My travelling pictures

I've visited Cordoba in 2010. Such a beautiful Andalusia City where the Roman and Islam used to rule. Driving around Cordoba with left hand drive car was challenging. I remember knocked a few side mirrors. I drove through a very thick fog and the GPS was not really helping. The hotel was opposite the great mosque of Cordoba, I have to go through gates in order to go inside the great mosque area. I didn't know that so I was driving in circle for about an hour before figured out how to get inside and it was late night. Anyway, Cordoba is really beautiful andy the architectures are amazing! Highly recommended to go.

Blogging

It's not difficult to write a few words but thus far blogging has just got out of the habit. Sometimes other things get in the way, sometimes I was wondering whether it's worth to pen out what I was thinking at the time. To be honest, I am not really sure whether I want this blog to be a plant pathology blog, a personal blog or a travel blog?? Such a mind boggling. Anyway, I think it's better just to write what I think worth it but to write only two entries in the space of one year potentially fatal for this blog. This blog must goes on!!!

Msc. of Science Graduation at UPM

After almost 5 years, Zetty and I finally has the opportunity to attend our Msc. od Science convocation. We couldn't attend it in 2008 because we were in the UK doing our PhD as soon as we sat for our Msc. viva. Luckily, the UPM school of graduate studies officer was kind enough to give us permission to attend our convocation. So we're both graduates with Msc. of Science in Mycology and Plant Pathology. Our late supervisor would have been proud of us if she's still around. This is for you Prof. Faridah Abdullah of Biology Department, Faculty of Science, UPM. You'll always be in our thought. Amin.

Q & A: Rare Earth Elements

What is rare earth elements?

First found by Lieutenant Carl Axel Arrhenius in 1787, at a quarry in the village of Ytterby, Sweden and it's developed from there where overtime a set of seventeen chemical elements in the periodic table, specifically the fifteen lanthanoids plus scandium and yttrium also considered as rare earth elements since they tend exhibit similar chemical properties as lanthanoids. In other words, rare earth having is 68 parts per million about as common as copper.

Rare earth distribution:

Although well over 90 percent of the minerals are produced in China, they are found in many places around the world, and, in spite of their name, are actually abundant in the earth's crust! Elsewhere, rare earth can be found from Mountain Pass mine in California, Nolans Project in Central Australia, the remote Hoidas Lake project in northern Canada, the Mount Weld project in Australia and northwestern Lai Châu Province, Vietnam.

There are several sites under consideration for mining such as Thor Lake in the Northwest Territories, various locations in Vietnam and a site in southeast Nebraska in the US, where Quantum Rare Earth Development, a Canadian company, is currently conducting test drilling and economic feasibility studies toward opening a niobium mine. Additionally, a large deposit of rare earth minerals was recently discovered in Kvanefjeld in southern Greenland and not to forget in Kuantan, Pahang, MALAYSIA!

So what is the function of rare earth?

Some of the elements such (neodymium and dysprosium) are used to make magnets that help generate torque in the motors of electric and hybrid cars and convert torque into electricity in large wind turbines (We thought hybrid car produces clean energy! Apparently...!!). Some are used to make green phosphors for flat-panel TVs, lasers, and high-efficiency fluorescent lamps. "You wouldn't have a laptop without these powerful magnets," source said. "It would have to weigh four to five times heavier."

The biggest exporter?

As I said before, China is the biggest exporter with 95% monopoly. On September last year, China has temporarily blocked exports of these materials to Japan alarming the risk of supply disruption in the short term. Worldwide demand for rare earth elements was 125,000 tons in 2010 and is expected to rise to 225,000 tons by 2015. With worldwide demand for the materials exploding, Mountain Pass has restarted it's mining last December after was shut down in 2002 due to severe environmental problems.

Buyers?

Obviously, most of the buyers are car producers because rare earth elements are lighter and smaller for their high end technologies.

Cost and profit?

Rare earth elements are not traded as gold or silver but they are mostly sold in private market, which makes their prices difficult to monitor and track. Nevertheless, prices are published periodically on websites such as mineralprices.com. With the lack of supply and high in demands, the prices for some rare earths have gone up more than 700% in the last 45 days! They are reality.

The danger? Impact?

