Improving image analysis in 2DGE-based redox proteomics by labeling protein carbonyl with fluorescent hydroxylamine

Recent advances in redox proteomics have provided significant insight into the role of oxidative modifications in cellular signalling and metabolism. At present, these techniques rely heavily on Western blots to visualize the oxidative modification and corresponding two dimensional (2D) gels for detection of total protein levels, resulting in the duplication of efforts. A major limitation associated with this methodology includes problematic matching up of gels and blots due to the differences in processing and/or image acquisition. In this study, we present a new method which allows detection of protein oxidation and total protein on the same gel to improve matching in image analysis. Furthermore, the digested protein spots are compatible with standard MALDI mass spectrometry protein identification. The methodology highlighted here may be useful in facilitating the development of biomarkers, assessing potential therapeutic targets and elucidating new mechanisms of redox signalling in redox-related conditions.     

Complete Genome Sequence of Desulfurococcus fermentans,a Hyperthermophilic Cellulolytic Crenarchaeon Isolated from a Freshwater Hot Spring in Kamchatka,Russia

Desulfurococcus fermentans is the first known cellulolytic archaeon. This hyperthermophilic and strictly anaerobic crenarchaeon produces hydrogen from fermentation of various carbohydrates and peptides without inhibition by accumulating hydrogen. The complete genome sequence reported here suggested that D. fermentans employs membrane-bound hydrogenases and novel glycohydrolases for hydrogen production from cellulose.     

Cloning and characterization of Arabidopsis and Brassica juncea flavin-containing amine oxidases

Polyamines (PAs) are low molecular weight metabolites involved in various physiological and developmental processes in eukaryotic and prokaryotic cells. The cellular PA level is regulated in part by the action of amine oxidases (AOs) including copper diamine oxidases (DAOs) and flavoprotein polyamine oxidases (PAOs). In this study, the isolation and characterization of flavin amine oxidases (FAOs) from Brassica juncea (BJFAO) and Arabidopsis (ATFAO1) are reported that were clustered in the same group as polyamine oxidases from maize (MPAO) and barley (BPAO1) and monoamine oxidases from mammalian species. ATFAO1 was temporally and spatially regulated in Arabidopsis and showed distinct expression patterns in response to different stress treatments. To investigate the in vivo function of FAO, transgenic Arabidopsis plants expressing sense, antisense, and double-stranded BJFAO RNAs were generated and those with altered activity of FAOs were selected for further characterization. It was found that the shoot regeneration response in transgenic plants was significantly affected by the modulated PA levels corresponding to FAO activities. Tissues that originated from transgenic plants with down-regulated FAO activity were highly regenerative, while those from transgenic plants with upregulated FAO activity were poorly regenerative. The shoot regeneration capacity in these transgenic plants was related to the levels of individual PAs, suggesting that FAO affects shoot regeneration by regulating cellular PAs. Furthermore, it was found that the effect of FAO activity on shoot regeneration was exerted downstream of the Enhancer of Shoot Regeneration (ESR1) gene, which may function in a branch of the cytokinin signalling pathway.     

Solution Structure of an Archaeal RNase P Binary Protein Complex: Formation of the 30-kDa Complex between Pyrococcus furiosus RPP21 and RPP29 Is Accompanied by Coupled Protein Folding and Highlights Critical Features for Protein-Protein and Protein-RNA Interactions

Ribonuclease P (RNase P) is a ribonucleoprotein (RNP) enzyme that catalyzes the Mg²⁺-dependent 5′ maturation of precursor tRNAs. In all domains of life, it is a ribozyme: the RNase P RNA (RPR) component has been demonstrated to be responsible for catalysis. However, the number of RNase P protein subunits (RPPs) varies from 1 in bacteria to 9 or 10 in eukarya. The archaeal RPR is associated with at least 4 RPPs, which function in pairs (RPP21-RPP29 and RPP30-POP5). We used solution NMR spectroscopy to determine the three-dimensional structure of the protein-protein complex comprising Pyrococcus furiosus RPP21 and RPP29. We found that the protein-protein interaction is characterized by coupled folding of secondary structural elements that participate in interface formation. In addition to detailing the intermolecular contacts that stabilize this 30-kDa binary complex, the structure identifies surfaces rich in conserved basic residues likely vital for recognition of the RPR and/or precursor tRNA. Furthermore, enzymatic footprinting experiments allowed us to localize the RPP21-RPP29 complex to the specificity domain of the RPR. These findings provide valuable new insights into mechanisms of RNP assembly and serve as important steps towards a three-dimensional model of this ancient RNP enzyme.     

Impact of the estrus cycle and reduction in estrogen levels with aromatase inhibition, on renal function and nitric oxide activity in female rats

Estradiol increases mRNA and/or protein expression of the nitric oxide synthase (NOS) isoforms in a variety of tissues including kidney. In this study we determined the relationship between cyclical variations in estradiol levels and renal function and total NO production in the virgin female rat. In addition, we used an aromatase inhibitor (Anastrozole), to inhibit synthesis of estradiol from testosterone. Estradiol levels were higher in proestrus vs. diestrus, and were markedly suppressed by 7 days treatment with aromatase inhibitor. There was no difference in total NO production (from urinary and plasma nitrate + nitrite = NO_X) between proestrus and diestrus but aromatase inhibition resulted in increases in total NO production. The renal cortical NOS activity and protein abundance also increased in aromatase-inhibited female rats. There were no differences in blood pressure (BP) in any group but the renal vascular resistance (RVR) was low in proestrus, increased in diestrus and did not change further after aromatase inhibition. In summary, the cyclical changes in renal function correlate with estradiol but not NO levels. Pharmacologic castration with aromatase inhibition leads to a marked increase in total and renal NOS. This contrasts to earlier work where surgical castration causes decreased NOS.     

