About Author: Ho Wei Seng (wsho)

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Next Generation Sequencing Technologies Workshop (NGST2011)

By
Ho Wei Seng (wsho)
– May 3, 2011

Background
Over the last several years, the advances in next generation sequencing (NGS) technologies have rapidly changing the landscape of life sciences and providing many novel biological applications to explore previously unanswered questions. The next-generation sequencing technologies are able to produce millions of short sequence reads in a high-throughput and cost-effective fashion. The emergence of these technologies has not only facilitated de novo genome sequencing but also to other applications such as RNA/transcriptome sequencing, exome sequencing, large-scale genome re-sequencing, epigenomics, metagenomics, small RNA discovery, deep SNP discovery, chromatin immunoprecipitation (ChIP), and etc.

The Next Generation Sequencing Technologies (NGST) 2011 workshop will be the first-of-its-kind gathering on next generation sequencing to be organized in Sarawak, the Land of the Hornbills. This workshop is jointly organized by the Faculty of Resource Science and Technology (UNIMAS), Genetics Society of Malaysia, illumina in partnering with ScienceVision Sdn Bhd and BGI (formerly known as Beijing Genomics Institute), China.

Objectives
a). To act as a platform to highlight the latest developments in NGS technologies.
b). To share experience and knowledge from the scientists who are successfully using the NGS technologies in their research.

Who Should Attend?
All researchers including academicians and postgraduate students thinking about or currently engaged in next generation sequencing research are encouraged to attend.

For more information and enquiries, please contact the organizer or visit the workshop official website:
Dr Ho Wei Seng
Email: wsho@frst.unimas.my
Tel: +60 82 – 58 2975;  F

ax: +60 82 – 58 3160

Workshop website:
http://ngst2011.wordpress.com

We look forward to receiving your registration form and hope you will be able to join us in Kuching in September 26-27, 2011 and we also greatly appreciate your kind assistance to publicize this event to those who may be interested to participant.

Thank you.

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Articles

By
Ho Wei Seng (wsho)
– November 16, 2010
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Forestry-SCORE

By
Ho Wei Seng (wsho)
– November 16, 2010

The timber-based industry accounted for 31.86 per cent, tourism — 21.72 per cent, oil-based industry – 20.27 per cent, aquaculture — 12.4 per cent, livestock — 4.34 per cent, aluminium – 3.13 per cent, steel – 2.09 per cent, palm oil – 1.8 per cent, marine engineering – 1.45 per cent and glass – 0.61 per cent.

Fatimah: SCORE manpower needs to be known soon
Tuesday, 16 November 2010 15:06

MIRI: The Sarawak Corridor of Renewable Energy’s (SCORE) manpower requirements will be known next month with the completion of a study by Universiti Malaysia Sarawak (Unimas).

CONGRATULATIONS: Fatimah presents a certificate to a graduate. Syed Mohamad Noor is at second left.

Minister in the Chief Minister’s Department Datin Fatimah Abdullah said the study looked into the detailed requirements of the 10 industries in SCORE.

“If there is a mismatch of supply and demand, then the next step is making recommendations to increase enrolment at training institutes or setting up more such institutes,” she explained.

Fatimah said this yesterday when representing Chief Minister Pehin Sri Abdul Taib Mahmud during the sixth convocation of Training Institutes for the Manpower Department (ILJTM) Eastern Region for ILP Miri, Labuan, Kota Kinabalu, Samarahan and Sandakan.

She said earlier projections for manpower requirements for SCORE was 1.6 million.

The timber-based industry accounted for 31.86 per cent, tourism — 21.72 per cent, oil-based industry – 20.27 per cent, aquaculture — 12.4 per cent, livestock — 4.34 per cent, aluminium – 3.13 per cent, steel – 2.09 per cent, palm oil – 1.8 per cent, marine engineering – 1.45 per cent and glass – 0.61 per cent.

“This is to show that there are abundant job opportunities to be made available in the eastern corridor particularly in Sarawak.

“Thus graduates should grab the opportunities by adopting life-long learning to equip themselves with skills needed by these industries,” she said.

The government on its part, she said, is committed to increasing the current 10 per cent average rate of enrolment in technical and vocational upper secondary schools to meet the nation’s industrial needs.

Fatimah pointed out that countries like Germany, which had a high rate of 60 to 70 per cent enrolment, had been successful in reducing the unemployment of graduates to a low three per cent, within one year upon graduating.

She said several other strategies would be used to realise this vision in line with the target of building Malaysia into a high income economy. Under the 10th Malaysia Plan (10MP), the government has allocated RM449.5 million to upgrade various training institutes and build new ones as well as purchase equipment.

