High efficiency degradation of tetrahydrofuran (THF) using a membrane bioreactor: identification of THF-degrading cultures of<Emphasis Type="Italic"> Pseudonocardia</Emphasis> sp. strain M1 and<Emphasis Type="Italic"> Rhodococcus ruber</Emphasis> isolate M2

A mixed microbial culture capable of growing aerobically on tetrahydrofuran (THF) as a sole carbon and energy source was used as the inoculum in a 10 l working volume membrane bioreactor. Following start-up, the reactor was operated in batch mode for 24 h and then switched to continuous feed with 100% biomass recycle. On average, greater than 96% of THF fed to the reactor was removed during the 8-month study. THF loading rates ranged from 0.62 to 9.07 g l^–1 day^–1 with a hydraulic retention time of 24 h. THF concentrations as high as 800 mg/l were tolerated by the culture. Biomass production averaged 0.28 kg total suspended solids/kg chemical oxygen demand removed, i.e., comparable to a conventional wastewater treatment process. Periodic batch wasting resulted in a solids retention time of 7–14 days. Reactor biomass typically ranged from 4 to 10 g/l volatile suspended solids and the effluent contained no solids. Pure THF-degrading cultures were isolated from the mixed culture based on morphological characteristics, Gram-staining and THF degradation. Based on 16S rDNA analysis the isolates were identified as Pseudonocardia sp. M1 and Rhodococcus ruber M2.     

Proteolytic cleavage of cyclin E leads to inactivation of associated kinase activity and amplification of apoptosis in hematopoietic cells

Cyclin E/Cdk2 is a critical regulator of cell cycle progression from G(1) to S in mammalian cells and has an established role in oncogenesis. Here we examined the role of deregulated cyclin E expression in apoptosis. The levels of p50-cyclin E initially increased, and this was followed by a decrease starting at 8 h after treatment with genotoxic stress agents, such as ionizing radiation. This pattern was mirrored by the cyclin E-Cdk2-associated kinase activity and a time-dependent expression of a novel p18-cyclin E. p18-cyclin E was induced during apoptosis triggered by multiple genotoxic stress agents in all hematopoietic tumor cell lines we have examined. The p18-cyclin E expression was prevented by Bcl-2 overexpression and by the general caspase and specific caspase 3 pharmacologic inhibitors zVAD-fluoromethyl ketone (zVAD-fmk) and N-acetyl-Asp-Glu-Val-Asp-aldehyde (DEVD-CHO), indicating that it was linked to apoptosis. A p18-cyclin E(276-395) (where cyclin E(276-395) is the cyclin E fragment containing residues 276 to 395) was reconstituted in vitro, with mutagenesis experiments, indicating that the caspase-dependent cleavage was at amino acid residues 272 to 275. Immunoprecipitation analyses of the ectopically expressed cyclin E(1-275), cyclin E(276-395) deletion mutants, and native p50-cyclin E demonstrated that caspase-mediated cyclin E cleavage eliminated interaction with Cdk2 and therefore inactivated the associated kinase activity. Overexpression of cyclin E(276-395), but not of several other cyclin E mutants, specifically induced phosphatidylserine exposure and caspase activation in a dose-dependent manner, which were inhibited in Bcl-2-overexpressing cells or in the presence of zVAD-fmk. Apoptosis and generation of p18-cyclin E were significantly inhibited by overexpressing the cleavage-resistant cyclin E mutant, indicating a functional role for caspase-dependent proteolysis of cyclin E for apoptosis of hematopoietic tumor cells.     

Isolation,chemical investigation and antiviral activity of polysaccharides from Gracilaria corticata (Gracilariaceae,Rhodophyta)

Polysaccharides were sequentially extracted from the agarophyte Gracilaria corticata. Chemical analysis combined with infrared spectroscopy showed that the cold water extracted material consists mainly of a high molecular weight sulfated galactan. Most of the sulfate groups are alkali labile and are located at C-4 of the 1,3-linked D-galactose units and C-6 of the 1,4-linked L-galactose residues. The autoclaved extracts contain agar type polysaccharide having a high pyruvate content and a variable degree of methylation, but were contaminated with floridean starch. 1H-NMR studies indicate that methoxyl groups, when present, occur at C-6 of the 1,3-linked D-galactose units and C-2 of the 1,4-linked L-galactose residues of agar polymer. Bioassays showed that a high molecular weight galactan sulfate, exhibited selective antiviral activity against herpes simplex virus types 1 and 2, likely due to an inhibition of the initial virus attachment to the host cell.     

