Life Sciences

<p>Shiv Nadar University is a comprehensive, multidisciplinary, research-focused, and student-centric University offering a full range of academic programs at the undergraduate, postgraduate and doctoral level. With state-of-the-art infrastructure, the University comprises of academic wings, sophisticated labs, international standard sports facilities, amphitheaters, auditorium, conference rooms and smart classrooms. The University&rsquo;s goal is to become internationally recognized for the quality of its research and creative endeavors and their applicability to improving quality of life, generating new insights and expanding the boundaries of human knowledge creativity. Committed to excellence in teaching, research and service, the University aims to serve the higher education needs of India and the world beyond.</p>

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Background. Stem cell factor (SCF) receptor c-Kit is recognized as a key signaling molecule, which transduces signals for the proliferation, differentiation and survival of stem cells. Binding of SCF to its receptor triggers transactivation, leading to the recruitment of kinases and phosphatases to the docking platforms of c-Kit catalytic domain. Tyrosine phosphatase-1 (Shp-1) deactivates/attenuates 'Kit' kinase activity. Whereas, Asp816Val mutation in the Kit activation loop transforms kinase domain to a constitutively activated state (switch off-to-on state), in a ligand-independent manner. This phenomenon completely abrogates negative regulation of Shp-1. To predict the possible molecular basis of interaction between c-Kit and Shp-1, we have performed an in silico protein-protein docking study between crystal structure of activated c-Kit (phosphorylated c-Kit) and full length crystal structure of Shp-2, a close structural counterpart of Shp-1. Findings. Study revealed a stretch of conserved amino acids (Lys818 to Ser821) in the Kit activation domain, which makes decisive H-bonds with N-sh2 and phosphotyrosine binding pocket residues of the phosphatase. These H-bonds may impose an inhibitory steric hindrance to the catalytic domain of c-Kit, there by blocking further interaction of the activation loop molecules with incoming kinases. We have also predicted a phosphotyrosine binding pocket in SH2 domains of Shp-1, which is found to be predominantly closer to a catalytic groove like structure in c-Kit kinase domain. Conclusions. This study predicts that crucial hydrogen bonding between N-sh2 domain of Shp-1 and Kit activation loop can modulate the negative regulation of c-Kit kinase by Shp-1. Thus, this finding is expected to play a significant role in designing suitable gain-of-function c-Kit mutants for inducing conditional proliferation of hematopoietic stem cells. © 2010 Mukhopadhyay et al; licensee BioMed Central Ltd.

(SoNS) School of Natural Sciences

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BMC Research Notes

The structural insights of stem cell factor receptor (c-Kit) interaction with tyrosine phosphatase-2 (Shp-2): An in silico analysis

Hyperactivation of phosphatidylinositol-3 kinase (PI3K) can occur as a result of somatic mutations in PIK3CA, the gene encoding the p110α subunit of PI3K. The HER2 oncogene is amplified in 25% of all breast cancers and some of these tumors also harbor PIK3CA mutations. We examined mechanisms by which mutant PI3K can enhance transformation and confer resistance to HER2-directed therapies. We introduced the PI3K mutations E545K and H1047R in MCF10A human mammary epithelial cells that also overexpress HER2. Both mutants conferred a gain of function to MCF10A/HER2 cells. Expression of H1047R PI3K, but not E545K PI3K, markedly upregulated the HER3/HER4 ligand heregulin (HRG). HRG siRNA inhibited growth of H1047R but not E545K-expressing cells and synergized with the HER2 inhibitors trastuzumab and lapatinib. The PI3K inhibitor BEZ235 markedly inhibited HRG and pAKT levels and, in combination with lapatinib, completely inhibited growth of cells expressing H1047R PI3K. These observations suggest that PI3K mutants enhance HER2-mediated transformation by amplifying the ligand-induced signaling output of the ErbB network. This also counteracts the full effect of therapeutic inhibitors of HER2. These data also suggest that mammary tumors that contain both HER2 gene amplification and PIK3CA mutations should be treated with a combination of HER2 and PI3K inhibitors. © 2010 Macmillan Publishers Limited All rights reserved.