Budget 2011 also gave great emphasis to development of human capital with several programmes such as the 1Malaysia Training programme to be implemented next year. Meanwhile, Manpower Department deputy director general Syed Mohamad Noor Syed Mat Ali said training institutes under the Ministry of Human Resources had achieved numerous successes.

Under the Ninth Malaysia Plan (9MP), five new training institutes were set up in Taiping, Kemaman, Jerantut, Bintulu and Marang, increasing the capacity from 5,000 to 23,000 trainees.

The Manpower Department has established 27 training institutes until November 2009, offering a total of 27 certificate level courses, 15 technology diploma level courses, four electrical diploma level courses and eight advanced diploma courses. Syed Mohamad Noor said for the sixth convention for the Eastern Region, a total of 1,990 graduates of ILJTM Sarawak and Sabah received their certificates in various courses.

“It is projected that in the coming years, there will be an increased number of enrolments and graduates and also the introduction of new courses such as microelectric, and courses in high end products such as ceramics, composite and polymer,” he said. This year, the department received recognition from competitions such as Robocon 2010 (Best Idea Award at National Level), Itex (Gold medal – Project Wireless Car Air Conditioner With E-IAQ Function and Bronze Medal – Project Dual Computer System), and National Skills 2010 (Anugerah Tangan Emas Perdana Menteri 2010 – Automobile Technology) winning three gold, four silver and four bronze medals.

Extracted from the Borneo Post.

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The Healing Effects of Forests

By
Ho Wei Seng (wsho)
– November 9, 2010


Maybe there’s something to that “hug a tree” idea.

“Many people,” says Dr. Eeva Karjalainen, of the Finnish Forest Research Institute, Metla, “feel relaxed and good when they are out in nature. But not many of us know that there is also scientific evidence about the healing effects of nature.”

Forests – and other natural, green settings – can reduce stress, improve moods, reduce anger and aggressiveness and increase overall happiness. Forest visits may also strengthen our immune system by increasing the activity and number of natural killer cells that destroy cancer cells.

Many studies show that after stressful or concentration-demanding situations, people recover faster and better in natural environments than in urban settings. Blood pressure, heart rate, muscle tension and the level of “stress hormones” all decrease faster in natural settings. Depression, anger and aggressiveness are reduced in green environments and ADHD symptoms in children reduce when they play in green settings.

In addition to mental and emotional well-being, more than half of the most commonly prescribed drugs include compounds derived from nature – for example Taxol, used against ovarian and breast cancer, is derived from yew trees, while Xylitol, which can inhibit caries, is produced from hardwood bark.

Dr. Karjalainen will coordinate a session on the health benefits of forests at the 2010 IUFRO World Forestry Congress in Seoul. “Preserving green areas and trees in cities is very important to help people recover from stress, maintain health and cure diseases.  There is also monetary value in improving people’s working ability and reducing health care costs.” she says.

(Adapted from http://theiufroblog.wordpress.com/2010/07/19/the-healing-effects-of-forests/)


HOME → The healing effects of forest

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From Conservation to Innovation: Building Research Capacity for Planted Forest Development in Sarawak

By
Ho Wei Seng (wsho)
– November 9, 2010

THINKING GLOBALLY, ACTING LOCALLY, FROM HERE…

The increase in global demand for wood requires increase in forest productivity. The alternative is to farm trees in plantations composed of fast-growing species with short rotation cycle (6-8 years). The rationale is that natural forests at the most produce about 3m3/ha/yr of commercial timber, whereas plantations can produce annually from 10m3/ha of hardwoods to 30m3/ha of softwoods and thus, decrease the effects of human pressure on our ecosystems while increasing the competitiveness of Sarawak’s forest industry.


Rapid socio-economic changes in the world are having profound impacts on all sectors, including forestry. While wood products demand is increasing, so is the demand for environmental services of forests. The increasing demand is triggered by population growth and rise in income (gross domestic income). Global demand for wood products is projected to increase from 3.5 billion m3 in 1990 to 6.4 billion m3 in 2020. Apart from that, the demand for environmental services of forest is also increasing whereby more natural forests will be excluded from wood production, and recently the bioenergy policy, the use of biomass, including wood is increasingly encouraged (Figure 1). Natural forests are unable to meet current global demand for wood due to the long generation intervals and slow growth rate, resulting in the loss and degradation of natural forests by logging. About 12 million ha of forests are lost every year. Africa, South East Asia and South America provide the best environment for tree growth but account for more than 75% of total losses.