Antimicrobial potentiality of a phenothiazine group of antipsychotic drug-prochlorperazine

The antipsychotic drug, prochlorperazine (Pcp), was tested for its antimicrobial efficacy against 103 strains belonging to both gram positive and gram negative bacteria. The drug was found to possess maximum activity against Staphylococcus aureus, Vibrio cholerae and Shigella spp. Pcp was moderately active against E. coli but most of the strains belonging to Bacillus spp, Klebsiella spp, Salmonella spp and Lactobacillus spp were found to be resistant to this drug. The drug was tested for its mode of antibacterial activity against Shigella dysenteriae 1 and it was found to be bacteriostatic in action. In in vivo studies, Pcp offered significant protection to Swiss albino mice at concentrations of 0.75 micro g/g (P < 0.01) and 1.5 microg/g (P < 0.001) body weight when challenged with 50 median lethal dose of Salmonella typhimurium NCTC 74. Thus the result depicts that prochlorperazine may emerge as a strong antimicrobial drug to replace the conventional antibiotics and to overcome the problem of drug resistance.     

Consumer-dependent responses of lake ecosystems to nutrient loading

The nutrient loading concept proposes that algal biomass, waterclarity and the processes of lake eutrophication are a functionof nutrient loading. We hypothesized that grazers play an importantrole in determining the impacts of nutrient loading on algalbiomass and water clarity, and the overall eutrophication process.To test how the contrasting grazer communities modify the fateof nutrients, we added nutrients (nitrate and phosphate) ata known loading rate to four large enclosures, but in two ofthe four enclosures large cladoceran grazers (Daphnia >1mm mean length) were allowed to develop by removing the planktivorousfish. In the remaining two enclosures, the development of largeDaphnia was prevented by adding planktivorous fish. The concentrationsof epilimnetic total phosphorus (TP) increased at a similarrate in all four enclosures. However, the daily accumulationof added phosphate into the participate or planktonic forms,especially into plankton <20 µm, was three times fasterwhen large Daphnia were absent than when large Daphnia wereabundant. In the enclosures with large Daphnia, added phosphatewas accumulated in the dissolved pool instead. At a constantnutrient loading, algal biomass (chlorophyll a) increased fourtimes faster in the enclosures without large Daphnia than inthose with large Daphnia. Similarly, Secchi depth declined from3.5 to <1 m when Daphnia were absent, but did not declinewhen Daphnia were common. Our results demonstrate that the samenutrient loading and the resultant increase in epilimnetic TPdo not produce the same trophic conditions, as indicated byalgal biomass and water clarity, if the grazers of the majorassimilators of nutrients (the fraction of plankton edible toDaphnia) are different. We suggest that stratified lake ecosystemshaving functionally dominant large grazer communities may beless prone to eutrophication than those lacking large grazers.Consistent with the nutrient loading concept, epilimnetic concentrationsof phosphorus increase proportionately with increased loadingof phosphorus, but the trophic conditions of ecosystems indicatedby algal biomass and water clarity do not follow the same patternsunder contrasting conditions of grazer communities. We suggestthat models predicting algal biomass from loading rates shouldaccount for the role of grazers.     

Differences in the chemical constituents of Mangifera indica, infected with Aspergillus niger and Fusarium moniliformae

The isolation and characterization of the chemical constituents of different parts of Mangifera indica, sound and infected with two pathogenic fungi, viz. Aspergillus niger and Fusarium moniliformae, are described. Natural occurrence of two polyketideshikimate-derived depsides is reported for the first time. Additionally, a number of xanthones, flavonoids, triterpenes and amino acids, not encountered before in this species, are reported. The co-occurrence of mangiferin, 1,3,6,7-tetra- and 1,3,5,6,7-pentaoxygenated xanthones and the quantitative variation of the latter two compounds with the growing of the plant and during the fungal infection are biochemically significant. The protector role of the flavonoids and other C₁₅ metabolites to M. indica from the ingress of the fungal hyphae is indicated. The two pathogenic fungi secreted a number of mycotoxins in different parts of the host species during its vegetation and flowering periods. During the elaboration of these toxic metabolites, the host-pathogen interaction played an important role. Evidence is presented for A. niger as a mycotoxin producing fungus.     

