Thursday, September 29, 2011

MSAB lecture : The FALSE promises of genetic engineering



In conjunction with Malaysian Society of Applied Biology (MSAB) Annual General Meeting on 16th August 2011, a public lecture on "The promises of genetic engineering in food and agriculture" was scheduled in the morning. The speaker is Dr. Micheal Hansen from USA Consumer Union. To our surprise, the actual title presented on that day is "The FALSE promises of genetic engineering in food and agriculture". Genetic engineering promises high yield, less pesticide, less herbicide, more healthy and safe food with the goal to feed to the world. Dr. Micheal Hansen explained why most of them are myths.

Myth 1 : US safety assessment is very high
Truth: There is no safety assessment conducted by FDA except for Favour Savior tomato. Some companies volunteer and submit summary to FDA but no specific details on how the assessment was done.

Myth 2: GM crops increase yield
Truth: The yield of Bt soybean is generally no better than the wild type variety. The yield drag makes sense because the energy to produce food will be channeled to produce resistance. Also, the yield depends on the variety used for transformation. Most high yield plant varieties are difficult to be transformed, and therefore, the varieties used in GM crops have lower yield. Generally, the yield is lower compared to conventional varieties as improved varieties (in terms of yield, disease and environmental resistance) are constantly released into the market. Therefore, a farmer planting conventional varieties produces higher yield each year than one that is planting GM crops. It's not possible for GM crops have to be commercialized at the same speed as conventional varieties.

Myth 3: GM crops reduce pesticides
Truth: Pesticide usage DO decrease in GE crops for the first few years BUT increase and exceed the conventional cultivar usage. Based on 9 year data, pesticide is used more on secondary pests. Surveys in china showed that Bt farmers reduce 46% pesticide on biolworm but spend 40% more on secondary pesticide.

Myth 4: GM crops reduce herbicides
Truth: Use of RR crops caused weeps to have roundup resistant. In some places, manual weep removal has to be applied because herbicides don’t work anymore. This is labour intensive and thus, increase the production cost.

Myth 5: GM crops do not cause allergy or immunology stimulation
Truth: GE crops do give some serious consequences in allergic and immunology reactions because the protein produced are not naturally found in the organisms. Some thinks this will increase our immunity which is a good thing but others don’t. A research looked for allegens using 6 amino acid search and found several proteins. Cry1A is a potent simulator of immune system and can survive digestion although there are claims that it will be digested in 30 seconds. There is a survey that showed Bt cotton cause allergic reactions in farmers and factory workers.

Golden Rice can save a million kids a year... think again!

In 2000, the headline "This rice can save a million kids a year" appeared in Time front cover. Golden rice is a variety of Oryza sativa produced through genetic engineering to synthesize beta-carotene (a precursor of pro-vitamin A) aimed to reduce blindness and malnutrition worldwide. The problem is an average person needs to eat 10kg a day to get enough daily intake of vitamin A. Then, comes GR2 in 2004 claimed to have 23 times more carotenoid than GR1. In this improved variety, two genes are transformed in rice which are responsible for converting lycopene to Beta carotene. Beta carotene can either be converted to Vitamin A or oxidized to form toxic which caused birth effects. There are doubts that vitamin A might be degraded during harvesting, storage and cooking. Since vitamin A is not a water soluble vitamin, GR has to be consumed with oil to allow its absorption. The other problem is GR is only available in Oryza sativa japonica (the temperate rice). Oryza sativa indica is widely planted in Asia such as Thailand and China. Importing golden rice will increase the price and reduce the number of people who can afford this staple food. I think this criticism is valid.

However, if you visit the GoldenRice website, you will find a FAQ here explaining: 1) GR is not expected to solve deficiency of vitamin A; 2) there is no danger of vitamin A toxicity 3) Natural lipid in rice will help absorption of vitamin A. Do note that most scientific references are 1995-2002.

So who's right and who's wrong?

This talk has got me start thinking about GE from a consumer aspect because I have been taught and repeatedly told about the advantages of GE. I remember Malaysia was being criticized by a representative from Sygenta for not planting GM crops during BioMalaysia Conference 3 years ago. The issues with GE are no longer about public acceptance of GMO and horizontal gene transfer. As a scientist, I think the real question is how to solve all these problems? The solutions are proteomic to understand allergic reactions, transformation efficiency and gene expression studies to increase yield ... resulting in more tax money put into research.