Figure 1: The current and future values of forests (Source: FAO, State of World Forests 2009)

Therefore, the increased demand for wood is likely to require increased forest productivity. The alternative is to farm trees in plantations composed of fast-growing species with short rotation cycle (6-8 years). With more research, particularly in the production of improved planting materials, tree selection and improvement, the plantations could produce more of the industrial timber by the end of the next 2 decades. The rationale is that natural forests at the most produce about 3 m3/ha/yr of commercial timber, whereas plantations can produce annually from 10 m3/ha of hardwoods to 30 m3/ha of softwoods. Furthermore, plantations are easier to manage due to the mono or double species mix compared to very diverse natural forest stands. Hence, plantations development will serve as a strategy for maintaining a sustainable supply of timber and at the same time, reducing the logging pressure on natural forests for wood production to an acceptable level.

In Sarawak, the state government has introduced the Forest (Planted Forest) Rules (1997) to encourage the development of commercial forest plantations and has set a target of 1.0 million hectares for forest plantations to be established by 2020. It is estimated that 30 million of high quality seedlings are required for the annual planting programme. Realizing the needs, a joint research programme (URL: http://fgilab.com) focusing on two selected fast growing indigenous tree species, namely Neolamarckia cadamba (Kelampayan) and Duabanga moluccana (Sawih) has been carried out to provide solutions, in addressing the shortage of quality planting materials for licensed planted forest areas in the state. The programme covers R&D activities on forest genomics, biotechnology and tree improvement geared towards enhancing commercial plantation forests as well as sustainable management of forest resources in Sarawak (Ho, 2008). Furthermore, the programme via the use of state-of-the-art technologies and approaches will help respond to the need to develop adequate tools for producing trees that are better adapted to local conditions, so that we may achieve economic benefits of great significance. Over the years, we have conducted projects with special focused on molecular genetic studies. Among others are the development of highly informative and polymorphic DNA markers specific for identifying the genetic makeup of two fast growing indigenous tree species, i.e. Kelampayan and Sawih; 2) the one step ‘Touch-incubate-PCR’ approach (aka fasTip-X Kit) for preparing plant tissues for high throughput genotyping, and 3) a genomic resource database, aka CADAMOMICS (10,368 ESTs) for wood formation in Kelampayan via high-throughput DNA sequencing.

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Why Neolamarkia cadamba and Duabanga moluccana?

Neolamarkia cadamba (Roxb.) Bosser, locally known as Kelampayan belongs to the family of Rubiaceae, has been identified as a promising fast growing species for planted forest development in Sarawak. Kelampayan is a large, deciduous and fast growing tree species, thus with characteristics which guarantee early economic returns within 8 to 10 years. Under normal conditions, it reaches a height of 17 m and diameter of 25 cm at breast height (dbh) within 9 years. It is a lightweight hardwood with a density of 290-560 kg/m3 at 15% moisture content. Thus, kelampayan is one of the best sources of raw material for the plywood industry, besides pulp and paper production. It can also be used as a shade tree for dipterocarp line planting, whilst its leaves and bark have medical application. The dried bark can be used to relieve fever and as a tonic, whereas a leaf extract can serve as a mouth wash. Another plantation tree species, Duabanga moluccana Blume or Sawih from the family of Sonneratiaceae can grow up to 45 meters tall and 100 cm in diameter. This tree is of great economic importance for the production of various wood works and products such as plywood, veneer and pulping. Additionally, it is also suitable for interior paneling, matches, moulding and pulping (CIRAD Forestry Department).



HOME → From conservation to innovation

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TRANSLATIONAL GENOMICS

By
Ho Wei Seng (wsho)
– November 8, 2010

Acacia Translational Genomics

The overall aim of this research project is to assess the quality of Acacia sp. wood available to the pulp, paper and board industries
through an understanding of wood properties and genetic analyses of wood quality traits/candidate genes. By associating
genotypes with phenotypes, we could determine what particular economic trait loci (ETL) or candidate genes are
involved and also how much of phenotypic variation could be explained by genetic variation on these genes via translational
genomics.


Projects: [Project Leader: Assoc. Prof. Dr. Ismail Jusoh; Co-researcher: Dr Ho Wei Seng]

  • Wood Density and Cleaved Amplified Polymorphic Sequence (CAPS) in Acacia sp.
  • Genetic Diversity of Acacia mangium Superbulk


Projects: [Project Leader: Dr Ho Wei Seng; Co-researcher: Assoc. Prof. Dr. Ismail Jusoh]

  • Evaluation of Genetic Relatedness Among Acacia mangium Superbulk and Acacia Hybrid (Acacia mangium x Acacia auriculiformis) Plus Trees Using DAMD Markers
  • Gene associated single nucleotide polymorphism (SNP) in cinnamate 4-hydroxylase (C4H) and cinnamy alcohol dehydrogenase (CAD) genes from Acacia mangium Superbulk trees.

