Research reading and comparing genomes. Covers disease redefinition, pangenome-guided breeding, crop pathogens, and reference genomes for neuroscience.
A study of 135 bacteria and 16 primitive microorganisms reveals large- and small-scale organizational patterns in their genomes, which are highly nonrandom. The findings suggest that evolution of prokaryotes is constrained by both gene content and genome arrangement on chromosomes.
The DOE JGI is accepting letters of intent for new CSP projects until January 13, 2006, with a focus on advancing the nation's energy security. The institute will prioritize proposals that translate genomic information into discoveries for developing cleaner domestic energy options.
Researchers at McMaster University have successfully sequenced the woolly mammoth genome, providing a new understanding of evolution and allowing for the potential recreation of extinct hybrid animals. The discovery has significant implications for fields such as conservation and genetics.
Scientists at The Institute for Genomic Research have sequenced the genome of Aspergillus fumigatus, a fungus that can cause human infections. The 28 Mb genome consists of 8 chromosomes with over 10,000 genes, which researchers are now searching to identify unique virulence factors.
Researchers have successfully sequenced the DNA of a woolly mammoth, comparing it to African and Indian elephant genomes. The study provides unprecedented insight into the evolution and extinction of the species.
Researchers harness dog genome data to study genetic diseases, breed characteristics, and skeletal variation. The findings highlight the dog's potential as a valuable model organism in genetics and medical research.
A new microbial genome sequence shows that C. hydrogenoformans can convert water and carbon monoxide to hydrogen, making it an excellent starting point for clean fuel production. The microbe's unique protein machines allow it to use carbon monoxide in different ways, making it more efficient than other species.
Scientists suggest prioritizing organisms based on evolutionary divergence to maximize sequence diversity, offering a more efficient approach than considering multiple factors simultaneously. This 'greedy strategy' allows centers to select the best candidates one at a time without compromising overall effectiveness.
The fourth version of IMG, a collaborative effort between DOE JGI and the Lawrence Berkeley National Laboratory, adds organism phenotype characterizations and enhances comparative analysis capabilities. The update features extended Analysis Carts and improved functional profiles across organisms.
A team of researchers has identified key genes responsible for the Spanish flu's extreme virulence, which could lead to the development of effective antivirals and vaccines. The study also suggests that certain FDA-approved flu medications may be effective against future strains of the virus.
Researchers at The Institute for Genomic Research predict that infinite genomes may never be fully described due to the continuous emergence of new genes in bacteria and viruses. By analyzing eight isolates of Group B Strep, TIGR scientists discovered a core genome with an average of 1806 genes present across all strains.
The latest version of IMG, a collaborative effort between the DOE JGI and Lawrence Berkeley National Laboratory, enables users to add annotations and save analysis results. The update also features improved comparative analysis capabilities and a new training workshop designed for teachers and students.
Researchers discovered that thermophilic bacteria have an abundance of disulfide bonds, which improve protein stability and boost heat-tolerance. The study identified a specific protein, protein disulfide oxidoreductase (PDO), playing a key role in forming these bonds.
A new technique called piggyBac has been developed to systematically inactivate genes in the mouse genome, enabling researchers to understand the functions of individual genes. This method uses a reliable gene-transposing tool that can insert itself into the genomes of human and mouse cells.
The completed rice genome sequence provides a raw material for studies aimed at improving the agricultural yield of the world's most important food source. The sequence reveals some 37,500 genes on the 12 chromosomes of rice, closely related to other major cereal grasses.
The complete sequence of the rice genome has been announced, providing a genetic toolkit for breeders to develop novel strains that are highly productive, disease-resistant, and environmentally friendly. This breakthrough has significant implications for global food security and sustainable agriculture.
A recent study reveals that symbiotic bacteria, such as Blochmannia, exhibit exceptional genomic stability despite rapid protein evolution. Genome sequencing of the black carpenter ant mutualist revealed that all shared genes were completely conserved in both genomes, indicating a striking lack of genetic change over millions of years.
Researchers discover key biochemical tools that cold-adapted bacteria use to survive in subzero temperatures, including cell membranes packed with polyunsaturated fatty acids and protective solutes inside cells. The study also reveals potential industrial applications for cold-hardy enzymes found in the Colwellia psychrerythraea genome.
A large-scale genomic study found that co-circulating minor variants of the flu virus can exchange genes and create novel, epidemiologically significant strains. This process can lead to an epidemic with just one or two more mutations, challenging the traditional view of epidemic flu.
