Seminar on biosecurity, Biodiversity & PGR

Seminar on Biosecurity, biodiversity and Plant Genetic Resources
Date: 4 May 2009 (Mon)
Time: 9.30 am -12.30 pm
Venue: Dewan Taklimat, Level 1, Administrative Building, UPM
Speaker: Prof. John Lovett, University of Tasmania

Go to http://www.biotech.upm.edu.my/main/images/news/MOSTIBrochure040509.pdf for more info and registration details. UKM transport will be arranged by Dr. Vani from PPBsBt. Please email vani@pkrisc.cc.ukm.my.

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Malaysian Biological Symposium 2009

Theme: Harnessing the potential of biodiversity
Date: 17-18 Nov 2009
Venue: Hotel Equatorial, Bangi
Organizer: Department of Biologi, Faculty of Science, UPM
Registration fees: RM400 (Students)/ RM500 (others)

More info on http://www.simbiomas2009.blogspot.com/

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Climate Change Seminar 16 May 09

Date: 16 May 2009 (Sat)
Time: 8:30 am - 5:00 pm
Venue: Hotel Equatorial, Bangi
Speakers: Profesor Dr. Fredolin Tangang (UKM), Dr. Liew Juneng (UKM), Profesor Dr. Khairulmaini Osman Salleh (UM), Ir.Hj Ahmad Jamaluddin b. Shaaban (NAHRIM), Ling Leong Kwok (MET)
Organizer: ASASI, IKD, KAS

Open registration at www.kesturi.net.

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De novo NGS Assembly: SOLiD Bioinformatics workshop part II

Sorry it took so long to post Part II of SOLiD bioinformatics workshop. Things that were puzzling to me two months ago all make sense now. I'm in debt with Dr. Sun JianDong for his kind explanation.

Dr. Sun spoke about de novo assembly. As we know, de novo assembly is fragment assembly without reference. Genome sequences and existing ESTs databases can be used as reference although the former has more advantages. Most assemblers used for Sanger sequencing cannot handle short reads generated by Next Generation Sequencing. Because of the length, short reads must be produced in large quantities and at greater coverage depths (Velvet 2008). Since the introduction of NGS, the science community has been very concerned with the development of algorithms that are suitable for these reads. Generally, there are TWO types of de novo NGS assemblers.

Hamilton Path

• also known as overlap-layout-consensus approach (Batzoglou 2005).
  
• each node is represented by one read and each detected read overlap as an arc between the appropriate nodes (Zerbino & Birney 2008)
• not suitable for short reads
• Examples: SSAKE, SHARCGS, SHORTY, Edena
  

Eulerian approach

• De Bruijn graph
• less complex and more accurate
• very sensitive to errors and low quality reads
• reads are mapped to the path based on k-mers.
• Examples: Velvet, Euler-SR
  

Programs that use De Bruijn graph are more accurate and faster compared to Hamilton path. However, these programs cannot tolerate the slighest error rates like 0.3%. (Chaisson et al 2009) Therefore, erroraneous ends must be trimmed and errors correction must be done. Latest version of Euler SR: Euler USR can assemble error-prone reads. Among all NGS assemblers, Velvet is still the widely used programs due to its fast and efficient assembly.

Next, he explained several metrics used in assembly evaluation:

• N50 contig length - Longer size is wanted
  
• Number of contigs - less number of contigs is desirable
  
• Length of contigs - longer contigs is better
  
• Coverage - higher coverage, better assembly.
  

(Note: N50 contig length = The size of contig such that 50% of the assembly is contained in contigs size of N50 or greater)

Here's another definition of N50. If we sort contigs from the largest to the smallest, and start covering the genome in that order. N50 is the length of contigs that just covers 50th percentile. Although longer contigs are better, N50 size deteriorates rapidly as low coverage region in the contigs increases in the attempt to obtain longer contigs. For microbial genome sequencing, the best assembly should only give one contig because the chromosome is circular. But in reality, that never happen.

Recent papers have revealed that paired-end reads are extremely useful in improving assembly and resolve some repeat problems. Read length also helps assembly but until it reaches a barrier according to Chaisson et al (2009). The barrier for E.coli is 35nt while assembly quality for yeast genome doesn't improve much after exceeding 60nt. This comes as a total suprise. The same goes with coverage issues. Assembly doesn't improve after coverage reaches certain threshold. Some repeats and sequence complexity cannot be resolved by high coverage.

