Biochemical and molecular markers in renal cell carcinoma: an update and future prospects

Cancer is a big problem in the developed world as well as in developing countries. Renal cell carcinoma (RCC) accounts for approximately 3% of adult malignancies and 90-95% of neoplasms arising from the kidney. RCC is more common in men than in women (2:1), and it most often occurs in patients between the ages of 50-70 years. In all cancers the cancerous cells release particular kind of proteins (called tumour markers) and blood tests are used to detect the presence of these markers. These tumour markers nowadays are an area of interest for oncologists who search for a possible solution in the detection and treatment of RCC. Different kinds of biochemical and molecular markers such as ferritin, MN/CA9, apoptotic index, p53, IL-2, gamma-enolase, CD44, CD95, chromosome instability and loss of heterozygosity have been tested in RCC, but so far no marker fulfils one or the other criteria to be considered as an ideal marker for RCC. This review gives basic and updated information about the different kinds of biomarkers studied in RCC and about the role implementation of genomics and proteomics in RCC.     

FliZ Is a posttranslational activator of FlhD4C2-dependent flagellar gene expression

Flagellar assembly proceeds in a sequential manner, beginning at the base and concluding with the filament. A critical aspect of assembly is that gene expression is coupled to assembly. When cells transition from a nonflagellated to a flagellated state, gene expression is sequential, reflecting the manner in which the flagellum is made. A key mechanism for establishing this temporal hierarchy is the sigma(28)-FlgM checkpoint, which couples the expression of late flagellar (P(class3)) genes to the completion of the hook-basal body. In this work, we investigated the role of FliZ in coupling middle flagellar (P(class2)) gene expression to assembly in Salmonella enterica serovar Typhimurium. We demonstrate that FliZ is an FlhD(4)C(2)-dependent activator of P(class2)/middle gene expression. Our results suggest that FliZ regulates the concentration of FlhD(4)C(2) posttranslationally. We also demonstrate that FliZ functions independently of the flagellum-specific sigma factor sigma(28) and the filament-cap chaperone/FlhD(4)C(2) inhibitor FliT. Furthermore, we show that the previously described ability of sigma(28) to activate P(class2)/middle gene expression is, in fact, due to FliZ, as both are expressed from the same overlapping P(class2) and P(class3) promoters at the fliAZY locus. We conclude by discussing the role of FliZ regulation with respect to flagellar biosynthesis based on our characterization of gene expression and FliZ's role in swimming and swarming motility.     

Dissociation (Ds) constructs, mapped Ds launch pads and a transiently-expressed transposase system suitable for localized insertional mutagenesis in rice

We have developed a transiently-expressed transposase (TET)-mediated Dissociation (Ds) insertional mutagenesis system for generating stable insertion lines in rice which will allow localized mutagenesis of a chromosomal region. In this system, a Ds containing T-DNA construct was used to produce Ds launch pad lines. Callus tissues, from single-copy Ds/T-DNA lines, were then transiently infected with Agrobacterium harbouring an immobile Ac (iAc) construct, also containing a green fluorescent protein gene (sgfpS65T) as the visual marker. We have regenerated stable Ds insertion lines at a frequency of 9–13% using selection for Ds excision and GFP counter selection against iAc and nearly half of them were unique insertion lines. Double transformants (iAc/Ds) were also obtained and their progeny yielded ~10% stable insertion lines following excision and visual marker screening with 50% redundancy. In general, more than 50% of the Ds reinsertions were within 1 cM of the launch pad. We have produced a large number of single-copy Ds/T-DNA launch pads distributed over the rice chromosomes and have further refined the Ds/T-DNA construct to enrich for “clean” single-copy T-DNA insertions. The availability of single copy “clean” Ds/T-DNA launch pads will facilitate chromosomal region-directed insertion mutagenesis. This system provides an opportunity for distribution of gene tagging tasks among collaborating laboratories on the basis of chromosomal locations. Electronic Supplementary Material Supplementary material is available for this article at and is accessible for authorized users.     

The rate of protein secretion dictates the temporal dynamics of flagellar gene expression

Flagellar gene expression is temporally regulated in response to the assembly state of the growing flagellum. The key mechanism for enforcing this temporal hierarchy in Salmonella enterica serovar Typhimurium is the sigma(28)-FlgM checkpoint, which couples the expression of the late flagellar (P(class3)) genes to the completion of the hook-basal body. This checkpoint is triggered when FlgM is secreted from the cell. In addition to the sigma(28)-FlgM checkpoint, a number of other regulatory mechanisms respond to the secretion of late proteins. In this work, we examined how middle (P(class2)) and late (P(class3)) gene expression is affected by late protein secretion. Dynamic analysis of flagellar gene expression identified a novel mechanism where induction of P(class2) activity is delayed either when late protein secretion is abolished or when late protein secretion is increased. Using a number of different approaches, we were able to show that this mechanism did not involve any known flagellar regulator. Furthermore, the changes in P(class2) activity were not correlated with the associated changes in P(class3) activity, which was found to be proportional to late protein secretion rates. Our data indicate that both P(class2) and P(class3) promoters are continuously regulated in response to assembly and late protein secretion rates. These results suggest that flagellar regulation is more complex than previously thought.     

Genetic structure,diversity, and allelic richness in composite collection and reference set in chickpea (<Emphasis Type="Italic">Cicer arietinum</Emphasis>L.)

