A statistical framework for the design of microarray experiments and effective detection of differential gene expression

Four reasons why you might wish to read this paper: 1. We have devised a new statistical T test to determine differentially expressed genes (DEG) in the context of microarray experiments. This statistical test adds a new member to the traditional T-test family. 2. An exact formula for calculating the detection power of this T test is presented, which can also be fairly easily modified to cover the traditional T tests. 3. We have presented an accurate yet computationally very simple method to estimate the fraction of non-DEGs in a set of genes being tested. This method is superior to an existing one which is computationally much involved. 4. We approach the multiple testing problem from a fresh angle, and discuss its relation to the classical Bonferroni procedure and to the FDR (false discovery rate) approach. This is most useful in the analysis of microarray data, where typically several thousands of genes are being tested simultaneously.Comment: 9 pages, 1 table; to appear in Bioinformatic

Straightforward and sensitive RT-qPCR based gene expression analysis of FFPE samples

Fragmented RNA from formalin-fixed paraffin-embedded (FFPE) tissue is a known obstacle to gene expression analysis. In this study, the impact of RNA integrity, gene-specific reverse transcription and targeted cDNA preamplification was quantified in terms of reverse transcription polymerase chain reaction (RT-qPCR) sensitivity by measuring 48 protein coding genes on eight duplicate cultured cancer cell pellet FFPE samples and twenty cancer tissue FFPE samples. More intact RNA modestly increased gene detection sensitivity by 1.6 fold (earlier detection by 0.7 PCR cycles, 95% CI = 0.593-0.850). Application of gene-specific priming instead of whole transcriptome priming during reverse transcription further improved RT-qPCR sensitivity by a considerable 4.0 fold increase (earlier detection by 2.0 PCR cycles, 95% CI = 1.73-2.32). Targeted cDNA preamplification resulted in the strongest increase of RT-qPCR sensitivity and enabled earlier detection by an average of 172.4 fold (7.43 PCR cycles, 95% CI = 6.83-7.05). We conclude that gene-specific reverse transcription and targeted cDNA preamplification are adequate methods for accurate and sensitive RT-qPCR based gene expression analysis of FFPE material. The presented methods do not involve expensive or complex procedures and can be easily implemented in any routine RT-qPCR practice

Heterogeneity in Ty1-copia group of retroelements in chickpea (Cicer arietinum) genome

Retrotransposons constitute a major fraction of plant genomes and these elements may have played a significant role in evolution and sequence organization of genomes. In order to access the diversity of Ty1-copia group of retroelements, reverse transcriptase (RT) sequences were amplified from chickpea genome, using the primers derived from two conserved domains of RT region. Thirty-six RT regions from independent amplicons were cloned and sequenced. On the basis of homology of deduced amino acids, the RT sequences could be grouped into three major families. The intra-family divergence at amino acid level ranges from 2 to 19%. Though intra-family RT sequences were conserved but no two sequences were identical. The results indicate a high degree of heterogeneity among the Ty1-copia group of retroelements from chickpea. It was possible to isolate RT specific sequences from RNA isolated from stressed seedlings, indicating that some of the retroelements may be functional under certain stress conditions

Style, Narrative, and Cultural Politics in Bullitt

Peter Yates’s 1968 film Bullitt cemented the reputation of its star, Steve McQueen, as “the essence of cool” – to borrow a phrase from the title of the 2005 documentary that reflects on the star’s legacy. As the film reveals, however, and the documentary explores, Bullitt is fraught with narrative problems, its now iconic set-pieces seemingly purchased at the expense of coherent and accessible plot development. Meanwhile the film’s formal experimentation – internally motivated by the thematic preoccupation with “noise” and freeways – heightens the ecstatic presentation of actor/protagonist as image (and of the autonomization of “style” in general), which in turn can be read as an ambivalent response to the cultural politics of the late 1960s. This paper explores the ways in which various elements of style, narrative, and cultural politics interact within the context of the film, placing Bullitt at a pivotal moment in both cinematic and cultural history.info:eu-repo/semantics/publishedVersio

Constraints of FL Motif on the Targeting and Function of Sodium-Bicarbonate Cotransporter 1

A C-terminal dihydrophobic FL motif plays a vital role in the basolateral targeting of sodium bicarbonate cotransporter 1. To further characterize the role of dihydrophobic FL motif, 1). the FL motif in wild type (PFLS) was reversed to LF (PLFS), 2). the FL motif (PFLS) was shifted upstream (FLPS), and 3). the FL motif (PFLS) was shifted downstream (PSFL). The wild type (PFLS) and its mutant (PLFS) were exclusively expressed on the basolateral membrane by con-focal microscopy, however, the mutant (FLPS) and (PSFL) were predominantly mistargeted to the apical membrane and the cytoplasm, respectively. Functional studies showed that the mutant (PSFL) displayed a remarkably reduced current (p value<0.05 vs wild type). The mutant (PSFL) displayed a more reduced membrane surface expression than the wild type and was co-localized with ER marker. The protein sequence spanning FL motif in kNBC1 C-terminal cytoplasmic tail shows a helical structure, mutants (PLFS) and (PSFL) reduce a-helical contents by circular dichroism study. Reversed FL isn't a constraint for basolateral targeting, but shifting it upstream and downstream are ones

Mass Dependent αS\alpha_S Evolution and the Light Gluino Existence

There is an intriguing discrepancy between \alpha_s(M_Z) values measured directly at the CERN $Z_0$-factory and low-energy (at few GeV) measurements transformed to $Q=M_{Z_0}$ by a massless QCD \alpha_s(Q) evolution relation. There exists an attempt to reconcile this discrepancy by introducing a light gluino \gl in the MSSM. We study in detail the influence of heavy thresholds on \alpha_s(Q) evolution. First, we consruct the "exact" explicit solution to the mass-dependent two-loop RG equation for the running \alpha_s(Q). This solution describes heavy thresholds smoothly. Second, we use this solution to recalculate anew \alpha_s(M_Z) values corresponding to "low-energy" input data. Our analysis demonstrates that using {\it mass-dependent RG procedure} generally produces corrections of two types: Asymptotic correction due to effective shift of threshold position; Local threshold correction only for the case when input experiment lies in the close vicinity of heavy particle threshold: $Q_{expt} \simeq M_h$. Both effects result in the effective shift of the \asmz values of the order of $10^{-3}$. However, the second one could be enhanced when the gluino mass is close to a heavy quark mass. For such a case the sum effect could be important for the discussion of the light gluino existence as it further changes the \gl mass.Comment: 13, Late