[Show abstract][Hide abstract] ABSTRACT: Purple aerobic anoxygenic phototrophs (AAPs) are the only organisms known to capture light energy to enhance growth only in
the presence of oxygen but do not produce oxygen. The highly adaptive AAPs compose more than 10% of the microbial community
in some euphotic upper ocean waters and are potentially major contributors to the fixation of the greenhouse gas CO2. We present the complete genomic sequence and feature analysis of the AAP Roseobacter denitrificans, which reveal clues to its physiology. The genome lacks genes that code for known photosynthetic carbon fixation pathways,
and most notably missing are genes for the Calvin cycle enzymes ribulose bisphosphate carboxylase (RuBisCO) and phosphoribulokinase.
Phylogenetic evidence implies that this absence could be due to a gene loss from a RuBisCO-containing α-proteobacterial ancestor.
We describe the potential importance of mixotrophic rather than autotrophic CO2 fixation pathways in these organisms and suggest that these pathways function to fix CO2 for the formation of cellular components but do not permit autotrophic growth. While some genes that code for the redox-dependent
regulation of photosynthetic machinery are present, many light sensors and transcriptional regulatory motifs found in purple
photosynthetic bacteria are absent.
Journal of Bacteriology 03/2007; 189(3):683-90. DOI:10.1128/JB.01390-06 · 2.81 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Yersinia pestis, the causative agent of plague, is responsible for some of the greatest epidemic scourges of mankind. It is widespread in the western United States, although it has only been present there for just over 100 years. As a result, there has been very little time for diversity to accumulate in this region. Much of the diversity that has been detected among North American isolates is at loci that mutate too quickly to accurately reconstruct large-scale phylogenetic patterns. Slowly-evolving but stable markers such as SNPs could be useful for this purpose, but are difficult to identify due to the monomorphic nature of North American isolates.
To identify SNPs that are polymorphic among North American populations of Y. pestis, a gapped genome sequence of Y. pestis strain FV-1 was generated. Sequence comparison of FV-1 with another North American strain, CO92, identified 19 new SNP loci that differ among North American isolates.
The 19 SNP loci identified in this study should facilitate additional studies of the genetic population structure of Y. pestis across North America.
PLoS ONE 02/2007; 2(2):e220. DOI:10.1371/journal.pone.0000220 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: We present an algorithm that indirectly makes N<sup>2</sup> sequence comparisons in O(N) with respect to the size of the genome. This algorithm is very applicable in assembling whole genomes from the thousands of DNA sequence fragments that are generated in shotgun sequencing. First, we assume that fragments that share k-mers should overlap in the final assembly. We then catalog all k-mers that exist in the shotgun library and infer links between fragments that share k-mers. These links are then used to represent edges in a graph. This graph is generated in O(N) yet represents the result of comparing every fragment to every other fragment.
3rd International IEEE Computer Society Computational Systems Bioinformatics Conference (CSB 2004), 16-19 August 2004, Stanford, CA, USA; 01/2004