could be excellent candidates for future drug therapy.
The HUSH complex is involved in normal brain development, neuronal individuality, and connectivity. The complex also regulates repetitive-like gene clusters, including protocadherin gene clusters, which are essential for neuron-to-neuron interactions.
A collaborative team at IGB discovered 30 new compounds, including three with antibacterial properties, using the Illinois Biological Foundry for Advanced Biomanufacturing. The platform allowed for rapid screening of hundreds of genes and pathways, enabling the researchers to identify potential anti-microbial compounds.
Rice University bioscientists have developed a novel approach to control the expression of 'silent' genes in bacteria using CRISPR technology. This strategy could lead to the discovery of new antibiotics and has potential applications in antifungal and anticancer agents, as well as agriculture.
A new statistical method called Association Plot facilitates the determination and analysis of marker genes in single-cell data. This allows researchers to trace back RNA molecules to their cell of origin, providing insights into cell-type specific genes.
Researchers at New York University have created artificial Hox genes using synthetic DNA technology and genomic engineering in stem cells. The findings confirm that clusters of Hox genes help cells learn and remember where they are in the body, with no other genes needed to be present.
A recent study identified 34 novel genes that contribute to endocrine resistance in breast cancer using dynamic gene expression analysis. The researchers found that these genes are differentially expressed in both estrogen receptor-positive and triple-negative breast cancers, suggesting shared genetic mechanisms underlying resistance d...
Researchers discovered hundreds of new gene functions in algae, which have counterparts in plants, enabling better understanding of photosynthesis, DNA repair, and stress responses. The findings can improve biofuel production and develop heat-tolerant crops.
A research team from the Max Planck Institute for Terrestrial Microbiology has identified 1,000 biosynthetic gene clusters, over half of which are previously unknown. These natural products have been found to be eukaryotic proteasome inhibitors that suppress the immune system of insects, as well as other virulence factors.
Scientists have identified a potential new antibiotic candidate from the rare soil microbe Lentzea flaviverrucosa. The discovery was made using genomics-based approaches and shows that this actinomycete produces two different bioactive molecules that are active against various types of cancer cells.
Researchers at Johns Hopkins Medicine discovered a critical step in the molecular circuitry of immune cells that mobilizes the immune system to fight off foreign invaders. The findings, published in iScience, shed light on subtle genetic variations among human populations that may explain individual responses to infections.
The study found that all 86 tridomain homologues of NDP-heptose synthetases are conserved in Actinobacteria, with three types of gene clusters encoding different natural products. The kinase domains of four selected proteins were found to be dysfunctional.
Researchers developed a combined approach to amplify the large-scale biosynthetic gene cluster, resulting in a 9.59-fold increase in bleomycin production. The method uses a ZouA-dependent DNA amplification system and double-reporters-guided recombinant selection.
Researchers at TU Wien propose a new method to interpret and mine fungal genomes to predict essential genes for the production of valuable substances. The FunOrder method identifies co-evolved genes that are functionally necessary, distinguishing them from gap genes.
Researchers at Washington University in St. Louis used comparative metabologenomics to study the genomes of Streptomyces bacteria and identify key factors that influence drug production. The study found that fine-tuning of specific nucleotides can control antibiotic production, offering new insights for next-generation drug discovery.
Scientists have successfully identified the complete avenacin biosynthetic pathway in oats, which provides resistance to soil-borne diseases like take-all. This discovery has implications for creating disease-resistant lines of wheat using modern technologies.
Researchers discovered a total of 23 new compounds in the endophytic fungus P. dangeardii, including azaphilone monomers, dimers, and trimers with unique structures. The compounds showed significant cytotoxicities, anti-inflammatory, or antioxidant activities.
Researchers at Earlham Institute created a new automated workflow using liquid handling robots to identify the genetic basis of preventing plant pathogens. The new technology screened 2,880 mutants in just 11 hours, identifying a gene cluster linked to growth inhibition of the common potato pathogen.
PML bodies are found to physically restrict access to DNA methylation enzymes, suppressing gene activation. The study sheds light on a new role of PML bodies in regulating gene expression by manipulating 3D nuclear organization.
Researchers have identified a cluster of over 800 genes that evolved to become 'plastic', allowing modern Daphnia to adjust its gene expression in response to phosphorus levels. This adaptability helps mitigate the effects of eutrophication, a major global threat to freshwater environments.
A new study found that certain gut bacteria, such as Bacteroides species, have acquired large immunity gene clusters to neutralize toxins from other bacteria. These clusters are actively acquiring new genes to protect against emerging threats.
A software tool called MetaMiner has been developed to identify bioactive molecules and their producing microbial genes for therapeutic use. The tool speeds up the discovery process, identifying 31 known RiPPs and seven new ones in about two weeks.