Background  

Plant genetic resources (PGR) are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program conceptualized the development of "composite collections" and extraction of "reference sets" from these for more efficient tapping of global crop-related genetic resources. In this study, we report the genetic structure, diversity and allelic richness in a composite collection of chickpea using SSR markers, and formation of a reference set of 300 accessions.     

An efficient leaf-disc culture method for the regeneration via somatic embryogenesis and transformation of grape (Vitis vinifera L.)

By manipulating hormone levels, light intensities and temperature, we have developed an efficient leaf-disc method for the regeneration of plants via embryogenesis and for transformation in four genotypes of Vitis vinifera L. In MS basal medium supplemented with 1 mg l^-1 6-benzylaminopurine (BAP) and 0.1 mg l^-1 2,4-dichlorophenoxyacetic acid, leaf discs cultured for 2 weeks under dark conditions produced calli in over 80% of the cultures. These subsequently differentiated into pro-embryos and embryos only if kept under conditions of low light intensity (15 µE m^-2 s^-1) for 2 weeks before being transferred to conditions of high light intensity (60 µE m^-2 s^-1). If the calli were directly transferred to high light intensity, the differentiation into embryos was blocked and the calli turned pink. The somatic embryos germinated at a frequency of about 10% on NN basal medium and about 32% on NN medium supplemented with 1 mg l^-1BAP and 0.1 mg l^-1 indole-3-butyric acid. The embryos, however, germinated when pre-exposed to a low temperature of 4°C for 2 weeks. If they were transferred directly to room temperature under conditions of high light intensity (60 µE m^-2 s^-1), shoot buds were produced, whereas under conditions of low light intensity (15 µE m^-2 s^-1) secondary embryogenesis was induced. About 90-95% of the in vitro grown plantlets could be successfully transferred to soil. The above method was also applicable for developing transgenic embryos whose transgenic nature was monitored using #-glucuronidase as a reporter gene.     

Ectopic expression of the spike protein of Rice Ragged Stunt Oryzavirus in transgenic rice plants inhibits transmission of the virus to insects

Rice ragged stunt oryzavirus (RRSV) replicates in both its insect vector, Nilaparvata lugens, and its plant host, rice, and has a complex multi-component particle bearing spikes on its outer surface. Transgenic rice lines expressing the 39 kDa spike protein showed good resistance to infection by RRSV. Furthermore, N. lugens fed on these plants prior to feeding on RRSV-infected plants were significantly protected against RRSV infection. The viral titre in insects initially fed on transgenic plants and then on RRSV-infected plants was inversely proportional to the levels of the 39 kDa protein expressed in the transgenic plants. This suggests that the 39 kDa protein interferes with the interaction between the intact virus particles and insect cell receptors and that the spike protein of RRSV contributes to vector specificity. This approach would probably be a more environment-friendly and sustainable method of virus control than by actual eradication of insect vectors.     

UV-B response of cucumber seedlings grown under metal halide and high pressure sodium/deluxe lamps

UV-B-sensitive (Poinsett) and -insensitive (Ashley) cultivars of cucumber ( Cucumis sativus L.) were grown in growth chambers at 600 μmol m⁻²s⁻¹ of photosynthetically active radiation provided by metal halide (MH) or high pressure sodium/deluxe (HPS/DX) lamps. Plants were irradiated 15 days from seeding for 6 h per day under 18. 2 kJ m⁻² day⁻¹ of biologically effective UV-B (UV-B_BE) radiation. One of the most pronounced effects of UV-B was a 27 to 78% increase in phenylalanine ammonialyase (PAL) activity. UV-B also increased total polyamines. Catalase and superoxide dismutase varied greatly in their response to UV-B. There were no interactive effects on PAL or catalase activity, or total polyamines. There was a UV × PAR source interaction for superoxide dismutase activity. UV-B increased chlorosis and decreased height, dry weight and leaf area. Stem elongation, biomass production, leaf enlargement and chlorosis were greater under HPS/DX lamps than under MH lamps. Chlorosis was greater in Poinsett than in Ashley and in lower leaves than in upper ones. Aside from chlorosis, there were no interactive effects of UV-B, PAR source or cultivar on any of the growth parameters measured, suggesting that the growth response of cucumber seedlings to UV-B is unaffected by PAR source or cultivar. Similarly, except for SOD activity, the biochemical response to UV-B was also not influenced by PAR source or cultivar.     

Heat shock tolerance and antioxidant activity in moth bean seedlings treated with tetcyclacis

Moth bean (Vigna aconitifolia (Jacq.) Marechal cv. Jaadia) seeds were germinated in the presence of 0, 18, or 36 M solutions of the gibberellin biosynthesis inhibitor, tetcyclacis. After 72 h, seedlings were exposed to 22 or 48°C for 90 min. The 48°C temperature dramatically increased total electrolyte and sugar leakage from the seedlings, particularly in the controls. Tetcyclacis reduced electrolyte and sugar leakage at 48°C by 15–35% compared to the 48°C controls. High temperature increased malondialdehyde concentration in control seedlings but not in treated seedlings indicating that tetcyclacis inhibited high temperature-induced lipid peroxidation. Relative to the control, tetcyclacis tended to increase the total activities of catalase and peroxidase in the seedlings. In contrast, tetcyclacis tended to decrease ascorbic acid oxidase activity, particularly at 48°C. These results suggest that tetcyclacis conferred at least some heat shock tolerance to moth bean seedlings. This increased tolerance was correlated with increased activities of some antioxidant systems.