Solid-phase oligonucleotide synthesis and flow cytometric analysis with microspheres encoded with covalently attached fluorophores

A novel combinatorial approach to synthesize oligonucleotides on fluorescently encoded microspheres based on flow sorting and segmental solid-phase synthesis is described. BODIPY dyes were covalently attached to polystyrene (8.8 microm, 55% DVB) microsphere particles to generate four fluorescently encoded sets. 20-mer oligonucleotide sequences can be synthesized on these microspheres with yields comparable to conventional CPG supports (80% overall yield, average stepwise yield = 99%). The concept of segmental solid-phase synthesis by flow sorting was demonstrated by synthesizing unique 20-mer oligonucleotide sequences on each of four fluorescently encoded microsphere sets by including a flow sorting step (after first eight base additions) and flow cytometric detection of sequences synthesized on each microsphere set by hybridization with fluorescently labeled complementary sequence.     

Codon bias and gene expression of mitochondrial ND2 gene in chordates

Background: Mitochondrial ND gene, which encodes NADH dehydrogenase, is the first enzyme of the mitochondrial electron transport chain. Leigh syndrome, a neurodegenerative disease caused by mutation in the ND2 gene (T4681C), is associated with bilateral symmetric lesions in basal ganglia and subcortical brain regions. Therefore, it is of interest to analyze mitochondrial DNA to glean information for evolutionary relationship. This study highlights on the analysis of compositional dynamics and selection pressure in shaping the codon usage patterns in the coding sequence of MT-ND2 gene across pisces, aves and mammals by using bioinformatics tools like effective number of codons (ENC), codon adaptation index (CAI), relative synonymous codon usage (RSCU) etc. Results: We observed a low codon usage bias as reflected by high ENC values in MT-ND2 gene among pisces, aves and mammals. The most frequently used codons were ending with A/C at the 3^rd position of codon and the gene was AT rich in all the three classes. The codons TCA, CTA, CGA and TGA were over represented in all three classes. The F1 correspondence showed significant positive correlation with G, T3 and CAI while the F2 axis showed significant negative correlation with A and T but significant positive correlation with G, C, G3, C3, ENC, GC, GC1, GC2 and GC3. Conclusions: The codon usage bias in MTND2 gene is not associated with expression level. Mutation pressure and natural selection affect the codon usage pattern in MT-ND 2 gene.     

SNVDis: A Proteome-wide Analysis Service for Evaluating nsSNVs in Protein Functional Sites and Pathways

Amino acid changes due to non-synonymous variation are included as annotations for individual proteins in UniProtKB/Swiss-Prot and RefSeq which present biological data in a protein-or gene-centric fashion. Unfortunately, proteome-wide analysis of non-synonymous singlenucleotide variations (nsSNVs) is not easy to perform because information on nsSNVs and functionally important sites are not well integrated both within and between databases and their search engines. We have developed SNVDis that allows evaluation of proteome-wide nsSNV distribution in functional sites, domains and pathways. More specifically, we have integrated human-specific data from major variation databases (UniProtKB, dbSNP and COSMIC), comprehensive sequence feature annotation from UniProtKB, Pfam, RefSeq, Conserved Domain Database (CDD) and pathway information from Protein ANalysis THrough Evolutionary Relationships (PANTHER) and mapped all of them in a uniform and comprehensive way to the human reference proteome provided by UniProtKB/Swiss-Prot. Integrated information of active sites, pathways, binding sites, domains, which are extracted from a number of different sources, provides a detailed overview of how nsSNVs are distributed over the human proteome and pathways and how they intersect with functional sites of proteins. Additionally, it is possible to find out whether there is an over-or under-representation of nsSNVs in specific domains, pathways or user-defined protein lists. The underlying datasets are updated once every 3 months. SNVDis is freely available at http://hive.biochemistry.gwu.edu/tool/snvdis.