DNA microspectrophotometry of bone sarcomas in tissue sections as compared to imprint and flow DNA analysis

The aim of the present study was to establish an upper limit of diploidy for microspectrophotometric (MSP) DNA measurements in sections of mesenchymal tissue analyzing DNA data of a large number of normal cell populations. The reliability of this upper limit of diploidy for discriminating between diploid and hyperploid bone sarcomas was tested by analyzing the same tumors by MSP in imprint preparations and flow cytometry (FCM). The median DNA value of control cells in tissue sections was given arbitrary value of DNA index (DI) 1.0, denoting the diploid DNA content. The proportion of cells with DNA values exceeding DI 1.25 (greater than DI 1.25) was determined for each normal cell population. The maximum percentage of cells with DNA values exceeding DI 1.25, encountered by analysis of 91 normal cell populations in tissue sections, was 31%. This percentage was set as an upper limit of diploidy. Hence, tumors with a higher percentage of cells greater than DI 1.25 were classified as hyperploid. When we applied this criterion, 31 of 36 sarcomas analyzed by MSP in tissue sections were hyperploid, which was in complete agreement with FCM and MSP in imprints of the same tumors. Apart from discriminating between diploid and hyperploid tumors, an attempt was made to determine peak DNA values of sarcomas analyzed in tissue sections. Peak DNA values, as defined by a minimum of 30% of the cells within a class width of DI 0.25, could be determined for 23 of 36 tumors. These peak DNA values correlated well with corresponding peaks obtained by FCM.(ABSTRACT TRUNCATED AT 250 WORDS)     

Quantitative plant proteomics

Quantitation is an inherent requirement in comparative proteomics and there is no exception to this for plant proteomics. Quantitative proteomics has high demands on the experimental workflow, requiring a thorough design and often a complex multi-step structure. It has to include sufficient numbers of biological and technical replicates and methods that are able to facilitate a quantitative signal read-out. Quantitative plant proteomics in particular poses many additional challenges but because of the nature of plants it also offers some potential advantages. In general, analysis of plants has been less prominent in proteomics. Low protein concentration, difficulties in protein extraction, genome multiploidy, high Rubisco abundance in green tissue, and an absence of well-annotated and completed genome sequences are some of the main challenges in plant proteomics. However, the latter is now changing with several genomes emerging for model plants and crops such as potato, tomato, soybean, rice, maize and barley. This review discusses the current status in quantitative plant proteomics (MS-based and non-MS-based) and its challenges and potentials. Both relative and absolute quantitation methods in plant proteomics from DIGE to MS-based analysis after isotope labeling and label-free quantitation are described and illustrated by published studies. In particular, we describe plant-specific quantitative methods such as metabolic labeling methods that can take full advantage of plant metabolism and culture practices, and discuss other potential advantages and challenges that may arise from the unique properties of plants.     

Quantitative profiling of polyacetylenes in tissue cultures and plant parts of three species of the Asteraceae

Polyacetylenes are a group of fatty-acid derived specialized metabolites with several C–C-triple bonds and derived compounds which are widely distributed in the plant kingdom, but are especially abundant and structurally diverse in the Asteraceae family. Despite their interesting structural and biological properties, the biosynthesis of polyacetylenes is only poorly understood. We have used three species of the Asteraceae (Carthamus tinctorius, Tagetes patula, and Arctium lappa) to compare their suitability for studies of polyacetylene biosynthesis when used after cultivation on soil or as tissue culture. The polyacetylene profiles detected in different plant parts together with information from the literature indicate that C. tinctorius seedlings and flowers as well as T. patula roots and flower buds are major sites of polyacetylene biosynthesis. Highest levels of polyacetylenes were detected in T. patula [about 30 µmol/g dry weight (d.w.) thiophenes in roots] while A. lappa contained less than 1 µmol/g d.w.. Methyljasmonate (MeJ)-induced T. patula hairy root cultures proved to be an excellent source of butenynyl-bithiophene (200 µmol/g d.w., 43 mg/g d.w.) while T. patula flower buds could serve as a source of pentenynyl-bithiophene and α-terthienyl (5–10 µmol/g d.w.) and C. tinctorius flowers or seedlings as a source of polyacetylenic C₁₃ hydrocarbons, the biosynthetic precursors of thiophenes (5–10 µmol/g d.w.). Upon addition of elicitors to tissue cultures, highest elicitation factors (between four and seven) were reached for 1,11-tridecadiene-3,5,7,9-tetrayne in C. tinctorius cell suspension cultures with 40 µM MeJ and α-terthienyl in T. patula hairy root cultures with 100 µM MeJ.     

Effects of inhibitors of RNA and protein synthesis on aspartate transcarbamylase activity in etiolated plant tissue

Aspartate transcarbamylase (ATCase) activity declines in etiolated cowpea (Vigna unguiculata L. Walp.) and soybean (Glycine max L. Merr.) hypocotyls between 3 and 11 days after planting. Treating cow-pea hypocotyls with cycloheximide (CH), actinomycin D (AMD), 6-methyl purine (6-MP), or cordycepin increases ATCase activity up to 740, 350, 465, and 305%, respectively, over water-treated controls 48 to 72 hours after treatment. In contrast erythromycin had no effect, and d-threo-chloramphenicol (CHL) reduced ATCase activity nearly 40%. CH, AMD, and CHL, whose effects were further characterized, each markedly reduced total RNA synthesis and protein synthesis. Respiration was stimulated by CH and AMD and reduced by CHL. In soybean, CHL-treated tissues and water-treated controls had comparable ATCase activities 48 hours after treatment, while AMD, 6-MP, and CH treatments reduced activities 29, 37, and 78%, respectively. The results suggest that the level of ATCase activity in etiolated cowpea hypocotyls is regulated by a mechanism or mechanisms that are interfered with by inhibition of RNA and protein synthesis. Possibly the mechanism is absent from etiolated soybean hypocotyls.     

RNA editing in plant mitochondria

RNA editing in plant mitochondria alters nearly all mRNAs by C to U and U to C transitions. In some species more than 400 edited sites have been identified with significant effects on the encoded proteins. RNA editing occurs in higher and lower plants and presumably has evolved before the differentiation of land plants. Current research focuses on the elucidation of the biochemistry and the specificity determinants of RNA editing in plant mitochrondria.     

Quantitative aspects of RNA silencing in metazoans

Small regulatory RNAs (microRNAs, siRNAs, and piRNAs) exhibit several unique features that clearly distinguish them from other known gene regulators. Their genomic organization, mode of action, and proposed biological functions raise specific questions. In this review, we focus on the quantitative aspect of small regulatory RNA biology. The original nature of these small RNAs accelerated the development of novel detection techniques and improved statistical methods and promoted new concepts that may unexpectedly generalize to other gene regulators. Quantification of natural phenomena is at the core of scientific practice, and the unique challenges raised by small regulatory RNAs have prompted many creative innovations by the scientific community.