P.S. Another interesting thing is 43 genes are up/down regulated in GM plant compared to wild type. Such a huge effect on gene expression due to the insertion of one gene!

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Saturday, September 3, 2011

Lecture on Management of forest fire and biomass burning in South East Asia



Here is the summary of the lecture on "Management of forest fire and biomass burning in South East Asia and its implication on climate change" presented by Prof. Dr. Peter Brimblecombe from University of East Anglia:

The history of haze in South East Asia
The forest fire in SE Asia is nothing new. It has been documented in Indonesia dated back to 1877-1878 where thick fog were seen in Padang, Palembang, Sabah, Ambon and Timor. Two months of fog were reported on Lake Toba on 1914. Ships complained smoke causing poor visibility and a fire destroyed 200 km2 in Sabah. Besides natural disaster such as drought, volcanic and duststorms, the expansion of rubber plantation is believed to contribute to the haze.

Health effects of haze
Forest fire releases both acids and alkali. The ecological impacts of haze are acid rain, effects on soil nutrients and pH, ozone phytotoxicity, lower sunlight which can reduce photosynthesis and crop yield. During haze, there is a higher number of particles (<3um) in the air that could get into the lung. Our lungs remove these particles by engulfing them using macrophages. However, this induces inflammation reactions and the worst consequences can be heart attack and stroke. Furthermore, transition metals can get into the blood stream and affect the antioxidant defences within the lung. Researchers found that there is a higher neuropsychological effect to the people who live closer to busy street (>10,000 cars a day), possible cause for Alzheimer disease. Long term effects on heart, lung, brain, eye and skin were feared.

My point of view : Who to blame for the haze in Malaysia?
We always point our fingers to our neighbouring country, Indonesia. There is no deny that the worst haze in 1997 and 2005 are caused by the timber industries in Borneo and Indonesia. The Indonesian government blamed the small farmers and El nino for the haze but satellite images proved otherwise. A detailed description of 1997-1998 haze can be found here. It’s possible that some peat forests are still burning until today because they are difficult to extinguish as they burn deep underground.

Time to start looking at ourselves! In Malaysia, there are reports of forest fires in pine and Acacia mangium forest plantations in the 1970s and 1980s. In fact, forest fires were observed in some part of Sarawak during 1997. Following the 1997 haze, the government had taken this matter seriously by enforcing laws and creating awareness.

Despite that, most Malaysian are not aware of how serious is air pollution in Malaysia. As Malaysian we like to burn, be it rubbish or dry leaves from our garden, whether we live in city or rural village. In KL, 65-75% of the PAH level were caused by automotive regardless of haze or non-haze conditions, and the rest by wood burning. As Malaysian we also like to drive cars and cheap subsidized fuel. One day the number cars will exceed the number of our population. Mind you Malaysia is ranked number 3 in the world with 641 vehicles per 1000 people (data probably dated 2009).

Solutions?
According to Prof. Dr. Peter Brimblecombe, the problem is ASEAN countries practised non interference policy. But I say we should increase fuel price, drive less cars, recycle more and use the dry leaves and leftover vegetables to make compose (just like me!).

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Friday, September 2, 2011

September 2011



3!!! That's the number of blogs I posted this year. What happened? I don't really know. I guess I'm busy with my project and editorial assistant tasks. Less traveling this year because it's my final year. There is a significant pressure and concern to finish my PhD in the coming semester. Luckily, I have extra 2 months time because the next (or current) semester was postponed from July to September. I hope to finish all my analysis by end of the semester and start completing my thesis and manuscript. Wish me luck!

What else is new?! Well, my long awaited publication in full text pdf is finally out last week (see link). I was very happy that the manuscript was accepted after one revision. Even happier to be the first one to publish among my peers. Sometimes it doesn't matter how fast you write, it's how fast you publish. I've started preparing for the manuscript since early last year. I spent a lot of time analyzing the data, RE-analyzing the data, draft the manuscripts and even more time revising it because it takes a week for my co-supervisor to read and another week for me to revise it and send it back. For 10 weeks, I was anxiously waiting for reviews. Once published, checking for number of views, comments and citations. It has been a good experience.

Recently, I attended a lecture and academic writing workshop by Prof Dr. Peter Brimblecombe. The lecture that focused on air pollution is eye-opening while the writing workshop is the best I have ever attended. I have written some notes and hope to post them soon. Keep your fingers crossed!