How can we forgot the impact and danger that happened in Bukit Merah Mine. Eight leukemia cases within 5 years in a community of 11,000 have been reported. What else, birth defects, clean up cost up to total of US$100 million! Severe environmental effects! Radioactive contaminated every where! Another case in Baotou, Inner Mongolia, where much of the world's rare earth supply is refined, has suffered major environmental damage! I was wondering can we trust that they will properly handling all these radioactive materials. Only a small leakage to water source can cost you even a human life.

Current technology and alternative to rare earth?

Stronger, lighter magnets could enter the market in the next few years, making more efficient car engines and wind turbines possible. Researchers are now working on new types of nanostructured magnets that would use smaller amounts of rare-earth metals than standard magnets. Nevertheless, it's not clear if the new magnets will get to market before the demand for rare-earth metals exceeds the supply. One example, Tesla Motor uses electromagnets rather than permanent rare-earth magnets. But such motors are larger and heavier than ones that use rare-earth magnets (My imagination is now running back through all those heavy cellphone in the 90's)!"The cost volatility going into the rare-earth permanent magnets was a concern," says JB Straubel, Tesla's chief technology officer. BMW's Mini E electric vehicle uses induction motors, and Tesla is supplying its drive trains to Toyota's upcoming electric RAV 4. Given the volatility of rare-earth supplies, and the advantages induction motors offer in high performance applications, "It makes sense for car companies to give serious thought to using induction motors," says Wally Rippel, senior scientist at AC Propulsion.


Should we have it in Pahang?

NO!

Companies? Board of director?

LYNAS. Who is going to be in the BOD? That is for you to think!

Chioww.....

From Hawaii with love!

Alohaaa!!

Yes, I have a bit of spare time while waiting for Andika to wake up so we can go to Yen Sushi and celebrate Zetty's post confinement! Enjoy the video taken in Honolulu and Big Island, Hawaii. We had a great time there!

Flamenco Dance at Corral de la Moreria.

Haallaaa Madrid.

I was very lucky to see the best flamenco in Madrid at the famous Corral de la Moreria "tablao" flamenco restaurant. We had the best table in the house and the atmosphere was great! We had such a great time and looking forward to having another great session with Flamenco. For me, the dance was so seductive and passionate. I love hearing the singers coz each of them has a very unique voice and style. Attached is a bit of Flamenco that we've seen that night.

The meaning of name.

Every parents want to name their baby as wonderful as they can. In certain ways, it has to be a name closed to their heart or unique or means something great. It took us a long time to think a name for our son. As far as I recalled we bought a book of Islamic's names but I think we never once open the book . For some reasons, we knew that the name will come in some ways without us looking for it.

It just did! During one of Zetty's regular baby scan, Andika's legs were really muscly and straight away I said he is a warrior (just like his great great grandfather; Panglima Ali of Kedah). Then, the name Andika spilled out. Zetty gave the name Raees to compliment Andika as Chief Warrior.

I remembered the first time his Tok heard his name, he said to Andika to live up to his name and I bet he will.

Our bundle of joy.

Our first born, Raees Andika Bin Mohd Hefni, arrived on Friday, 22 April 2011, 16:39 at Royal United Hospital, Bath, UK.

Alhamdulillah. Andika is truly our bundle of joy. He is five weeks old today and we really love him so much. Andika was over due for 10 days.After almost 26 hours since the start of the first contraction, he was born. I couldn't believe it then and I am still amazed every time I see him. We are blessed with one cutie little boy. Unfortunately, tokwan and tok mak Andika had to go home before they can't see him as they came wee bit earlier. Luckily, Andika's tok and nanny were there.

Zetty is still in confinement though we already went out twice now! Never mind that, as long as we are concerned with her health and well being than I think she is fine. She hasn't got any major stitches but still we need to be careful about that.


Anyway, there you go I am a father now and it's truly a life changing experience and I will leave you guys with a video I made for Zetty's first Mother's Day!

Supermoon

I've got an opportunity to take this supermoon picture shining across the Windsor Castle.

Naturalist is better than politician?

Since I continue my PhD, my interest on politic is fading away slowly. My interest in nature is getting obvious over time. Though I have to admit, politic situation in Malaysia has make me sick of it. The thing is, do I want to be one of them or I'm different? Next question is how can I change things if I'm not a decision maker? Do I have the right attitude and determination? These questions always linger in my mind.