Oncogene

H1047R phosphatidylinositol 3-kinase mutant enhances HER2-mediated transformation by heregulin production and activation of HER3

This article delineates preliminary results obtained from three newly set up very low frequency (VLF) radio receiver observation stations at low latitude Indian sites Allahabad (16.49°N), Nainital (20.48°N) and Varanasi (15.41°N), during 2007. These stations were set up by collaboration between the Indian Institute of Geomagnetism, Mumbai and Stanford University, USA under the International Heliophysical Year 2007/United Nations Basic Space Science Initiative (UNBSSI) program. VLF stations are part of Atmospheric Weather Electromagnetic System for Observation, Modeling and Education (AWESOME) network being operated globally to study the ionosphere and the magnetosphere with the help of electromagnetic waves in extremely low frequency (ELF) and VLF bands. The new set up of VLF receiver is a marked improvement over the traditional recording and analysis systems in India. It provides additional facilities to study the VLF phenomena at low latitudes which were not studied earlier, like direction finding of events like whistlers, emissions, etc. and D-region ionospheric perturbation caused by the geophysical phenomena such as solar flares, lightning induced electron precipitations, cosmic gamma ray flares, terrestrial gamma rays flares, geomagnetic storm effect, etc. Simultaneous observation at multiple sites will provide opportunity to study in more detail the application of ELF/VLF data as earthquake precursors. Some of the initial results obtained from the preliminary analysis are presented to show the probing potentiality of ELF/VLF waves in ionosphere/magnetosphere studies.

Current Science

Initial results from AWESOME VLF receivers: Set up in low latitude Indian regions under IHY2007/UNBSSI program

Genetic variability, heritability and genetic advance as per cent of mean for 14 characters in 7 elite and diverse genotypes of chilli (Capsicum annuum L.) were studied. The phenotypic coefficient of variation was higher than the respective genotypic coefficient of variation for all the 14 characters under study. Considerable amounts of GCV and PCV were observed for capsaicin content, number of fruits per plant, fruit length, fruit diameter, leaf area and total fresh yield per plant indicating the existence of greater diversity for these characters. Heritability, in broad sense, was found appreciably high (&gt;90%) for the characters: number of primary branches, leaf area, fruit length, number of fruits per plant, total fresh yield per plant and the total dry yield per plant. High heritability estimates have been found to be helpful in making selection of superior genotypes on the basis of phenotypic performance with respect to quantitative characters. High heritability coupled with high degree of genetic advance was noted for total fresh yield per plant, number of fruits per plant and ascorbic acid content in both, the F1s and parents. High heritability coupled with high genetic advance and genetic coefficient of variation reflects that the above characters are under the control of additive gene effects, and could be relied upon for yield improvement.

Vegetos

Genetic Architecture in the improvement of Chilli (Capsicum annuum L.) Crops

K-antigen capsule synthesis is an important virulence determinant of the oral anaerobe Porphyromonas gingivalis. We previously reported that the locus required for synthesis of this surface polysaccharide in strain W83 (TIGR identification PG0106 to PG0120) is transcribed as a large (∼16.7-kb) polycistronic message. Through sequence analysis, we have now identified a 77-bp inverted repeat located upstream (206 bp) of the start codon of PG0106 that is capable of forming a large hairpin structure. Further sequence analysis just upstream and downstream of the capsule synthesis genes revealed the presence of two genes oriented in the same direction as the operon that are predicted to encode DNA binding proteins: PG0104, which is highly similar (57%) to DNA topoisomerase III, and PG0121, which has high similarity (72%) to DNA binding protein HU (β-subunit). In this report, we show that these two genes, as well as the 77-bp inverted repeat region, are cotranscribed with the capsule synthesis genes, resulting in a large transcript that is ∼19.4 kb (based on annotation). We also show that a PG0121 recombinant protein is a nonspecific DNA binding protein with strong affinity to the hairpin structure, in vitro, and that transcript levels of the capsule synthesis genes are downregulated in a PG0121 deletion mutant. Furthermore, we show that this decrease in transcript levels corresponds to a decrease in the amount of polysaccharide produced. Interestingly, expression analysis of another polysaccharide synthesis locus (PG1136 to PG1143) encoding genes involved in synthesis of a surface-associated phosphorylated branched mannan (APS) indicated that this locus is also downregulated in the PG0121 mutant. Altogether our data indicate that HU protein modulates expression of surface polysaccharides in P. gingivalis strain W83. Copyright © 2010, American Society for Microbiology. All Rights Reserved.

Journal of Bacteriology

HU protein affects transcription of surface polysaccharide synthesis genes in Porphyromonas gingivalis

The co-chaperone Hep1 is required to prevent the aggregation of mitochondrial Hsp70 proteins. We have analyzed the interaction of Hep1 with mitochondrial Hsp70 (Ssc1) and the determinants in Ssc1 that make it prone to aggregation. The ATPase and peptide binding domain (PBD) of Hsp70 proteins are connected by a linker segment that mediates interdomain communication between the domains. We show here that the minimal Hep1 binding entity of Ssc1 consists of the ATPase domain and the interdomain linker. In the absence of Hep1, the ATPase domain with the interdomain linker had the tendency to aggregate, in contrast to the ATPase domain with the mutated linker segment or without linker, and in contrast to the PBD. The closest homolog of Ssc1, bacterial DnaK, and a Ssc1 chimera, in which a segment of the ATPase domain of Ssc1 was replaced by the corresponding segment from DnaK, did not aggregate in Δhep1 mitochondria. The propensity to aggregate appears to be a specific property of the mitochondrial Hsp70 proteins. The ATPase domain in combination with the interdomain linker is crucial for aggregation of Ssc1. In conclusion, our results suggest that interdomain communication makes Ssc1 prone to aggregation. Hep1 counteracts aggregation by binding to this aggregation-prone conformer. © 2010 by The American Society for Biochemistry and Molecular Biology, Inc.

