Table of Contents
1. Project Proposal: High Performance Computers for Plant Sciences Department
Project Title: Seeking funds for upgrading computer facilities in the Department of Plant Sciences of the University of Colombo for the Bioinformatics Special Degree Students
Funds to be raised: $2750 x 2 =5500
After reviewing the proposal submitted to the executive committee of CUFSAA by the plant science department, CUFSAA has undertaken the task to raise funds to purchase two high performance computers to the plant science department at University of Colombo. Currently the department does not have adequate computational facilities to serve the Bioinformatics special degree students. Bioinformatics is a promising research field and in the last few years the field has grown enormously. The plant science department plans to train the current bio informatics students suitable to the needs of the field and needs these high performance computers. Bioinformatics based research projects require significant amount of dedicated and continuous computer time to do the analysis and run programs which sometimes last for a couple of hours or days. Currently the department receive around 6-8 bioinformatics special degree students every year and all of them are required to conduct a final year research project in addition to the academic courses and other training programs. In particular, most of the final year research projects require continuous use of high-end computer facilities for long periods and having their own high end computer facility will help the faculty to train the students for today’s job market. CUFSAA also discussed whether cluster based computing can provide a good enough solution. However, many students lack adequate computer and networking facilities to connect to a cluster. Also, given the number of students and their course loads, flexibility becomes a crucial issue. CUFSAA also looked for expert opinion and found flexibility to be a very important practical aspect in this type of research and is planning to fund one computer initially with an external hard drive (< 5 TB) to facilitate data storage and based on the progress to fund the second computer in the future.
The Department of Plant Science wishes to set up a high-performance computer facility to enhance applied bioinformatics skills among undergraduate students and initiate genome-scale research projects. In this regard, the Department wishes to purchase two high-performance computers to meet the current requirement. The Head of the department of Plant Sciences, Dr. C. M. Nanayakkara sent CUFSAA a Request for Funding and the association expressed its willingness to support the project. CUFSAA also discussed whether cluster based computing can provide a good enough solution. However, the bioinformatics special degree students and faculty require longer uninterrupted flexible time to complete their research projects which can take a couple of hours or days. Hence given the number of students and their course loads, flexibility becomes a crucial issue. CUFSAA also looked for expert opinion and found flexibility to be a very important practical aspect in this type of research.
Please review the complete project proposal and support us. The complete project proposal is here.
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To post a paper check to CUFSAA, please make your checks payable to CUFSAA and add Plant Science Project on the memo line.
The postal address to send the donations is:
Colombo University Faculty of Science Alumni Association c/o Dr. Saliya De Silva 393 Valley Road River Edge NJ 07661 USA.
Thank you for your support!
2. A List of Recent Bioinformatics related undergraduate Projects
- Uncovering gene regulatory networks controlling plant embryogenesis: Gene regulatory networks (GRNs) underlie almost all cellular phenomena. Our primary goal is to predict GRNs underlying plant developmental processes from transcriptomic datasets using statistical and machine learning approaches. Although many efforts have been taken to elucidate the underlying molecular aspect of embryogenesis, the architecture of GRNs controlling plant embryogenesis is still poorly understood. Therefore, we use ‘plant embryogenesis’ as our primary experimental system.
- Transcriptome analysis of Arabidopsis POL2 mutants – an insight to gene functions at a global scale: RNA Sequencing (RNA-Seq) is a powerful technique for characterizing and quantifying the transcriptome. Today, a large number of bioinformatics software tools are available for transcriptome reconstruction and expression quantification. The functional characterization of Arabidopsis DNA polymerase epsilon catalytic subunit A (AtPOL2a, At1G08260) gene and its duplicated gene copy, AtPOL2b(At2G27120) gene is hampered due to the functional redundancy of these two genes. Thus, this study aimed at performing a comparative analysis of atpol2 mutants’ and wild type Arabidopsis (accession Col-0) transcriptome datasets generated using RNA-Seq. The specific objectives of the study were to evaluate different Bioinformatics analysis pipelines for the detection of differentially expressed genes (DEGs) between mutants and wild type Arabidopsis and predict biological pathways associated with DEGs.
