Reproducible gene expression measurement among multiple laboratories obtained in a blinded study using standardized RT (StaRT)-PCR

BACKGROUND

A method that provides standardized data and is relatively inexpensive and capable of high throughput is a prerequisite to the development of a meaningful gene expression database suitable for conducting multi-institutional clinical studies based on expression measurement. Standardized RT (StaRT)-PCR has all these characteristics. In addition, the method must be reproducible. StaRT-PCR has high intralaboratory reproducibility. The purpose of this study is to determine whether StaRT-PCR provides similar interlaboratory reproducibility.

METHODS AND RESULTS

In a blinded interlaboratory study, expression of ten genes was measured by StaRT-PCR in a complementary DNA sample provided to each of four laboratories. The average coefficient of variation for interlaboratory comparison of the nine quantifiable genes was 0.48. In all laboratories, expression of one of the genes was too low to be measured.

CONCLUSION

Because StaRT-PCR data are standardized and numerical and the method is reproducible among multiple laboratories, it will allow development of a meaningful gene expression database.

Development of a 1.4-Mb BAC/PAC contig and physical map within the critical region for complete X-linked congenital stationary night blindness in Xp11.4

A physical map internal to the markers DXS1368 and DXS228 was developed for the p11.4 region of the human X chromosome. Twenty-four BACs and 10 PACs with an average insert size of 149 kb were aligned to form a contig across an estimated 1.4 Mb of DNA. This contig, which has on average fourfold clone coverage, was assembled by STS and EST content analysis using 46 markers, including 8 ESTs, two retinally expressed genes, and 22 new STSs developed from BAC- and PAC-derived DNA sequence. The average intermarker distance was 30 kb. This physical map provides resources for high-resolution mapping as well as suitable clones for large-scale sequencing efforts in Xp11.4, a region known to contain the gene for complete X-linked congenital stationary night blindness.

Construction of a 1.5-Mb bacterial artificial chromosome contig in Xp11.23, a region of high gene content

To generate sequence-ready templates for the gene-rich Xp11.23 region, we have constructed a 1.5-Mb bacterial artificial chromosome (BAC) contig spanning the interval between the DNA markers OATL1 and DXS255. The contig includes 28 BACs, ranging in size from 58 to 258 kb with an average size of 135 kb, which provide 2.5-fold coverage of the region. The BAC contig was constructed based entirely on the content of 40 DNA markers from a previously established YAC contig and 11 new markers developed from BAC-end DNA sequences, 4 of which were required to close gaps in the map. There was no evidence of rearrangement, instability, or chimerism in any of the BAC clones. The BAC cloning system appears to provide robust and total physical coverage of this gene-rich region with clones that are suitable for DNA sequencing.

Localization by fluorescence in situ hybridization (FISH) of human mitochondrial polymerase gamma (POLG) to human chromosome band 15q24-->q26, and of mouse mitochondrial polymerase gamma (Polg) to mouse chromosome band 7E, with confirmation by direct sequence analysis of bacterial artificial chromosomes (BACs)

Cloned cDNAs for the human mitochondrial DNA polymerase gamma (POLG) were identified by homology with the yeast mitochondrial DNA polymerase catalytic subunit (MIP). Fluorescence in situ hybridization (FISH) of human and mouse bacterial artificial chromosomes (BACs), hybridized by radioactively labeled POLG cDNAs, mapped to human chromosome band 15q24-->q26, as well as to mouse chromosome band 7E. Direct sequencing of the BAC DNA without subcloning confirmed the presence of both human POLG and mouse mitochondrial DNA polymerase gamma (Polg) in the respective BACs.

Proteolysis of V antigen from Yersinia pestis

Lcr-plasmids of yersiniae are known to mediate a unique low calcium response characterised by restriction of growth in vitro with induction of putative virulence factors including yersiniae outer membrane-peptides (YOPs) and V antigen (Lcr+). A medium was developed that permitted expression of high yields of V by Yersinia pestis KIM in large fermenter vessels. Immunoblots of specific precipitates prepared by prior molecular sieving showed that native unaggregated V exists as a monomeric 37,000 dalton peptide. Fractionation by precipitation with (NH4)2SO4 and chromatography on phenyl-Sepharose, DEAE cellulose, Sephacryl S200, calcium hydroxyapatite, and Sephadex G200 yielded highly purified antigen as judged by sodium dodecyl sulfate-polyacrylamide gel electrophoresis of parallel preparations from Lcr+ and Lcr- yersiniae. However, yields of V obtained by this process were unexpectedly low. As determined from immunoblots with monospecific polyclonal and monoclonal anti-V, this loss of activity occurred as a function of evident degradation at every step of purification yielding antigenic fragments of about 36,000, 34,000, 31,000, 30,000, and 28,000 daltons. Neutral or acidic pH favored hydrolysis; insignificant cleavage occurred in viable Lcr+ cells of Y. pestis or in culture supernatant fluids. V in neutral cytoplasm from Yersinia pseudotuberculosis or Yersinia enterocolitica did not undergo comparable degradation.

