It's vacation time!

Yeah! The long-awaited vacation is just around the corner. Then, I'll leave Malaysia to do an attachment. See you next year! :p

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Some recent thoughts (August 09)

Busy... seems like the only word I always use to describe my life. lol... I think people are tired of hearing that word from me.

At the end of August, I attended the MSMBB post-conference symposium. After looking at the programme and speaker list, there's no way I can miss this. I was right. Not only did I gain so much knowledge, it's a nice break from my busy life for a couple of days. It gives me new ideas and directions on my work. When I interact with other researchers, I feel very excited about the new things i can do. Enthuasiasm is contagious. I took the advice of the organizer to go home, think about what I wanna do next and write it down. Suddenly, I feel that those few days are so well-spent.

So next time you feel like you can't breathe or what my housemate call "living everyday like a photocopy machine", just take a break to attend a seminar or conference. Go home, think, and write a note.

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GRA vacancy

GRA vacancies at INBIOSIS, UKM
BSc (Honors) in biochemistry, food science or analytic chemistry & >CGPA 3.0 required.Deadline is 8 Sept 09. Please email CV to Dr. Syarul Nataqain nataqain@ukm.my or Dr. Maizom maizom@ukm.my


GRA vacancy at UPM

• Background in biology/genetics/biotechnology/biochemistry/forestry
• CGPA> 3.5
• will pursue a MSc/PhD
• preferably with own transport
• project involves gene cloning and characteristics

Please email Dr. Rozi rozimohd@putra.upm.edu.my with GRA subject heading.

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A lecture on AH1NI

This is not a post that is related to my research but I will share what I can understand clearly from the talk. It begins with an introductory speech on "genetic variation key to survivor" by MGRC founder, Dr. Robert Hercus. It’s interesting as I was not aware of the fact that viruses such as HIV has millions of variants. There are more than 4 types of dengue viruses. A virus genome is about 10kb, so it’s fairly easy to sequence thousands of variants per day. Before getting to the eminent speaker lecture by Dr. John McCauley from National Institute for Medical Research (UK), Prof. Ramlan from UPM gave us a talk on animal influenza and some insights into virology.

What are influenza virus?
According to Wikipedia, influenza viruses are RNA viruses of the family Orthomyxoviridae that cause flu in birds and mammals. The viruses can be classified according to species ABC, strains and genotypes which can be divided into claudes. The surface proteins, HA and NA subunits play important roles in infection. Therefore, most viruses are named based on these proteins: H5N1, H1N1 etc. It's important to note that the AH1N1 virus contains RNA genome instead of DNA. The genome is divided into 8 segments. The reassortment of genes is a major concern.

So is H1N1 new?

The answer is NO. The Spanish flu 1918 originated from a subtype of H1N1. The common types of swine flu found in pigs are H1N1, H1N2 and H3n2. There are about 1.5 million pigs in Malaysia. Based on a survey carried out by Prof. Ramlan and his team, classic influenza virus are detected in some of the 800 samples tested. The common detection method used is RT-Elisa-PCR while researchers all over the world use Real-time PCR to confirm the presence of AH1N1 virus accurately.

"A phylogenetic estimate of the gaps in genetic surveillance indicates a long period of unsampled ancestry before the S-OIV outbreak, suggesting that the reassortment of swine lineages may have occurred years before human emergence." -Smith et al. 2009, Nature.

According to this paper published in Nature, the new virus is the combination of several other influenza viruses. Based on the phylogeny study of the proteins, it's closely related to Hong Kong H1N1 virus. It's interesting to see that bioinformatics play such a big role in this discovery.

Why did the new virus go undetected for years?

Dr. John McCauley explained that this is due to the lack of swine flu prevention measures taken by all the countries. The flu symptoms are mild i.e. lose weight and abortion.

When will the vaccine be available?
Autumn. Exact date? Unknown.

Why is the vacinne taking so long?

It definitely is taking faster than any other vaccine production. Bear in mind that it's a long process. The right virus strains must be first identified. The virus is incubated in the egg. Optimization is crucial to ensure large-scale production. Clinical trial and quality control must be carried out. Lastly, it involves licensing and other legal actions to make it available in the market.

What lessons can we learn?
Governments have to invest heavily on influenza viruses R&D. More effective prevention measures must be taken by all the countries on the next outbreak. Faster drugs and vaccines development. It's a matter of time before the virus become resistant to Tamilflu. Nobody can tell where all this is all going. Everyone is waiting to see what happens next.

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Short lecture on basic in Bioinformatics

I'm attending a MSMBB post-conference workshop right now. Prof. Shoba just gave a brief lecture on basics in Bioinformatics. I'll just post a quick note with my own opinion added.

Bioinformatics is the application of computational methods in system biology. Bioinformatician deals mainly with protein and DNA sequences. The sequences are treated as linear sequences. It means that the backbone of the DNA or protein is ignored and only residues are important. They also have to deal with 3D structures using specific software. Bioinformatics helps biologist to understand a biological process and shorten the time of lab work. Therefore, they also spend a lot of time communicating with biologists and reading about the subject.

Let's take a look at the history of bioinformatics that is focused mainly on DNA sequences. In 1980, bioinformatics projects were initiated to look at protein structures. When Sanger sequencing was introduced, more works are carried out in analyzing DNA sequences. In 1990, the Human Genome Sequencing project was announced and was completed in 2000. Everyone was very excited about the sequences. That was when what people call the "false dawn of bioinformatics era". The real dawn of bioinformatics came when the Next Generation Sequencing was introduced in 2005. Subsequently to be replaced by 3rd Generation Sequencing. Expertise in these fields are highly sought after in the market.

