Ice cream party: Eat all you want!

Wow! Free Ice cream?!

When? 31 Mac 09: 11-3pm
Where? Bangunan Biologi foyer in front of FST cafe
What's the catch? Lotsa products catalog and demos from Cole-Parmer await you. All postgrad, staff and lecturer are welcome.

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PGM seminar PowerPoint available now!

Download all the PGM seminar presentations at http://www.persatuangenetikmalaysia.com/articles.htm

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MGRC seminar Part II: Plant Genomics

This talk is presented by Dr. Jane Rogers. She was the Head of Sequencing in Wellcome Trust Sanger Institute before joining The Genome Analysis Centre, JIC. She started her presentation with a brief introduction on genome sequencing methods and the types of genome sequences based on sequence quality. The sequence quality measure based on human genome project is showed below:


The main problem in genome sequencing is closing the gaps between large contigs which is thought to be caused by large repeats. According to Dr. Rogers, there are about 340 gaps in the human genome project completed in 2003. Recent studies showed that these gaps are caused by copy number variations (CNV) and different clones that are used for sequencing. This is a fascinating discovery!

Out of nearly 50 plant genome sequencing projects, only complete Arabidopsis and rice genome are obtained. The rest produce draft genome sequences. So why do we need to sequence so many plant genome? The ultimate goal is crop breeding. Genomics assisted selection program is expected to take at least 9 years time before phenotypic selection can be carried out.

Polyploidy plants are the most difficult species to sequence due to huge genome size, repetitive regions and complexity. One example is hexaploid wheat. 80% of this genome is repetitive. Physical mapping of wheat genome using BAC clones has been initiated in 2005. Now Dr. Rogers and her team are interested in sequencing chromosome 3DL of wheat.

Most sequencing projects involve plants with small genome size. Besides Arabidopsis, poplar and Medicago trunculata is used as model plant for tree and legume. Medicago trunculata is a nitrogen fixing plant. The original size of this plant is thought to be 200 Mb but may reach up to 300 Mb. Almost 2600 BAC clones have been sequenced up until Oct 2008. Additional shotgun sequencing using 454 and Illumina platforms are used. The scientists are interested to study nodulation pathway of this plant using genomic approach.

Another important application of genomics is to understand plant resistance. She elaborated on the recent work of Prof. Jonathan Jones which is highly cited. His team sequenced two strains of Arabidopsis white rust using Illumina platform. The 36 bp short reads are assembled using Velvet. Comparison of these two genomes has successfully identified candidate effectors in host resistance mechanism.

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MGRC seminar Part I: John Innes Centre (JIC)

An introduction of John Innes Centre (JIC) is given by Prof. Chris Lamb, the director of JIC. JIC founded in 1910 at the bequest of John Innes. Most of the funding comes from BBSRC and only a small portion comes from the industry and charity. The JIC sites include JIC, The Genome Analysis Center (which is newly established), Sainsbury Laboratory, The Norwich BioIncubator and Plant Biosciences Ltd.

One of the centre’s goals is to understand science and use that information to benefit the society. JIC’s main strength is excellency in fundamental research of plant sciences and microbiology. Out of ~800 members, there 17 % PhD students.

Most major crop production has declined compared to 1964-1994. Rice, maize, canola and wheat fall in that category. Therefore, JIC’s research is focusing on wheat, canola and a bit of work on rice .

The centre has identified several Grand Challenges:
1. Science for enchanced breeding
2. Adapting to climate change
3. reduced footprint, input, ghg
4. enhancing yield, yield resilience
5. output trials
6. Delivery mechanism
7. (missing in my note)

One of their researches on transgenic plants received a lot of attentions lately. Their team has produced purple tomatoes by transferring two genes from snapdragon that can increase production of anthocyanin. Increase level of this antioxidant caused the observed colour change. Findings showed that anthocyanins can significantly reduce the growth of colon cancer cells. Feeding of purple tomatoes to mutant mice prone to cancer can prolong the mice’s lifespan. Here’s how it looks like:
This presentation will be posted up soon on http://www.mgrc.com.my as part of MGRC eminent speaker series.

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Taman Negara 3-5 April 09 RM30 only!

i-Club UKM is orgranizing a leadership camp at Taman Negara, Pahang to promote environmental awareness.
Date: 3-5 April 09
Activities: Plants labelling, Jungle trekking, cave exploration...
Organizer: GE, i-club UKM, Perhilitan and UKM
For UKM students only.

