A tracked approach for automated NMR assignments in proteins (TATAPRO)

A novel automated approach for the sequence specific NMR assignments of ¹H^N, ¹³C, ¹³C, ¹³C/¹H and ¹⁵N spins in proteins, using triple resonance experimental data, is presented. The algorithm, TATAPRO (Tracked AuTomated Assignments in Proteins) utilizes the protein primary sequence and peak lists from a set of triple resonance spectra which correlate ¹H^N and ¹⁵N chemical shifts with those of ¹³C, ¹³C and ¹³C/¹H. The information derived from such correlations is used to create a `master_list' consisting of all possible sets of ¹H^N _i, ¹⁵N_i, ¹³C _i, ¹³C _i, ¹³C_i/¹H _i, ¹³C _i–1, ¹³C _i–1 and ¹³C_i–1/ ¹H _i–1 chemical shifts. On the basis of an extensive statistical analysis of ¹³C and ¹³C chemical shift data of proteins derived from the BioMagResBank (BMRB), it is shown that the 20 amino acid residues can be grouped into eight distinct categories, each of which is assigned a unique two-digit code. Such a code is used to tag individual sets of chemical shifts in the master_list and also to translate the protein primary sequence into an array called pps_array. The program then uses the master_list to search for neighbouring partners of a given amino acid residue along the polypeptide chain and sequentially assigns a maximum possible stretch of residues on either side. While doing so, each assigned residue is tracked in an array called assig_array, with the two-digit code assigned earlier. The assig_array is then mapped onto the pps_array for sequence specific resonance assignment. The program has been tested using experimental data on a calcium binding protein from Entamoeba histolytica (Eh-CaBP, 15 kDa) having substantial internal sequence homology and using published data on four other proteins in the molecular weight range of 18–42 kDa. In all the cases, nearly complete sequence specific resonance assignments (> 95%) are obtained. Furthermore, the reliability of the program has been tested by deleting sets of chemical shifts randomly from the master_list created for the test proteins.     

Luminescence properties of green‐emitting Ca2MgSi2O7:Eu2+ phosphor by a solid‐state reaction method

A europium (Eu)‐doped di‐calcium magnesium di‐silicate phosphor, Ca₂MgSi₂O₇:Eu²⁺, was prepared using a solid‐state reaction method. The phase structure, particle size, surface morphology, elemental analysis, different stretching mode and luminescence properties were analyzed by X‐ray diffraction (XRD), transmission electron microscopy (TEM), field emission scanning electron microscopy (FESEM) with energy dispersive X‐ray spectroscopy (EDX), Fourier transform infrared (FTIR) spectroscopy, photoluminescence (PL) and mechanoluminescence (ML). The phase structure of Ca₂MgSi₂O₇:Eu²⁺ was an akermanite‐type structure, which belongs to the tetragonal crystallography with space group P4?2₁m; this structure is a member of the melilite group and forms a layered compound. The surface of the prepared phosphor was not found to be uniform and particle distribution was in the nanometer range. EDX and FTIR confirm the components of Eu²⁺‐doped Ca₂MgSi₂O₇ phosphor. Under UV excitation, the main emission peak appeared at 530 nm, belonging to the broad emission ascribed to the 4f⁶5d¹→4f⁷ transition of Eu²⁺. The ML intensity of the prepared phosphor increased linearly with increasing impact velocity. A CIE color chromaticity diagram and ML spectrum confirmed that the prepared Ca₂MgSi₂O₇:Eu²⁺ phosphor would emit green color and the ML spectrum was similar to that of PL, which indicated that ML is emitted from the same center of Eu²⁺ ions. Copyright © 2015 John Wiley & Sons, Ltd.     

Evaluation of Hs-CRP Levels and Interleukin 18 (-137G/C) Promoter Polymorphism in Risk Prediction of Coronary Artery Disease in First Degree Relatives

Background

Coronary Artery Disease (CAD) is clearly a multifactorial disease that develops from childhood and ultimately leads to death. Several reports revealed having a First Degree Relatives (FDRS) with premature CAD is a significant autonomous risk factor for CAD development. C - reactive protein (CRP) is a member of the pentraxin family and is the most widely studied proinflammatory biomarker. IL-18 is a pleiotrophic and proinflammatory cytokine which is produced mainly by macrophages and plays an important role in the inflammatory cascade.

Methods and Results

Hs-CRP levels were estimated by ELISA and Genotyping of IL-18 gene variant located on promoter -137 (G/C) by Allele specific PCR in blood samples of 300 CAD patients and 300 controls and 100 FDRS. Promoter Binding sites and Protein interacting partners were identified by Alibaba 2.1 and Genemania online tools respectively. Hs-CRP levels were significantly high in CAD patients followed by FDRS when compared to controls. In IL-18 -137 (G/C) polymorphism homozygous GG is significantly associated with occurrence of CAD and Hs-CRP levels were significantly higher in GG genotype subjects when compared to GC and CC. IL-18 was found to be interacting with 100 protein interactants.

