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Human BAC ends quality assessment and sequence analyses.
End sequences from bacterial artificial chromosomes (BACs) provide highly specific sequence markers in large-scale sequencing projects. To date, we have generated >300,000 end sequences from >186,000 human BAC clones with an average read length of >460 bp for a total of 141 Mb covering approximately 4.7% of the genome. Over 60% of the clones have BAC end sequences (BESs) from both ends representing more than fivefold coverage of the human genome by the paired-end clones. Our quality...
Sequence and analysis of the 60 kb conjugative, bacteriocin-producing plasmid pMRC01 from Lactococcus lactis DPC3147.
The complete sequence of pMRC01, a large conjugative plasmid from Lactococcus lactis ssp. lactis DPC3147, has been determined. Using a shotgun sequencing approach, the 60,232 bp plasmid sequence was obtained by the assembly of 1056 underlying sequences (sevenfold average redundancy). Sixty-four open reading frames (ORFs) were identified. Analysis of the gene organization of pMRC01 suggests that the plasmid can be divided into three functional domains, with each approximately 20 kb region...
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...
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...
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...