Industrial Crops and Products 55 (2014) 75–82
Contents lists available at ScienceDirect
Industrial Crops and Products journal homepage: www.elsevier.com/locate/indcrop
Correlation and functional differentiation between different markers to study the genetic diversity analysis in medicinally important plant Plumbago zeylanica Raja Feroz Ahmad Haji a , Mili Bhargava b , Bashir A. Akhoon c , Amandeep Kumar d , Narshima B. Brindavanam d , Vijeshwar Verma a,∗ a
Department of Biotechnology, Shri Mata Vaishno Devi University, Katra, Jammu and Kashmir 182320, India Biotechnology Division, CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow 226015, India c Department of Bioinformatics, System Toxicology Group, CSIR-Indian Institute of Toxicology Research, Lucknow 226001, India d Dabur Research & Development Centre, Dabur India Ltd., Ghaziabad 201010, India b
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Article history: Received 30 September 2013 Received in revised form 23 January 2014 Accepted 27 January 2014 Available online 5 March 2014 Keywords: Plumbago zeylanica Genetic diversity Phylogenetic analysis SSR SRAP ITS
a b s t r a c t The plant species Plumbago zeylanica (P. zeylanica) is a multipurpose medicinal herb of family Plumbaginaceae. This plant is a natural gift to mankind credited with potential medicinal properties such as anti-cancer, anti-atherogenic, cardiotonic, hepatoprotective, anti-fungal, diabetes and neuroprotective assets to list of few. In this study, genetic diversity and relationships among various Plumbago accessions, collected from different geographical regions of India, was assessed using simple sequence repeat (SSR), sequence related amplified polymorphism (SRAP) and internal transcribed spacer (ITS) markers. SSR and SRAP markers showed highest values of Nei’s genetic diversity and Shannon information index among populations. We also observed statistically significant genetic differentiations among and within populations (P < 0.01 in the AMOVA tests). Additionally, both Un-weighted paired group method with arithmetic average (UPGMA) and principal coordinate analysis (PCoA) grouped P. zeylanica populations into similar clusters which corroborate the above analysis to be useful for genetic diversity analysis of this plant. Our data signifies that SSR and SRAP are both reliable and effective tools for analyzing genetic diversity in P. zeylanica. However, based on our chosen dataset, we find ITS marker less significant for the genetic diversity analysis of this multifaceted plant. This information would be useful towards the identification, characterization and conservation of this species at the molecular level. © 2014 Elsevier B.V. All rights reserved.
1. Introduction
Abbreviations: AFLP:, Amplified Fragment Length Polymorphism; AMOVA:, Analysis of molecular variance; ARE:, Antioxidant responsive element; CTAB:, Cetyl trimethylammonium bromide; dNTPs:, Deoxynucleotide Triphosphates; EDTA:, Ethylenediaminetetraacetic acid; HGT:, Horizontal gene transfer; ISSR:, InterSimple Sequence Repeat; ITS:, Internal Transcribed Spacer; mTOR:, Mammalian target of rapamycin; NCBI:, National center for biotechnology information; NEB:, New England Biolabs; NRF:, Nuclear factor erythroid; PCoA:, Principal coordinate analysis; PCR:, Polymerase chain reaction; POP:, Population; PVP:, Polyvinylpyrrolidone; SAHN:, Sequential Agglome rative Hierarchical Nested; SIMQUAL:, Similarity for Qualitative Data; SRAP:, Sequence-related amplified polymorphism; SSR:, Simple sequence repeat; TE:, Tris-EDTA; UPGMA:, Un-weighted paired group method with arithmetic average; VEGFR:, Vascular endothelial growth factor receptor. ∗ Corresponding author. Tel.: +91 1991 285692. E-mail addresses:
[email protected],
[email protected] (V. Verma). 0926-6690/$ – see front matter © 2014 Elsevier B.V. All rights reserved. http://dx.doi.org/10.1016/j.indcrop.2014.01.045
Plumbago zeylanica is a perennial flowering plant (commonly known as white chitarak) that belongs to the family Plumbaginaceae. It is a fast growing, much branched evergreen shrub that reaches about 2 m and is native to warm temperate-tropical regions of the world. The plant is supposed to be originated in SouthEast Asia (Inamdar and Patel, 1970) and grows wild in India and Sri Lanka (Kirtikar et al., 1993). In India, the plant grows commonly wild or in cultivation due to its more therapeutic uses (Chetty et al., 2006) and is widely distributed from Central India to West Bengal, Maharashtra and various parts of Southern India. The plant has multidimensional uses and exhibit varying degrees of therapeutic values in the treatment of viral, fungal, malaria and bacterial pathogens. The plant also shows various other medicinal activities like anti-inflammatory, antioxidant, anti-invasive,