Conclusion

Our results indicate that Hs-CRP levels and IL-18-137(G/C) polymorphism may help to identify risk of future events of CAD in asymptomatic healthy FDRS.     

Stocking density‐dependent growth and survival of Asian sun catfish,Horabagrus brachysoma (Gunther 1861) larvae

The aim of the experiment was to evaluate the growth and survival of Horabagrus brachysoma larvae at different stocking densities (3, 7, 13, 20, 27 and 33 larvae L^?1) during their hatchery phase. Total length and wet weight of the larvae consistently decreased (P < 0.05) at the end of 14 and 28 days of rearing as the density increased. The specific growth rate was significantly (P < 0.05) highest at three larvae L^?1 compared to the other five densities. The percent weight gain and survival of larvae was also highest at lowest density. The observation corroborates that catfish larvae can be reared at low densities in stagnant water conditions. Considering the value of larval growth, survival and overall weight gain, the stocking density of seven larvae L^?1 has been identified as the maximum for larval rearing of H.  brachysoma under hatchery conditions.     

Research on marine actinobacteria in India

Marine actinobacteriology is one of the major emerging areas of research in tropics. Marine actinobacteria occur on the sediments and in water and also other biomass (mangrove) and substrates (animal). These organisms are gaining importance not only for their taxonomic and ecological perspectives, but also for their unique metabolites and enzymes. Many earlier studies on these organisms were confined only to the temperate regions. In tropical environment, investigations on them have gained importance only in the last two decades. So far, from the Indian peninsula, 41 species of actinobacteria belonging to 8 genera have been recorded. The genus, Streptomyces of marine origin has been more frequently recorded. Of 9 maritime states of India, only 4 have been extensively covered for the study of marine actinobacteria. Most of the studies conducted pertain to isolation, identification and maintenance of these organisms in different culture media. Further, attention has been focused on studying their antagonistic properties against different pathogens. Their biotechnological potentials are yet to be fully explored.     

Effect of seed soaking with sulphydryl compounds on the photochemical efficiency and antioxidant defence system during the growth of pearl millet under water limiting environment

Pearl millet (Pennisetum glaucum L. cv. HHB-67) seeds were pre-soaked in sulphydryl compounds (dithiothreitol, thioglycollic acid, thiourea, and cysteine). In plants at 59 and 67 d after sowing (DAS), activities of photosystem (PS) 2 (ferricyanide site) and PS1, both chloroplastic and total superoxide dismutase, glutathione reductase, and glutathione-S-transferase increased after all sulphydryl pre-treatments at both stages of plant development. Also dry matter of plant parts sampled at 55 DAS was higher after thiol-treatments in comparison with control.     

Wide dynamic range phase-sensitive surface plasmon resonance biosensor based on measuring the modulation harmonics

In this study, a novel phase-sensitive surface plasmon resonance (SPR) setup, based on temporal modulation of a pumping beam by a photoelastic modulator, and subsequent extraction of phase information at the second and the third harmonics of the modulation frequency, has been developed to study biomolecular interactions on SPR-supporting gold. We demonstrated that the design setup provides ultra-high phase sensitivity, together with a wide dynamic range of measurements. In particular, the proposed scheme was used to study real-time interaction of biotin-protein and streptavidin-BSA complexes. We have found that the proposed technique has a detection limit as high as 2.89 x 10(-7) in terms of refractive index units (RIU). In terms of biosensing performance, a detection sensitivity of 1.3 nM from the streptavidin-maleimide/thiolated BSA complex binding reaction has also been demonstrated.     

Reduced Severity of Experimental Autoimmune Encephalomyelitis in GMF-Deficient Mice

Glia maturation factor (GMF), a highly conserved brain-specific protein, isolated, sequenced and cloned in our laboratory. Overexpression of GMF in astrocytes induces the production and secretion of granulocyte-macrophage-colony stimulating factor (GM-CSF), and subsequent immune activation of microglia, expression of several proinflammatory genes including major histocompatibility complex proteins, IL-1β, and MIP-1β, all associated with the development of experimental autoimmune encephalomyelitis (EAE), the animal model for multiple sclerosis. Based on GMF’s ability to activate microglia and induce well-established proinflammatory mediators, including GM-CSF, we hypothesize that GMF is involved in the pathogenesis of inflammatory disease EAE. In this present investigation, using GMF-deficient mice, we study the role of GMF and how the lack of GMF affects the EAE disease. Our results show a significant decrease in incidence, delay in onset, and reduced severity of EAE in GMF-deficient mice, and support the hypothesis that GMF plays a major role in the pathogenesis of disease.     

The Hha–TomB toxin–antitoxin module in Salmonella enterica serovar Typhimurium limits its intracellular survival profile and regulates host immune response

Cell Biology and Toxicology - The key to bacterial virulence relies on an exquisite balance of signals between microbe and hosts. Bacterial toxin–antitoxin (TA) system is known to play a...