Fragments of mitochondrial DNA (mtDNA) transferred to the nuclear genome are called nuclear mitochondrial DNAs (NUMTs). We report here a comparison of NUMT content between genomes from two species of the same genus. Analysis of the genomes of Phytophthora sojae and R ramorum revealed large differences in the NUMT content of the two genomes: 16.27… [Read More]

Prochlorococcus ecotypes are a useful system for exploring the origin and function of diversity among closely related microbes. The genetic variability between phenotypically distinct strains that differ by less that 1% in 16S ribosomal RNA sequences occurs mostly in genomic islands. Island genes appear to have been acquired in part by phage-mediated lateral gene transfer,… [Read More]

Pathogenic bacteria dispersed into the outdoor air from natural events or human activity are an important concern affecting public health, agriculture, ecological health and international security. Recent studies in atmospheric microbiology have contributed to our ability to detect bacterial pathogens in air samples, increased our knowledge of the spatial and temporal dispersal of aerosolized bacteria… [Read More]

A newly compiled data set of nearly complete sequences of the large subunit of the nuclear ribosome (LSU or 28S) sampled from 31 diverse medusozoans greatly clarifies the phylogenetic history of Cnidaria. These data have substantial power to discern among many of the competing hypotheses of relationship derived from prior work. Moreover, LSU data provide… [Read More]

Bacterial species with high DNA sequence similarity to pathogens could affect the specificity of assays designed to detect biological threat agents in environmental samples. The natural presence of four pathogenic bacteria, Bacillus anthracis, Clostridium perfringens, Francisella tularensis, and Yersinia pestis and their closely related species, was determined for a large collection of soil and aerosol… [Read More]

Microbiologists conducting surveys of bacterial and archaeal diversity often require comparative alignments of thousands of 16S rRNA genes collected from a sample. The computational resources and bioinformatics expertise required to construct such an alignment has inhibited high- throughput analysis. It was hypothesized that an online tool could be developed to efficiently align thousands of 16S… [Read More]

In this paper, a new classifier design methodology, confidence-based classifier design, is proposed to design classifiers with controlled confidence. This methodology is under the guidance of two optimal classification theories, a new classification theory for designing optimal classifiers with controlled error rates and the C.K. Chow’s optimal classification theory for designing optimal classifiers with controlled… [Read More]

A 16S rRNA gene database ) addresses limitations of public repositories by providing chimera screening, standard alignment, and taxonomic classification using multiple published taxonomies. It was found that there is incongruent taxonomic nomenclature among curators even at the phylum level. Putative chimeras were identified in 3% of environmental sequences and in 0.2% of records derived… [Read More]

This paper proposes a new active learning approach, confidence- based active learning, for training a wide range of classifiers. This approach is based on identifying and annotating uncertain samples. The uncertainty value of each sample is measured by its conditional error. The approach takes advantage of current classifiers’ probability preserving and ordering properties. It calibrates… [Read More]

The HYDIN gene located in human chromosome band 16q22.2 is a large gene encompassing 423 kb of genomic DNA that has been suggested as a candidate for an autosomal recessive form of congenital hydrocephalus. We have found that the human HYDIN locus has been very recently duplicated, with a nearly identical 360-kb paralogous segment inserted… [Read More]