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Category Archives: Genetics

Nepal Agriculture Research Council (NARC), Biotechnology Unit is organizing ” National Biotechnology Conference 2011″ with theme ” Biological Revolution through Biotech” on 12-13 July 2011 at Khumaltar, Lalitpur, Nepal. You are cordially invited for the participation of the program. This program will be inaugurated by Honorable Minister of Agriculture and Cooperatives, Nepal.

Venue: National Agriculture Research Institute Hall, Khumaltar, Lalitpur, Nepal

Conformed Speakers:

  1. Dr. Dilip Panthee (Asso. Prof. North Carolina State University, NC, USA)

Deadline for Abstract Submission: 17 June 2011
The abstract should be within 250 words and the topic should relate to theme of the conference. Similarly, you will be notified about its acceptance. The topic of the article should be purely research based except for status and policy papers.

Areas for the abstract submission:

  1. Status of the biotechnology research, production and development
  2. Tissue culture and in-vitro techniques
  3. Biodiversity conservation and utilization using biotechnology tools.
  4. Breeding and genetics using biotechnology tools.
  5. Vaccine and medical biotechnology
  6. Policy on biotechnology research, production and development

For further information, please contact Raj K. Niroula (rkn27st@yahoo.com) and Resham B. Amgai (reshamamgain@yahoo.com) at Biotechnology Unit (Phone: +977 1 5539658).

For details please download the document below

Notice & Program Biotech Conference 2011

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Click on the picture for enlarged version.

Chandra Prasad Risala, b, Tadashi Yokoyamac, Corresponding Author Contact Information, E-mail The Corresponding Author, Naoko Ohkama-Ohtsud, Salem Djedidia and Hitoshi Sekimotoe

a United Graduate School of Agri. Science, Tokyo Univ. of Agri. and Tech., Tokyo 183-8509, Japan

b Soil Management Directorate, Dept. of Agriculture, Hariharbhawan 552-0314, Nepal

c Institute of Agriculture, Tokyo Univ. of Agri. and Tech., Saiwai-cho 3-5-8, Fuchu, Tokyo 183-8509, Japan

d Women’s Future Devt. Organization, Tokyo University of Agri. and Tech., Tokyo 183-8509, Japan

e Faculty of Agriculture, Utsunomiya University, Utsunomiya 321-8505, Japan

Received 2 April 2010.
Available online 20 September 2010.
Systematic and Applied Microbiology
Volume 33, Issue 7, November 2010, Pages 416-425

Abstract

Soybean-nodulating bradyrhizobia are genetically diverse and are classified into different species. In this study, the genetic diversity of native soybean bradyrhizobia isolated from different topographical regions along the southern slopes of the Himalayan Mountains in Nepal was explored. Soil samples were collected from three different topographical regions with contrasting climates. A local soybean cultivar, Cobb, was used as a trap plant to isolate bradyrhizobia. A total of 24 isolates selected on the basis of their colony morphology were genetically characterized. For each isolate, the full nucleotide sequence of the 16S rRNA gene and ITS region, and partial sequences of the nifD and nodD1 genes were determined. Two lineages were evident in the conserved gene phylogeny; one representing Bradyrhizobium elkanii (71% of isolates), and the other representing Bradyrhizobium japonicum (21%) and Bradyrhizobium yuanmingense (8%). Phylogenetic analyses revealed three novel lineages in the Bradyrhizobium elkanii clade, indicating high levels of genetic diversity among Bradyrhizobium isolates in Nepal. B. japonicum and B. yuanmingense strains were distributed in areas from 2420 to 2660 m above sea level (asl), which were mountain regions with a temperate climate. The B. elkanii clade was distributed in two regions; hill regions ranging from 1512 to 1935 m asl, and mountain regions ranging from 2420 to 2660 m asl. Ten multi-locus genotypes were detected; seven among B. elkanii, two among B. japonicum, and one among B. yuanmingense-related isolates. The results indicated that there was higher species-level diversity of Bradyrhizobium in the temperate region than in the sub-tropical region along the southern slopes of the Himalayan Mountains in Nepal.

Keywords: Bradyrhizobium; Genetic diversity; 16S rRNA gene; Himalaya; Nepal

– by Dr. Sameer M. Dixit and Prof. Dr. Meeta Singh

Cervical cancer is the most preventable cancer in women. Ironically, it is also the biggest killer amongst all cancers in Nepali women. All women that are sexually-active are at risk of contracting it. Although there are no clear reports, it is estimated that 20 percent of all female cancers is linked to cervical cancer, most of those being in advanced clinical stages. Annually, in Nepal, there are an estimated 1,100 deaths due to cervical cancer.

Research worldwide has shown that Human Papillomavirus (HPV) is the major cause of cervical cancer in women. Specifically, about 5 types of HPV (16, 18, 31, 32 and 45) among about 100 known strains have been linked to cervical cancer. According to literature, persistence infection with one of 15 high-risk HPV types is considered a necessary cause for cervical cancer. Estimates worldwide have suggested that types 16 and 18 account for 70 percent of all cervical cancers. In Asia, this has been liked to 67 percent of all cervical cancers, with Southern Asia (where Nepal is located) linked to 80 percent of all cervical cancers.

There are preventive vaccines already developed and being used in developed countries against at least four of the high-risk HPV groups. Gardasil (manufactured by Merck) protects against HPV 6, 11, 16 and 18. Cervarix (manufactured by Glaxo Smithkline) protects against 16 and 18. These are recommended for young girls in three shots (primary and booster dosage).