Researchers at the University of Illinois have discovered a new biochemical trick used by microbes to produce an antimicrobial compound effective against malaria. The discovery reveals a completely unknown production pathway, which may lead to the development of more efficient and cost-effective methods for producing similar compounds.
Scientists at the University of Illinois have developed a technique to activate large silent gene clusters in Streptomyces bacteria, yielding new natural products and potential anti-microbial drugs. By using transcription factor decoys, researchers successfully expressed genes that had previously remained dormant.
Researchers at the University of Warwick have discovered a novel acid antibiotic, Scleric Acid, by engineering DNA from soil bacteria. The compound shows moderate antibacterial activity against Mycobacterium tuberculosis and has potential applications as a biocatalyst for manufacturing high-value chemicals.
Scientists deciphered the biosynthetic gene cluster for furanosteroid demethoxyviridin, a nanomolar-potency inhibitor of phosphatidylinositol 3-kinase (PI3K). The research group identified key enzymes involved in the biosynthesis pathway.
Scientists have developed a systematic approach to screen for molecules produced by molds, finding 17 new natural products in three species. The technology, called FAC-MS, uses genomics and data analytics to identify gene clusters that produce valuable chemicals.
Researchers at Princeton University have discovered a master switch that 'switches on' silent biosynthetic gene clusters in bacteria, leading to the production of new compounds with anti-parasitic properties. The global regulator, scmR, acts as a gatekeeper for expression and can be eliminated genetically to release molecules of interest.
Researchers use CRISPR-Cas9 gene-editing technology to activate silent genes in Streptomyces bacteria, revealing potential new compounds with distinct structures that could lead to novel classes of drugs. The study aims to combat antibiotic resistance and cancer by identifying new chemical scaffolds.
Scientists have examined the globin gene cluster in zebrafish to understand 3D genome folding and its relationship to gene expression. They found that adult and embryonic globin genes are spatially separated in the genome, with distinct chromatin domains and organization.
Researchers developed software RODEO to identify clusters of genes indicating an organism's ability to synthesize therapeutically promising molecules. The tool uses machine learning approach to recognize predictive genomic features and has been successfully applied to a class of molecules called lasso peptides.
Researchers at Uppsala University found that genes frequently collaborate in large clusters or networks to regulate traits. This study highlights the importance of considering gene interactions when predicting genetic effects on individuals.
Scientists at MIT and HHMI use a new imaging technique to observe short-lived enzyme clusters that play a central role in triggering mRNA production and controlling gene transcription. These clusters, which remain stable for up to 24 seconds, can significantly impact gene expression.
A newly discovered photosynthetic bacterium has been found to be abundantly present in diverse environments, including freshwater lakes and water treatment plants. Researchers believe this bacterium holds promise for producing biofuels by transferring its genes to other organisms.
Researchers at the University of Illinois have developed a database that analyzes microbial genomic data to speed up the discovery of new therapeutic drugs. The database allows scientists to identify promising gene clusters and predict the production of natural products, enabling them to target specific bacterial strains for study.
A recent study identifies rare variants in the APOB gene in families with exceptional longevity, highlighting its potential role in lipid transport and cholesterol metabolism. The findings suggest that genetic factors influencing lipid metabolism may contribute to human longevity.
A new strategy to quickly screen whole libraries of compounds has been developed to find elicitors that turn on silent gene clusters. Two silent gene clusters were successfully activated, leading to the discovery of a new metabolite.
Researchers analyzed genomic data from The Cancer Genome Atlas and identified three molecular clusters in lower-grade brain tumors. Tumors with IDH1/IDH2 mutations and co-deletion of chromosome arms 1p and 19q have a median survival of around eight years, while those without these mutations have a median survival of only 18 months.
Researchers have developed a novel DNA engineering technique to discover potentially valuable functions hidden within bacterial genomes. By reprogramming gene expression, they were able to increase the production of previously unknown compounds with useful biomedical applications.
Scientists demonstrate the existence of two distinct regulatory domains controlling arm and hand formation, revealing a complex genetic switch that enables wrist emergence. The study sheds light on the molecular processes governing limb development, highlighting the intricate dialogue between genes and regulatory elements.
Researchers analyzed the genome of C. botulinum bacteria to understand how they acquired their deadly neurotoxin gene cluster. The study found that the bacteria picked up the cluster in a single event and discovered fragments of other toxin genes, suggesting a 'hotspot' for gene transfer.
Researchers at University of York and GlaxoSmithKline have identified a complex gene cluster responsible for producing the medicinal compound noscapine. This discovery will accelerate breeding of high-noscapine poppy varieties, which could provide a reliable source of this valuable medicine.