Journal of Biological Chemistry

ATPase domain and interdomain linker play a key role in aggregation of mitochondrial Hsp70 chaperone Ssc1

Observation of whistler-mode chorus emissions recorded at the Indian Antarctic station, Maitri (lat=70°46′S, long=11°50′E, L=4.5), during a quiet period on 5 February 2001 has been reported. The detailed spectral analysis of recorded chorus emissions shows that each chorus element originates from the upper edge of the underlying hiss band. To explain the observed dynamic spectra of these chorus emissions, a possible generation mechanism is presented based on the recent nonlinear theory. It is observed that the seeds of chorus emissions with rising frequency are generated near the magnetic equator as a result of a nonlinear growth mechanism that depends on the wave amplitude. On the basis of this theory, the frequency sweep rate of chorus emission is computed and compared with that of our experimentally observed values, which in general shows good agreement. © 2010 The Royal Swedish Academy of Sciences.

Physica Scripta

An explanation of the observation of whistler-mode chorus emissions at the Indian Antarctic station, Maitri (L = 4.5)

Genetic diversity among 48 ber genotypes from different eco-geographical regions of India was investigated using random amplified polymorphic DNA (RAPD) and intersimple sequence repeat (ISSR) markers. Forty-six RAPD and 18 ISSR primers generated a total of 368 and 167 amplification products of which 271 (74.15%) and 152 (89.94%) were polymorphic, respectively. The average numbers of polymorphic fragments were 5.89 (RAPD) and 8.44 (ISSR) per primer with number of amplified bands ranging between 2 to 17 and 4 to 12 for RAPD and ISSR respectively. RAPD primer OPD-3 (9.00 Rp and 0.29 PIC) and ISSR primer UBC-880 (5.63 Rp and 0.29 PIC) were the most informative primers. Out of the 18 ISSR primers 14 were anchored, of which 12 were 3'-anchored and 2 were 5'-anchored. Fourteen ISSR primers produced distinct bands contained dinucleotide repeats. Primers based on (AC)n and (AG)n repeats produced the most polymorphic bands. Based on mantel matrix correlation between two marker systems it is suggested that the two markers amplify different genomic regions. The genetic similarity among 48 ber genotypes ranged from 47.62% (Thornless and Seov) to 88.97% (Narma and Banarsi Karaka) that suggested a wide genetic base for the ber germplasm collection. The study suggests superiority of ISSR marker system over RAPD for studying genetic diversity in ber.

Indian Journal of Genetics and Plant Breeding

Comparative evaluation of genetic relationships among ber (Ziziphus sp.) genotypes using RAPD and ISSR markers

Transport of essentially all matrix and a number of inner membrane proteins is governed, entirely or in part, by N-terminal presequences and requires a coordinated action of the translocases of outer and inner mitochondrial membranes (TOM and TIM23 complexes). Here, we have analyzed Tim50, a subunit of the TIM23 complex that is implicated in transfer of precursors from TOM to TIM23. Tim50 is recruited to the TIM23 complex via Tim23 in an interaction that is essentially independent of the rest of the translocase. We find Tim50 in close proximity to the intermembrane space side of the TOM complex where it recognizes both types of TIM23 substrates, those that are to be transported into the matrix and those destined to the inner membrane, suggesting that Tim50 recognizes presequences. This function of Tim50 depends on its association with TIM23. We conclude that the efficient transfer of precursors between TOM and TIM23 complexes requires the concerted action of Tim50 with Tim23. © 2009 by The American Society for Cell Biology.

Molecular Biology of the Cell

Role of tim50 in the transfer of precursor proteins from the outer to the inner membrane of mitochondria

This paper reports quasi-periodic pulsing hiss emissions recorded during daytime in the frequency range of 50 Hz-15 kHz at low latitude station Jammu (geomag. lat. = 22°26'N; L = 1.17). It is noted that pulsing VLF emissions are a rare phenomena at low latitudes. The various spectrograms of pulsing VLF hiss emissions presented in this paper clearly show band limited spectrums regularly pulsing with almost equal period of the order of few seconds in the frequency range of ̃3-8kHz. Generation and propagation mechanism of these emissions are briefly discussed. © Printed in India.