Ashok K. Dubey

Aβ aggregation and possible implications in Alzheimer's disease pathogenesis

•  Introduction •  Amyloid Structure •  Mechanism of Amyloid aggregation •  Aβ: a natively unfolded protein? •  Ambiguities in synthetic Ab studies •  Formation of Amyloid plaques •  Role of Ab in AD Pathogenesis •  Conclusion

Metabolic burden as reflected by maintenance coefficient of recombinant Escherichia coli overexpressing target gene

Metabolic burden as a consequence of overexpression of target gene in a recombinant strain of E. coli 1727 has been analyzed with respect to maintenance energy coefficient (m). The values of ‘m’ for the host, uninduced recombinant and IPTG induced recombinant were determined to be 0.12, 0.17 and 0.32 g.g-1.h-1 respectively. Transient plasmid instability and nearly 33% fall in maximum specific growth rate were observed under conditions of enhanced requirements for maintenance energy.

KINETIC MECHANISM OF CYTOSINE DNA METHYLTRANSFERASE MSPI

A kinetic analysis of MspI DNA methyltransferase (M.MspI) is presented. The enzyme catalyzes methylation of λ-DNA, a 50-kilobase pair linear molecule with multiple M.MspI-specific sites, with a specificity constant (k cat/K M ) of 0.9 × 108 m −1s−1. But the values of the specificity constants for the smaller DNA substrates (121 and 1459 base pairs (bp)) with single methylation target or with multiple targets (sonicated λ-DNA) were less by an order of magnitude. Product inhibition of the M.MspI-catalyzed methylation reaction by methylated DNA is competitive with respect to DNA and noncompetitive with respect to S-adenosylmethionine (AdoMet). TheS-adenosylhomocysteine inhibition of the methylation reaction is competitive with respect to AdoMet and uncompetitive with respect to DNA. The presteady state kinetic analysis showed a burst of product formation when AdoMet was added to the enzyme preincubated with the substrate DNA. The burst is followed by a constant rate of product formation (0.06 mol per mol of enzyme s−1) which is similar to catalytic constants (k cat = ∼0.056 s−1) measured under steady state conditions. The isotope exchange in chasing the labeled methyltransferase-DNA complex with unlabeled DNA and AdoMet leads to a reduced burst as compared with the one involving chase with labeled DNA and AdoMet. The enzyme is capable of exchanging tritium at C-5 of target cytosine in the substrate DNA in the absence of cofactor AdoMet. The kinetic data are consistent with an ordered Bi Bi mechanism for the M.MspI-catalyzed DNA methylation where DNA binds first.

Structural and functional analysis of various globulin proteins from soy seed.

Storage proteins of soybean mostly consist of globulins, which are classified according to their sedimentation coefficient. Among 4 major types: 2S, 7S, 11S, and 15S of globulins, 7S and 11S constitute major fraction. The 11S fraction consists only of glycinin and 7S fraction majorly consists of β-conglycinin, small amounts of γ-conglycinin and basic 7S globulin (Bg7S). Glycinin exist as a hexamer while β-conglycinin as a trimer and Bg7S as a tetramer. Glycinin subunits are coded by 5 genes of a family, whereas about 15 genes are present for β-conglycinin subunits. Bg7S gene is present in four copies in soybean genome. Synthesis of all proteins takes place as a single polypeptide chain, which is cleaved after folding to yield different chains or subunits. Glycinin and β-Conglycinin are made for storage purpose. However, Bg7S has potential xylanase inhibition activity and protein kinase activity. Primary structure of Bg7S reveals 12 conserved cysteine residues involved in forming 6 disulfide bonds, which provides appreciable stability to protein. Secondary structure is predominately rich in β-sheets with few alpha helices. Bg7S shares structural similarity with various aspartic-proteases. In this review, our aim is to discuss sequence, structure, and function of various globulins present in Glycine max.