RM30 only!!! Don't miss out this great opportunity!!! Call Brenda now at 017-3292813!

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First Call for IUFRO-APAFRI joint conference 2010

A joint conference of IUFRO Working Parties 2.04.01 (Population, ecological and conservation genetics) and 2.04.10 (Genomics) entitled "Conserving and Enhancing Productivity of Forests in the Genomics Era" will be held from *8-12 March 2010 at Kuala Lumpur, Malaysia. This is a joint effort by FRIM and UKM. For more information, click here.

IUFRO- the International Union of Forest Research Organizations
APAFRI- Asia Pacific Association for Forest Research Institutions
*Subject to changes

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Scientific writing for FST graduate students

Speaker: Alena Sahudi, FST editorial consultant
Date: 26 Mac 2009 (Thurs)
Time: 2.30 pm
Venue: Faculty meeting room, DAM, FST.

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PGM seminar summary

Who would have guess UPM have 3 different locations of Fakulti Pertanian? And, who would have thought that the Pak Guard gave the wrong direction? For the first time, I don’t even feel ashamed upon late arrival.

The first talk is on “using molecular markers to explore rice genetic diversity” by Dr.Leocardio S.Sebastian. He’s a very experienced and well-known rice researcher in Philippine. Looking at his bibliography makes me think that the PGM should organize one session focus only on his experience as rice breeder. He is now working with Bioversity based in Serdang. I missed the front part of the presentation but I can tell that his talk is all about Single Nucleotide Polymorphisms (SNPs) and Association Mapping in rice varieties.

Next, Ass. Prof Dr. Zilfalil started his talk about medical genetics. The Human Genome Center in USM which he directed has been involved in research on less known diseases that affect Malaysia populations. He explained why gene-based approach should be given attention in clinical trials and gave some examples on SMN1 and NAIP gene which play a big role in Spinal Muscular Atrophy (SMA) disease. The speaker also shared some Pan Asia SNPs initiative results on Malay populations. They found out that the Malay in Kelantan might be “the first Malay” in Malaysia. A small portion of their genes are similar to Indian genes while the DNA of Malays from south Peninsular Malaysia is closest to Indonesians. When all the major ethnic groups in Asia are compared, Chinese is the closest group to Malay. This didn’t come as a surprise because migration hypothesis and previous studies have supported this theory.

The last talk is on fish breeding, triplody induction and sperm cryopreservation. The species of interest is Catfish such as Baung, Keli and Patin (local names of different catfishes). It was only last week I was told that ikan Keli is a hardy fish that can survive without water for a period of time and live in dirty water ( such as drain and muddy area). That’s why very few people want to eat ikan Keli. But things are changing now with the advancement in aquaculture. So why breed triploid fish? Triploid fish is sterile. Most hybrids will have larger size than the parental species. In theory, the energy used for gonad growth is shifted towards somatic growth. Thus, explains the higher growth rate. Dr. Anuar, the speaker later relate to us how Patin (Pangasius sp.) turned into “Cinderella” in Vietnam.

New: Powerpoint presentations can be obtained at http://www.persatuangenetikmalaysia.com/articles.htm

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Inbiosis seminar 27 Mac 2009

Title: Microbial Metabolomics
Presenter: Dr. Silas Villas Boas from University of Auckland
Date: 27 Mac 2009 (Fri)
Time: 9-10.30 am
Venue: Bilik Seminar, INBIOSIS, UKM.

The workshop will be held on 24-26 Mac 2009. For more information, please email inbiosis.seminar.series@gmail.com

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SOLiD bioinformatics workshop Part I

I almost missed this workshop because I was told by my colleague that it’s just another seminar on SOLiD. Luckily I emailed the sales rep and received the agenda the night before. I think Analisa Resources Sdn. Bhd did a great job organizing this workshop. Not to mention the wonderful buffet lunch at Hotel Equatorial. :p

Illumina Solexa and SOLiD are two NGS platforms that came up almost the same time. Despite similar read length, SOLiD can generate twice the amount of sequence at a slightly lower cost. Judging from the number of publications, it is assumed that most people favour Solexa over SOLiD. But, the scenario is changing.

SOLiD differs from other platforms in which the reads are mapped in colour space. Its 2-base encoding system allows better SNPs detection by differentiating a SNP from sequencing error. Two colour change will indicate a SNPs while single colour change indicates an error.