Research collaborators:

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PARTNERSHIP CONTACT

By
Ho Wei Seng (wsho)
– November 8, 2010

We are always looking for new collaborations and partnerships. Please do not hesistat to contact us to explore opportunities.

Ho Wei Seng (PhD.)
Coordinator, Forest Genomics & Informatics Laboratory (fGiL)
Universiti Malaysia Sarawak (UNIMAS)
Tel: +6082 581000 ext.2975;  Fax: +6082 583160
Email: wsho@frst.unimas.my / howeiseng@gmail.com

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PEOPLE

By
Ho Wei Seng (wsho)
– November 8, 2010
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POSTGRADS

By
Ho Wei Seng (wsho)
– November 8, 2010

Researchers / Postgrads:

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Phui Seng Loi (UNIMAS/SFC)  

Project Title: Development of SSR Markers for Neolamarckia Cadamba (Roxb.) Bosser (Kelampayan)

Reliable information on the distribution of genetic variation is a crucial point for applicability and efficiency of any breeding, preservation and conservation programmes for forest trees. The emergence of DNA marker technologies have revolutionized the field of plant genetics by providing new tools for rapid genetic analysis, fingerprinting and studying relatedness among cultivars of many forest tree species. Recently, development of an ideal DNA marker system which is genetically co-dominant and multiallelic is becoming a major concern due to the genetic complexity of breeder’s populations and high levels of heterozygosity in individual genotypes. Simple sequence repeat (SSR) marker is a polymerase chain reaction (PCR)-based marker system of this kind, and becoming the excellent markers of choice for comparative genetic and genomic analysis, individual genotyping and studies of gene flow in forest trees. In this study, Neolamarckia cadamba was chosen due to its commercial value and fast growing ability. Although N. cadamba is important in ecosystems and tropical forestry and becoming one of the most frequently planted trees in the tropics, but genetic information about member species is limited. To date, none of the DNA markers has been developed from N. cadamba, compared with that from others economically important tropical tree. Therefore, in order to discover, investigate and determine the genetic diversity and structure of N. cadamba, the main goal of this study is to develop simple sequence repeat (SSR) markers specific for genotyping N. cadamba trees. The developed SSR markers later can be used to estimate the genetic diversity of natural and planted populations of Kelampayan.

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Liew Kit Siong (FRST-UNIMAS) 

Project Title: Development and Polymorphism of Simple Sequence Repeat (SSR) DNA Markers for Duabanga moluccana Blume

Efficient management of forest genetic resources whether for genetic improvement or conservation programmes requires accurate and rapid assessment of genetic diversity. With the advent of DNA sequencing, data analysis and polymerase chain reaction (PCR) technology, there has been a remarkable progress in the development of an array of potential DNA molecular markers in order to better characterize forest genetic diversity and address genetic resources questions. In recent year, simple sequence repeats (SSRs) are considered markers of choice in genetic studies because they are PCR-based,  high discriminatory power, high information content arising from their multiallelic nature, co-dominant, small amount of DNA template necessary, randomly distributed throughout the genome, robust and reproducible assay, and transferability across closely related taxa. However, the isolation and characterization of SSR marker for a forest trees is limited until now because involves highly time-consuming and development cost. In this study, SSR markers will be developed for Duabanga moluccana Blume based on a simple method as reported by Lian et al. (2001). D. moluccana was chosen for study due to its economically and ecologically important. To date, baseline genetic information for this species is limited and none of the DNA-based markers has been developed. In order to determine the genetic diversity and structure of D. moluccana, thus, the main objective of this study is to develop a set of SSR markers specific for genotyping D. moluccana trees.

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Grace Ting Jen Ching (FRST-UNIMAS) 

Project Title: Development of SCAR Markers for Sex Typing in Canarium odontophyllum Miq. (Dabai)

Dabai, being a Sarawak’s specialty fruit is well-known with its unique sexual characteristic. The female Dabai trees bear fruits while male Dabai trees do not and are normally removed 4 years later when the plants are reproductively mature.  This lengthy life cycle along with inability to determine gender at early stage can result in undesirable waste of time, space, resources and nursery cost. Therefore, an ideal solution to overcome this constraint is to develop a Sequence Characterized Amplified Region (SCAR) marker to determine the Dabai sex-type at seedling stage. Through RAPD, sex-related diagnostic band can be identified and subsequently transformed into a co-dominant SCAR marker by means of cloning and sequencing. Once developed, SCAR marker has the massive potential to assist in Dabai crop management program and thereby in advance, proposing and economic and yet profitable planting approach for Dabai plantation.

