Application of the common base method to regression and analysis of covariance (ANCOVA) in qPCR experiments and subsequent relative expression calculation.

BACKGROUND: Quantitative polymerase chain reaction (qPCR) is the technique of choice for quantifying gene expression. While the technique itself is well established, approaches for the analysis of qPCR data continue to improve. RESULTS: Here we expand on the common base method to develop procedures for testing linear relationships between gene expression and either a measured dependent variable, independent variable, or expression of another gene. We further develop functions relating variables to a relative expression value and develop calculations for determination of associated confidence intervals. CONCLUSIONS: Traditional qPCR analysis methods typically rely on paired designs. The common base method does not require such pairing of samples. It is therefore applicable to other designs within the general linear model such as linear regression and analysis of covariance. The methodology presented here is also simple enough to be performed using basic spreadsheet software.

A soil bacterium alters sex determination and rhizoid development in gametophytes of the fern Ceratopteris richardii.

Gametophytes of the fern Ceratopteris richardii develop into either hermaphrodites or males. As hermaphrodites develop, they secrete antheridiogen, or ACE, into the environment, inducing male development in undifferentiated gametophytes. Hermaphrodites are composed of archegonia, antheridia, rhizoids and a notch meristem, while males consist of antheridia and rhizoids. Much of the research on sexual and morphological development concerns gametophytes grown in sterile environments. Using biochemical and molecular techniques we identify a soil bacterium and explore its effects on sexual and rhizoid development. Hermaphrodite and male gametophytes were exposed to this bacterium and the effects on sexual development, rhizoid length and rhizoid number were explored. The bacterium was identified as a pseudomonad, Pseudomonas nitroreducens. Gametophytes grown in the presence of the pseudomonad were more likely to develop into hermaphrodites across all gametophyte densities. Across all gametophyte sizes, hermaphrodites had rhizoids that were 2.95× longer in the presence of the pseudomonad while males had rhizoids that were 2.72× longer in the presence of the pseudomonad. Both hermaphrodite and male gametophytes developed fewer rhizoids in the presence of the pseudomonad. Control hermaphrodites produced 1.23× more rhizoids across all gametophyte sizes. For male gametophytes grown in the absence of the pseudomonad, the rate of increase in the number of rhizoids was greater with increasing size in the control than the rate of increase in males grown in the presence of the pseudomonad. The pseudomonad may be acting on gametophyte sexual development via several potential mechanisms: degradation of ACE, changes in nutrient availability or phytohormone production. The pseudomonad may also increase rhizoid number through production of phytohormones or changes in nutrient availability.

A common base method for analysis of qPCR data and the application of simple blocking in qPCR experiments.

BACKGROUND: qPCR has established itself as the technique of choice for the quantification of gene expression. Procedures for conducting qPCR have received significant attention; however, more rigorous approaches to the statistical analysis of qPCR data are needed. RESULTS: Here we develop a mathematical model, termed the Common Base Method, for analysis of qPCR data based on threshold cycle values (C q ) and efficiencies of reactions (E). The Common Base Method keeps all calculations in the logscale as long as possible by working with log10(E) ∙ C q , which we call the efficiency-weighted C q value; subsequent statistical analyses are then applied in the logscale. We show how efficiency-weighted C q values may be analyzed using a simple paired or unpaired experimental design and develop blocking methods to help reduce unexplained variation. CONCLUSIONS: The Common Base Method has several advantages. It allows for the incorporation of well-specific efficiencies and multiple reference genes. The method does not necessitate the pairing of samples that must be performed using traditional analysis methods in order to calculate relative expression ratios. Our method is also simple enough to be implemented in any spreadsheet or statistical software without additional scripts or proprietary components.

Synthesis and characterization of inorganic-organic hybrid gallium selenides.

Two semiconducting hybrid gallium selenides, [Ga6Se9(C6H14N2)4][H2O] (1) and [C6H14N2][Ga4Se6(C6H14N2)2] (2), were prepared using a solvothermal method in the presence of 1,2-diaminocyclohexane (1,2-DACH). Both materials consist of neutral inorganic layers, in which 1,2-DACH is covalently bonded to gallium. In 1, the organic amine acts as a monodentate and a bidentate ligand, while in 2, bidentate and uncoordinated 1,2-DACH molecules coexist.

[C7H10N][In3Se5]: a layered selenide with two indium coordination environments.

A new layered indium selenide, [C(7)H(10)N][In(3)Se(5)] (1), has been prepared solvothermally using 3,5-dimethylpyridine as a solvent and structure-directing agent. This material, which was characterized by single-crystal and powder X-ray diffraction, thermogravimetric analysis, UV-vis diffuse-reflectance spectroscopy, IR spectroscopy, and elemental analysis, crystallizes in the monoclinic space group P2(1)/c [a = 3.9990(4) Å, b = 16.7858(15) Å, c = 23.930(2) Å, and ß = 94.728(4)°]. The crystal structure of 1 contains anionic layers of stoichiometry [In(3)Se(5)](-) in which indium atoms with octahedral and tetrahedral coordination coexist. The [In(3)Se(5)](-) layers are interspaced by monoprotonated 3,5-dimethylpyridinium cations. A closely related material, [C(7)H(10)N][In(3)Se(5)] (2), was obtained when using 2,6-dimethylpyridine instead of 3,5-dimethylpyridine.

Diminished expression of C/EBPalpha in skin carcinomas is linked to oncogenic Ras and reexpression of C/EBPalpha in carcinoma cells inhibits proliferation.

The basic leucine zipper transcription factor, CCAAT/enhancer binding protein alpha (C/EBPalpha) is involved in mitotic growth arrest and has been implicated as a human tumor suppressor in acute myeloid leukemia. We have previously shown that C/EBPalpha is abundantly expressed in mouse epidermal keratinocytes. In the current study, the expression of C/EBPalpha was evaluated in seven mouse skin squamous cell carcinoma (SCC) cell lines that contain oncogenic Ha-Ras. C/EBPalpha mRNA and protein levels were greatly diminished in all seven SCC cell lines compared with normal primary keratinocytes, whereas C/EBPbeta levels were not dramatically changed. Reexpression of C/EBPalpha in these SCC cell lines resulted in the inhibition in SCC cell proliferation. To determine whether the decrease in C/EBPalpha expression observed in the SCC cell lines also occurred in the carcinoma itself, immunohistochemical staining for C/EBPalpha in mouse skin SCCs was conducted. All 14 SCCs evaluated displayed negligible C/EBPalpha protein expression and normal C/EBPbeta levels compared with the epidermis and all 14 carcinomas contained mutant Ras. To determine whether oncogenic Ras is involved in the down-regulation of C/EBPalpha, BALB/MK2 keratinocytes were infected with a retrovirus containing Ras12V, and C/EBPalpha protein, mRNA and DNA binding levels were determined. Keratinocytes infected with the retrovirus containing oncogenic Ras12V displayed greatly diminished C/EBPalpha protein, mRNA and DNA binding levels. In addition, BALB/MK2 cells containing endogenous mutant Ras displayed diminished C/EBPalpha expression and the ectopic expression of a dominant-negative RasN17 partially restored C/EBPalpha levels in these cells. These results indicate that oncogenic Ras negatively regulates C/EBPalpha expression and the loss of C/EBPalpha expression may contribute to the development of skin SCCs.