And how exactly does what I mentioned has anything to do with SOLiD bioinformatics? Nothing ...because most assemblers mentioned aboved (except Velvet) cannot read colour space data. hehe... I think I have to write another post to come to the points of this SOLiD Bioinformatics Workshop.

Related posts:
SOLiD Bioinformatics Part I : Introduction
SOLiD Bioinformatics Part III: SOLiD softwares

Reference:
Zerbino & Birney 2008. Velvet: Algorithms for de novo short read assembly using De Bruijn graphs
Chaisson et al 2009. De novo fragment assembly with short mate-paired reads: Does the read length matter?

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Seminar on DSSAT and Climate Change

A workshop on Decision Support System for Agro-technology Transfer (DSSAT 4) and Climate Change was held in FST, UKM from 30 Mac to 10 April 2009. One of my labmates was attending the workshop. After I discovered how interesting this workshop is, I didn't hesitate to attend the seminar which was held on 6 April 09. (Hehe. I know this post is late.)

We know that the climate 10 years from now will be quite different. The climate change can affect the crop production significantly. By predicting how the climate change can influence the yield, researchers and plant breeders can take measures to ensure sufficient food supply. Here's how DSSAT can play a role.


So what is DSSAT? It's nothing new. DSSAT 4 is a software package that integrates the effect of soil, crop phenotype, weather and management options to help users in crop management strategies. It's only suitable for annual crop . There are lots of information of major crops in the existing databases. In simple words, we can put all the data about soil, weather and crop measurement or yield into DSSAT to predict the yield next year.

During the seminar, the speaker showed an example how climate change affect the yield of two Thai rice varieties. Rice production in most places in Thailand are predicted to decrease due to draught. By predicting the area which will be badly affected, the scientists and the government can take appropriate measures such as improved draught resistant varieties.

That was actually the second part of the talk. The first speaker is Dr. Wilkens from IFDC. This organization aids to transfer technology to developing countries. Part of his work is to help The International Nitrogen Initiative to come up with ways to reduce negative nitrogen effect in developing countries.


Nitrogen deposition is a serious environmental problem particularly in Asia. Agricultural activities is the main contributor. Rice has been given a lot of attention because it's the staple food in Asia. Unlike any other crop, paddy required certain depth of water to grow. Thus, most farmers would throw the fertilizers onto the water-filled paddy field. This practice resulted in large nitrogen leakage when the flood water runs off to river or drain. It cause a waste because the plants are not able to absorb these nutrients.

And the solutions? A new fertilizing technology known as Urea deep placement. This method has been demostrated in Bangladesh. This controlled release method encapsulate the fertilizer with ultra thin polymer to prodoce briquette. 4 briqueetes will be placed around each plant at a depth of 7-10 cm to allow efficient release of nutrients. The advantage is fertilization is only done once and less 50% fertilizer is used. However, the labour cost for deep placement is high. Further studies showed that overall cost has not increased due to higher yield and less spending on fertilizer. Besides that, farmers have to worry less about weeds. Click here for a similar powerpoint presentation.

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A blogger's problem

When I first started blogging two months ago, I put lots of efforts in customizing my blog. If you haven't notice, the template theme is green, the nice tropical calender and the digital clock. It wasn't until recently, I noticed all the features are similar to other blogs. Malaysia4biotech.blogspot is using the same template as mine (Wait, it was there before?). It seems the same calender is used by another blogger (Worst! She's from UKM as well). There are just too many coincidences, isn't it?

Well, it's time to change a new template. Thinking of expanding the width of the blog post too. Hope I don't mess things up like the last time I tried. Hehe... stay tuned!

Also, I'm thinking of changing the blog's tagline. Just "Almost everything about forest & biotechnology". Throw away the word "Malaysia". And probably add "genomics" since my main interest is in plant genomics. Thus, "Almost everything about forest, biotechnology and genomics. ". Suddenly it sounds a bit too much. :p Any idea?

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Biotechnology career fair & exhibition 2009

Biocareer fair and exhibition 09
Date: 25 & 26 Apr 09 (Sat & Sun)
Venue: Kuala Lumpur Convention Center
Organizer: Biotech Corp.