Researchers have identified gene sequences involved in the host-parasite relationship and parasite metabolism, providing potential vaccine candidates. The sequencing of trypanosome genomes has significant challenges due to repetitive sequences but promises to advance tropical medicine by helping develop new drugs against these diseases.
Researchers have discovered a shared genetic core among three deadly parasites, which could lead to the development of new drugs targeting these diseases. The genome studies found that the parasites share approximately 6,200 conserved genes, providing potential targets for treatment.
Researchers have identified 34 mutations resulting in embryonic lethality, attributing it to defects in cellular proliferation, gastrulation, and other developmental processes. The study predicts that between 13.7% and 19% of all mouse genes are necessary for embryonic viability.
Researchers found nearly equal proportions of two different sexes in a worldwide collection of 290 specimens, indicating recent evolutionary history of sexual activity. This discovery could lead to new strains with increased ability to cause disease and infect humans.
A genome study of the beneficial microbe Pseudomonas fluorescens Pf-5 has identified new chemical pathways that may help boost plant health and combat plant diseases. The research, published in Nature Biotechnology, reveals the potential for this microbe to produce new antibiotic compounds.
DOE JGI scientists have overcome major challenges to sequence DNA from ancient cave bear specimens, yielding 40,000-year-old genomic data. The breakthrough enables comparison with modern brown bears and polar bears, shedding light on human predecessors.
The new IMG 1.1 version features enhanced capabilities to improve the efficiency of genome analysis, including a function to compare gene occurrence profiles and support infrastructure for comparative organism statistics. The tool continues to be updated quarterly with new public and DOE JGI genomes.
The University of Wisconsin-Madison's Grid Laboratory of Wisconsin (GLOW) is a campus-wide distributed computing environment that harnesses spare processing power from hundreds of individual computers. This allows researchers to sort through massive DNA sequences and power simulations in a fraction of the time previously required. By a...
A study of gene expression in a microbial community found over 2,000 proteins produced by five key species, including unique enzymes that maintain protein structure in acidic conditions. The community thrives in hot, highly acidic environments, with large numbers of proteins not resembling any other known proteins.
Researchers developed Environmental Genomic Tags (EGTs) to assess environment vitality and signal progress in remediating contaminated environments. The EGT approach captures a DNA profile of a particular niche, reflecting the presence and levels of nutrients, pollutants, and other environmental features.
Researchers analyzed whale skeletons and farm soil using metagenomics, discovering specialized bacteria that thrive in these environments. The study provides a new understanding of the diversity of microbial life on earth, with potential applications in fields such as agriculture and medicine.
The study reveals novel receptors that enable the fungus to recognize its environment, as well as secreted proteins used to damage rice plants. The M. grisea genome contains retro-elements, which may contribute to its rapid evolution of new strains.
The DOE JGI has launched a public online microbial genome data clearinghouse, IMG, to facilitate the analysis and comparison of microbial genomes. The platform offers a comprehensive system for exploring and annotating DOE JGI-sequested genomes, enabling scientists to tap into the diversity of microbial environments.
Researchers have discovered three new bacterial species, Wolbachia wAna, wSim, and wMoj, in the genomes of Drosophila fruit flies. The discovery was made by scanning raw genomic data from the Trace Archive, a public repository of sequencing projects.
Scientists have found that functional forms of missing tRNA genes can be created by copying from distant DNA sequences and joining them. This discovery sheds light on the evolution of extremophiles in the Archaea kingdom.
The genome sequence of V. fischeri reveals surprising parallels with Vibrio cholerae and other pathogens, indicating toxin activity genes. The research sheds light on the connection between quorum sensing and global regulatory networks in bacterial cell communication.
A new method assigns biological functions to unknown genes, enabling genome comparison, by integrating experimental and computational analyses. This approach identifies functional proteins in 97% of hypothetical genes and provides a framework for ranking their precision and confidence.
Researchers at New York University have discovered over 150 additional genes required to make an embryo, bringing the total estimated number of genes needed to around 2,600. The study also sheds light on how these genes work in humans and provides clues for understanding human diseases.
Researchers found evidence of meiosis in Giardia intestinalis, a unicellular protist parasite, suggesting that eukaryotes have been capable of sex for a long time. The discovery provides insight into the evolution of sexual reproduction in eukaryotic cells.
Researchers have mapped the genome of Cryptococcus neoformans, a fungus that causes severe inflammation of the brain in people with HIV and those taking chemotherapy or steroid treatments. The study identified 30 new genes involved in the fungus's biosynthesis, offering potential targets for treatment.
