Up regulated virulence genes in M. tuberculosis H37Rv gleaned from genome wide expression profiles

Identification of up regulated virulence genes in M. tuberculosis H37Rv using genome wide expression profiles is of interest in drug discovery for the disease. Hence, we report 17 up-regulated PPIN (Protein-Protein Interaction Network) enriched potential virulence linked genes using expression data available at the Gene Expression Omnibus (GEO) database for further consideration.     

The genes of the Green Revolution

The spectacular increases in wheat and rice yields during the 'Green Revolution', were enabled by the introduction of dwarfing traits into the plants. Now, identification of the genes responsible for these traits shows that they interfere with the action or production of the gibberellin (GA) plant hormones. We knew that the wheat Rht genes encode growth repressors that are normally suppressed by GA, and recent work shows that the rice sd1 gene encodes a defective enzyme in the GA-biosynthetic pathway.     

State-space search strategies gleaned from animal behavior: a traveling salesman experiment

A widespread search strategy employed by predators in both vertebrate and invertebrate phyla is the well-known area-restricted search strategy. The generality, simplicity, and effectiveness of this strategy have made it emerge many times during the course of natural selection. In this work, an artificial intelligence state-space search procedure is developed using search guidelines gleaned from the foraging behavior of predators. This procedure, which we call predatory search, has been implemented on a NP-Hard combinatorial problem: the traveling salesman problem. Numerical results are presented for a limited set of benchmark problems, and area-restricted search seems to be effective: We have been able to find the optimal solution to, among others, a 400-city Manhattan problem. Received: 9 July 1997 / Accepted in revised form: 24 November 1997     

Identification of Sorghum genes responsible for resistance to Green bug

Genes responsible for resistance to greenbug (Schizaphis graminum Rond.) were identified in sorghum. The dominant (Sgr1) and recessive (Sgr2) genes for resistance were revealed in sample k-457 (PI264453, United States). The samples i-589430 (PI264453, Spain) and k-3852 (Sarvasi, Hungary) carry gene Sgr1. These accessions are assumed to also have gene Sgr2. The samples k-9921 (Shallu, United States) and k-9922 (KS-30, United States) have incompletely dominant resistance gene Sgr3. A symbol Sgr4 was assigned to the dominant gene from sample k-6694 (Deer, United States). The dominant Sgr5 and recessive Sgr6 genes were revealed in the samples k-1362 (Durra Belaya, Syria) and k-1240 (Dzhugara Belaya, China). The cultivar Sorgogradskoe (k-9436, Rostovskaya oblast) has gene Sgr5. The samples k-10092 (Odesskii 360, Ukraine) and k-5091 (Cherhata, Marocco) are assumed to have genes Sgr5 and Sgr6. Sample k-924 (Dzhugara Belaya, China) is protected by the dominant gene Srg7 and recessive gene Sgr8. Sample k-923 (Dzhugara Belaya, China) has at least one of these genes. Two dominant complementary genes for resistance (Sgr9 and Sgr10) were revealed in sample k-930 (Dzhugara Belaya, China). One of two dominant genes of sample k-1237 (Dzhugara Belaya, China) was assigned the symbol Sgr11. Genes Sgr5-Sgr11 responsible for resistance to greenbug are new and were not previously used in breeding.     

Visual information gleaned by observing grasping movement in allocentric and egocentric perspectives

One of the major functions of vision is to allow for an efficient and active interaction with the environment. In this study, we investigate the capacity of human observers to extract visual information from observation of their own actions, and those of others, from different viewpoints. Subjects discriminated the size of objects by observing a point-light movie of a hand reaching for an invisible object. We recorded real reach-and-grasp actions in three-dimensional space towards objects of different shape and size, to produce two-dimensional 'point-light display' movies, which were used to measure size discrimination for reach-and-grasp motion sequences, release-and-withdraw sequences and still frames, all in egocentric and allocentric perspectives. Visual size discrimination from action was significantly better in egocentric than in allocentric view, but only for reach-and-grasp motion sequences: release-and-withdraw sequences or still frames derived no advantage from egocentric viewing. The results suggest that the system may have access to an internal model of action that contributes to calibrate visual sense of size for an accurate grasp.     

The egg white and yolk interactomes as gleaned from extensive proteomic data

Combinatorial peptide ligand libraries have recently allowed considerable advances in the mapping of chicken egg yolk and white proteomics. Data from literature have been regrouped and elaborated for network and pathway analyses in order to convey a unified view of these proteomes. Redundant proteins were excluded, while isoforms of the same proteins were maintained to reach a total of 260 distinct gene products for egg yolk and 148 for egg white having a match in the database. From these analyses, a role for proteins involved in cell development, proliferation and migration, cell-to-cell interaction and hematological system development emerged. Although it might turn out that, notwithstanding the extensive mapping, the currently available datasets might be still incomplete, a valuable insight could still be obtained about specific proteins playing a crucial role in antimicrobial responses, mainly histones, lysozyme and vitamin-binding proteins. In particular, SERPINB3 (ovalbumin Y, or Squamous Cell Carcinoma Antigen, SCCA1) was individuated in 8 out of 10 top score pathways in egg yolk and in 6 out 10 in egg white. SERPINB3 is a member of the ov-serpin family, participating in coagulation and inflammation responses. However, it is yet to be assessed how these observations could correlate with previous analyses about the role of egg yolk derived proteins in counteracting blood coagulation.     