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Nurfaziah Binti Matra (FRST-UNIMAS) 

Project Title: Seeds Cryopreservation, Viability and Mating System of Neolamarckia cadamba (Roxb.) Bosser

The supply of timber from natural forests has been rapidly declining over recent years as a result of previous over logging in some areas of tropical rain forests which has led the country to adopt sustainable forest management policies to maintain the existing natural resources. The cryopreservation of Neolamarckia cadamba (kelampayan) seeds can be an important complementary approach to the safeguarding of woody plant biodiversity, assuming that the development of a low-input and widely-applicable technology is pursued. The mating system is an important determinant of the genetic structure and evolutionary inherent of natural populations because it establishes the pattern of uniting gametes to form the next generation. The objectives of this study are: 1) to assess the viability and germination of N. cadamba seed lots; 2) to determine the influence of storage environments on viability and germination of N. cadamba seeds; 3) to determine suitable conditions of environment for storage of N. cadamba seeds for long-term conservation, and 4) to determine the mating system of N. cadamba using simple sequence repeat (SSR) DNA markers.

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Tchin Boon Ling (FRST-UNIMAS) 

Project Title: Gene-associated SNP Discovery and Molecular Cloning of Full-length cDNA of Cinnamate 4-hydroxylase (C4H) and Cinnamyl Alcohol Dehydrogenase (CAD) in Kelampayan (Neolamarckia cadamba)

Genetic association or the correlation between the phenotypes and genotypes (i.e. SNPs) in candidate gene; is a powerful method for identification of the genes or loci that contribute to variation in complex traits. Once the quantitative trait nucleotides (QTNs) are identified, such powerful approach provides significant advantages to the forest industry. As the early selection of planting materials encoded desired traits can be performed at early seedling stages, thus better economic return in shortest period of time and at reasonable cost is achievable. Therefore, the objectives of this study are to (i) isolate and in silico characterizing the full length cDNA of cinnamyl alcohol dehydrogenase (CAD) and cinnamate 4-hydroxylase (C4H) from kelampayan; and determine gene-associated SNP in CAD and C4H genes from kelampayan. Sequence variations within these two genes in 30 kelampayan trees will be examined and an array of wood properties namely, specific gravity, wood density, fiber-length, cell wall thickness and microfibril angle will be meausred. Statistical analysis will be carried out to test for the association. It is expected that the full-length cDNA sequence of C4H and CAD will be obtained and in silico characterized. Moreover, gene-associated SNP discovery in C4H and CAD genes from kelampayan will be conducted.


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Tiong Shing Yiing (FRST-UNIMAS)  

Project Title: Full-length cDNA cloning and SNP discovery of xyloglucan endotransglycosylase (XET) and cellulose synthase (CesA) genes in kelampayan (Neolamarckia cadamba)

Neolamarckia cadamba or commonly known as kelampayan is one of the important forest tree species in Malaysia. This fast growing tree species is used in reforestation. Kelampayan is also involved in forest plantation for commercial purposes due to its wood characteristics that are suitable to produce different products, such as plywood and paper. Therefore, the study of wood quality is needed to monitor the quality of the trees planted.  Molecular study of wood formation and wood properties of this tropical tree species is needed to choose the desired trait of kelampayan to be planted in forest plantation. A DNA marker, SNP has been chosen to determine the genetic variation of xyloglucan endotransglycosylase (XET) and cellulose synthase (CesA) in N. cadamba because it is a direct marker that gives more accurate genetic variation information. Xyloglucan endotransglycosylase and cellulose synthase are proteins that play an important role in regulating wood formation. XET is the enyme that regulate cell wall expension while CesA acts as a central catalyst in the generation of plant cell wall biomass. In this study, full length cDNA of XET and CesA will be cloned and SNP will be discovered. In silico characterization of these two gene sequences and the gene-associated SNP study will also be carried out. The association genetic study can help in identification of associations between variation in phenotypic traits and allelic polymorphism in known genes. This is useful in plant improvement programme to choose the desired traits of N. cadamba. A more economical and efficient forest planting then can be carried out and hence increases the source of income in forest field.

