Institute of Biochemistry, Molecular Biology and Biotechnology

The Institute of Biochemistry, Molecular Biology and Biotechnology of the University of Colombo is fully equipped with the state of the art instruments and facilities to carry out advance research activities where the researchers can take full advantage to carry out their experiments.

This activities will contribute to the development of high quality man power for the development of Sri Lanka. Several research programmes are currently in progress in the areas of :

Molecular Biological Approaches to Filariasis

Filariasis in Sri Lanka is caused by the filarial nematode parasite, Wuchereria bancrofti. The disease is transmitted by the vector mosquito, Culex quinquefaciatus. According to WHO data, currently more than 125 million people in tropical countries of the globe are infected. In the past few years we have been successful in the development of rapid and highly sensitive DNA based diagnostic techniques and also similar DNA based methods to detect the vector mosquito.

There are only two drugs presently available for the treatment of the disease, carbamazine and ivermectin. There is, therefore a great need to develop new drugs and identify potential drug targets in the parasite. The enzyme, cyclo-oxygenase, in the parasite has been hypothesized as a potential target for drug development. Partial purification and characterization of this enzyme was completed.

The filarial parasite W. bancrofti causing lymphatic filariasis cannot be cultured. Only source of parasite material is from night blood samples collected from patients. This source is not sufficient to undertake molecular studies. A related cattle filarial parasite is Setaria digitata. The adult worm of this parasite can be obtained in large quantities from the abdominal cavity of cattle slaughtered at abattoirs. Using this parasite a cDNA library was established. The screening of this library for parasite specific genes is being continued and myosin light chain gene and several other genes have been sequenced. These are likely to provide potential diagnostic methods or therapeutic targets for the development of new drugs for filariasis.

A Probationary Lecturer in Parasitology at the Faculty of Medicine, University of Jaffna carried out MPhil studies under this project. DNA sequences generated are providing the basis for an MPhil degree registered at University of Colombo, School of Computing.

Related studies are being carried out by a student registered at the Faculty of Science for MPhil degrees. This project aims to study function of nematode specific proteins from the cattle filarial parasite Setaria digitata and to study its organelle localization. Experiments are conducted at the IBMBB.

Molecular Medicine

Several projects in biomedical sciences are carried out requiring either human or animal experimentation. These include studies on cancer, pregnancy and fetal growth, endometrial function, pregnancy induced hypertension and human DNA variation etc.

Cancer Genetics

Mutation Analysis of DNA from clinically confirmed Breast Cancer Patients

Most cancers are now known to have a genetic predisposition. Two candidate genes, BRCA1 and BRCA2 are now implicated in the development of familial type of breast cancer. The prevalence of all forms of cancer and breast cancer in particular appear to show a global upward trend. Although cancer was regarded as a disease of the affluent society, this is now changing and according to experts at the Cancer Hospital at Maharagama, the trend in Sri Lanka is also on the increase.

Although mutation analysis per se is neither a cure nor a prevention, the collection of such data for the Sri Lankan population is extremely important, as mutations are known to vary among populations. In addition, it may also help the person carrying such a mutation to resort to regular screening such as mammography.

One PhD student who worked on analysis of BRCA-1 gene mutations satisfactorily completed her examination. Another MPhil/PhD student is currently studying BRCA-2 mutations. This study is a collaborative study with the National Cancer Institute, Maharagama and Faculty of Medicine, University of Colombo.

Human DNA Variation

Although all humans are 99.9% identical, the differences among them provide tools for genetic identification of individuals. Some of the methods used are not suitable when the material available is very limited or degraded and in such instances analysis of mitochondrial DNA has proved to be useful. In order to establish a data base of mitochondrial D loop.

Reproductive & Developmental Biology

  • A Genomic and a Proteomic Study of Low Birth Weight

In view of the importance of placental function in fetal growth and paucity of data on placental gene expression, a study is being conducted to investigate placental gene expression in relation to fetal growth. This is a collaborative study with Castle Street Hospital for Women. Role of insulin like growth factor system in relation to birth weight is also being investigated and is described below. One MPhil student worked on placental gene expression.

  • Role of Leptin in Endometrial Function

In view of the effects of leptin on reproductive function and the presence of leptin receptors in the human endometrium a study had been in progress to investigate the effect of leptin on rodent endometrial function.

