Nucleotide sequence analysis of the inversion termini located within IS3 elements α3β3 and β5α5 of Escherichia coli K-12

This paper presents the first detailed structural analysis of termini of an inversion mediated by recombination between Escherichia coli native IS elements. The complete nucleotide sequence of the inversion termini in the lactose region of Escherichia coli K-12 confirms our previous suggestion that the inversion occurred by homologous recombination between α3β3 and β5α5 IS3 elements (D.J. Savic, J. Bacteriol. 140:311-319, 1979; D.J. Savic, S. Romac, and S.D. Ehrlich, J. Bacteriol. 155:943-946, 1983). The data show a slight structural divergence of α3β3 and β5α5 elements, but they do not reveal new sequences within recomhined IS3 elements that could influence the expression of nearby genes

РЫНОЧНАЯ ОЦЕНКА АКТИВОВ ОТЕЧЕСТВЕННЫХ КРЕДИТНЫХ ОРГАНИЗАЦИЙ: ОСОБЕННОСТИ И МЕТОДЫ ПРОВЕДЕНИЯ

N this article, the author summarizes the accumulated experience of methodological approaches to the valuation of variousproperty and analyzes their application tothe banking sector, namely for different occasions and objectives of the valuation(revaluation) of assets of credit institutions in the current economic conditions; formulates some suggestions to improveboth the approaches to market valuationof an object such as banking assets, andthe methods of its implementation in Russian conditions.Вданнойстатьеавторобобщаетнакопленныйметодологическийопытподходов к стоимостной оценке различных объектовсобственностиианализирует их применение к банковской сфере, а именно для различных случаев и задач проведения стоимостной оценки (переоценки) активов кредитных организацийвсовременныхэкономических условиях; формулирует некоторые предложения по совершенствованию как самихподходовкрыночнойоценке такогообъекта, какбанковскиеактивы, так иметодовеепроведениявроссийских условиях

Alternative splicing enriched cDNA libraries identify breast cancer-associated transcripts

<p>Abstract</p> <p>Background</p> <p>Alternative splicing (AS) is a central mechanism in the generation of genomic complexity and is a major contributor to transcriptome and proteome diversity. Alterations of the splicing process can lead to deregulation of crucial cellular processes and have been associated with a large spectrum of human diseases. Cancer-associated transcripts are potential molecular markers and may contribute to the development of more accurate diagnostic and prognostic methods and also serve as therapeutic targets. Alternative splicing-enriched cDNA libraries have been used to explore the variability generated by alternative splicing. In this study, by combining the use of trapping heteroduplexes and RNA amplification, we developed a powerful approach that enables transcriptome-wide exploration of the AS repertoire for identifying AS variants associated with breast tumor cells modulated by <it>ERBB2</it> (<it>HER-2/neu</it>) oncogene expression.</p> <p>Results</p> <p>The human breast cell line (C5.2) and a pool of 5 ERBB2 over-expressing breast tumor samples were used independently for the construction of two AS-enriched libraries. In total, 2,048 partial cDNA sequences were obtained, revealing 214 alternative splicing sequence-enriched tags (ASSETs). A subset with 79 multiple exon ASSETs was compared to public databases and reported 138 different AS events. A high success rate of RT-PCR validation (94.5%) was obtained, and 2 novel AS events were identified. The influence of <it>ERBB2</it>-mediated expression on AS regulation was evaluated by capillary electrophoresis and probe-ligation approaches in two mammary cell lines (Hb4a and C5.2) expressing different levels of <it>ERBB2</it>. The relative expression balance between AS variants from 3 genes was differentially modulated by <it>ERBB2</it> in this model system.</p> <p>Conclusions</p> <p>In this study, we presented a method for exploring AS from any RNA source in a transcriptome-wide format, which can be directly easily adapted to next generation sequencers. We identified AS transcripts that were differently modulated by <it>ERBB2</it>-mediated expression and that can be tested as molecular markers for breast cancer. Such a methodology will be useful for completely deciphering the cancer cell transcriptome diversity resulting from AS and for finding more precise molecular markers.</p

Transcriptomic Analysis of Human Retinal Detachment Reveals Both Inflammatory Response and Photoreceptor Death