Independent mechanisms of stimulation of polynucleotide kinase/phosphatase by phosphorylated and non-phosphorylated XRCC1

XRCC1 plays a central role in mammalian single-strand break repair. Although it has no enzymatic activity of its own, it stimulates the activities of polynucleotide kinase/phosphatase (PNKP), and this function is enhanced by protein kinase CK2 mediated phosphorylation of XRCC1. We have previously shown that non-phosphorylated XRCC1 stimulates the kinase activity of PNKP by increasing the turnover of PNKP. Here we extend our analysis of the XRCC1-PNKP interaction taking into account the phosphorylation of XRCC1. We demonstrate that phosphorylated and non-phosphorylated XRCC1 interact with different regions of PNKP. Phosphorylated XRCC1 binds with high affinity (K_d = 3.5 nM and 1 : 1 stoichiometry) to the forkhead associated (FHA) domain, while non-phosphorylated XRCC1 binds to the catalytic domain of PNKP with lower affinity (K_d = 43.0 nM and 1 : 1 stoichiometry). Under conditions of limited enzyme concentration both forms of XRCC1 enhance the activities of PNKP, but the effect is more pronounced with phosphorylated XRCC1, particularly for the kinase activity of PNKP. The stimulatory effect of phosphorylated XRCC1 on PNKP can be totally inhibited by the presence of excess FHA domain polypeptide, but non-phosphorylated XRCC1 is not susceptible to competition by the FHA domain. Thus, XRCC1 can stimulate PNKP by two independent mechanisms.     

Design,synthesis and evaluation of (E)-α-benzylthio chalcones as novel inhibitors of BCR-ABL kinase

Novel (E)-α-benzylthio chalcones are reported with preliminary in vitro activity data indicating that several of them are potent inhibitors (comparable to imatinib, the reference compound) of BCR-ABL phosphorylation in leukemic K562 cells, known to express high levels of BCR-ABL. The ability of such compounds to significantly inhibit K562 cell proliferation suggests that this scaffold could be a promising lead for the development of anticancer agents that are able to block BCR-ABL phosphorylation in leukemic cells.     

Substituted polyaniline/chitosan composites: Synthesis and characterization

Substituted polyaniline/chitosan(PANIs/Ch) composites were chemically synthesized by using ammonium peroxydisulfate as oxidant and characterized by measurements of conductivity, FTIR, UV–vis, SEM and TGA techniques. FTIR spectra of the composites revealed that there is a strong interaction between substituted polyanilines and chitosan. Among the substituted polyaniline/chitosan composites synthesized, poly(N-ethylaniline)/chitosan PNEANI/Ch has the highest conductivity with a value of 1.68 × 10^?4 S/cm. The P2EANI/Ch composite exhibited higher thermal stability than the other composites. SEM images of the composites showed an agglomerated granular morphology of substituted polyaniline particles coated on the surface of chitosan.     

Expression,purification and biological characterisation of recombinant human irisin (12.5 kDa)

Fibronectin type III domain containing 5 (FNDC5) is a transmembrane protein. Upon cleavage, it yields a peptide called irisin that is supposedly bind to an unknown receptor and facilitates browning of white adipose tissue (WAT). Increased levels of irisin are associated with increased levels of energy expenditure markers PGC-1α, UCP-1, besides abundance of beige adipocytes in WAT. Though varied sizes of irisin were reported in humans and rodents it is not yet clear about the actual size of the irisin produced physiologically. Hence, we cloned and expressed human irisin (32–143 aa of FNDC5) in Escherichia coli based on the proposed cleavage site that yields 12.5?kDa peptide to study its antigenicity and other biological functions in vitro. We purified recombinant human irisin (rh-irisin) to 95% homogeneity with simple purification method with a yield of 25?mg/g wet cell pellet. rh-irisin has been detected by commercially available antibodies from different sources with similar antigenicity. Biological activity of the rh-irisin was confirmed by using 3T3-L1 pre-adipocyte differentiation by Oil red O staining. Further, rh-irisin treatment on pre-adipocytes showed increased expression of markers associated with energy expenditure. As it is involved in energy expenditure process, it could be considered as potential therapeutic option for various metabolic diseases.     

Phyto-assisted synthesis of zinc oxide nanoparticles using Cassia alata and its antibacterial activity against Escherichia coli

Zinc oxide, an established inorganic metal oxide in nanoparticles form exhibits tremendous anti-bacterial activity. The present study focuses on determining the anti-bacterial activity of green synthesized zinc oxide nanoparticles (ZnO NPs). Results clearly validate the effective synthesis of spherical shaped nanoparticles with average size range of 60–80 nm. SEM and EDAX data buttresses the results obtained by XRD pattern in terms of size and purity. ZnO NPs exhibited dose-dependent anti-bacterial activity against Escherichia coli (E. coli) and the IC₅₀ value was calculated to be around 20 μg/mL. Growth kinetics study was conducted in the presence of nanoparticles which demonstrated the bacteriostatic effect of ZnO NPs. The study recommends the potential use of ZnO NPs in industries like food, pharmaceutical, agriculture, cosmetic industries for its anti-bacterial activity.