Despite what paper reviews said about SOLiD, here’s the things they can’t tell you
• Since Invitrogen has acquired Applied Biosystems (not the other way around) last year, Applied Biosystems now provide end-to-end solutions from sample preparation to sequencing.
• SOLiD can run two slides per run. Each slide can be divided up to 8 chambers. With its barcoding system, up to 320 samples can be run each time (with 20 barcodes).
• Both 454 and SOLiD uses emulsion PCR concept but the difference is SOLiD places the bead randomly on the flow cell (That’s how they claim the throughout is increased). But now, they are looking into ways to increase bead density by arranging beads on the slide.
• The new SOLiD version 3 allows users to view the sequencing process via the internet and control the process remotely.
• SOLiD will give forward and reverse reads (This is new to me. I wonder if other platforms can do the same)
• Besides higher accuracy 99.96%, SOLiD offers different size of insert size up to 4 kb to enable scaffolding. Scaffolding is important to form larger contigs.
• Unlike other sequencing platform, SOLiD user can download data analysis softwares from the website and sample data. http://www.solidsoftwaretools.com

Related posts:
SOLiD Bioinformatics Part II: de novo assembly
SOLiD Bioinformatics Part III: SOLiD softwares

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Graduate positions in forest biotechnology

Found a few GRA openings advertised on a website when I was goggling forest biotechnology. There are quite a few interesting areas in forest biotech such as biomass and biofuel, bioinformatics and cellulose synthesis of poplars. Click here for more information.

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Some recent thoughts (Mac 09)

Ever since I came back from my vacation, I have been so busy. Suddenly it seems like a bad time to go on holidays. The trip is tiring… I don’t know why. It took me two days to recover from the fatigue.

On Thursday, I joined a visit to Asiatic Centre for Genome Technology (ACGT) in Technology Park Malaysia. ACGT is a BioNexus company under Genting Group that specialize in oil palm genome sequencing and other related research. Besides oil palm, ACGT is also interested in Jatropha genome sequencing, matagenomics analysis and biomarkers discovery for crop improvement. I’m curious about ACGT because the company has been relatively mouth shut about the outcome of their oil palm genome sequencing in Biomalaysia 2008 conference. Naturally, we would expect MPOB to be the first in oil palm genome sequencing but we were wrong. During the visit, we were impressed by their facilities such as re-sequencing pipeline using PCR robots, five ABI 3730xl DNA Analyzer, a nice computer cluster called AGNES and in-house databases with updates once every 2 weeks. The company will be sending a few staff to J Craig Venter Centre each year for internship in bioinformatics. How cool! If you are interested to join the company, it’s not too late. Job vacancies are available, just email hrad@asiatic.com.my.

I have been keeping an eye on high performance laptops lately. Can’t wait for the next PC fair. Haven’t you heard about my laptop tragedy?! Long story cut short: laptop + water = it’s time to get a new one! Hahaha…

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Seminar on genome analysis of cattle blood parasite

Title: The current status of Theileria orientalis genome analysis
Presenter: Prof Dr.Chihiro Sugimoto from Hokkaida University, Japan
Date: 17 Mac 2009 (Tues)
Time: 2.30pm
Venue: G143BB FST, UKM.

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Real-time PCR workshop

Date: 18 Mac 2009 (Wed)
Time: 9am-5pm
Venue: Lab 4183 (wetlab) and G143 (lecture)

Only for 4183 students. Lunch will be prepared.

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Summary: Career talk by Biotech Corp

Here's the summary of the Biotechnology career talk given by Biotech Corp since not many people attend it just now. The important things to note:

• BiotechCorp is providing training for fresh Biotech graduates through BeST programme (Biotechnology entrepreneurship Special Training) to prepare them for the biotech industry. This training which combines training (obviously!), lab work and industrial internship will last for 3 months. Wow... super-intensive! The trainees will be given a monthly allowance of RM1000 (Rub my eyes again!). There are 3 intakes: April/May, August and December.
  