Gene duplication within the Green Lineage: the case of TEL genes

Recent years have witnessed a breathtaking increase in the availability of genome sequence data, providing evidence of the highly duplicate nature of eukaryotic genomes. Plants are exceptional among eukaryotic organisms in that duplicate loci compose a large fraction of their genomes, partly because of the frequent occurrence of polyploidy (or whole-genome duplication) events. Tandem gene duplication and transposition have also contributed to the large number of duplicated genes in plant genomes. Evolutionary analyses allowed the dynamics of duplicate gene evolution to be studied and several models were proposed. It seems that, over time, many duplicated genes were lost and some of those that were retained gained new functions and/or expression patterns (neofunctionalization) or subdivided their functions and/or expression patterns between them (subfunctionalization). Recent studies have provided examples of genes that originated by duplication with successive diversification within plants. In this review, we focused on the TEL (TERMINAL EAR1-like) genes to illustrate such mechanisms. Emerged from the mei2 gene family, these TEL genes are likely to be land plant-specific. Phylogenetic analyses revealed one or two TEL copies per diploid genome. TEL gene degeneration and loss in several Angiosperm species such as in poplar and maize seem to have occurred. In Arabidopsis thaliana, whose genome experienced at least three polyploidy events followed by massive gene loss and genomic reorganization, two TEL genes were retained and two new shorter TEL-like (MCT) genes emerged. Molecular and expression analyses suggest for these genes sub- and neofunctionalization events, but confirmation will come from their functional characterization.     

Green tea polyphenols reduce body weight in rats by modulating obesity-related genes

Beneficial effects of green tea polyphenols (GTP) against obesity have been reported, however, the mechanism of this protection is not clear. Therefore, the objective of this study was to identify GTP-targeted genes in obesity using the high-fat-diet-induced obese rat model. A total of three groups (n?=?12/group) of Sprague Dawley (SD) female rats were tested, including the control group (rats fed with low-fat diet), the HF group (rats fed with high-fat diet), and the HF+GTP group (rats fed with high-fat diet and GTP in drinking water). The HF group increased body weight as compared to the control group. Supplementation of GTP in the drinking water in the HF+GTP group reduced body weight as compared to the HF group. RNA from liver samples was extracted for gene expression analysis. A total of eighty-four genes related to obesity were analyzed using PCR array. Compared to the rats in the control group, the rats in the HF group had the expression levels of 12 genes with significant changes, including 3 orexigenic genes (Agrp, Ghrl, and Nr3c1); 7 anorectic genes (Apoa4, Cntf, Ghr, IL-1β, Ins1, Lepr, and Sort); and 2 genes that relate to energy expenditure (Adcyap1r1 and Adrb1). Intriguingly, the HF+GTP group restored the expression levels of these genes in the high-fat-induced obese rats. The protein expression levels of IL-1β and IL-6 in the serum samples from the control, HF, and HF+GTP groups confirmed the results of gene expression. Furthermore, the protein expression levels of superoxide dismutase-1 (SOD1) and catechol-O-methyltransferase (COMT) also showed GTP-regulated protective changes in this obese rat model. Collectively, this study revealed the beneficial effects of GTP on body weight via regulating obesity-related genes, anti-inflammation, anti-oxidant capacity, and estrogen-related actions in high-fat-induced obese rats.     

Biological evaluation,molecular docking and DNA interaction studies of coordination compounds gleaned from a pyrazolone incorporated ligand

Abstract

In this work, we have synthesized a few novel mononuclear complexes of Cu(II), Co(II), Ni(II) and Zn(II) using a pyrazolone-derived Schiff base ligand. They were characterized by spectroscopic and analytical methods. The elemental analyses, UV-Vis, magnetic moment values and molar conductance of the complexes reveal that the complexes adopt an octahedral arrangement around the central metal ions. The interaction of complexes with CT-DNA was studied by absorption spectral titration and viscosity measurements. The observed data show that the complexes bind with CT-DNA via an intercalation mode. Efficient pUC18 DNA cleavage ability of the synthesized compounds was explored by gel electrophoresis. The antimicrobial activity of these compounds against a set of bacterial and fungal strains reveals that the complexes exhibit better activity than the free ligand. Moreover, all the complexes were evaluated against two cancer (HeLa and HepG2) and one normal (NHDF) cell lines. The data were compared with cisplatin. Anti–inflammatory activity has been experimentally validated which proves that theoretical predictions concur with the experimental results. In addition, molecular docking studies have been performed to consider the nature of binding mode and binding affinity of these compounds with DNA (1BNA) and protein (3hb5). These studies reveal that the mode of binding is intercalation and the complexes have higher binding energy scores than the free ligand.     

