C-terminal region of Mad2 plays an important role during mitotic spindle checkpoint in fission yeast <Emphasis Type="Italic">S</Emphasis>c<Emphasis Type="Italic">hizosaccharomyces pombe</Emphasis>

The mitotic arrest deficiency 2 (Mad2) protein is an essential component of the spindle assembly checkpoint that interacts with Cdc20/Slp1 and inhibit its ability to activate anaphase promoting complex/cyclosome (APC/C). In bladder cancer cell line the C-terminal residue of the mad2 gene has been found to be deleted. In this study we tried to understand the role of the C-terminal region of mad2 on the spindle checkpoint function. To envisage the role of C-terminal region of Mad2, we truncated 25 residues of Mad2 C-terminal region in fission yeast S.pombe and characterized its effect on spindle assembly checkpoint function. The cells containing C-terminal truncation of Mad2 exhibit sensitivity towards microtubule destabilizing agent suggesting perturbation of spindle assembly checkpoint. Further, the C-terminal truncation of Mad2 exhibit reduced viability in the nda3-KM311 mutant background at non-permissive temperature. Truncation in mad2 gene also affects its foci forming ability at unattached kinetochore suggesting that the mad2-?CT mutant is unable to maintain spindle checkpoint activation. However, in response to the defective microtubule, only brief delay of mitotic progression was observed in Mad2 C-terminal truncation mutant. In addition we have shown that the deletion of two β strands of Mad2 protein abolishes its ability to interact with APC activator protein Slp1/Cdc20. We purpose that the truncation of two β strands (β7 and β8) of Mad2 destabilize the safety belt and affect the Cdc20-Mad2 interaction leading to defects in the spindle checkpoint activation.     

Analysis of Delta-Notch interaction by molecular modeling and molecular dynamic simulation studies

Notch is a single-pass transmembrane receptor protein. Delta (member of the DSL protein family), a Notch ligand, is also single-pass transmembrane protein that can interact with Notch to form the Delta-Notch complex. It has been demonstrated that of the 36 Epidermal Growth Factor (EGF) repeats of Notch, 11th and 12th are sufficient to mediate interactions with Delta. Crystal structure of mammalian Notch1 extracellular ligand binding domain shows the presence of 11th and 12th EGF-like repeats. Here a portion of the Drosophila Delta protein, known to interact with Notch extracellular domain, has been modeled using homology modeling. The structure of the Delta-Notch complex was subsequently modeled by protein-docking method using GRAMM. Molecular dynamic simulations of the modeled structures were performed. The probable structures for Delta-Notch complex have been proposed based on interaction energy parameter and planarity studies.     

Design of an ON/OFF mist duty cycle in mist bioreactors for the growth of hairy roots

In this study, we designed a strategy for selecting the operating conditions of a mist reactor for the growth of hairy roots. This was accomplished by developing a mathematical model to optimize the ON/OFF mist duty cycle for the specified growth of hairy roots. The availability and rate of transport of nutrients to the roots are important parameters in the design and operation of the reactor. The thin liquid film over the root surface, which continuously builds up during the ON cycle, is a major factor that limits mass transfer. The same film also acts as a finite reservoir of nutrients in the absence of any replenishment during the OFF cycle. This reservoir gets depleted as growing roots continue to consume the nutrients. As a result of this depletion the duration of the OFF cycle must be limited such that the nutrient concentration does not go below the critical value required for the specified growth rate. The depleted reservoir is then replenished during the next ON cycle to an extent that depends on feed concentration and duration of the next ON cycle. It was shown that the use of increasing feed concentrations in the fed-batch mode of operation could maintain a specified growth rate in the reactor. Interestingly, this also resulted in the efficient operation of the reactor whereby the reactor operated at slightly above the required concentration and close to the point of minimum mass transfer resistance.     