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Lai Pei Sing (FRST-UNIMAS) 

Project Title: Development and Characterization of EST-SSR markers for kelampayan (Neolamarckia cadamba (Roxb.) Bosser)

Expressed Sequence Tag-Simple Sequence Repeat (EST-SSR) markers are markers which are embedded in functional gene sequences and lead to the identification of genes controlling these traits. Apart from distinguish cultivars from the same species, the transferability of these markers helps to distinguish the relationship between related species. These markers are valuable for the study of variations and polymorphisms of the plant species. The application of ‘Touch-n-Go’ approach and FTA® technology will be used to further reduce the time and cost requirement in this study. The objectives of this study are to develop the one-step ‘Touch-n-Go’ approach and FTA® technology in preparation of plant tissue for PCR analysis, in silico analysis on the frequency and distribution of the identified EST-SSR markers, and determine the characteristics and polymorphisms of each newly developed EST-SSR markers. Computer software will be used to identify the EST-SSRs from kelampayan expressed sequence tag (EST) database (dbEST) and the primer pairs which flank those regions will be designed. The primers will be used in the amplification of DNA obtained through ‘Touch-n-Go’ approach and FTA® technology. Then, each SSR locus will be characterized and the genetic diversity parameter will be determined. ‘Touch-n-Go’ approach and FTA® technology will be successfully developed for high throughput genotyping, frequency and distribution of the identified EST-SSR markers will be determined, and the characteristics and polymorphisms of each newly developed EST-SSR markers will be determined. These newly developed markers will facilitate the selection of interested genotype and enhance the breeding in plantation forestry with kelampayan. Besides, the breeding period and the field workload will be reduced correspondently.

______________________________________________________________________________________________________________

Angela Tida Anak Henry (FRST-UNIMAS)

under construction!

______________________________________________________________________________________________________________

Hafizah Abdul Razak (FRST-UNIMAS)

under construction!

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UNDERGRADS

By
Ho Wei Seng (wsho)
– November 8, 2010

Undergrads: Final Year Projects

No. FYP Title Student
1. Sequence polymorphism of arabinogalactan gene in kelampayan (Neolamarkia cadamba)

Supervisor: Dr Ho Wei Seng

Co-supervisors: Dr Pang Shek Ling (Researcher, Sarawak Forestry)

 Tang Leh Ee (22510)
2 Molecular cloning of hypervariable regions (HVR II) from cellulose synthase gene in kelampayan (Neolamarkia cadamba)

Supervisor: Dr Ho Wei Seng

Co-supervisors: Dr Pang Shek Ling (Researcher, Sarawak Forestry)

 Meldon Calvin Sim Wee Yang (21436)
3. DNA barcoding of selected kelampayan (Neolamarkia cadamba) genotypes from Kelampayan Provenance Trial Plot (Block 4) using ISSR markers

Supervisor: Dr Ho Wei Seng

 Diyanah Musfirah Bt Jamal (20873)
4. Molecular cloning of cDNA encoding for alpha-amylase inhibitor from kelampayan (Neolamarkia cadamba)

Supervisor: Dr Ho Wei Seng

Co-supervisors: Dr Pang Shek Ling (Researcher, Sarawak Forestry)

 Chin Siaw Yin (20800)
5. DNA barcoding of kelampayan (Neolamarkia cadamba) progenies (half-sib family) using ISSR markers

Supervisor: Dr Ho Wei Seng

 Ivy Moh Heng Shi (21089)
6. Sequence polymorphism of heat shock protein 70 (hsp70) gene in kelampayan (Neolamarkia cadamba)

Supervisor: Dr Ho Wei Seng

Co-supervisors: Dr Pang Shek Ling (Researcher, Sarawak Forestry)

 Choo Hui Yik (208081)
7. Sequence polymorphism of sucrose synthase gene in kelampayan (Neolamarkia cadamba)

Supervisor: Dr Ho Wei Seng

Co-supervisors: Dr Pang Shek Ling (Researcher, Sarawak Forestry)

 Amber Chin Yen Siew (20640)
8. Molecular cloning of cDNA encoding for trypsin inhibitor from kelampayan (Neolamarkia cadamba)

Supervisor: Dr Ho Wei Seng

Co-supervisors: Dr Pang Shek Ling (Researcher, Sarawak Forestry)

 Melanie Perera (21435)
9. Sequence polymorphism of the COBRA gene in kelampayan (Neolamarkia cadamba)

Supervisor: Dr Ho Wei Seng

Co-supervisors: Dr Pang Shek Ling (Researcher, Sarawak Forestry)

 Aaron Bong Sing Woei (20575)
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SAWIH