Background Retinal detachment often leads to a severe and permanent loss of vision and its therapeutic management remains to this day exclusively surgical. We have used surgical specimens to perform a differential analysis of the transcriptome of human retinal tissues following detachment in order to identify new potential pharmacological targets that could be used in combination with surgery to further improve final outcome. Methodology/Principal Findings Statistical analysis reveals major involvement of the immune response in the disease. Interestingly, using a novel approach relying on coordinated expression, the interindividual variation was monitored to unravel a second crucial aspect of the pathological process: the death of photoreceptor cells. Within the genes identified, the expression of the major histocompatibility complex I gene HLA-C enables diagnosis of the disease, while PKD2L1 and SLCO4A1 -which are both down-regulated- act synergistically to provide an estimate of the duration of the retinal detachment process. Our analysis thus reveals the two complementary cellular and molecular aspects linked to retinal detachment: an immune response and the degeneration of photoreceptor cells. We also reveal that the human specimens have a higher clinical value as compared to artificial models that point to IL6 and oxidative stress, not implicated in the surgical specimens studied here. Conclusions/Significance This systematic analysis confirmed the occurrence of both neurodegeneration and inflammation during retinal detachment, and further identifies precisely the modification of expression of the different genes implicated in these two phenomena. Our data henceforth give a new insight into the disease process and provide a rationale for therapeutic strategies aimed at limiting inflammation and photoreceptor damage associated with retinal detachment and, in turn, improving visual prognosis after retinal surgery

Cultured adult rat jejunal explants as a model for studying regulation of CYP3A

Enzymes within the CYP3A subfamily are major Phase I drug-metabolizing enzymes present in hepatocytes and small bowel enterocytes. These enzymes are highly inducible in the liver by many structurally diverse compounds, including a number of commonly used medications. Studies indicate that CYP3A enzymes present in small bowel enterocytes are also inducible. However, the regulation of CYP3A enzymes in this tissue has not been well characterized, in part because in vivo studies are difficult, especially in humans. Our goal was to develop an in vitro model to study the regulation of CYP3A in enterocytes. To this end, we defined culture conditions under which adult rat jejunal explants maintained viable appearing villi for 21 hr. When dexamethasone, the prototypical inducer of CYP3A1 in rat hepatocytes, was added to the culture medium, there was a time-dependent induction of CYP3A1 mRNA and CYP3A protein in explant enterocytes which was essentially indistinguishable from the time course of induction of CYP3A1 mRNA and protein in enterocytes in vivo. This effect of dexamethasone appeared to be specific since dexamethasone had no consistent effect on the explant concentration of another enterocyte specific mRNA, intestinal fatty acid binding protein. Using this explant culture model, we found that CYP3A1 mRNA was also inducible by clotrimazole but we were unable to detect induction by rifampicin or troleandomycin. Our observations suggest that jejunal explants may provide an appropriate model for the study of the regulation of CYP3A and other drug-metabolizing enzymes.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/30618/1/0000258.pd

Transcriptional analysis of the bovine herpesvirus 1 Cooper isolate

Blot hybridization analysis of infected bovine herpesvirus 1 (BHV-1) cellular RNA isolated at various times post infection and after treatment with specific metabolic inhibitors was used to characterize transcription of the BHV-1 Cooper isolate. Synthesis of BHV-1 RNA was detected as early as 3 h post infection and reached a maximum at six to eight hours post infection. The most transcriptionally active area of the genome was between map units 0.110 to 0.195, within the Hin dIII I fragment. From the entire genome a total of 59 transcripts ranging in size from approximately 0.6 to 10 kilobases were characterized as belonging to one of three distinct classes. Using the protein synthesis inhibitor cycloheximide, three immediate-early transcripts were identified as originating from the internal inverted repeat region between map units 0.734 and 0.842, corresponding to the Hin dIII D fragment. Using phosphonoacetic acid to prevent virus DNA synthesis by inhibition of the BHV-1 DNA polymerase, 28 early transcripts were recognized. The remaining 28 transcripts, classified as late RNA, were detected without the use of metabolic inhibitors at 6 to 8 h post infection. Transcription of early and late RNA was not restricted to any specific area of the genome. Eighty percent of the transcripts from both the Hin dIII A fragment, between map units 0.381 to 0.537 within the unique long segment, and the Hin dIII K fragment, between map units 0.840 to 0.907 of the unique short segment, were designated as belonging to the early class.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/41672/1/705_2005_Article_BF01316744.pd