Previous studies examined the effect of leptin on endometrial IGF I, prolactin and IGFBP-1 synthesis, three proteins implicated in molecular events of implantation using a primary endometrial cell line from virgin rats. Pattern of leptin and leptin receptor expression in the uterus and in the oviduct in relation to the estrus cycle was also investigated. In order to examine gene expression in response to leptin stimulation selected genes were studied. These studies support an MPhil project.

  • Leptin System and other Proteomic Markers for early detection of pregnancy induced hypertension/ Pre-Eclamptic Toxaemia

Pregnancy induced hypertension (PIH)/pre-eclamptic toxaemia (PE) are pregnancy complications with serious consequences for the baby and the mother. To date there are no biochemical or genetic markers that can identify women predisposed to PIH/PE. A collaborative study with the Castle Street Hospital for women, Colombo continued to evaluate the feasibility of using biochemical and genetic markers related to the leptin system for early detection of PIH/PE before clinical manifestation. Results todate have shown that maternal leptin levels, free leptin index and the leptin genotype are likely to identify those predisposed to developing PE/PIH. This programme funded by SAREC and NRC supported one PhD student and two MSc students.

  • Insulin-like growth factor system in Pregnancy and Fetal Growth

A PhD project which commenced in 2006 to study IGF genotype in relation to fetal growth was continued in 2009. Blood samples were collected from mothers, fathers and newborns (cord blood) and analysis of plasma levels of IGF I, IGF II and IGFBP-1 as well as IGF-II Apa polymorphism studies were completed in 2008. IGF-I genotyping and H 19 genotyping continued. This project is supported by SAREC Grant and National Research Council Grant to Prof. Tennekoon. One MSc student was also supported by this project.

Genetic Variation between the Populations of Aedes Aegypti and AE. Albopictus

Aedes aegypti and Aedes albopictus are the major dengue vectors in Sri Lanka. A thorough understanding of the vector population is of paramount importance to develop effective strategies for combating the disease. Pattern of genetic diversity of Aedes aegypti and Aedes albopictus were examined by analyzing Ribosomal DNA (r-DNA) variations. 70 individual mosquitoes from 6 populations of A. aegypti and 70 individual mosquitoes from 5 populations of A. albopictus were analyzed for ITS2 based variations. A significant polymorphism was found even among mosquitoes caught from the same locality. Based on the results obtained both species could be divided into 2 major groups.

One MPhil student carried out this work which is a collaborative programme with University of Sri Jayawardenapura and Medical Research Institute.

Development of Molecular Markers to identify Corynespora leaf fall disease in Rubber (Hevea Brasiliensis)

Corynespora Leaf Fall (CLF) caused by Corynespora cassiicola is currently considered as the most destructive leaf disease of Rubber (Hevea brasiliensis) in Asia & African continents. Pathogen affects the young & old leaves on immature & mature rubber plants causing leaf fall through out the year. The disease affects all susceptible clones causing defoliation & die-back. Chemical control of CLF is practiced only in nurseries. It cannot be used in the field because it wastes not only the chemicals but also the time & labour.

The identified effective method for control of CLF is development of resistant clones through plant breeding. Conventionally, for screening & identification of resistant clones for CLF requires lots of labour & time. And it requires 22-30 years to release such a clone. Therefore to reduce the time of the breeding & selection cycle, use of effective DNA fragment specific for the resistant trait is of paramount importance.

Resistant gene analog (RGA) markers were used to develop a method to identify rubber plants resistant to CLF. Experiments are in progress to characterize a DNA fragment which was specific for the resistant clones. This work was carried out by one MPhil student supported by SAREC.

Genetic Differentiation of Sri Lankan Traditional Rice Varieties using AFLP Markers

Rice production in Sri Lanka has increased during the past 30 years. This has mainly been due to the effort of rice breeders developing new rice varieties. Most of the rice varieties currently grown in Sri Lanka belong to the category of New Improved Varieties (NIV), which were developed using foreign rice varieties. Although NIV’s produce high yields, there is an increasing demand in export market for Sri Lankan traditional rice varieties because of their grain qualities such as high fiber content. Therefore analysis of the genetic diversity of these traditional varieties will be beneficial to plant breeders when developing new varieties. Fluorescent Amplified Fragment Length Polymorphism (AFLP) and resistance gene analog markers are being used to assess the genetic variation and the genes conferring biotic and abiotic resistance in these varieties. This work is carried out by an MPhil student who is a probationary lecture of the Department of Botany, University of Jaffna and undergraduate students of Wayamba University supervised by an IBMBB staff member. Research is supported by SAREC and National Research Council Grant to Dr. Jagath Weerasena.