Insights into the human oral microbiome

Human oral cavity harbors the second most abundant microbiota after the gastrointestinal tract. The expanded Human Oral Microbiome Database (eHOMD) that was last updated on November 22, 2017, contains the information of approximately 772 prokaryotic species, where 70% is cultivable, and 30% belong to the uncultivable class of microorganisms along with whole genome sequences of 482 taxa. Out of 70% culturable species, 57% have already been assigned to their names. The 16S rDNA profiling of the healthy oral cavity categorized the inhabitant bacteria into six broad phyla, viz. Firmicutes, Actinobacteria, Proteobacteria, Fusobacteria, Bacteroidetes and Spirochaetes constituting 96% of total oral bacteria. These hidden oral micro-inhabitants exhibit a direct influence on human health, from host’s metabolism to immune responses. Altered oral microflora has been observed in several diseases such as diabetes, bacteremia, endocarditis, cancer, autoimmune disease and preterm births. Therefore, it becomes crucial to understand the oral microbial diversity and how it fluctuates under diseased/perturbed conditions. Advances in metagenomics and next-generation sequencing techniques generate rapid sequences and provide extensive information of inhabitant microorganisms of a niche. Thus, the retrieved information can be utilized for developing microbiome-based biomarkers for their use in early diagnosis of oral and associated diseases. Besides, several apex companies have shown keen interest in oral microbiome for its diagnostic and therapeutic potential indicating a vast market opportunity. This review gives an insight of various associated aspects of the human oral microbiome.

Mechanisms Underlying the Opposing Effects of P2Y Receptors on the Cell Cycle

The purinergic P2Y receptors are critical determinants of physiological function playing diverse roles in cell proliferation, differentiation, and survival. However, in cancer cells they have been reported to assume contradictory roles at times, thus causing inhibition of proliferation, cell death, and apoptosis. A critical evaluation and analysis of the existing experimental data show that this response is caused by multiple mechanisms at the level of the ligand, receptor, G protein, intracellular signaling, such as the mitogen activated protein kinase pathways and surface expression. This review addresses the impact of these factors in determining the outcome of P2Y receptor activation. Working in conjunction, these factors can act to produce the observed opposing effects on the cell cycle. Thus, they are important factors in the pathogenesis and control of cancer.

Expression parameters for target gene cloned in Escherichia coli in response to phosphate supply

SummaryRecombinant strain of E.coli 1727 overexpressed target gene at enhanced level when supplied with excess of inorganic phosphate. Rate of target gene expression, yield coefficient for target gene product and plasmid copy number increased significantly: 50%, 100% and 40% respectively at 125 mM excess phosphate. This was, however, accompanied by 26% decrease in specific growth rate and 30% in cellular growth yield coefficient.

Analytical Methods for the Assessment of Maillard Reactions in Foods

The aim of this chapter is to give a reliable overview of analytical methods for the quantitative and qualitative evaluation of Maillard reaction products in foods during processing and storage steps. At present, the importance of Maillard reactions in food processing is correlated with the appearance of sensorial alterations in foods: colours, flavours, and odours can be seriously compromised. Maillard reaction-related modifications may be a distinctive advantage in certain foods. On the other side, the attention of researchers in the area of public health is often focused on safety aspects of selected molecules or classes of substances such as furfurals, furosine, 3-deoxyglucosone, and other chemicals such as acrylamide. This chapter describes the Maillard reaction in detail. Moreover, many problems concerning the real comprehension of this group of chemical reactions depend on the peculiarity of analysed food products and analyte features. As a result, the choice of the ‘right’ analytical procedure should take into account these aspects related to peculiar analytes: a brief introduction to the problem is presented here.

Alzheimer's Amyloid-β Rescues Yeast from Hydroxide Toxicity

Amyloid-beta(Abeta42), which is known to be toxic to neuronal cells, protects yeast cells from severe sodium hydroxide toxicity. More than 85% cell death was caused by treatment with 1 mM NaOH and approximately 95% was observed at a 2 mM concentration. However, greater than 55% cells survived the treatment in the presence of Abeta42. A strong protective effect of the peptide was also evident from the differential staining of the treated culture with propidium iodide.

High-level expression of a heterologous gene in Escherichia coli in response to carbon-nitrogen source and C/N ratio in a batch bioreactor

Overexpression of the target gene in a recombinant strain of Escherichia coli has been analyzed in view of changes in the carbon−nitrogen source and as a function of C/N ratio. The rate of target gene expression varied over a range of 200%, and the yield coefficient for the target gene product changed over 400% with change in carbon source at 10 g L−1 in M9 medium. With variation in nitrogen source, however, only marginal changes (10–15%) occurred in these parameters of overexpression. Higher concentration, for example 2.5 g L−1, of any nitrogen source adversely affected heterologous expression as rate of target gene expression declined in the range 35%−50% and the yield coefficient of foreign protein decreased between 45% and 60%. A C/N ratio of 15 was found to be optimum for both parameters for overexpression and host specific parameters such as specific growth rate and observed yield coefficient for cellular growth. An analysis with respect to temperature and pH revealed that host and expression parameters were quite susceptible to changes in these factors.