Ras oncogene mutations in urine sediments of patients with bladder cancer

Early detection of bladder cancer is particularly important since it dramatically affects the survival rates. However, neither urinary cytology nor tumor markers that are currently used are sensitive enough for the early detection of bladder cancer or recurrent disease. The ras genes are frequently mutated in cancer. In this study, we investigated the diagnostic potential of ras mutation analysis in urinary sediments of patients with bladder cancer using a single-strand conformation polymorphism analysis and polymerase chain reaction. Mutation in codon 12 of the H-ras gene was observed in 39% of the patients. Our results indicate that this approach may significantly improve diagnostic sensitivity in detecting bladder tumors.     

Database and tools for metabolic network analysis

Metabolic network analysis has attracted much attention in the area of systems biology. It has a profound role in understanding the key features of organism metabolic networks and has been successfully applied in several fields of systems biology, including in silico gene knockouts, production yield improvement using engineered microbial strains, drug target identification, and phenotype prediction. A variety of metabolic network databases and tools have been developed in order to assist research in these fields. Databases that comprise biochemical data are normally integrated with the use of metabolic network analysis tools in order to give a more comprehensive result. This paper reviews and compares eight databases as well as twenty one recent tools. The aim of this review is to study the different types of tools in terms of the features and usability, as well as the databases in terms of the scope and data provided. These tools can be categorised into three main types: standalone tools; toolbox-based tools; and web-based tools. Furthermore, comparisons of the databases as well as the tools are also provided to help software developers and users gain a clearer insight and a better understanding of metabolic network analysis. Additionally, this review also helps to provide useful information that can be used as guidance in choosing tools and databases for a particular research interest.     

New diprenylated dihyrochalcones from leaves of Artocarpus elasticus

Two new diprenylated dihydrochalcones, elastichalcone A 1 and elastichalcone B 2 and three known compounds were isolated from the leaves of Artocarpus elasticus. Their structures were determined by various spectroscopic techniques (UV, IR, MS, 1D-NMR and 2D-NMR). Elastichalcone B 2 and a known compound exhibited good free radical scavenging activity with IC₅₀ values of 11.30 and 11.89 μg/ml, respectively.     

Procaryotic and eucaryotic traits of DNA methylation in spiroplasmas (mycoplasmas).

Differences in the type of base methylated (cytosine or adenine) and in the extent of methylation were detected by high-pressure liquid chromatography in the DNAs of five spiroplasmas. Nearest neighbor analysis and digestion by restriction enzyme isoschizomers also revealed differences in methylation sequence specificity. Whereas in Spiroplasma floricola and Spiroplasma sp. strain PPS-1 5-methylcytosine was found on the 5' side of each of the four major bases, the cytosine in Spiroplasma apis DNA was methylated only when its 3' neighboring base was adenine or thymine. In Spiroplasma sp. strain MQ-1 over 95% of the methylated cytosine was in C-G sequences. Essentially all of the C-G sequences in the MQ-1 DNA were methylated. Partially purified extracts of S. apis and Spiroplasma sp. strain MQ-1 were used to study substrate and sequence specificity of the methylase activity. Methylation by the MQ-1 enzyme was exclusively at C-G sequences, resembling in this respect eucaryotic DNA methylases. However, the MQ-1 methylase differed from eucaryotic methylases by showing high activity on nonmethylated DNA duplexes, low activity with hemimethylated DNA duplexes, and no activity on single-stranded DNA.     

<Emphasis Type="Italic">Cupriavidus malaysiensis</Emphasis> sp. nov., a novel poly(3-hydroxybutyrate-<Emphasis Type="Italic">co</Emphasis>-4-hydroxybutyrate) accumulating bacterium isolated from the Malaysian environment