Careers in Bioinformatics

Genomics:

• Genome sequencing
• Comparative genomics
• annotation and mapping
• gene discovery

Pharmacogenomics:

• SNPs
  
• therapeutic target recognition
  
• pathway effects
  
• drug and expression effects

Proteomics:

• proteomics
• protein profiling
• alternate splice
• structural genomics
• drug and vaccine design

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Useful ways to prevent email hacking

Recently, I received several emails from a few colleagues that has similar content. First, they said they were trapped in a hotel room without any reception (except internet access). They were asking for my help to get them out of there. For example, bank in USD20,000 into this account before this particular time. I swear they came to work on that day. So, there's no other explanation other than their email accounts are hacked!

This is a serious problem. This cannot happen to me! So, how can I prevent my account from being hacked? First of all, use a difficult password with capital letters and numbers. Change the password regularly. Do not leave any important emails in your inbox for the fear of losing them.

Sounds easy but the truth is these tips will never work! Hackers can easily download a free software online and get it running at no time. To know how to prevent, we must first know how email account hacking software works. The key is to think like a hacker! :p

Here's some useful tips I found:

• Do not open any email if you don't know the sender.
• Never reply any email that ask for your email or password. Can't believe people still fall for this!
• Another trick hackers used is to create an identical webpage similar to your login page. Once you type in your account and password, your email account is gone.
• Never download any files from unknown sender. You might install the hacking software into your computer. It can run automatically like a trojan horse and send your information to the hacker. Your anti-virus might not be able to detect it.
  
• Safeguard your computer. Never give anyone a chance to install the hacking software in your computer.

For safety reasons, I will delete any blog comments containing email address.

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International Conference on Natural Resources and Environmental

International conference on Natural Resources and Environmental Management and Environmental Safety and Health 2009

Theme: Understanding the causes and impacts of climate change
Date: 24-26 November 2009
Venue: Hilton Hotel, Kuching, Malaysia
registration fees: RM300 (Student)

KUCHINGGGG!!!!!

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MSMBB seminar on Next Generation Sequencing analysis

MSMBB post-conference seminar on genomics data management

Date: 21 & 22 Aug 2009 (Fri & Sat)
Duration: one and a half day
Venue: Rimba Ilmu, UM
Registration: Rm100

The Malaysian Society for Molecular Biology and Biotechnology (MSMBB), in collaboration with Illumina and Science Vision Sdn Bhd will be organizing the Post Conference Seminar, entitled “The Agri-Genomics Data Management Symposium”, on 21-22nd August 2009 at Rimba Ilmu, University of Malaya. Distinguished speakers from Illumina, Beijing Genomincs Institute, CLC bio, LGM, MGI and Macquarie University (Australia) are invited to share their knowledge and views. A chance not to be missed by local NGS users.

Click here to see the programme. Click here to find out more.

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My AH1N1 false alarm

AH1N1 has been around for a few months. There are over 2000 cases in Malaysia with 43 fatal cases. Some people take it for granted and some are really paranoid. And I fall in the middle category: always keep myself up to date and living my normal life. Some of the schools and universities were closed for a short period of time. I wonder when will UKM suffer the same fate. Please don't let it happen before I finish my work!

I was sick 2 weeks ago. One morning I woke up with fever and an infected throat. A few days before that, I met a few overseas friends, took the ktm and went to several public places. I'm at high risk of being infected by AH1N1. The two questions playing in my mind were: should I go to lab or see a doctor straight away. I'm too busy to be ill but I didn't want to put anyone else at risk. In the end, I dragged myself to the clinic. To my relief, the doctor concluded I have normal fever and assured me there's nothing to worry about. He then gave me a surgical mask (it's orange!) and taught me how to use it. Can you imagine my shock when I found out that I've been wearing it wrongly all this time!

When my fever was gone the next day, I went back to lab and joked about how I was overreacting. A week later, I get a text message from a friend. Asking if I have AH1N1 (in indirect manner) because my friend was having fever. Now I know I'm not the only person overreacting. :p

I noticed more and more people are wearing surgical masks in public places. I think it funny since that type of mask won't protect you from the virus. The doctor's advice is to wear mask if you have coughs. The best way to reduce your risk is to travel less. Speaking of traveling, I'm going to travel a lot starting october. And I won't let AH1N1 stop me from enjoying the much anticipated time of my life. :D

On wednesday, I attended an eminent speaker lecture on AH1N1 research organized by MGRC. It's an very interesting talk. Stay tuned!

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Pesta Konvokesyen ke-37

Pesta Konvokesyen ke-37
Date: 12-18 August 2009
Venue: Where else? Dewan Gemilang

Pesta Konvo is back! Food, games, shopping and lepak. It also means that we have to spend money buying gifts for our friends and juniors. It's a tradition. Good thing I only have a short gift list this year. Can't wait to visit the Vegetarian food stall again. Yummy.

I have picked a few activities that sound interesting:

• Riang Ria bersama Pizza Hut (Pizza!)
• Evolusi seni tani (This can be fun)
  
• International culture show
• Majlis malam penutup (Would be nice if they let me in)

Click here for the programmes throughout Pesta Konvo.

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