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The construction of Arabidopsis expressed sequence tag assemblies. A new resource to facilitate gene identification.
The generation of large numbers of partial cDNA sequences, or expressed sequence tags (ESTs), has provided a method with which to sample a large number of genes from an organism. More than 25,000 Arabidopsis thaliana ESTs have been deposited in public databases, producing the largest collection of ESTs for any plant species. We describe here the application of a method of reducing redundancy and increasing information content in this collection by grouping overlapping ESTs representing the...
Revealing Roles of Uncultivated Species in the Oral Microbiome
Many human microbial infectious diseases including oral caries are polymicrobial in nature, and closely associated with ecological conditions of the microbial communities. Oral caries disease is one of the most prevalent and costly bacterial infections in humans. Understanding the metabolism and gene expression profiles as well as inter-species interactions within these complex microbial communities are necessary steps in studying the diseases and finding new treatment solutions. While...
Human Hair Microbiota
Human hair samples are an important trace evidence type for providing leads in forensic investigations. They are used to determine the race, gender, and identity of the individual responsible for a criminal act. Hair also supports its own microbial habitat that is intra- and inter-personal variable, and as such, this little explored substrate has significant potential in forensics microbiome research due to the unique signatures that are available on an individual. We explored...
Optical mapping of Plasmodium falciparum chromosome 2.
Detailed restriction maps of microbial genomes are a valuable resource in genome sequencing studies but are toilsome to construct by contig construction of maps derived from cloned DNA. Analysis of genomic DNA enables large stretches of the genome to be mapped and circumvents library construction and associated cloning artifacts. We used pulsed-field gel electrophoresis purified Plasmodium falciparum chromosome 2 DNA as the starting material for optical mapping, a system for making ordered...
Maternal carriage of Prevotella during pregnancy associates with protection against food allergy in the offspring.
In mice, the maternal microbiome influences fetal immune development and postnatal allergic outcomes. Westernized populations have high rates of allergic disease and low rates of gastrointestinal carriage of Prevotella, a commensal bacterial genus that produces short chain fatty acids and endotoxins, each of which may promote the development of fetal immune tolerance. In this study, we use a prebirth cohort (n = 1064 mothers) to conduct a nested case-cohort study comparing 58 mothers of...
A shotgun optical map of the entire Plasmodium falciparum genome.
The unicellular parasite Plasmodium falciparum is the cause of human malaria, resulting in 1.7-2.5 million deaths each year. To develop new means to treat or prevent malaria, the Malaria Genome Consortium was formed to sequence and annotate the entire 24.6-Mb genome. The plan, already underway, is to sequence libraries created from chromosomal DNA separated by pulsed-field gel electrophoresis (PFGE). The AT-rich genome of P. falciparum presents problems in terms of reliable library...
French Road Sampling Trip Saves Sorcerer II From More Rough Weather!
September 28th 2010 With one last sample to collect and the weather still rough in the Mediterranean, we made the decision to make the Banyuls sample a road sampling trip. So Jeremy and I loaded up a rental car with carboys and headed out at 5 am to drive the 125 miles (200km) to Banyuls France from Barcelona Spain. Driving to Banyuls After being on the boat for a few months straight, the 2 hour drive was a welcome adventure, even with the 5 am departure! We...
Analysis of the complete genome of smallpox variola major virus strain Bangladesh-1975.
We analyzed the 186,102 base pairs (bp) that constitute the entire DNA genome of a highly virulent variola virus isolated from Bangladesh in 1975. The linear, double-stranded molecule has relatively small (725 bp) inverted terminal repeat (ITR) sequences containing three 69-bp direct repeat elements, a 54-bp partial repeat element, and a 105-base telomeric end-loop that can be maximally base-paired to contain 17 mismatches. Proximal to the right-end ITR sequences are another seven 69-bp...
A quality control algorithm for DNA sequencing projects.
Heterologous DNA sequences from rearrangements with the genomes of host cells, genomic fragments from hybrid cells, or impure tissue sources can threaten the purity of libraries that are derived from RNA or DNA. Hybridization methods can only detect contaminants from known or suspected heterologous sources, and whole library screening is technically very difficult. Detection of contaminating heterologous clones by sequence alignment is only possible when related sequences are present in a...
Precision medicine screening using whole-genome sequencing and advanced imaging to identify disease risk in adults.
Reducing premature mortality associated with age-related chronic diseases, such as cancer and cardiovascular disease, is an urgent priority. We report early results using genomics in combination with advanced imaging and other clinical testing to proactively screen for age-related chronic disease risk among adults. We enrolled active, symptom-free adults in a study of screening for age-related chronic diseases associated with premature mortality. In addition to personal and family medical...