Green lacewing phylogeny, based on three nuclear genes (Chrysopidae, Neuroptera)

Abstract.  Systematic relationships among higher taxa within Chrysopidae, a large and agriculturally significant neuropteran family, are poorly understood. A molecular phylogenetic survey of Chrysopidae was performed with three nuclear genes, namely wingless (546 bp), phosphoenolpyruvate carboxykinase (483 bp), and sodium/potassium ATPase alpha subunit (410 bp). We examined 83 species in 24 genera, mainly from Japan, Eurasia and Africa. Parsimony and Bayesian analyses of combined datasets of a total of 1439 bp demonstrated that (1) monophyly of the subfamily Chrysopinae was supported but the relationship between Nothochrysinae and Apochrysinae was unclear, although the two subfamilies together may constitute the sister taxon of Chrysopinae; (2) of the three tribes examined within Chrysopinae (Ankylopterygini, Belonopterygini and Chrysopini), monophyly of Ankylopterygini and Belonopterygini was supported, but the relationships among the three remain unclear; (3) seven sub-clades in Chrysopini were indicated, namely (i) Brinckochrysa , (ii) Chrysemosa  +  Suarius , (iii) Chrysotropia  +  Nineta , (iv) Mallada  +  Chrysoperla  +  Peyerimhoffina , (v) Cunctochrysa  +  Meleoma  +  Nipponochrysa  +  Apertochrysa albolineatoides , (vi) Chrysopa  +  Plesiochrysa , and (vii) Dichochrysa  +  Apertochrysa eurydera ; and (4) most genera were monophyletic, except for Apertochrysa and Cunctochrysa , each of which was shown to have two distinct origins. Our molecular analysis allowed the assignment of several species of uncertain affinities to known genera. There was some disagreement between the molecular and previously published morphological phylogenies, but in general our results confirmed existing morphological hypotheses of evolution within the family.     

Slicing a protease: structural features of the ATP-dependent Lon proteases gleaned from investigations of isolated domains

ATP-dependent Lon proteases are multi-domain enzymes found in all living organisms. All Lon proteases contain an ATPase domain belonging to the AAA(+) superfamily of molecular machines and a proteolytic domain with a serine-lysine catalytic dyad. Lon proteases can be divided into two subfamilies, LonA and LonB, exemplified by the Escherichia coli and Archaeoglobus fulgidus paralogs, respectively. The LonA subfamily is defined by the presence of a large N-terminal domain, whereas the LonB subfamily has no such domain, but has a membrane-spanning domain that anchors the protein to the cytoplasmic side of the membrane. The two subfamilies also differ in their consensus sequences. Recent crystal structures for several individual domains and sub-fragments of Lon proteases have begun to illuminate similarities and differences in structure-function relationships between the two subfamilies. Differences in orientation of the active site residues in several isolated Lon protease domains point to possible roles for the AAA(+) domains and/or substrates in positioning the catalytic residues within the active site. Structures of the proteolytic domains have also indicated a possible hexameric arrangement of subunits in the native state of bacterial Lon proteases. The structure of a large segment of the N-terminal domain has revealed a folding motif present in other protein families of unknown function and should lead to new insights regarding ways in which Lon interacts with substrates or other cellular factors. These first glimpses of the structure of Lon are heralding an exciting new era of research on this ancient family of proteases.     

Green tea polyphenols function as prooxidants to inhibit Pseudomonas aeruginosa and induce the expression of oxidative stress-related genes

Green tea polyphenols (GTP) are widely believed to function as antioxidants and antimicrobial agents. Here we observed that GTP and epigallocatechin gallate, the most abundant catechin in GTP, could also function as prooxidants and produce hydrogen peroxide (H₂O₂) to inhibit the growth of Pseudomonas aeruginosa. pH value of the medium was the key factor that affected prooxidant versus antioxidant property of GTP. Under weakly acidic conditions (pH 5.5–6.5), GTP showed antioxidant activity by eliminating H₂O₂; whereas, under neutral and weakly alkaline conditions (pH 7.0–8.0), GTP showed prooxidant activity and inhibited the growth of P. aeruginosa. Furthermore, we studied the effects of GTP on gene expression profiles of a few oxidative stress-related genes by quantitative real-time PCR analysis. After 10 min to 1 h of exposure under weakly alkaline condition, GTP significantly up-regulated expression levels of katB, sodM, ohr, lexA, and recN gene. These findings highlight that the pH-dependent H₂O₂ production by GTP contributes to the antibacterial activity and can induce oxidative stress-related responses in P. aeruginosa.     

Green City

This research analyzes the Green City project in the town of Três Coroas, Brazil. We describe its management system, evaluating the change process and the economic, social, and environmental benefits since the recycling center has been in service. We demonstrate a successful case of operational and cultural change in the disposal of industrial waste, describing the key points that helped the adoption of a new set of procedures, and illustrating the role of the champion in the implementation of a symbiotic cluster.