Looking for career opportunities in biotechnology? Bring along your resume and other documents to Biocareer 2009. On-site interview will be held.

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Seminar at FRIM 28 Apr 09

Title: Biotechnology and other research activities in the School of Plant Science, University of Tasmania (UTAS)
Speaker: Assoc Prof Dr Anthony Koutoulis (Head of School of Plant Science, University of Tasmania)
Date: 28 Apr 09 (Tues)
Time: 10 -11am
Venue: Licuala Room (next to the Auditorium), FRIM, Kepong

Topics includes ploidy manipulation in Acacia, omega-3 oils & various ‘omics’ research (genomics, proteomics and metabolomics) in Hop (Humulus lupulus ). For more information, contact Brian (Tel: 014-6264694 or email brian@frim.gov.my)

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EndNote workshop

Title: EndNote workshop
Speaker: Dr. Talib
Date: 22 April 09 (Wed)
Time: 11.30 am
Venue: G139
For 4183 lab members only.

EndNote is a commercial software that can help researchers to manage bibliographies and references when writing journal articles. Trial version can be downloaded from here.

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DECTAR on 17 April 09 (Fri)

Majlis Syarahan Naib Canselor
Title: Membina momentum menatar keunggulan; Ekosistem Ilmu UKM sebagai Wahana
Date: 17 April 2009
Time: 8.30 am
Venue: DECTAR UKM.

Karnival Komuniti Lestari UKM
Date: 17 April 2009
Time: 9 am - 5 pm
Venue: Panggung Seni, UKM. Just next to DECTAR

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Join 2009 Conferences now!

This blog has been inactive lately. The thing is there's fewer activity going on in campus (is it so?). Another thing is I'm busy. I have been involved in the organizing committee of IUFRO Joint Conference 2010 (excuses excuses!). Plus, I'm still not done with posting Taman Negara Merapoh (bla bla bla).

There are quite a number of conferences in Q3 2009. Here's some:

The 8th Malaysia Genetic Congress,
Date: 4-6 August 2009
Venue: Awana Genting Resort, Pahang
For more information, visit http://www.persatuangenetikmalaysia.com/

Agricultural Biotechnology International Conference (ABIC) 2009
Date: 22-25 Sept 2009
Venue: Bangkok, Thailand
For more information, visit http://www.abic.ca/abic2009/home/About.php

Not forgetting International Conference on Bioinformatics InCoB 2009. View my post here.

Here's another one:
Agriculture Congress 2009
Theme: Tropical agriculture in a changing climate and energy scenario
Date: 27-29 October 2009
Venue: Palace of the Golden Horses, Selangor
For more information, visit http://www.agri.upm.edu.my/agcongress09/index.html

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Fungi diversity at Taman Negara Merapoh

Fungi is a common sight in Taman Negara Merapoh. You can find different types, colour and morphology of fungi or mushroom along the trail. I'm no expert in mycology but I can tell that the fungi diversity is high. Many species that can be hardly spotted are found here. So get ready your camera to snap some really nice pictures!

We discovered at least 20 species of fungi during our 2-day jungle trekking including a rare mushroom like Dictyophora sp. or Stinkhorn.


The forest floor and almost every fallen tree trunks are covered with mushrooms. The sight of it is just amazing. This is what people call mushrooms after the rain.


We stumbled upon this special fungus when we took a wrong turn. It has grey whitish fruiting bodies and a black middle stalk with buddings shaped like asparagus in the middle.


My favourite photo is the C. tricholoma or red cup fungi.


There are many more photos that I would like to share because I realized that there's little online information on tropical forest mushroom. However, it's impossible to post all. Photos are available upon request (for education and research purposes only).

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Taman Negara Merapoh: introduction

Taman Negara is the oldest national park in Malaysia. It’s established in 1938-39. It was named King George V National Park when it first started. It covers a total area of 4,343 km2 spreading over three states (Pahang, Kelantan and Terengganu). The two main entrances to Taman Negara are Kuala Tahan and Merapoh. Taman Negara holds the highest peak in Peninsular Malaysia, Gunung Tahan which is 2,187m above sea level. Here’s the activities you can do:

Jungle trekking – There are 6 trails to choose from: Rentis Interpretif (535m), Rentis Palas (1.6 km), Rentis Gajah (5.5km), Rentis Negeram (4.1 km), Rentis Bunian and Rentis Berjalan Malam (nightwalk). Rentis Interpretif and Rentis Palas are short and located near the campsite. Suitable for the kids' education purposes because the trees on the path are labeled. Thanks to iClub members plant labeling effort. Rentis Gajah is more challenging. This trail will bring you to Gua Gajah and it takes at least 2 hours. to get there It’s forbidden to go without a guide!