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Monday, July 18, 2011

Seminars in July 2011





Public Lecture on Ocean, Climate and Infectious disease
Date: 27 July 2011
Time: 9.30 - 11.30 am
Venue: Auditorium MyGenome, Genome Malaysia/MGI
Speaker: Rita R. Colwell
Organizer: The Malaysian Society of Microbiology
For registration, visit www.mymicro.org

Academic Writing Workshop
Title: “Typing Pool - Developing Writing Skills for Journal Publication”
Date: 28-29 July 2011
Speaker : Prof. Dr. Peter Brimblecombe, University of East Anglia
Organizer: IKLIM, FST, UKM
For registration, email Pn. Halimatun (halimatunmuhamad@gmail.com) before 15 July.

Seminar on biomass burning and forest fire in Southeast Asia: impact on climate change

Date: 28 July 2011
Time: 9am
Venue: FST meeting room, FST, UKM
Speaker : Prof. Dr. Peter Brimblecombe, University of East Anglia
Organizer: IKLIM, FST, UKM

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Thursday, June 9, 2011

Seminars in June 2011






Invited Professor Lecture
Date: 10 June 2011 (Friday)
Time: 3pm
Title: DArT provides a powerful tool for population genetics analysis and phylogeny reconstruction in Eucalyptus
Speaker: Dr. Dorothy Steane, University of Tasmania, Australia
Venue: G143, Bangunan Biologi, FST, UKM

FRIM Open Day
Date: 11 June 2011
Activities : Nature Walk, Fun Walk, Car boot sales etc
Admission: Free

Rintis Muhibah
Date: 18 June 2011
Venue: FRIM
Organizer: Kebajikan Kakitangan PPBsBt

High throughput Multiplex Gene Expression Seminar
Date: 21 June 2011
Time: 10 am
Venue: UPM IBS Auditorium
For registration, email : dana@3s.com.my

MGRC Eminent Speaker Seminar
Title : Origin, Implications and Prediction of Genetic Variation Effects
Speaker: Prof. Mauno Vihinen, University of Tampere, Finland.
Date: 23 June 2011
Time: 2 - 5pm
Venue: Westside Room 1-4, Level 8, Bouvelard Hotel, Mid Valley

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Saturday, April 9, 2011

Seminar on Molecular Biology as Platform Technology (12/4/11)





Seminar on Molecular Biology as Platform Technology


Date : 12th April 2011 (Tues)
Time : 10am -1pm
Venue : Auditorium MyGenome, MGI
Speakers :
1) Prof. Dr. Rofina Yasmin Othman (BIOTEK, MOSTI)
2) Prof. Dr. Ken-ichi Arai (A-IMBN)
3) Prof. Jeongbin Yim (A-IMBN/Seoul National University)
4) Dr. Matthew Meyrick Salter (Macmillan Scientific Communications)

Lunch is provided. Limited seats. For registration, please email shahrul_izwan85@yahoo.com.

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Saturday, November 13, 2010

Lecture on experience from University of East Anglia



In early October, I attended a talk by Prof. Peter Brimblecombe about "Excellence in environmental science: An experience from University of East Anglia". The history of UAE is relatively new, dating from 1970s. Sometime after scientists realized a need to create a new disciplinary called environmental sciences. It's always easier to create non-tradisional courses in young university.

Prof. Brimblecombe pointed out that one major challenge in science is interdisciplinary. I totally agree. Take genomics as example, it requires knowledge and expertise in molecular biology, genetics, bioinformatics and statistics etc (acquired through learning or collaboration). He noticed that Malaysian researchers lack international collaborators. With internet, communication has never been easier. Then again, communication between scientists and policy makers should be strengthen. Staff support and their sense of loyalty is important too.

The professor also showed a copy of Personal and Professional Development (PPD), a programme book designed for PhD students. They offer a variety of short courses from how to prepare for viva to learning Perl. Instantly, memories of my attempt to pick up Python a year ago lashed back. How I wished I can attend all those training courses in the booklet. Although more than half of these courses are offered in our universities, they are mainly offered to undergraduates but not postgraduate students.

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Thursday, October 28, 2010

Pasoh International Symposium





Pasoh International Symposium 2010
Date: 10 -12 Nov 2010
Venue: Auditorium, Forest Research Institute Malaysia (FRIM)
Day 1 & 2 programme includes talks on collaborative projects between FRIM and STRI, population dynamics and modeling, biodiversity and climate change.
Day 3 field trip to FRIM Research Centre in Pasoh, N.Sembilan.
50 free seats are available to local students. For more information, click here.