By
Ho Wei Seng (wsho)
– November 8, 2010

Sawih

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PHOTO GALLERY

By
Ho Wei Seng (wsho)
– November 8, 2010
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DABAI

By
Ho Wei Seng (wsho)
– November 8, 2010
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CADAMOMICS DEVELOPMENT

By
Ho Wei Seng (wsho)
– November 8, 2010

APPROACH

Despite the high economic value of tropical wood, little is known about the genetic control of wood formation or xylogenesis for this species compared to loblolly pine (59,797 ESTs), poplars (25,218 ESTs) and spruce (16,430 ESTs). Wood or secondary xylem is manufactured through the process of cell division, cell expansion, secondary cell wall formation (involving cellulose, hemicellulose, cell wall proteins, and lignin biosynthesis and deposition) and programmed cell death. These processes are strongly interlinked and modulation of any one aspect of wood formation may affect many other aspects.

The use of a functional genomics approach can rapidly provide information on the regulation of not just one gene, but an entire pathway or several pathways at the same time. As of October, 2008, no kelampayan EST information is available in the NCBI GenBank. Therefore, we applied genomics approaches to explore the molecular basis of wood formation in kelampayan via high-throughput DNA sequencing of cDNA clones derived from developing xylem tissues.


Developing xylem tissues were collected by scraping a thin layer from the exposed xylem surface (after removal of the bark) at breast height to investigate the molecular basis of wood formation in kelampayan. A 2-year old tree was sampled at Kota Samarahan, Sarawak in April 2008. The collected tissues were put in a clean plastic bag and immediately frozen in liquid nitrogen in the field, and then kept in -80 °C for later RNA isolation.

Total RNA was extracted using RNeasy Midi Kit (Qiagen, Germany) with modification. Poly(A)+ mRNA was isolated from the total RNA using using Micro-FastTrackTM 2.0 Kits (Invitrogen, USA). A total of 105 µg total RNA was used for mRNA isolation. The purity and quality for both total RNA and mRNA were checked by agarose gel electrophoresis and spectrophotometry.

The cDNA library was constructed using CloneMinerTM cDNA Library Construction Kit (Invitrogen, USA) according to the manufacturer’s protocol. About 0.6 µg mRNA was used as starting template for 1st strand cDNA synthesis. The attB1 adaptor was then ligated at the 5’ end of the double stranded cDNA.

The cDNA was then subjected to size fractionation using cDNA Size Fractionation Columns supplied with the kit. A total of 80 ng size-fractionated cDNA and 250 ng pDONRTM 222 plamid were used for BP recombination reaction. The cDNA was then transformed into ElectroMAXTM DH10B T1 phage resistant cells using MicroPulserTM electroporator (Bio-Rad, USA) and grown on LB-kanamycin agar plates overnight at 37 oC.

cDNA clones were manually picked and cultured overnight with shaking in 96-well culture blocks. Glycerol stocks for each clone were prepared and kept in a duplicate 96-well plate format. All glycerol stocks were kept in -80 °C for later use. The titer of the cDNA library was 1.09 X 107 cfu, indicating that the cDNA library is comprehensive.

A total of 10,368 cDNA clones were randomly selected and used in high-throughput plasmid preparation using Montage Plasmid Miniprep96 and MultiScreen Separation System (Milipore, USA). cDNA inserts were sequenced from the 5’ end using an M13F primer and the ABI PRISMTM Ready Reaction BigDyeTM Terminator Cycler Sequencing kit (Applied Biosystems, USA).

High-throughput DNA sequencing was performed on an ABI 3730xl automated DNA Analyzer (Applied Biosystems, USA). Sequencing and bioinformatics analyses were conducted at the Malaysia Genome Institute (MGI), MOSTI.

All the sequences were quality checked before clustering and annotation. Raw ABI-formatted chromatogram reads were base-called using Phred (Ewing et al., 1998; Ewing and Green, 1998) with a threshold value of 20. Vector sequences were masked using Cross-Match.

The trimming and removal of vectors, adaptors and low quality nucleotides was done using customized Perl scripts. Only high quality ESTs with a minimum of 100 bases and fewer than 4 % N were retained. The high quality ESTs were matched against the NCBI non-redundant database by using the blastx algorithm prior to clustering and assembling of the ESTs.

Sequences with blastx E-value > 10-10 were categorized as having no significant similarity. Multiple sequence alignment, clustering, assembly and the generation of consensus contigs was done using StackPACK (Miller et al., 1999). The StackPACK contains d2_cluster (Burke et al., 1999), PHRAP (Laboratory of PHIL GREEN) and CRAW (Chou and Burke, 1999).