Ikan Kelah fish sanctuary – Take a 4WD to Kuala Juram (14 km away from main campsite) to reach Sungai Juram where Ikah Kelah awaits you. Here, you can feed Ikan Kelah or Malaysian Mahseer (Tor Tambra) . If the water is clear, you can see the ikan Kelah swimming against the current with their mouths wide open. In addition, you can see the fish up close at the Ikan Kelah Breeding Centre at the main campsite.


Cave exploration – Two limestone caves can be found in Taman Negara Merapoh: Gua Gajah and Gua Peningat. Gua Gajah is a small cave often visited by the elephants. Along the trail, you can see elephant footprints and droppings. Follow the tunnel in the cave and you will find yourself surrounded by thousands of bats in the dark. Don’t forget to bring torchlight! Gua Peningat is much more larger than Gua Gajah. It’s located further away from the main campsite.

Gua Gajah

Wildlife watching - There are a few watch towers to observe wildlife such as Bukit Seraya (see picture below) and Bumbun Rimau. Menara Tinjau Bukit Seraya is situated on the way to Kuala Juram. It offers a scenic view of Tahan moutain range (picture showed at the bottom). It is restricted to 20 people on the tower at one time. On the other hand, Bumbun Rimau is a popular spot for nightlife watching. It's located just in front of a hangout place for animals like tiger, leopard, mouse deer, Asian golden cat and sun bear. If you're lucky, you'l get to see all the animals. If you're not, come again! There are beds where you can spend the night. You need to take a 4WD and follow a short jungle trekking trail (300m) in order to get there.


Climbing Gunung Tahan – Taman Negara Merapoh is the best way to climb up Gunung Tahan (2,183m) because the trip is shorter (4 days) compared to Kuala Tahan way (7 days). Only 48 people per day are allowed to hike the mountain. Hiring guide is compulsory (RM 950 for 12 persons). Other procedure such as luggage examination is required. Alternatively, you can follow the path from Sg Relau (Merapoh) to Kuala Tahan. Many experienced hikers claim that Gunung Tahan as the most difficult track in Malaysia.

Gunung Tahan view from Bukit Seraya

For more information on other activities and how to get to Taman Negara Merapoh, Click here.

Note: All the facts are given by Perhilitan staff unless otherwise stated.

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Jom Taman Negara, Jom Merapoh!

It’s been a week since my last post. Last week, I was busy solving Real-time PCR mystery. I spent my weekend at Taman Negara and only arrived home at 11pm last night. Despite all that, I came to work this morning.

The scenic view of Taman Negara Pahang on the way to Kuala Juram
The Taman Negara trip was awesome! Being the oldest protected forest area in Malaysia, it’s a MUST-GO for every nature lovers. There are two main entrances to Taman Negara Pahang: Kuala Tahan and Sg Relau via Merapoh. The entrance we used is Merapoh, a small town north of Pahang which is surrounded by limestone caves. It offers most scenic and tranquil experience to visitors.

Group photo of iClub Taman Negara Camp participators
This trip will not be made possible without iClub. iClub is a new club in UKM and the only one sponsored by an industrial company, GE or General Electric. The club is open to all UKM student regardless of races. iClub is different from other environmental clubs because it organizes various leadership, communication and motivation events to benefit UKM graduates. I’ll keep posting their upcoming activities so stay tuned!

Besides that, this trip is also sponsored by PERHILITAN. Perhilitan has provided us help and accommodation. Although they have limited resources, they are very kind to assist us in every way to make this trip enjoyable. The problems they faced are little funding, lack of publicity and limited staff. iClub has to come up with ways to promote this place and to create public awareness. Therefore, this week I’ll be sharing my experience in promoting Merapoh as the choice of entrance for Taman Negara Pahang. Just look out for many more interesting pictures.

Jom Taman Negara, Jom Merapoh!

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