A Quest for miRNA Bio-Marker: A Track Back Approach from Gingivo Buccal Cancer to Two Different Types of Precancers

Deregulation of miRNA expression may contribute to tumorigenesis and other patho-physiology associated with cancer. Using TLDA, expression of 762 miRNAs was checked in 18 pairs of gingivo buccal cancer-adjacent control tissues. Expression of significantly deregulated miRNAs was further validated in cancer and examined in two types of precancer (leukoplakia and lichen planus) tissues by primer-specific TaqMan assays. Biological implications of these miRNAs were assessed bioinformatically. Expression of hsa-miR-1293, hsa-miR-31, hsa-miR-31* and hsa-miR-7 were significantly up-regulated and those of hsa-miR-206, hsa-miR-204 and hsa-miR-133a were significantly down-regulated in all cancer samples. Expression of only hsa-miR-31 was significantly up-regulated in leukoplakia but none in lichen planus samples. Analysis of expression heterogeneity divided 18 cancer samples into clusters of 13 and 5 samples and revealed that expression of 30 miRNAs (including the above-mentioned 7 miRNAs), was significantly deregulated in the cluster of 13 samples. From database mining and pathway analysis it was observed that these miRNAs can significantly target many of the genes present in different cancer related pathways such as “proteoglycans in cancer”, PI3K-AKT etc. which play important roles in expression of different molecular features of cancer. Expression of hsa-miR-31 was significantly up-regulated in both cancer and leukoplakia tissues and, thus, may be one of the molecular markers of leukoplakia which may progress to gingivo-buccal cancer.     

Flexibility of alpha-helices: results of a statistical analysis of database protein structures

Alpha-helices stand out as common and relatively invariant secondary structural elements of proteins. However, alpha-helices are not rigid bodies and their deformations can be significant in protein function (e.g. coiled coils). To quantify the flexibility of alpha-helices we have performed a structural principal-component analysis of helices of different lengths from a representative set of protein folds in the Protein Data Bank. We find three dominant modes of flexibility: two degenerate bend modes and one twist mode. The data are consistent with independent Gaussian distributions for each mode. The mode eigenvalues, which measure flexibility, follow simple scaling forms as a function of helix length. The dominant bend and twist modes and their harmonics are reproduced by a simple spring model, which incorporates hydrogen-bonding and excluded volume. As an application, we examine the amount of bend and twist in helices making up all coiled-coil proteins in SCOP. Incorporation of alpha-helix flexibility into structure refinement and design is discussed.     

Genetic diversity and evolution of the human leptin locus tetranucleotide repeat

To better understand the evolutionary history of the gene region containing the multifunctional adipose tissue hormone leptin, we genotyped 1,957 individuals from 12 world populations for a highly variable tetranucleotide repeat polymorphism located 476 bp 3' of exon 3 of the leptin gene. Common alleles shared among populations, alleles specific to geographically defined populations, and the homologous alleles in the common and pygmy chimpanzee, the gorilla and the orangutan, were sequenced to define the allelic variation at the nucleotide level. These data reveal a common set of alleles shared among world populations, presumed to have arisen from a great ape ancestral allele prior to the divergence of the major geographical subdivisions of the human population, a subset of alleles specific to populations of African ancestry and a second set of alleles that arose by tandem duplication of the core repeat unit following the separation of African and non-African populations. These findings emphasize the complex evolutionary history of this locus and raise cautions about the pooling of alleles at this locus in association studies.     

Effect of heavy ion irradiation on DNA DSB repair in Methanosarcina barkeri

Archaea are expected to be highly repair proficient since they survived the vicious onslaught of radiation damage at the time of their early appearance. The DNA double strand break repairing ability of mesophilic archaea Methanosarcina barkeri (DSM 804) was studied using (7)Li, (12)C and (16)O heavy ions and compared with that of (60)Co gamma-rays. They can repair double strand breaks and, as in eukaryotes, the nature as well as extent of induction and its subsequent repair were dependent on the linear energy transfer of the radiation source.