News Update on Nucleotide: Jun 2020

The International Nucleotide Sequence Database Collaboration

The International Nucleotide Sequence Database Collaboration (INSDC; http://www.insdc.org) comprises three global partners committed to capturing, preserving and providing comprehensive public-domain nucleotide sequence information. The INSDC establishes standards, formats and protocols for data and metadata to make it easier for individuals and organisations to submit their nucleotide data reliably to public archives. This work enables the continuous, global exchange of information about living things. Here we present an update of the INSDC in 2015, including data growth and diversification, new standards and requirements by publishers for authors to submit their data to the public archives. The INSDC serves as a model for data sharing in the life sciences. [1]

The general stochastic model of nucleotide substitution

DNA sequence evolution through nucleotide substitution may be assimilated to a stationary Markov process. The fundamental equations of the general model, with 12 independent substitution parameters, are used to obtain a formula which corrects the effect of multiple and parallel substitutions on the measure of evolutionary divergence between two homologous sequences. We show that only reversible models, with six independent parameters, allow the calculation of the substitution rates. Simulation experiments on DNA sequence evolution through nucleotide substitution call into question the effectiveness of the general model (and of any other more detailed description); nevertheless, the general model results are slightly superior to any of its particular cases. [2]

Cyclic nucleotide phosphodiesterases

Cyclic nucleotide second messengers (cAMP and cGMP) play a central role in signal transduction and regulation of physiologic responses. Their intracellular levels are controlled by the complex superfamily of cyclic nucleotide phosphodiesterase (PDE) enzymes. Continuing advances in our understanding of the molecular pharmacology of these enzymes has led to the development of selective inhibitors as therapeutic agents for disease states ranging from cancer and heart failure to depression and sexual dysfunction. Several PDE types have been identified as therapeutic targets for immune/inflammatory diseases. This article briefly reviews the available in vitro, preclinical, and clinical data supporting the potential for selective PDE inhibitors as immunomodulatory agents. (J Allergy Clin Immunol 2001;108:671-80.) [3]

Association of MMP 9-1562 C/T Single Nucleotide Polymorphism with the Susceptibility to Lung Cancer Disease in South Iranian Population

Aims: The aim of this study was to investigate the association of MMP9 -1562 C /T single nucleotide polymorphism with lung cancer in south Iranian population. Matrix metalloproteinases (MMPs) are a family of highly conserved metal-dependent proteolytic enzymes that are able to degrade ECM components and regulate various cell behaviors. Among several candidate genes, MMP9 is one of the most important genes known to play a key role in relation to lung cancer initiation and progression. A common -1562(C/T) single nucleotide polymorphism in the promoter region of MMP9 was reported to have an association with lung cancer disease.

Study Design: A case – control study was carried out using 90 lung cancer patients and 100 healthy controls.

Place and Duration of Study: Cellular and Molecular Gerash Research Center, Shiraz University of Medical sciences, shiraz, Iran, between 2010-2012. [4]

Correlation Effect of the Van-der-Waals and Intramolecular Forces for the Nucleotide Chain – Metallic Nanoparticles Binding in a Carbon Nanotube Matrix of Periodic Boundaries

Using molecular dynamics simulation method we investigated the correlation effects between the weak Van der Waals forces and intramolecular vibrations for the molecular system consisting of a small nucleotide chain, gold nanoparticles and carbon nanotube with periodic boundaries. The molecular system represents a great interest in many aspects of modern research and applied sciences. For example, in bio-nano-technologies the application aspects include the development of electronic mobile diagnostic facilities, nanorobotic design for a drug delivery inside living cell, and so on. For the molecular system we have built up a series of the models with different configurations and performed their analysis. The entire system was allowed to interact with each other by the only VdW forces. The Lennard-Jones short-ranged interaction was assumed between the nucleotide chain, nanoparticles and carbon nanotube. For the carbon nanotube a many-body Tersoff potential having a quantum-chemistry nature was used. So far, the so-called hybrid MD approach was realized, where the quantum-chemistry potential in combination with a classical trajectory calculation applied. The peculiarities of the nucleotide chain – nanoparticle interaction and bond formation inside of a carbon nanotube matrix of the periodic boundaries were investigated along with the structural and dynamical behavior. [5]

Reference

[1]  Cochrane, G., Karsch-Mizrachi, I., Takagi, T. and Sequence Database Collaboration, I.N., 2016. The international nucleotide sequence database collaboration. Nucleic acids research44(D1), pp.D48-D50.

[2] Rodriguez, F.J.L.O.J., Oliver, J.L., Marin, A. and Medina, J.R., 1990. The general stochastic model of nucleotide substitution. Journal of theoretical biology, 142(4), pp.485-501.

[3] Essayan, D.M., 2001. Cyclic nucleotide phosphodiesterases. Journal of Allergy and Clinical Immunology, 108(5), pp.671-680.

[4] Jafari, M., Pirouzi, A., Mohsenzadeh, M., Kusari, A. and Hajihosseini, S. (2014) “Association of MMP 9-1562 C/T Single Nucleotide Polymorphism with the Susceptibility to Lung Cancer Disease in South Iranian Population”, Journal of Advances in Medicine and Medical Research, 4(13), pp. 2494-2502. doi: 10.9734/BJMMR/2014/6795.

[5] Khusenov, M. A., Dushanov, E. B. and Kholmurodov, K. T. (2015) “Correlation Effect of the Van-der-Waals and Intramolecular Forces for the Nucleotide Chain – Metallic Nanoparticles Binding in a Carbon Nanotube Matrix of Periodic Boundaries”, Current Journal of Applied Science and Technology, 8(3), pp. 313-323. doi: 10.9734/BJAST/2015/16619.

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