Bacterial classification on the basis of a polyphasic approach was conducted on three poly(3 hydroxybutyrate-co-4-hydroxybutyrate) [P(3HB-co-4HB)] accumulating bacterial strains that were isolated from samples collected from Malaysian environments; Kulim Lake, Sg. Pinang river and Sg. Manik paddy field. The Gram-negative, rod-shaped, motile, non-sporulating and non-fermenting bacteria were shown to belong to the genus Cupriavidus of the Betaproteobacteria on the basis of their 16S rRNA gene sequence analyses. The sequence similarity value with their near phylogenetic neighbour, Cupriavidus pauculus LMG3413^T, was 98.5%. However, the DNA–DNA hybridization values (8–58%) and ribotyping analysis both enabled these strains to be differentiated from related Cupriavidus species with validly published names. The RiboPrint patterns of the three strains also revealed that the strains were genetically related even though they displayed a clonal diversity. The major cellular fatty acids detected in these strains included C15:0 ISO 2OH/C16:1 ω7c, hexadecanoic (16:0) and cis-11-octadecenoic (C18:1 ω7c). Their G+C contents ranged from 68.0  to 68.6 mol%, and their major isoprenoid quinone was Ubiquinone Q-8. Of these three strains, only strain USMAHM13 (= DSM 25816 = KCTC 32390) was discovered to exhibit yellow pigmentation that is characteristic of the carotenoid family. Their assembled genomes also showed that the three strains were not identical in terms of their genome sizes that were 7.82, 7.95 and 8.70 Mb for strains USMAHM13, USMAA1020 and USMAA2-4, respectively, which are slightly larger than that of Cupriavidus necator H16 (7.42 Mb). The average nucleotide identity (ANI) results indicated that the strains were genetically related and the genome pairs belong to the same species. On the basis of the results obtained in this study, the three strains are considered to represent a novel species for which the name Cupriavidus malaysiensis sp. nov. is proposed. The type strain of the species is USMAA1020^T (= DSM 19416^T = KCTC 32390^T).     

A supernumerary chromosome with an accumulation mechanism in the lecanoid genetic system

Summary The supernumerary chromosomes of a mealy bug,Pseudococcus obscurus Essig are heterochromatic but show a variable heteropycnosis. In the female, they are weakly heteropyonotic in most tissues, but in a few tissues the individual supernumeraries form striking chromocenters. At oogenesis, they remain unassociated and divide equationally during the first division; during the second, they pair and disjoin. Pairing is usually accomplished by twos so that an unpaired supernumerary is found whenever an odd number, or only one, is present; the unpaired entity is twice as likely to go to the second polar body as to the egg.The normal spermatogenesis in the mealy bugs is a highly modified meiosis in which the paternal heterochromatic set is eliminated from the genetic continuum; during this sequence the supernumeraries are fully heterochromatic up until late prophase I. They then undergo a sharp change in pycnosis and become negatively heteropycnotic. In the second meiotic division they usually segregate with the maternal euchromatic set. Their behavior during spermatogenesis thus becomes an accumulation mechanism since an unreduced number, or nearly that, is transmitted by the males.The variable behavior of the supernumeraries affords further insight into the problem of heterochromatization in the mealy bugs.The supernumeraries may have originated from fragments followed by subsequent duplications. The accumulation mechanism may have been an important factor in their establishment.In genetic systems in which the supernumeraries have an accumulation mechanism, an elimination mechanism might evolve to stabilize the number of supernumeraries. Such elimination mechanisms are known for other genetic systems but have not yet been developed in this mealy bug.The material in this paper is part of a dissertation submitted to the graduate school of the University of California in partial satisfaction of the requirements for the degree of Doctor of Philosophy. This work was supported in part by a National Science Foundation Grant (G-9772) to ProfessorSpencer W. Brown.Predoctoral Trainee in Genetics, National Institutes of Health, 1960–1961.     

Reproduction in the Mediterranean endemic gorgonian Spinimuricea klavereni (Anthozoa,Octocorallia, Plexauridae)

Spinimuricea klavereni is a Mediterranean endemic gorgonian that is rarely encountered, probably because it typically occurs at depths below 50 m. It is exceptionally common in the northern Marmara Sea, with an unusually shallow upper depth limit of ~20 m. The reproductive biology of this species was studied during a one year period off Büyükada, in the northeastern Marmara Sea. Spinimuricea klavereni is a gonochoric broadcast spawner with an almost even sex ratio. Colonies were ~15 cm in height at first reproduction. Gametogenesis was continuous, characterized by high male and female fecundities year‐round. Oocytes and sperm sacs of all developmental stages were found throughout the year, with small‐sized oocytes and sperm sacs dominant throughout the year. The reproduction of S. klavereni did not seem to exhibit any marked seasonal pattern, unlike most other studied Mediterranean octocorals. Modest variation in gamete output was probably related to slight alterations in food availability and temperature. The non‐seasonal reproductive pattern we observed may be related to the low intra‐annual variation in temperature in the Marmara Sea, and the fact that the mesotrophic‐eutrophic level of productivity in the Marmara Sea can support the energetic requirements of continuous gametogenesis in this gorgonian. Whether these patterns are local adaptations or intrinsic characteristics for this Mediterranean endemic species remains to be studied.