In the United States, the Center for Disease Control recommends that female patients start regular cervical cancer screening at the age of 21 or within three years after first having sexual intercourse. The first test for the screening test for cancer of the cervix is the pap test which detects precancerous or cancers cells. The second recommended test is the HPV test, which looks for the human papillomavirus that can cause these cell changes leading to cervical cancer. While the smear test can be carried out by most pathology laboratories, HPV test requires advanced laboratory setup. In US and other developed countries, early intervention is now made possible by molecular detection technologies such as polymerase chain reaction (PCR) or real-time PCR. These tests enable detection of high-risk HPV in the cervix rather than relying on histopathological results alone. Thus, by regular screening for HPV, it is now possible to reduce the risk of developing cancer in women worldwide.

For a developing country like Nepal, accurate screening of cases of cancer of the cervix in Nepal continues to be a major problem. Very little, if any, literature reports exist on the type of HPV present in the population, and in cervical cancer cases. Even World Health Organization (WHO) does not have data on Nepali context to come up with an effective solution to the problem. Even though vaccines exist, without the knowledge of the HPV type prevalent here, the usefulness of such vaccines in Nepal is not proven.

Women who are sexually-active should visit their gynecologist for cervical cancer screening. Cervical cancer is totally preventable, so there is no excuse for not getting tested for it.

Molecular detection of HPV and its strain identification has never been tried in Nepali laboratories before. The primary screening method used in Nepal is the Pap Test – Pap smears can detect cervical cancers if smears are taken properly and interpreted by an experienced expert cytologist. Pap smears may not provide accurate detection of all suspect cases if the smear sample is not taken properly. However, if we can even screen some of the early stage cervical cancer patients using novel molecular tools such as PCR, we could be saving many more lives. PCR could be the preferred and more efficient method of detection of HPV and thereby detect cancer cervix in our country where there are very few pathologists. It must be taken into account that just the presence of HPV in the cervix does not necessarily indicate cervical cancer risk. In most cases, the low-risk viruses are shed off by the body automatically. However, detection of the virus provides the gynecologist evidence to screen the patient at regular intervals, thereby enabling early detection of abnormal cellular morphology in the case of cancer. Identification of any of the high-risk HPV is thus the key to early intervention of cervical cancer.

It is, therefore, highly recommended for all women who are sexually-active to visit their preferred gynecologist for cervical cancer screening. HPV type molecular screening is also now available in the city. October of every year is dedicated to cancer, worldwide. Cervical cancer is totally preventable, so there is no excuse for not getting tested for it.

Dr. Dixit is associated with the Center for Molecular Dynamics Nepal (CMDN). Dr. Singh is Head of Department, Gynecology/Obstetrics, Tribhuvan University Teaching Hospital (TUTH). CMDN in collaboration with Dept of Gynecology/Obstetrics, TUTH, is in the process of initiating HPV type study into cervical cancer in Nepal.

s.dixit@cmdn.org

This article has been taken from The Republica National Daily http://myrepublica.com/portal/index.php?action=news_details&news_id=24761

DR SAMEER M DIXIT & PROF DR MEETA SINGH

The Himalayan Times National Daily, 31st October 2010

Mitochondrial and Y-chromosome diversity of the Tharus (Nepal): a reservoir of genetic variation.

BMC Evol Biol. 2009 Jul 2;9:154.

Fornarino S, Pala M, Battaglia V, Maranta R, Achilli A, Modiano G, Torroni A, Semino O, Santachiara-Benerecetti SA.

Dipartimento di Genetica e Microbiologia, Università di Pavia,Pavia, Italy. fornarin@pasteur.fr

Abstract

BACKGROUND: Central Asia and the Indian subcontinent represent an area considered as a source and a reservoir for human genetic diversity, with many markers taking root here, most of which are the ancestral state of eastern and western haplogroups, while others are local. Between these two regions, Terai (Nepal) is a pivotal passageway allowing, in different times, multiple population interactions, although because of its highly malarial environment, it was scarcely inhabited until a few decades ago, when malaria was eradicated. One of the oldest and the largest indigenous people of Terai is represented by the malaria resistant Tharus, whose gene pool could still retain traces of ancient complex interactions. Until now, however, investigations on their genetic structure have been scarce mainly identifying East Asian signatures.

RESULTS: High-resolution analyses of mitochondrial-DNA (including 34 complete sequences) and Y-chromosome (67 SNPs and 12 STRs) variations carried out in 173 Tharus (two groups from Central and one from Eastern Terai), and 104 Indians (Hindus from Terai and New Delhi and tribals from Andhra Pradesh) allowed the identification of three principal components: East Asian, West Eurasian and Indian, the last including both local and inter-regional sub-components, at least for the Y chromosome.

CONCLUSION: Although remarkable quantitative and qualitative differences appear among the various population groups and also between sexes within the same group, many mitochondrial-DNA and Y-chromosome lineages are shared or derived from ancient Indian haplogroups, thus revealing a deep shared ancestry between Tharus and Indians. Interestingly, the local Y-chromosome Indian component observed in the Andhra-Pradesh tribals is present in all Tharu groups, whereas the inter-regional component strongly prevails in the two Hindu samples and other Nepalese populations.The complete sequencing of mtDNAs from unresolved haplogroups also provided informative markers that greatly improved the mtDNA phylogeny and allowed the identification of ancient relationships between Tharus and Malaysia, the Andaman Islands and Japan as well as between India and North and East Africa. Overall, this study gives a paradigmatic example of the importance of genetic isolates in revealing variants not easily detectable in the general population.

PMID: 19573232 [PubMed – indexed for MEDLINE]PMCID: PMC2720951Free PMC Article

Pubmed: http://www.ncbi.nlm.nih.gov/pubmed/19573232

Full Text Article (PubMed Central): http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2720951/pdf/1471-2148-9-154.pdf