Anyway, first thing in my mind now is to finish up my study. This is my stepping stone. Then I can be whoever I want to be..(politician + naturalist + plant pathologist + a husband and a father).

At last after almost 2 years I've been trying to design Foe specific primers, I have made it!! I'm happy coz I know things are falling together now. If it is not because of my soil experiment (which is on the way from Malaysia), I think I should be able to finish my PhD on time. Nevermind, I can use my extension for traveling.

Things are going good with Zetty and baby as well. We have bought everything and I think mentally we are ready to have our baby soon. Though, I haven't bought a car yet which I will very soon!!

Genetic engineering: The world's greatest scam?

Borneo Says No to Dirty Energy

Borneo Says No to Dirty Energy

Sabah says NO to coal-fired plant!

We should never trade our proud forests with dirty energy! I'm glad to hear Sabah is not falling for that coal-fired plant. No matter what it is, we must keep our forest healthy and vibrant!

http://www.time.com/time/health/article/0,8599,2052627,00.html

Manuscript reviewer.

I was over the moon when I was invited to review a manuscript by the editor of Plant Pathology Journal. First thing that cross my mind was, at last my work has been acknowledge by an expert. Second thing that cross my mind was, OMG I have to read a lot as the other reviewer was a big shot in this molecular research. At least you don't want show any spark contrast between your report and his. Immediately, I started to feel a bit pressure mounting on my shoulder. Obviously, you want to do well for your first review as your reputation is at stake.

They gave me two weeks to review that paper. The recommendation that I should made were:

1. Accept with minor revision
2. Accept with major revision
3. Reject and resubmit
4. Reject

The thing was, the second reviewer made his review in one night!! Clearly, I'm not at his level but I told myself that I'm still learning and you'll reach that stage very soon. I think the most important thing are whether the basic work of the paper is sound, the display of results, the interpretation and overall writing style ( I'm not good at this; still working!!) and quality should be acceptable. One fact, about 70% of the paper submitted to journal were rejected. I guess you have to describe carefully what are you trying to interpret and reveal, you must not forget that every things need some clarifications. Otherwise, you'll be bombarded with questions, comments and possible rejection .

I remember, I took about 6 months before my first paper been accepted and more or less the same time for my second paper. So, you have to spend a lot of time writing a paper and I suggest when you do it, do it carefully with a critical thinking. You've got to make sure that you have enough information and be prepared to do more experiments if needed. I have to remind you that plagiarism is not a good idea as most reviewer can detect it. Remember they are the expert and I'm sure they are fully aware of previous and current papers in the area of their research expertise.

As a young researcher, you might ask whether to publish 2-3 papers of your research in low impact factor journal or higher impact factor journal. I think it depend to your work, in Malaysia the question is always how many papers have you published? In the UK, in which journal have you published? My strategy at the moment is......well it depend on my results really . I am aiming for at least 2 publications. I still think I can get another two publications from my Msc. thesis.

Anyway, back to the manuscript, sorry but I have rejected that paper. Ohh..the second reviewer also rejected that paper :-)

POTENTIAL PROBIOTICS FOR BIOCONTROL OF DISEASES IN OYSTER CULTURE

Aquaculture sustainability is an important key in the wake of fthe declining seafood supply in Malaysia. I think development of aquaculture industry through green technologies can drive the industry forward. However, some of the projects have come under scrutiny by environmentalists. Thus, this industry demands green technologies. I guess Universiti Putra Malaysia (UPM) along with the government agencies are the drivers to make these technologies become reality. Seafood should be viewed as the source of food to meet the ever increasing food demand in the future, said an official of the Asian Pacific Chapter of the World Aquaculture Society at a meeting in Kuala Lumpur recently.

Here I would like to share a study done by a young researcher Murni Karim, from UPM. Currently she is doing her PhD research at the University of Rhode Island, USA. Her interesting research is about biocontrol activity of bacterial against Roseovarius crassostreae. She won 2^nd place in World Aquaculture Conference this year. Congratulations and all the best Mrs. Murni Karim.