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PhD scholarship 2010





Hong Kong PhD fellowship Scheme
135 scholarships are available each year. Students are given a monthly stipend of HK$ 20,000 and travel grant worth HK$ 10,000. The areas of studies included science, medicine, engineering and technology and other non-science fields. Click here for more information.


Industrial Biotechnology PhD scholarships 2011
12 PhD scholarships are open for application. The programmes will be conducted in Germany, namely TU Dortmund University, Bielefeld University and University of Düsseldorf. The projects span many topics such as "Omics" technologies, bioinformatics, expression, biocatalysis and downstream processing. Students have a chance to attend 3-month industrial internship and receive a monthly stipend of 1500 euro for 36 months. Deadline is 12 Nov 2010. Click here for more information.

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Thursday, September 30, 2010

Notes from ETNA Summer School 2010






Prof. Atanas Atanassov from JGC giving a speech

This year ETNA Summer School is jointly organized by Joint Genomic Centre (JGC) and AgroBioInstitute (ABI) which are located at the Department of Biology in Sofia University. After a tour around the facilities, we were given an interesting introduction about the research interests in Bulgaria. Besides rose oil and grapewine(and Black Sea!), this country has a lot more economically important areas. ABI also focused on important crop such as wheat, barley, berries, lactic acid bacteria, thermophile bacteria, honey bee, medicinal herbs, and animal breeding.

The first day is followed by 10 presentations. Most plant-specific talks focused on grapevine genomics and breeding. A plant totally unfamiliar to me. Grapevine or vitis vinifera is grown for wine and table grapes. Wine yard covers 59% of Europe. It’s a perennial crop, grafted and high in genetic diversity, Quality of wine is greatly influenced by environment . The sugar content in the grape is important for fermentation. Although the genome sequences are available, many genes are still unknown and unannotated. Many are unique to the grapevine. It's a highly heterozygous plant. Difficult transformation. It’s an ancient allopolyploid before going through diploidization 2(6+6+7)=38. However, the American grapewine (such as Muscadinia) contains 40 chromosomes. The studies focused on disease resistant, cold or drought tolerant, budding responses and berry development using a combination of transcriptomic (mainly using microarray) and metabolomics.


Visiting the wine yard in Starosel

Metabolomic is an important component of this course. Something new to me. The participants were introduced to basic concepts of metabolomics, sample preparation, detection using GC-MS and most importantly analysing metabolomic data using bioinformatics tools. Every metabolite profile is closely associated to phenotype. For example, different developmental stages of grapewine berry has different concentration of compounds. Metobolomic helps scientists to link the change of metabolites to phenotype such as taste or colour. It's interesting how metabolomic can be integrated with transcriptomic data to produce more biological significant results.


Practical sessions

The most interesting talk is epigenetics in plant breeding presented by Prof. Atanasios Tsaftaris. First, he explained the methylation and histone modification mechanisms and some classical examples of plant epigenetics. Epi- means "above" so epigenetics means "above genetics". It's genetics that doesn't follow Mendel's law. I also learn Genetics Imprinting - Expression of only one allele from the parents due to suppression of the other allele caused by methylation. It's now known that epigenetics play an important role in sensing the environment, control of flowering time and seed development. It is also the cause of somaclonal variation in plant tissue culture and why clones in the field don't perform the same. Two years ago, a Nature paper about Arabidopsis epigenome was published but one can't truly appreciate that paper until he/she understand epigenetics and its implication in plant biology. Read this paper!

This summer school has provided me great opportunity to interact with researchers and students. The topic about funding problem was brought up during coffee break. Research funding has been reduced due to economic crisis and I believed it happens everywhere. The grant application criteria in every country are different. In Europe, there's national and EU funding. A national funding is supported by the government. In the Netherlands, the project must be supported by a few private companies before getting grant approval from government. To secure a EU funding, the project must involve two or more countries with a common research interest. In Malaysia, almost all research funding came from the government. Compared to Bulgaria, Malaysia government or universities have been very supportive to postgrad students by providing scholarship and tuition fees waiver. Now I finally have to agree that we have lots of funding and opportunities in Malaysia. It's up to the Malaysian researchers' initiative and creativity to make use of the available resources. So this is one BIG take home message that I wanna tell my colleagues.

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