A combined computational-experimental analyses of selected metabolic enzymes in Pseudomonas species

Comparative genomic analysis has revolutionized our ability to predict the metabolic subsystems that occur in newly sequenced genomes, and to explore the functional roles of the set of genes within each subsystem. These computational predictions can considerably reduce the volume of experimental studies required to assess basic metabolic properties of multiple bacterial species. However, experimental validations are still required to resolve the apparent inconsistencies in the predictions by multiple resources. Here, we present combined computational-experimental analyses on eight completely sequenced Pseudomonas species. Comparative pathway analyses reveal that several pathways within the Pseudomonas species show high plasticity and versatility. Potential bypasses in 11 metabolic pathways were identified. We further confirmed the presence of the enzyme O-acetyl homoserine (thiol) lyase (EC: 2.5.1.49) in P. syringae pv. tomato that revealed inconsistent annotations in KEGG and in the recently published SYSTOMONAS database. These analyses connect and integrate systematic data generation, computational data interpretation, and experimental validation and represent a synergistic and powerful means for conducting biological research.     

Synthesis of some novel imidazole-based dicationic carbazolophanes as potential antibacterials

Synthesis of fluorescent imidazole-based dicationic carbazolophanes incorporating various spacer units is described. Interestingly, the cyclophanes 2a and 5a incorporating a pyridine moiety exhibited superior antibacterial activity against most of the pathogenic bacteria in the tested concentrations as compared to the other cyclophanes as well as the test control, benzalkonium chloride (BAC), cetylpyridinium chloride (CPC) and tetracycline.     

Role of thymine in protein coding frames of mRNA sequences

Distribution of thymine in protein coding mRNA sequences has been studied here. Our study suggest that thymine in protein coding sequences are not randomly distributed but with probability. Frame1 prefers to have definite amount of thymine. It is observed that the thymine content of frame 4 is also involved in protein coding. Frame 3 prefers to have least amount of thymine. However, frame 2 and frame 6 shows a variable degree of thymine content. The mRNA sequences of heterosexual animals, particularly, the human show a different distribution profile (less thymine in frame 1) compared to that of yeast and plants.     

Photophysics of ruthenium(II) complexes carrying amino acids in the ligand 2,2′-bipyridine and intramolecular electron transfer from methionine to photogenerated Ru(III)

New ruthenium(II) complexes carrying methionine and phenylalanine in the bipyridine ligand, [Ru(bpy)₂(4-Me-4′-(CONH-l-methionine methyl ester)-2,2′-bipyridine)](PF₆)₂ (IV) and [Ru(bpy)₂(4-Me-4′-(CONH-l-phenylalanine ethyl ester)-2,2′-bpy)](PF₆)₂(V) have been synthesized and characterized and their photophysical properties studied. Flash photolysis measurements of complex IV, in the presence of an electron acceptor, methyl viologen (MV²⁺) show that an intermolecular electron transfer from the excited state of Ru(II) in complex IV, to MV²⁺ takes place, forming Ru(III) and the methyl viologen cation radical, MV⁺. The formation of MV⁺ in this system is confirmed using time-resolved transient absorption spectroscopy. This intermolecular electron transfer is followed by intramolecular electron transfer from the thioether moiety (methionine) to the photogenerated Ru(III), regenerating Ru(II).     

Synthesis and anti-microbial activity of pyrazolylbisindoles--promising anti-fungal compounds

A series of pyrazolylbisindole derivatives have been synthesized by reacting substituted pyrazole aldehydes with substituted indoles using phosphotungstic acid, a Keggin type heteropoly acid as catalyst. The synthesized pyrazolylbisindoles were evaluated for anti-microbial activities. The effect of pyrazolylbisindoles on the mycelial growth of plant pathogenic fungi is revealed. Entries 3c and 3d emerged as the most interesting compounds in this series exhibiting excellent anti-fungal activity.     

Synthetic analogues of mycobacterial arabinogalactan linkage-disaccharide part II: synthesis and preliminary screening of lipophilic O-alkyl glycosides

Lipophilic analogues of the linkage-disaccharide found in the mycobacterial cell wall were synthesized and the synthetic analogues when biologically evaluated showed promising antimycobacterial property with MIC value in the range 3.13–12.50 μg/mL against Mycobacterium tuberculosis H₃₇Rv.     

Systematic CpT (ApG) Depletion and CpG Excess Are Unique Genomic Signatures of Large DNA Viruses Infecting Invertebrates

Differences in the relative abundance of dinucleotides, if any may provide important clues on host-driven evolution of viruses. We studied dinucleotide frequencies of large DNA viruses infecting vertebrates (n = 105; viruses infecting mammals = 99; viruses infecting aves = 6; viruses infecting reptiles = 1) and invertebrates (n = 88; viruses infecting insects = 84; viruses infecting crustaceans = 4). We have identified systematic depletion of CpT(ApG) dinucleotides and over-representation of CpG dinucleotides as the unique genomic signature of large DNA viruses infecting invertebrates. Detailed investigation of this unique genomic signature suggests the existence of invertebrate host-induced pressures specifically targeting CpT(ApG) and CpG dinucleotides. The depletion of CpT dinucleotides among large DNA viruses infecting invertebrates is at least in part, explained by non-canonical DNA methylation by the infected host. Our findings highlight the role of invertebrate host-related factors in shaping virus evolution and they also provide the necessary framework for future studies on evolution, epigenetics and molecular biology of viruses infecting this group of hosts.     

Synthesis and evaluation of anti-HIV activity of isatin beta-thiosemicarbazone derivatives

On the basis of pharmacophoric modelling studies of existing NNRTIs, a series of isatin beta-thiosemicarbazone derivatives was synthesized and evaluated for their anti-HIV activity in HTLV-III(B) strain in the CEM cell line. Three compounds showed significant anti-HIV activity, whereupon compound 6 was found to be the most active compound with an EC(50) value of 2.62 microM and a selectivity index of 17.41, while not being cytotoxic to the cell line at a CC(50) value of 44.90 microM. Other tested compounds exhibited marked activity below their toxicity threshold.     

Emodin Suppresses Migration and Invasion through the Modulation of CXCR4 Expression in an Orthotopic Model of Human Hepatocellular Carcinoma

Accumulating evidence(s) indicate that CXCL12-CXCR4 signaling cascade plays an important role in the process of invasion and metastasis that accounts for more than 80% of deaths in hepatocellular carcinoma (HCC) patients. Thus, identification of novel agents that can downregulate CXCR4 expression and its associated functions have a great potential in the treatment of metastatic HCC. In the present report, we investigated an anthraquinone derivative, emodin for its ability to affect CXCR4 expression as well as function in HCC cells. We observed that emodin downregulated the expression of CXCR4 in a dose-and time-dependent manner in HCC cells. Treatment with pharmacological proteasome and lysosomal inhibitors did not have substantial effect on emodin-induced decrease in CXCR4 expression. When investigated for the molecular mechanism(s), it was observed that the suppression of CXCR4 expression was due to downregulation of mRNA expression, inhibition of NF-κB activation, and abrogation of chromatin immunoprecipitation activity. Inhibition of CXCR4 expression by emodin further correlated with the suppression of CXCL12-induced migration and invasion in HCC cell lines. In addition, emodin treatment significantly suppressed metastasis to the lungs in an orthotopic HCC mice model and CXCR4 expression in tumor tissues. Overall, our results show that emodin exerts its anti-metastatic effect through the downregulation of CXCR4 expression and thus has the potential for the treatment of HCC.