For d2_cluster, the sequences were grouped together if there were at least 96 % sequence similarity in any window of 150 bases. The loose clusters were then aligned using PHRAP and subsequently CRAW. The contigs and singletons generated from the clustering were considered as a set of putative unique genes (unigenes).

References

Burke J, Davison D and Hide W.  (1999).  d2_cluster: a validated method for clustering EST and full-length cDNA sequences. Genome Res. 9: 1135-1142.

Chou A and Burke J.  (1999).  CRAWview: for viewing splicing variation, gene families and polymorphism in clusters of ESTs and full-length sequences. Bioinformatics 15: 376-381.

Ewing B, Hillier LAD, Wendl MC and Green P.  (1998).  Base-calling of automated sequences traces using Phred. Genome Res. 8: 175-185.

Ewing B and Green P. (1998).  Base-calling of automated sequences traces using Phred. II. Error probabilities. Genome Res. 8: 186-194.

Laboratory of PHIL GREEN,  http://www.phrap.org. (March 24, 2009).

0

fGiL Lecture Series

By
Ho Wei Seng (wsho)
– November 6, 2010

fGiL LECTURE SERIES: MIND POWER, INSIDE OUT


BACKGROUND
Biotechnology has been identified as one of the key strategic sectors that will support the growth of the Malaysian economy. It is anticipated that growth in this sector will contribute approximately 2.5% of national GDP by 2010, 4.0% by 2015 and 5.0% by 2020. This is supported by leveraging on the strength of the country’s diverse natural resources. However, the capacity and capability of Malaysian talent in biotechnology will determine the growth and progress of this sector. Emerging regional neighbours, such as Singapore, India and Taiwan are gradually extending their influence in the international biotech arena and this was mainly due to their strong emphasis on their human capital development initiatives.

Hence, this fGiL Lecture Series will be an important avenue for biotech workforce including undergraduate and postgraduate students to enhance efficiency and knowledge capabilities as well as competitiveness in the global biotechnology platform in the future. This is also in line with the government initiatives to enhance the quality of domestic biotech workforce. Furthermore, it also provides a platform for a gathering and sharing of experiences among the undergraduate and postgraduate students at the fGiLab.

Objectives:
To build the self-confidence of researchers in scientific discourse;
To improve critical thinking skill of researchers in solving problems and issues involving scientific investigations;
To enhance research culture and to improve competitiveness among researchers, and
To build a stimulating environment to nurture Great Minds.

List of Speakers:

Lecture Series Speaker Name(s) Topic Remarks
LS01/2010

Oct 8, 2010

 Speaker 1: Phui Seng Loi Development of microsatellite markers for Neolamarckia Cadamba (Roxb.) Bosser (Kelampayan)
LS02/2010

Oct 29, 2010

 Speaker 1: Grace Ting Sex determination
Speaker 2: Meldon Sim Cellulose synthase and Hypervariable (HVRII) region
LS03/2010

Dec 10, 2010

 Speaker 1: Liew Kit Siong Molecular markers
Speaker 2 : Choo Hui Yik HSP70 gene
Year: 2011 (Date and topic will be confirmed later)
LS04/2011

Jan xx, 2011

 Speaker 1: Tiong Shing Yiing Role of cellulose synthase (CesA) in wood formation
Speaker 2: Diyanah Musfirah ISSR markers
LS05/2011

Jan xx , 2011

 Speaker 1: Pang Shek Ling To be confirmed
Speaker 2: Amber Chin Sucrose synthase in Kelampayan.
LS06/2011

Feb xx, 2011

 Speaker 1: Lai Pei Sing EST-SSR markers
Speaker 2: Tang Leh Ee Arabinogalactan gene in Kelampayan.
LS07/2011

Mac xx, 2011

 Speaker 1: Tchin Boon Ling SNP markers
Speaker 2: Chin Siaw Yin Alpha-amylase inhibitors
LS08/2011

Mac xx, 2011

 Speaker 1: Nurfaizah Matra To be confirmed
Speaker 2: Ivy Moh Heng Shi DNA Barcoding: ISSR markers
LS09/2011

Apr xx, 2011

 Speaker 1: To be identifed To be confirmed
Speaker 2: Melanie Ann Trypsin inhibitors and plant defense
LS10/2011

Apr xx, 2011

 Speaker 1: Ho Wei Seng To be confirmed
Speaker 2: Aaron Bong COBRA gene
LS11/2011

May xx, 2011


LS01
LS02
LS03

LS04
LS05
LS06

LS07
LS08
LS09



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