Dehalococcoides bacteria can adapt to various environmental conditions through the use of mobile genetic elements, allowing them to degrade chlorinated pollutants. The genome sequence of Strain 195 reveals its ability to turn genes on and off in response to environmental cues.
Researchers have completed the first complete genome sequence of Dehalococcoides ethenogenes, a bacterium that dechlorinates major groundwater pollutants. The study reveals the microbe's unique metabolic capabilities, including 19 reductive dehalogenases and five hydrogenase complexes.
The UGA/Penn team aims to develop a single-access point for genomic and related information about Apicomplexa parasites, enabling accelerated vaccine, diagnostic, and therapeutic development. The database will link existing databases for Plasmodium species, Toxoplasma gondii, and Cryptosporidum parvum.
The sequencing of S. pomeroyi, an ocean bacterium, provides valuable tools to understand its functions and impact on the atmosphere. Early investigation reveals 4,283 regions in the genome that predict protein synthesis and cellular machinery.
The study of Silicibacter pomeroyi's genome reveals that marine bacterioplankton use inorganic compounds for energy, enabling efficient carbon use in low-nutrient oceans. The research also shows the microbe's adaptability to ocean hot spots, rich areas of organic matter.
The root-knot nematode causes more than half of $100 billion in annual crop and plant damage worldwide. Researchers will sequence its genome for a better understanding of its attack mechanisms.
The NIDCR-launched study aims to detect unique patterns of gene expression in oral bacterial communities that predict periodontal diseases. The researchers will store biological information in a searchable online database, allowing for more precise diagnosis and treatment.
Researchers find that transposable elements, called Pack-MULEs, copy themselves prolifically and rearrange genes, making them newly discovered players in evolution. The discovery elevates these little-considered elements to potentially major players in the process of evolution.
The Lancet editorial advocates for free access to genome data, highlighting its benefits in accelerating research on diseases such as SARS. This open-access policy promotes international cooperation, trust, and altruism, offering a compelling alternative to bioweapons.
The study reveals that methanotrophs, including M. capsulatus, have multiple pathways for using methane and can respond to environmental changes by switching between different chemical pathways. This flexibility could make them a valuable tool for reducing methane emissions.
Researchers have cracked the genetic code of B. mallei, a highly evolved pathogen that causes glanders, an infectious equine disease. The study reveals a tightly regulated set of virulence genes and genomic instability, which may explain why B. mallei can evade host immune responses.
A multidisciplinary team reports the first complete genome sequence of Methylococcus capsulatus, a methane-loving bacterium that can consume methane and produce protein. The genome provides insights into methanotroph biology and its potential for bioremediation, reducing greenhouse gas emissions and degrading pollutants.
A team of researchers has developed a fast-track method to identify regulatory sequences in the genome that control cell growth and development. The study, published in Science, used a unique algorithm called Improbizer to predict where these regulatory sequences might be found in the genome.
A study by Rachel Mueller and David Wake rewrites the evolutionary history of salamanders, finding inconsistencies with accepted classifications. The research suggests that some terrestrial salamanders regained their larval stage after moving back to water, contradicting previous assumptions.
Scientists have developed a new method to quickly identify the precise landing sites of gene regulators in yeast, which are essential for understanding how genes and their regulators 'talk' to each other. This breakthrough could lead to a better understanding of diseases such as diabetes and cancer.
A study found that pigs have more babies due to gene duplication, which allowed them to adapt to climate change. The researchers used a multi-disciplinary approach to investigate the evolution of aromatase genes and their role in altering reproductive biology.
Using fruit flies, scientists confirm bursicon's role in hardening exoskeletons after molting and enabling wing development. The discovery could lead to precise timing of pest control measures for migratory locust outbreaks.
Researchers have successfully mapped the genomes of two devastating fungal pathogens, Phytophtora sojae and Phytophtora ramorum, which causes sudden oak death disease. The genome sequences will aid in developing better detection methods and tracking the spread of the disease.
The 'tango array' device can sort particles ranging from bacterial cells to DNA segments in a matter of seconds, distinguishing them by size. This breakthrough technology has the potential to greatly accelerate biological research and replace some centrifuge devices.
Researchers developed a novel method to pinpoint rapidly evolving genes in pathogens, revealing potential drug targets for tuberculosis and malaria. The technique analyzes genome sequences to identify genes under selective pressure, allowing for the discovery of previously unknown genes.
Researchers have decoded the genome of Desulfovibrio vulgaris, a microbe responsible for microbially-influenced corrosion. The analysis provides insights into the microbe's capacity and flexibility to reduce metals, potentially leading to new methods for preventing corrosion and remediating metallic pollutants.