Murni Karim, David Rowley, Marta Gómez-Chiarri

Dept. of Fisheries, Animal and Veterinary Science

University of Rhode Island 169 CBLS,

120 Flagg Road,

Kingston, RI 02881, USA

msh_712@yahoo.com

Roseovarius crassostreae is a bacterial pathogen of oysters Crassostrea virginica that is responsible for juvenile or Roseovarius oyster disease (ROD). ROD causes high seasonal mortalities of juvenile C.virginica in the Northeast US. Several Vibrio spp. also have been reported as the cause of mortality in shellfish hatcheries. Increased concern about this problem has led to research for alternative disease prevention methods, including the use of microorganisms such as bacteria as biocontrol agents. The introduction of selected beneficial bacterial isolates for biocontrol of R. crassostreae and vibriosis might eventually replace the current use of antibiotics, which could reduce their ecotoxicological and ill effects on human health.

This study was undertaken to screen and characterize marine bacterial isolates as potential agents to control pathogenic R. crassostreae and V. tubiashii. Screening of 64 isolates from Rhode Island marine organisms using agar-based assay methods led to the isolation of candidates RIO6-95 and S4. Each isolate displayed strong antibiotic effect against pathogens tested. In an oyster challenge model, pretreatment of larval and seed oysters with RIO6-95 and S4 protected against mortality due to challenge with R. crassostreae and V. tubiashii. Oysters were treated with 10² to 10⁶cfu/ml of the test strains 24 to 48 hours prior to exposure of 10⁵ to 10⁶ cfu/ml of the pathogens. The results suggest the potential of marine isolates RI06-95 and S4 bacteria to serve as biocontrol agents to reduce ROD and vibriosis in C. virginica culture.

Poor little pigeon

About 20 minutes ago, I found this poor pigeon struggling to fly. She just laid down calmly as I approached her. At first, I thought her neck was broken but apparently it was her left wing. I brought her to the Biodiversity Lab trying to seek their attentions. Nobody knew and some even suggested to kill her. I couldn't and obviously I didn't want to!! I didn't know what to do. Just now, she died. I hope she knew I wanted to save her.....Rest in peace my friend.....

Sampling and studying ants in the high canopy of a tropical rainforest by Kalsum M. Yusah

Entomology has always been special to me. It is one of my favorite subjects during my undergraduate study. This subject is mesmerizing and appealing. Its open a door to a diverse and complex nature of insects world. The list of entomologists through recorded history is enormous, and includes such notable figures as Charles Darwin, Jean-Henri Fabre, Vladimir Nabokov, Karl von Frisch (winner of the 1973 Nobel Prize in Physiology or Medicine) and two time Pultizer Prize winner E.O. Wilson.

Here I would like to share a study done by a young researcher Kalsum M. Yusah, from Sabah and currently she is in her 3rd year of her PhD research at the University of Cambridge,UK. Her interesting research is about ants.

Although research in the past few decades has established that the rainforest canopy harbours an exceptionally rich diversity of arthropods, we still know very little about the ecology of these important animals. This is principally because it is difficult to sample and study animals that live so high above the ground. We report here on methods that we have developed for studying ants, the dominant arthropod taxon, in the canopy of the dipterocarp forest of the Danum Valley Conservation Area in Sabah, Malaysia. We show that methods that work well on the ground need to be significantly modified before they can be applied in the challenging condition of the high canopy.

The most flexible method of accessing the tree crowns is to use the double-rope technique, and it is also essential that the scientist becomes sufficiently confident in using branch-walking techniques such that she is able not only to move freely but also to make rigorous observations within the canopy. For efficient sampling of canopy ants, fogging is a useful general method, but needs to be modified by raising the trays high into the crowns to produce a focused sample with little loss of the crown ant species or contamination by ants from lower in the canopy. Traditional baits work well in the canopy, but in order actually to collect ants at the baits, it is necessary to use a modified trap that can be closed without the disturbance caused by walking on the branch near the ants. We show in detail how this purse-string trap works. Pitfall traps can also be used in the canopy but are quite poor at collecting ants. For observing ant behaviour, we used video cameras which both reduces disturbance of the ants and minimizes the amount of time that the researcher needs to spend in the tree crown.

We present quantitative data on the effectiveness of these different sampling methods, and show that a combination of baiting and fogging appears to capture approximately 90% of the ant species in a tree crown.

p/s: Thanks for letting me share your research Kalsum. Great job! Here is a link to entomologist blogger from UKM.