One MSc student worked on the development of PCR primers from putative disease resistant gene identified from rice variety “Rathuheenti and identification of disease resistant gene analogs from Sri Lankan rice varieties.

Molecular Characterization of Tea (Camellia Sinensis L) Cultivars in Sri Lanka

The tea-breeding programme, aimed at improving quality and growth traits, is in progress at the Tea Research Institute of Sri Lanka (TRI) although very little is known about the pattern of genetic variation in breeders’ collection. Therefore, effective conservation and use of genetic resources of tea are essential for sustainability and for increasing productivity of this vital export plantation crop. One PhD student who is a junior scientist from TRI carried out genetic studies on Tea and is now writing his Thesis.

DNA Phylogeny, Morphology Pathogenecity of Macrophoma Theicola Petch the causual agent of Stem Cenker in Tea

Low country stem canker caused by the ascomycete Macrophoma theicola petch, is the most serious stem disease of Camellia sinensis L. (tea) at lower elevations in Sri Lanka. It causes branch canker or kills the young shoots and in severe attacks may kill the entire bush by girdling the stem. The objectives of this study are to use molecular methods and morphological characteristics to compare the isolates of M. theicola obtained from different locations of Sri Lanka and to identify induced genes of Camellia sinensis in response to M. theicola infection. Morphological characterization of the pathogen is almost completed for different isolates of M. theicola

A junior scientist from TRI registered for an MPhil is working in this project.

Differentiation of Sri Lankan Mustard (Brassica Juncea) varieties using AFLP Markers and altering their Fatty Acid Profile by Interspecific Hybridization

Mustard (Brassica juncea) is the most important species of the genus Brassica. predominant cruciferous species in the Indian subcontinent. Mustard has been grown as a crop for hundreds of years and seeds are used widely in cooking in Sri Lanka. However, mustard has high levels of fatty acids such as erucic acid which are unfavourable for human health, and leads to heart disease. A closely related species, Brassica napus (Canola) has a fatty acid profile more favourable for protection against heart disease. This project is aimed at differentiating Sri Lankan mustard (Brassica juncea) varieties using molecular markers. Interspecific hybridization with Brassica napus is being attempted aimed at improving fatty acid profile of mustard. Amplified fragment length polymorphism showed a significant polymorphism in mustard and canola accessions tested. Agronomic characteristics were assessed to document morphological differences among accessions. Antifungal activities of plant extracts of mustered varieties were tested for several plant pathogenic fungi.

This is a collaborative study between IBMBB (Co-investigator: Dr. Jagath Weerasena) and the Open University (PI: Dr. Mrs. S. R. Weerakoon), supported by National Science Foundation. One MPhil student wa supported by this project and he is now writing the Thesis.

Biological Control of Agricultural Pests by Bacillus Thuringiensis

The development of microbial pesticides for effective pest control in the context of sustainable agriculture will be a major challenge and priority for the country. This research project aims at developing biological pesticides using Sri Lankan environmental isolates of Bt as an active ingredient, which could find use against major Lepidopteran, Coleopteran and Dipteran pests on agricultural crops. The objectives of the research are to determine insecticidal activity of Sri Lankan isolates of Bt against vegetable, fruit, rice and Tea pests, to develop microbial insecticides from Bt, to isolate and characterize toxins from Bt and to develop quality assurance procedures for microbial insecticides. Characterization of Bt strains by PCR based Cry gene identification is currently in progress.

This is a collaborative study between IBMBB (Co-investigator: Dr. Jagath Weerasena) and the Industrial Technology Institute, Colombo (PI: Dr. R. Samarasekera), supported by National Science Foundation and National Research Council, Sri Lanaka. One MPhil student is supported by this project.

Generic Differentiation of Finger Millet Accessions in Sri Lanka

Finger millet is the primary food source of millions of people in many regions of the world. Great attention has been paid on the improvement of this crop through breeding programmes. Substantial and smaller germplasm collections are available and hence the understanding of genetic diversity of those germplasms is very important to improve the crop. This study was carried out to understand the genetic diversity of finger millet accessions available in Sri Lanka. SSR markrs based PCR amplification was used in this study. This is a collaborative study between IBMBB (Co-investigator: Dr. Jagath Weerasena) and the Dept. of Botany, University of Sri Jayawardanapura (Dr. Mrs. P.N. Dassanayake), one MSc student of IBMBB worked in this project.