Transmembrane electrical potential in Rickettsia prowazekii and its relationship to lysine transport

The transmembrane electrical potential (delta psi) generated by Rickettsia prowazekii metabolizing glutamic acid or ATP was determined by flow dialysis with the lipophilic cation tetraphenylphosphonium and with lysine. At pH 7.0, the rickettsiae generated a delta psi as measured by tetraphenylphosphonium distribution of 90 mV. Under similar conditions, cells of R.prowazekii concentrated lysine to a gradient indicating a delta psi of 90 mV. Energy-starved cells of R. prowazekii were able to utilize exogenously supplied ATP as well as glutamic acid to generate a delta psi of 110 mV at pH 8.0. Lysine transport was markedly affected by environmental pH, the optimum pH ranging from 8.0 to 8.5. delta psi as measured with tetraphenyl-phosphonium was similarly affected in this system, with values ranging from 70 mV at pH 6.0 to 100 mV at pH 8.0. Respiration rates were also affected by the external pH, with a maximum rate of 28 nmol of O2 consumed per min per mg of rickettsial protein occurring at pH 8.0. The pH effects were readily reversible and with a rapid onset.

Effect of exogenous nucleotides on Ca2+ dependence and V antigen synthesis in Yersinia pestis

Cells of Yersinia pestis strain EV76 are known to cease growth after a shift from 26 to 37 degrees C in neutral Ca2+-deficient medium; this effect is potentiated by Mg2+. With 2.5 mM Mg2+ and no added Ca2+, restriction was relaxed at elevated pH at which maximum cell yields occurred in the presence of 20 mM exogenous ATP. This ATP-dependent growth was inhibited by Ca2+ or 20 mM Mg2+; the nucleotide was neither transported into the organism nor hydrolyzed extracellularly. With strain EV76, ATP could be replaced by GTP but not other nucleotides, nucleosides, free bases, or pyrophosphate. CTP and UTP also promoted growth of strain KIM, in which limited division also occurred with nucleoside di- and monophosphates. Intracellular V antigen was detected 1 h after temperature shift in Ca2+-deficient medium containing 20 mM Mg2+, a time corresponding to the earliest known events associated with restriction (shutoff of stable RNA synthesis and reduction of adenylate energy charge). Maximum yield of V was obtained 2 h later when cell division ceased; the titer of the antigen remained constant thereafter. The specific activity of V in cells grown with ATP was significantly reduced, especially at elevated pH. These results would be expected if exogenous nucleotides promote growth by sequestering sufficient Mg2+ to prevent restriction of cell division mediated by V antigen.

Plague virulence antigens from Yersinia enterocolitica

The virulence of Yersinia enterocolitica, biotype 2, serotype O:8, in mice is related to its ability to produce plague V and W antigens. V and W antigens in Y. enterocolitica are shown to be immunologically identical to the previously described V and W antigens of Yersinia pestis and Yersinia pseudotuberculosis.

Consequences of Ca2+ deficiency on macromolecular synthesis and adenylate energy charge in Yersinia pestis

A 37 but not 26 degrees C virulent Yersinia pestis is known to require at least 2.5 mM Ca2+ for growth; this requirement is potentiated by Mg2+. After shift of log-phase cells (doubling time of 2 h) from 26 to 37 degrees C in Ca2+-deficient medium, shutoff of net ribonucleic acid synthesis preceded that of protein and cell mass. With 2.5 mM Mg2+, about two doublings in cell mass and number occurred before restriction with synthesis of sufficient deoxyribonucleic acid to account for initiation and termination of two postshift rounds of chromosome replication. Temperature shift with 20 mMMg2+ resulted in a single doubling of cell mass and number with one round of chromosome replication. Subsequent to shutoff of ribonucleic acid accumulation, ribonucleoside but not deoxyribonucleoside triphosphate pools became reduced to about 50% of normal values and the adenylate energy change fell from about 0.8, typical of growing cells, to about 0.6. Excretion of significant concentrations of adenine nucleotides under both permissive and restrictive conditions was observed. Only trace levels (less than 0.01 microM ol/g [dry weight]) of guaninosine 5'-diphosphate 3'-diphosphate accumulated under restrictive or permissive conditions; guanosine 5'-triphosphate 3'-diphosphate was not detected. Return of fully restricted cells from 37 to 26 degrees C with Ca2+ resulted in prompt growth, whereas addition of Ca2+ at 37 degrees C was ineffective. This finding indicates that the observed temperature-sensitive lesion in ribonucleic acid synthesis that results in restriction can be prevented but not reversed by cultivation with Ca2+.