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1.  Allele Distributions at Hybrid Incompatibility Loci Facilitate the Potential for Gene Flow between Cultivated and Weedy Rice in the US 
PLoS ONE  2014;9(1):e86647.
The accumulation of independent mutations over time in two populations often leads to reproductive isolation. Reproductive isolation between diverging populations may be reinforced by barriers that occur either pre- or postzygotically. Hybrid sterility is the most common form of postzygotic isolation in plants. Four postzygotic sterility loci, comprising three hybrid sterility systems (Sa, s5, DPL), have been recently identified in Oryza sativa. These loci explain, in part, the limited hybridization that occurs between the domesticated cultivated rice varieties, O. sativa spp. japonica and O. sativa spp. indica. In the United States, cultivated fields of japonica rice are often invaded by conspecific weeds that have been shown to be of indica origin. Crop-weed hybrids have been identified in crop fields, but at low frequencies. Here we examined the possible role of these hybrid incompatibility loci in the interaction between cultivated and weedy rice. We identified a novel allele at Sa that seemingly prevents loss of fertility in hybrids. Additionally, we found wide-compatibility type alleles at strikingly high frequencies at the Sa and s5 loci in weed groups, and a general lack of incompatible alleles between crops and weeds at the DPL loci. Our results suggest that weedy individuals, particularly those of the SH and BRH groups, should be able to freely hybridize with the local japonica crop, and that prezygotic factors, such as differences in flowering time, have been more important in limiting weed-crop gene flow in the past. As the selective landscape for weedy rice changes due to increased use of herbicide resistant strains of cultivated rice, the genetic barriers that hinder indica-japonica hybridization cannot be counted on to limit the flow of favorable crop genes into weeds.
doi:10.1371/journal.pone.0086647
PMCID: PMC3904945  PMID: 24489758
2.  A Census of Human Soluble Protein Complexes 
Cell  2012;150(5):1068-1081.
SUMMARY
Cellular processes often depend on stable physical associations between proteins. Despite recent progress, knowledge of the composition of human protein complexes remains limited. To close this gap, we applied an integrative global proteomic profiling approach, based on chromatographic separation of cultured human cell extracts into more than one thousand biochemical fractions which were subsequently analyzed by quantitative tandem mass spectrometry, to systematically identify a network of 13,993 high-confidence physical interactions among 3,006 stably-associated soluble human proteins. Most of the 622 putative protein complexes we report are linked to core biological processes, and encompass both candidate disease genes and unnanotated proteins to inform on mechanism. Strikingly, whereas larger multi-protein assemblies tend to be more extensively annotated and evolutionarily conserved, human protein complexes with 5 or fewer subunits are far more likely to be functionally un-annotated or restricted to vertebrates, suggesting more recent functional innovations.
doi:10.1016/j.cell.2012.08.011
PMCID: PMC3477804  PMID: 22939629
3.  Effects of Amino Acid Supplementation on Porin Expression and ToxR Levels in Vibrio cholerae 
Infection and Immunity  2012;80(2):518-528.
Vibrio cholerae responds to environmental changes by altering the protein composition of its outer membrane. In rich medium, V. cholerae expresses almost exclusively the outer membrane porin OmpU, whereas in minimal medium, OmpT is the dominant porin. The supplementation of a minimal medium with a mixture of asparagine, arginine, glutamic acid, and serine (NRES) promotes OmpU production and OmpT repression at levels similar to those seen with rich media. Here we show that the altered Omp profile is not due to an increase in the growth rate in the presence of supplemental amino acids but requires the addition of specific amino acids. The effects of the NRES mix on Omp production were mediated by ToxR, a known regulator of omp gene expression. No changes in the Omp profile were detected in a toxR mutant. Supplementation with the NRES mix resulted in significantly higher levels of ToxR, and the elevated ToxR levels were sufficient to cause a switch in Omp synthesis. The increase in the level of the ToxR protein correlated with an increase in toxR mRNA levels and was observed only when toxR was expressed from its native promoter. ToxS, which is required for ToxR activity, was necessary for NRES-mediated omp gene regulation but not for the increase in ToxR levels. The growth of V. cholerae in the presence of bile acids also resulted in Omp switching, and this required ToxR. However, unlike the NRES mix, bile acids did not increase either ToxR protein or toxR mRNA levels, suggesting a different mechanism of omp gene regulation by bile than that by amino acids.
doi:10.1128/IAI.05851-11
PMCID: PMC3264288  PMID: 22144480
4.  Protein abundances are more conserved than mRNA abundances across diverse taxa 
Proteomics  2010;10(23):4209-4212.
Proteins play major roles in most biological processes; as a consequence, protein expression levels are highly regulated. While extensive post-transcriptional, translational and protein degradation control clearly influence protein concentration and functionality, it is often thought that protein abundances are primarily determined by the abundances of the corresponding mRNAs. Hence surprisingly, a recent study showed that abundances of orthologous nematode and fly proteins correlate better than their corresponding mRNA abundances. We tested if this phenomenon is general by collecting and testing matching large-scale protein and mRNA expression datasets from seven different species: two bacteria, yeast, nematode, fly, human, and plant. We find that steady-state abundances of proteins show significantly higher correlation across these diverse phylogenetic taxa than the abundances of their corresponding mRNAs (p=0.0008, paired Wilcoxon). These data support the presence of strong selective pressure to maintain protein abundances during evolution, even when mRNA abundances diverge.
doi:10.1002/pmic.201000327
PMCID: PMC3113407  PMID: 21089048
5.  Characterization of Vibrio cholerae RyhB: the RyhB Regulon and Role of ryhB in Biofilm Formation  
Infection and Immunity  2005;73(9):5706-5719.
Vibrio cholerae encodes a small RNA with homology to Escherichia coli RyhB. Like E. coli ryhB, V. cholerae ryhB is negatively regulated by iron and Fur and is required for repression of genes encoding the superoxide dismutase SodB and multiple tricarboxylic acid cycle enzymes. However, V. cholerae RyhB is considerably longer (>200 nucleotides) than the E. coli RNA (90 nucleotides), and it regulates the expression of a variety of genes that are not known to be regulated by RyhB in E. coli, including genes involved in motility, chemotaxis, and biofilm formation. A mutant with a deletion in ryhB had reduced chemotactic motility in low-iron medium and was unable to form wild-type biofilms. The defect in biofilm formation was suppressed by growing the mutant in the presence of excess iron or succinate. The wild-type strain showed reduced biofilm formation in iron-deficient medium, further supporting a role for iron in normal biofilm formation. The ryhB mutant was not defective for colonization in a mouse model and appeared to be at a slight advantage when competing with the wild-type parental strain. Other genes whose expression was influenced by RyhB included those encoding the outer membrane porins OmpT and OmpU, several iron transport systems, and proteins containing heme or iron-sulfur clusters. These data indicate that V. cholerae RyhB has diverse functions, ranging from iron homeostasis to the regulation of biofilm formation.
doi:10.1128/IAI.73.9.5706-5719.2005
PMCID: PMC1231101  PMID: 16113288

Results 1-5 (5)