I am falling in love with Borneo. Amazing photos by Malaysian photographer: Mr. Cede Prudente

Breath taking view of Crocker Range

I truly adore Borneo. Borneo has got many magnificent views of flora and fauna. Millions of visitors from all over the world came to witness one of the greatest places in earth. I'm speechless to see all these pictures. Of course there are a lot more than this. Mr. Cede has captured the best of Borneo. His works are breathtakingly beautiful. I would love to embrace into our own nature. They are just beautiful!! I hope we do appreciate what ever mother nature gives to us. We really need to conserve our exceptional and unique rain forest and wild animals. Therefore, start taking care of of them. Nobody else has got it except us.

I love it and I hope you all will love it too! It's our treasure!

Thanks to Mr. Cede for sharing your world with us. I think he has produced lots of books about Borneo. Check it out. I'm sure it's amazing! You can buy all his books here:
http://www.amazon.com/s/ref=ntt_athr_dp_sr_2?_encoding=UTF8&sort=relevancerank&search-alias=books&field-author=Cede+Prudente

Rhinoceros Hornbill


Orang Utan


Wild Bornean Elephants


Kinabatangan Crocodylus porosus


Red Giant flying squirrel


DANCE OF THE ARGUS


Proboscis Monkeys aka. The Flying Dutchman


Mr. Cede Prudente

Zetty Norhana Balia Yusof: Best Poster Award at the 14th International Conference on the Cell and Molecular Biology of Chlamydomonas

Zetty has done it again! She has been awarded The Best Poster Award at the 14th International Conference on the Cell and Molecular Biology of Chlamydomonas held in Wheaton College, Boston, USA. Congratulations dear!!

I guess this has been a very significant award for her. An international award which every young scientist craving to achieve. I remember she told me that her supervisor said to her just to use the old poster or just updated or added a little bit more data using her previous poster template. However, being her (as I know), she was very determined to do a new poster. She knows what she wants and she always do and IT'S WORTH THE EFFORTS! She won $300 sponsored by Genetics Society of America (GSA). Superb!

I think her poster was excellent and all rounded! Lots of of informations but simple and easy to understand with those cartoons. I bet she explained it really well to the judges as well as the visitors. I am very proud of you dear! I think there will be many more achievements to come from her. She always ask me can she be a good scientist errr...YES YOU CAN!!

Attached is her poster's abstract.

The effect of a single base change in THI4 riboswitch on TPP binding in C. reinhardtii

Zetty Norhana Balia Yusof, Michael Moulin, Haruka Tamura and Alison G. Smith

Department of Plant Sciences, University of Cambridge, Cambridge CB2 3EA, UK

In bacteria, many genes involved in the biosynthesis of cofactors such as TPP are regulated by riboswitches. Riboswitches are genetic control elements located mainly within the 5’ untranslated regions of messenger RNAs. Upon binding of regulatory signals, which include vitamins, amino acids, nucleobases and uncharged tRNA, these RNA elements undergo conformational changes that modulate gene expression. The thiamin pyrophosphate (TPP)-binding riboswitch is found in all three kingdoms of life and can regulate gene expression via premature termination of transcription, initiation of translation and mRNA splicing. In the green alga Chlamydomonas reinhardtii, we have found that TPP riboswitches are found in THI4 and THIC, the genes encoding the first enzymes of the thiazole and pyrimidine branches respectively of the thiamine biosynthesis pathway. In this study we report an in vivo expression analysis of the effect of mutations in conserved bases located in P2 and P4 stems of the C. reinhardtii THI4 riboswitch. We performed an analysis of mutants with single base substitutions in the riboswitch linked with a luciferase gene and observed the expression with the absence or presence of thiamin. We observed high expression of luciferase activity without the presence of thiamin and low expression with the presence of thiamin in the non-mutated riboswitch. When a single base located in the P2 stem was changed to mimic the pyr1 mutant (pyrithiamine resistant mutant), the luciferase activity was maintained even in the presence of thiamine. A single base change of one the conserved residues in the P4 stem also resulted in a stable luciferase activity in the presence of thiamine. The results confirm the participation of bases located in P2 and P4 stems in the recognition of TPP as well as the consequence of binding of TPP towards the expression of THI4 gene in C. reinhardtii.