• Besides that, BiotechCorp also offers internship and incubation programme. Incubation Programme is aimed to help young biotech entrepreneurs.
• A biotechnology career fair is coming soon. It's known as BioCareer Fair & Exhibition and will be held in KL Convention Centre from 25-26 April 2009
  

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The Next Generation Sequencing Status in Malaysia

Since the introduction of Next Generation Sequencing (NGS) in 2005, the science community in Malaysia has been increasingly aware of it due to the rapid development of NGS technology in various applications. Here are the major local players in Malaysia’s NGS field to look out for:

Synamatix Sdn. Bhd. It is the most experienced company in NGS bioinformatics. It is founded in 2002. Synamatix has successfully established itself overseas with the introduction of SXoligoSearch. This software will align Illumina reads against a range of Refseq RNA or NCBI genome builds for a number of organisms. Synamatix also provides outsourcing NGS service. MGRC, a wholly-owned subsidiary of Synamatix Sdn Bhd. has been actively engaging in talks with potential NGS users and conducting NGS-related seminar and workshop.

Novocraft Technologies Sdn. Bhd. It is another Malaysia-based software company that has gained BioNexus status recently. Its product Novoalign is a fast and efficient tool for Illumina Solexa reads. Unlike SXoligoSearch, Novoalign is free for academic and non-profit use. The company is the official vendor in Malaysia for Cofactor Genomics. Cofactor Genomics is a US-based company that offers Illumina Solexa Seqeuncing. Besides cheaper and better quality of sequencing, it offers transparency in sequencing price and sample queue to its customers.

Two other companies are Science Vision Sdn. Bhd. and Analisa Resources Sdn. Bhd., the official representative for Illumina and Applied Biosystems respectively. Both have something in common. Besides organizing NGS-related seminar and workshop and offering sequencing service via outsourcing, they work closely with their Singaporean counterparts.

After so much talk and expectation, the first NGS platform has finally landed in Malaysia! UiTM has bought one unit of Illumina GAII. I'm sure the local researchers will be looking forward to cheaper Solexa sequencing from UiTM.

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Next Generation Sequencing: Era of short reads

I thought that I should do a brief introduction on Next Generation Sequencing (NGS) before my next post.

Next Generation Sequencing is, as the name infers, a new DNA sequencing technology compared to the traditional sequencing (Sanger sequencing).When people ask me what’s the difference between NGS and Sanger, I’ll say no cloning, cheaper, higher accuracy, higher throughput in one breath! However, NGS produce shorter reads compared to Sanger sequencing.

The NGS platforms that are currently running in the labs are 454 GS-FLX Titanium (replacing GS-FLX), Illumina Solexa GAII (Will be replaced by GAIIx) and ABI SOLiD 3. 454 sequencing is the only NGS technology that can sequence up to 400bp but it has lower throughput compared to the rest (180Mb/run for GS-FLX Titanium). Both Solexa and SOLiD is expected to achieve 100bp in length and up to 10 Gb/run this year. Among the applications of NGS are whole genome sequencing, transcriptome sequencing, gene expression (RNA-seq), microRNA, Chip-Seq etc.

Despite all the advantages of NGS technology, the main challenge when handling short reads is bioinformatics. The assembly of short reads will produce more contigs due to repeats problem. Again don't want to elaborate on that.

I would recommend this paper by Elaine Mardis. It’s a very comprehensive review on NGS. Please bear in mind that most paper in 2006 will compare Sanger and 454 sequencing. After the emergence of Illumina Solexa and ABI SOLiD in 2007, the papers would compare all 3 platforms. For those who are interested to know more about the challenges of NGS, click here to check out October 2008 issue of Nature Biotechnology.

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Seminar on Plant genomics

Title: Recent advances in plant genomics research and analysis
Presenter: Prof. Chris Lamb, Director of John Innes Centre, UK &
Dr. Jane Rogers, Director of The Genome Analysis Centre, UK.
Date: 26 Mac 2009 (Thurs)
Time: 1.30-4.15 pm
Venue: Sky view 7, Level 29, The Gardens, Mid valley, KL.
Organizer: MGRC

By invitation. If you have not heard about this seminar, either you haven't check your emails or you're not in MGRC mailing list.

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Health & peace talk by Nobel Laureate winner

Title: Biomedical science, world health and world peace
Presenter: Prof Howard Robert Horvitz,
Nobel prize winner of Medicine in 2002
Date: 16 Mac 2009 (Mon)
Time: 2 pm
Venue: Bilik Senat, Canselori, UKM.

Open to everyone.

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Career in Biotechnology 13 Mac 09

Title: Career in Biotechnology
Orgnizer: Malaysia Biotechnology Sdn. Bhd.
Date: 13 Mac 2009 (Fri)
Time: 3-5pm
Venue: G129BB, Bangunan Biologi, FST, UKM.