- Computational analysis of OsNRAMP5 in selected Sri Lankan rice varieties: Heavy metal contamination, especially Cadmium (Cd), in paddy soils has become a critical issue worldwide.It can be easily absorbed by rice plants and accumulated in grains. Therefore, Cd contaminated rice has become a serious threat to public health. Natural Resistance-Associated Macrophage Proteins (NRAMPs) is a large family of metal ions transporters found in all organisms.To understand the sequence diversity of OsNRAMP5 in Sri Lankan rice varieties, an attempt was made to analyze the OsNRAMP5 promoter and peptide sequences in 54 sequenced localrice genomes.
- Genome-wide analysis of AP2/ERF gene familyinTheobroma cacao: The AP2/ERF is one of the key families of transcription factors in plants. They play an important role in regulating plant growth and development, and responses to various abiotic and biotic stresses. The AP2/ERF transcription factor family has been identified in many plant species including model plants. However, little research has been conducted on this transcription factor family in cacao, which is an economically important crop. In this study, a comprehensive genome-wide analysis was conducted to predict the genes encoding AP2/ERF in cacao. We believe that the findings of this study form a foundation for further studies of the functional characterization of cacao AP2/ERF genes and genetic improvement in cacao.
- Analysis of bacterial community profiles in rhizosphere under different fertilizer regimes using metagenomics approaches: The objective of the project is to analyze bacterial community profiles in the rhizosphere using metagenomics approaches, with the aim of finding alterations in soil bacterial communities due to different nitrogen fertilizer applications.
- Genome-wide Identification and Analysis of Late Embryogenesis Abundant (LEA) Genes in Musa acuminata (Banana): An insight into motif and gene structure arrangement: The objective of the research was to identify LEA genes in M.acuminata and perform an in-silico analysis to obtain the structural and functional properties of the genes and encoding proteins.
- Analysis of Kranz Anatomy: The objective of this study was to analyze the identified genes associated with Kranz anatomy in the three classes of plants namely C3, C3-C4 intermediates and C4. For example, one of the genes investigated in the project was the SCARECROW which is identified to be a factor necessary for the formation of Kranz anatomical features in C4 plants. Multiple Sequence Alignments were carried out for each class and key nucleotide differences in domains were examined to determine whether they are attributable to Kranz anatomical differences among the three classes. Moreover, the protein structures was also studied as a part of the research.
- Investigation of variation of genes associated with varied levels of drought tolerance at nucleic acid and amino acid sequence level using Bioinformatics tools: In this research project the selected protein coding genes known to associate with drought tolerance in plant species with varied drought tolerance levels were investigated at the nucleic acid and protein level with the use of bioinformatics tools with sub objectives of investigating drought tolerance associated genes, coding important proteins in the process of stress tolerance using literature as resources and identifying the sequences of the relevant protein coding genes and the proteins from available data to analyze protein coding genes at the DNA level and the relevant proteins at the amino acid sequence and structural level and identifying crucial amino acids responsible. And finally the variation in drought tolerance with the differences in the crucial amino acids at the active site were compared.
- Level of genomic differentiation of an avian hybrid zone determined using markers generated through Illumina RAD NGS tools: In this research genomic differentiation among Dinopium psarodes, D.benghalensis and their hybrids was determined. Apart from that, the genetic hybrid index was also created to check the gene flow and the introgression between parental species and the hybrids. For this, the short sequence reads generated by illumina RAD- seq of the individuals were assembled using denovo assembly method. Partially and fully informative species specific markers (SNP) were identified. Using the identified markers, GHI and the Fst were calculated.
- Phylogeny Of Oncogenic Human Papillomavirus Types: A Worldwide Systematic Analysis: Of over 170 HPV types belonging to the Papillomaviridae around 15 have been classified as high-risk. HPV infections, recognized as one of the most common sexually transmitted infections globally is identified as one of the main etiological factors for cervical cancer in addition to being linked to cancers of oral and oropharyngeal, lung, anal and penile. The specific objectives of the study were to establish phylogenetic relations and population indices among cervical cancer, lung cancer and oral and oropharyngeal cancer-causing HPV types. The study was conducted with a total of 161 HPV genome records, across six countries.