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Whole-genome random sequencing and assembly of Haemophilus influenzae Rd.
An approach for genome analysis based on sequencing and assembly of unselected pieces of DNA from the whole chromosome has been applied to obtain the complete nucleotide sequence (1,830,137 base pairs) of the genome from the bacterium Haemophilus influenzae Rd. This approach eliminates the need for initial mapping efforts and is therefore applicable to the vast array of microbial species for which genome maps are unavailable. The H. influenzae Rd genome sequence (Genome Sequence DataBase...
Antarctic Epiblog: Leaving McMurdo
Ice formation outside McMurdo Station After we took our samples out at the ice edge, we returned to McMurdo Station for several intense days of demobilization. We had to return all of the large drills, power equipment and camping gear, and spent a considerable time preparing our own gear for shipment back to the United States. Our samples and some of our critical gear will go by air transport to Port Huemene in California, and the rest will be shipped back to the US by...
Assembly of eukaryotic algal chromosomes in yeast.
Synthetic genomic approaches offer unique opportunities to use powerful yeast and Escherichia coli genetic systems to assemble and modify chromosome-sized molecules before returning the modified DNA to the target host. For example, the entire 1 Mb Mycoplasma mycoides chromosome can be stably maintained and manipulated in yeast before being transplanted back into recipient cells. We have previously demonstrated that cloning in yeast of large (> ~ 150 kb), high G + C (55%)...
Maintaining a Healthy Upper Respiratory Tract Microbiome May Help Prevent Secondary Infections in Influenza A Patients
(La Jolla, California)—May 26, 2020—Scientists from the J. Craig Venter Institute (JCVI), Icahn School of Medicine at Mount Sinai, and Pontificia Universidad Católica de Chile examined changes in the upper respiratory tract (URT) microbiome during an influenza A virus (IAV) infection. The study examined the URT microbiome in both healthy and IAV-infected human and ferret cohorts. Humans and ferrets share similar lung physiology, and both are known to be susceptible to and transmit...
The Human Microbiome and Cancer.
Recent scientific advances have significantly contributed to our understanding of the complex connection between the microbiome and cancer. Our bodies are continuously exposed to microbial cells, both resident and transient, as well as their byproducts, including toxic metabolites. Circulation of toxic metabolites may contribute to cancer onset or progression at locations distant from where a particular microbe resides. Moreover, microbes may migrate to other locations in the human body and...
Identification of individuals by trait prediction using whole-genome sequencing data.
Prediction of human physical traits and demographic information from genomic data challenges privacy and data deidentification in personalized medicine. To explore the current capabilities of phenotype-based genomic identification, we applied whole-genome sequencing, detailed phenotyping, and statistical modeling to predict biometric traits in a cohort of 1,061 participants of diverse ancestry. Individually, for a large fraction of the traits, their predictive accuracy beyond ancestry and...
TIGR, IBEA, and TCAG to Create New High-Throughput Genomic Sequencing Facility
August 15, 2002 ROCKVILLE, MD--August 15, 2002--The Institute for Genomic Research (TIGR), Institute for Biological Energy Alternatives (IBEA) and The Center for the Advancement of Genomics (TCAG), all not-for-profit organizations supported by the J. Craig Venter Science Foundation, announced today their plan to create a next generation, high-throughput DNA sequencing facility in Rockville, Maryland. The sequencing of the first two genomes of free-living organisms in 1995 at TIGR...
The malaria genome sequencing project: complete sequence of Plasmodium falciparum chromosome 2.
An international consortium has been formed to sequence the entire genome of the human malaria parasite Plasmodium falciparum. We sequenced chromosome 2 of clone 3D7 using a shotgun sequencing strategy. Chromosome 2 is 947 kb in length, has a base composition of 80.2% A + T, and contains 210 predicted genes. In comparison to the Saccharomyces cerevisiae genome, chromosome 2 has a lower gene density, a greater proportion of genes containing introns, and nearly twice as many proteins...
Physiological basis for xenotransplantation from genetically modified pigs to humans.
The collective efforts of scientists over multiple decades have led to advancements in molecular and cellular biology-based technologies including genetic engineering and animal cloning that are now being harnessed to enhance the suitability of pig organs for xenotransplantation into humans. Using organs sourced from pigs with multiple gene deletions and human transgene insertions, investigators have overcome formidable immunological and physiological barriers in pig-to-nonhuman primate...
Inflammation-driven deaminase deregulation fuels human pre-leukemia stem cell evolution.
Inflammation-dependent base deaminases promote therapeutic resistance in many malignancies. However, their roles in human pre-leukemia stem cell (pre-LSC) evolution to acute myeloid leukemia stem cells (LSCs) had not been elucidated. Comparative whole-genome and whole-transcriptome sequencing analyses of FACS-purified pre-LSCs from myeloproliferative neoplasm (MPN) patients reveal APOBEC3C upregulation, an increased C-to-T mutational burden, and hematopoietic stem and progenitor cell (HSPC)...