Open to all final year students and staff.

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SOLiD Bioinformatics workshop, 10 Mac 09

Today, Analisa Resources and Applied Biosystems organized a great seminar and workshop as an introduction to SOLiD data analysis in Malaysia Genome Institute (MGI).

I apologize because I didn't post this up earlier. I only received the agenda last night. I'm glad I went. I hope I have time to write a nice post on this next week.

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Inbiosis seminar 11 Mac 09

Title: The use of microarray in investigating asthma
Presenter: Prof. Madya Dr. Roslan Harun, UMBI.
Date: 11 Mac 2009 (Wed)
Time: 4-5pm
Venue: Bilik Seminar, Inbiosis, UKM.

Open seminar. For more information, please email inbiosis.seminar.series@gmail.com

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Jungle trekking in Pulau Redang

The weather is perfect. The sun is shining brightly despite the predicted rainstorm The blue ocean is inviting. The sunlight is reflected on the surface as the sea wrinkles and crawls to the beach. That was my first impression when I arrived at Redang island last wednesday.

I’m sure everyone is familiar with Redang. It is an island in Terengganu famous for its beautiful beaches and rich marine life. Not many people know that actually Pulau Redang is also rich in both flora and fauna. Among the species that can be found are macaque monkeys, mousedeer, monitor lizard, snake, geckos, over 50 species of birds, 84 species of butterflies etc. If you are tired of snorkeling, you might consider spending 2 hours for jungle trekking.

The jungle trekking trail starts from the backyard of Coral Redang Resort and it leads to Berjaya resort. All you need to do is follow the orange TNB (Tenaga National Berhad) pipeline. Also, look out for ropes or tree trunks that are painted in red.

On the second day of my trip, we headed out after lunch. We were lucky because the trail is quite dry. We found a snake skeleton after a mere 5 min walk. As we proceed cautiously, I saw a Sang Kancil (mousedeer) running away from me after hearing my loud footsteps. The track gets more exciting as we crossed several rivers and climb up the hills. It took us awhile to figure out where is the trail when it’s impossible to walk next the orange pipe.

What amazes me the most is to find a few Monkey cups plants (Nepenthes sp. or pitcher plant). It got its name because monkeys are often spotted drinking water from the plant. These plants growing out from the vines can run several meters. To the Chinese, Monkey cups are signs of prosperity. The local Chinese saying is 朱笼进水十八十八 .When it’s pronounced in Cantonese, it means that if you collect 18 monkey cups, you’ll be rich when the water enters them (This is my translation version). Usually the first thing I'll do is to peek into the cup for any trapped insect and then pour the water out. Old habit hard to die. Monkey cups are rare these days SO PLEASE DO NOT DAMAGE the plant or remove the cup from the leaf!!!

When walking through the forest, always be alert of any surrounding sound. Try to look up the trees when you heard birds chirping. This is how I spotted two exotic bird species with long tails. Due to my "over-sensitiveness", I was surprised several times at the loud noises made by some tiny lizards.

After trekking for 50 mins, we stopped at the sight of monkeys fighting on the trees. We were so close to our destination because we can hear the sounds of waves crashing onto the shore! Yet, we have no choice but to head back to the resort for our 2.30 pm snorkeling trip.

I would say that this trail is a bit challenging because there’s a place that is very steep. You need to hold on to the ropes which had been tied to the trees to get down the hill. I have done even steeper trekking in Hulu Langat last year at NIGHT! If I were to rank this trail, I would give it a 7 in terms of challenge and 9 out of 10 in terms of biodiversity. One of the best adventures I had because there’s so much to see.

Note:
Unfortunately, I wasn’t able to visit the turtle sanctuary in Redang because according to the resort staff, that place can only be reached by boat. The turtle volunteer program is offered every year. For more information, visit www.umt.edu.my/turtle.

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On Vacation

This blog will be inactive for a few days because I'll be on vacation. Finally!!!

I’m going to Redang! I was lucky to find really cheap flight tickets to KT and got an early bird 3D2N snorkeling package promotion. I have been waiting for my next snorkeling trip since I returned from Sabah for more than a year. Getting tan is the only thing I don’t look forward in this trip. I also hope to write a nice post on turtle conservation in Pulau Redang that I have heard so much recently.

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