Journal of Molecular Graphics and Modelling 28 (2010) 664–669
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In silico designing and optimization of anti-breast cancer antibody mimetic oligopeptide targeting HER-2 in women Bashir A. Akhoon a,*, Shishir K. Gupta b, Vijeshwar Verma a, Gagan Dhaliwal b, Mugdha Srivastava b, Shailendra K. Gupta c, Raja Feroz Ahmad d a
Centre of Bioinformatics, Department of Biotechnology, SMVD University, Jammu, India Society for Biological Research & Rural Development, Lucknow 226010, UP, India Indian Institute of Toxicology Research, CSIR, Lucknow, UP, India d Department of Biotechnology, SMVD University, Jammu, India b c
A R T I C L E I N F O
A B S T R A C T
Article history: Received 9 December 2009
Overexpression of HER-2 is of frequent (20–30%) occurrence in breast cancer. Therapeutic targeting of HER-2 with humanized antibody derived oligopeptide may be a promising approach to the treatment of breast cancer. HER-2 gene is part of a family of genes that play critical roles in regulating transmembrane growth of breast cancer cells. Pertuzumab, a recombinant humanized monoclonal antibody (2C4), binds to extracellular domain II of the HER-2 receptor and inhibits its ability to dimerize with other HER receptors blocking the cell growth, signaling and apoptosis induction. The unique binding pocket on HER-2 for pertuzumab provides an important target domain for creation of new anticancer drugs. In the present work an efficient oligopeptide was designed by our computational method that interacts with pertuzumab binding sites of HER-2. In silico docking study demonstrated the best specific interaction of RASPADREV oligopeptide with the dimerization domain in the HER-2 molecule among various screened oligopeptides. ADMET and SAR properties prove the drug likeness of designed oligopeptide as having value 0.98. ß 2010 Elsevier Inc. All rights reserved.
Accepted 9 January 2010 Available online 18 January 2010 Keywords: Breast cancer HER-2 Pertuzumab Oligopeptide designing Anticancer drug
1. Introduction Breast cancer is the 2nd leading cause of deaths in women today and it is the most common cancer among women. The two strong risk factors for developing breast cancer include being female (only 1% of cases are diagnosed in males) and increasing age. 1 of 8 women is affected by breast cancer and one third of women die from breast cancer [1,2]. Infiltrating ductal carcinoma is the most common type of breast cancer, representing 78% of all malignancies. It in infiltrated through the wall of the duct then invades the fatty tissue of the breast and at this point it may be metastasize [2,3]. Studies show that approximately 25% of breast cancer patients have tumors that are human epidermal growth factor receptor 2 (HER-2) positive [4]. HER-2 positive tumors tend to grow and spread more quickly than tumors that are not HER-2 positive. HER-2 gene is part of a family of genes that promotes the
* Corresponding author at: BIF centre, Department of Biotechnology, Shri Mata Vaishno Devi University Campus, Sub P.O. SMVD University, Katra 182320, J&K, India. Tel.: +91 9906751249/9451157798. E-mail address:
[email protected] (B.A. Akhoon). 1093-3263/$ – see front matter ß 2010 Elsevier Inc. All rights reserved. doi:10.1016/j.jmgm.2010.01.002
growth of cancer cells. A fraction of breast cancers, as part of their development, undergo gene amplification [5,6]. Instead of having two gene copies of the HER-2 gene in a normal cell, there are multiple copies. As a result, there is far more expression of the HER2 protein on the cell surface, resulting in aberrant cell growth. An estimated 20–25% of breast cancers make these extra copies of the HER-2 gene. A normal breast cell might have 20,000 HER-2 receptors; a breast cancer cell could have as many as 1.5 million. Approximately 40,000 women are diagnosed each year in the United States with HER-2 positive breast cancer [2]. HER proteins are transmembrane growth factor receptors that activate intracellular signaling pathways in response to extracellular signals [3]. The structure of extracellular region of HER-2 is divided into four domains, designated domain I (extracellular ligand-binding domain), domain II (transmembrane domain), domain III (intracellular catalytic tyrosine kinase domain) and domain IV (carboxyl terminal signaling tail). Domain I extends from 1 to 195 residues, domain II extends from 196 to 320 residues, domain III proceeds from 321 to 488 and domain IV starts from 489 and ends in 560 [2]. Upon ligand binding, the extracellular domain changes into its active conformation leading to receptor dimerization and transphosphorylation of their C-terminal tails. Dimeriza-