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1.  Statistical Methods for Comparative Phenomics Using High-Throughput Phenotype Microarrays* 
We propose statistical methods for comparing phenomics data generated by the Biolog Phenotype Microarray (PM) platform for high-throughput phenotyping. Instead of the routinely used visual inspection of data with no sound inferential basis, we develop two approaches. The first approach is based on quantifying the distance between mean or median curves from two treatments and then applying a permutation test; we also consider a permutation test applied to areas under mean curves. The second approach employs functional principal component analysis. Properties of the proposed methods are investigated on both simulated data and data sets from the PM platform.
PMCID: PMC2942029  PMID: 20865133
functional data analysis; principal components; permutation tests; phenotype microarrays; high-throughput phenotyping; phenomics; Biolog
2.  SARS in Hospital Emergency Room 
Emerging Infectious Diseases  2004;10(5):782-788.
Thirty-one cases of severe acute respiratory syndrome (SARS) occurred after exposure in the emergency room at the National Taiwan University Hospital. The index patient was linked to an outbreak at a nearby municipal hospital. Three clusters were identified over a 3-week period. The first cluster (5 patients) and the second cluster (14 patients) occurred among patients, family members, and nursing aids. The third cluster (12 patients) occurred exclusively among healthcare workers. Six healthcare workers had close contact with SARS patients. Six others, with different working patterns, indicated that they did not have contact with a SARS patient. Environmental surveys found 9 of 119 samples of inanimate objects to be positive for SARS coronavirus RNA. These observations indicate that although transmission by direct contact with known SARS patients was responsible for most cases, environmental contamination with the SARS coronavirus may have lead to infection among healthcare workers without documented contact with known hospitalized SARS patients.
PMCID: PMC3323223  PMID: 15200809
Severe acute respiratory syndrome; healthcare workers; environmental contamination; real-time reverse transcriptase–polymerase chain reaction
4.  A 60-Kilodalton Immunodominant Glycoprotein Is Essential for Cell Wall Integrity and the Maintenance of Cell Shape in Streptococcus mutans 
Infection and Immunity  2001;69(11):6987-6998.
We have demonstrated previously by Western blotting that in naturally sensitized humans, the serum or salivary antibody response to Streptococcus mutans was directed predominantly to a protein antigen with a size of approximately 60-kDa. To identify this immunodominant antigen, specific serum antibodies were eluted from immunoblots and five positive clones with inserts ranging in length from 3 to 8 kb from identical chromosomal loci were obtained by screening a genomic expression library of Streptococcus mutans GS-5. Amino acid sequencing established the identity of this immunodominant antigen, a 60-kDa immunodominant glycoprotein (IDG-60), to be a cell wall-associated general stress protein GSP-781, which was originally predicted to have a molecular mass of approximately 45 kDa based on the derived nucleotide sequence. Discrepancy in the molecular mass was also observed in recombinant his-tagged IDG-60 (rIDG-60) expressed from Escherichia coli. Glycosylation, consisting of sialic acid, mannose galactose, and N-acetylgalactosamine, was detected by lectin binding to IDG-60 in cell wall extracts from S. mutans and rIDG-60 expressed in vivo or translated in vitro. Despite the presence of multiple Asn or Ser or Thr glycosylation sites, IDG-60 was resistant to the effect of N-glycosidase F and multiple O-glycosidase molecules but not to β-galactosidase. Insertional inactivation of the gene encoding IDG-60, sagA, resulted in a retarded growth rate, destabilization of the cell wall, and pleiomorphic cell shape with multifold ingrowth of cell wall. In addition, distinct from the parental GS-5 strain, the isogenic mutant GS-51 was unable to survive the challenge of low pH and high osmotic pressure or high temperature. Expression of the wild-type gene in trans within GS-51 from plasmid pDL277 complemented the growth defect and restored normal cell shape. These results suggested that IDG-60 is essential for maintaining the integrity of the cell wall and the uniformity of cell shape, both of which are indispensable for bacteria survival under stress conditions.
PMCID: PMC100079  PMID: 11598074
5.  Metabolic Instability of Escherichia coli Cyclopropane Fatty Acid Synthase Is Due to RpoH-Dependent Proteolysis 
Journal of Bacteriology  2000;182(15):4288-4294.
Cyclopropane fatty acids (CFAs) are generally synthesized as bacterial cultures enter stationary phase. In Escherichia coli, the onset of CFA synthesis results from increased transcription of cfa, the gene encoding CFA synthase. However, the increased level of CFA synthase activity is transient; the activity quickly declines to the basal level. We report that the loss of CFA activity is due to proteolytic degradation dependent on expression of the heat shock regulon. CFA synthase degradation is unaffected by mutations in the lon, clpP, and groEL genes or by depletion of the intracellular ATP pools. It seems likely that CFA synthase is the target of an unidentified energy-independent heat shock regulon protease. This seems to be the first example of heat shock-dependent degradation of a normal biosynthetic enzyme.
PMCID: PMC101943  PMID: 10894739
6.  d-Allose Catabolism of Escherichia coli: Involvement of alsI and Regulation of als Regulon Expression by Allose and Ribose 
Journal of Bacteriology  1999;181(22):7126-7130.
Genes involved in allose utilization of Escherichia coli K-12 are organized in at least two operons, alsRBACE and alsI, located next to each other on the chromosome but divergently transcribed. Mutants defective in alsI (allose 6-phosphate isomerase gene) and alsE (allulose 6-phosphate epimerase gene) were Als−. Transcription of the two allose operons, measured as β-galactosidase activity specified by alsI-lacZ+ or alsE-lacZ+ operon fusions, was induced by allose. Ribose also caused derepression of expression of the regulon under conditions in which ribose phosphate catabolism was impaired.
PMCID: PMC94189  PMID: 10559180
7.  Effect of ppGpp on Escherichia coli Cyclopropane Fatty Acid Synthesis Is Mediated through the RpoS Sigma Factor (ςS) 
Journal of Bacteriology  1999;181(2):572-576.
Strains of Escherichia coli carrying mutations at the relA locus are deficient in cyclopropane fatty acid (CFA) synthesis, a phospholipid modification that occurs as cultures enter stationary phase. RelA protein catalyzes the synthesis of guanosine-3′,5′-bisdiphosphate (ppGpp); therefore, ppGpp was a putative direct regulator of CFA synthesis. The nucleotide could act by increasing either the activity or the amount of CFA synthase, the enzyme catalyzing the lipid modification. We report that the effect of RelA on CFA synthesis is indirect. In vitro and in vivo experiments show no direct interaction between ppGpp and CFA synthase activity. The relA effect is due to ppGpp-engendered stimulation of the synthesis of the alternative sigma factor, RpoS, which is required for function of one of the two promoters responsible for expression of CFA synthase.
PMCID: PMC93412  PMID: 9882672
8.  Inhibition of Colicin E2 Activity by Bacterial Lipopolysaccharide 
Journal of Bacteriology  1970;104(3):1106-1109.
Lipopolysaccharide isolated from colicin E2-sensitive Escherichia coli and from “receptor-minus” mutants inhibits the activity of colicin E2. Lipid A and the polysaccharide fraction obtained by mild acid hydrolysis of lipopolysaccharide are inactive either alone or when tested in combination. Periodate oxidation of lipopolysaccharide destroys over 85% of its inhibition activity.
PMCID: PMC248266  PMID: 16559082

Results 1-8 (8)