My journey to Lindau Nobel Laurate Meeting

Time flies by!

Last couple of months were kind of hectic for me with SwapnoJaatra! Its nice to have a break!

Four or five months back, I got this chain email from one of my subscribed group that the Lindau Council at Bangladesh asked for online application from interested individuals for Interdisciplinary Lindau Nobel Meeting 2010. I was hesitant initially. Fortunately, for me, Mustak bhaya insisted that I should apply. I had two days in my hand (the last date was knocking at the door :p). Collected all the documents and applied. There has been a number of steps, initially I was selected from Bangladesh, then I had to apply at the Lindau Committee.

I think it was sometime around May! I got this email from the Lindau Committee congratulating me for being selected! That's a WOW!

Time passed by, required documents started to come to us (Me and Tania apu). Then an email came asking for application from those individuals who are interested to attend EUROSCIENCE OPEN FORUM 2010 @ Torino, Italy meeting after Lindau Conference. I thought, why not? But I wasn't sure about this one, 40 to be selected out of 650! It was a pleasant surprise at the end, I was selected based on my write-up!

Two weeks of Europe tour: 1 week @ Lindau, Germany and 1 week at Torino, Italy.... the journey has just began!

My laptop is running out of its battery charge :( There is no option of plugging power cable at Dhaka Intl Airport, I guess I've to stop now!

Conscious learning at Vegetative state!

As mentioned in one of my previous posts, I'm not a fan of neuroscience per se, but I find deep interest in human psychology and cognition. Its only interest though, I've not yet done my home-works on these subjects!

I first read about the condition in New Scientist, its been a while... (may be I took that issue from Chittagong British Council which means it was at least 4 years back!) The article was patients who lost their motor function, yet have unaffected sensory perception. I wish I could do something for them. Being trapped inside the body and no communication with the world around you... its hard for me imagine how it feels! But we, the human being, survive.

The issue is closely intertwined with the patients in vegetative state, as declared by doctors. In a recent research, it was revealed that some of the patients in this state have their conscious learning part intact and their ability of conscious learning correlates with their prospect of recovering later on. This is an interesting result indeed. I would recommend reading the following link:

http://www.scientificamerican.com/article.cfm?id=learning-in-vegetative-state

After 19 days... Jackson still going strong in charts

I was checking out this week's last.fm chart, Micheal Jackson at the top: expected. But the way he was leading... most loved, top artist, top track, even in hyped track (some of the less famous tracks of Michael)... hyped artist included Jacksons and Michael's brother Jermaine!

10 Apple top album includes 3 Michael ones!

19 days and still leading all the charts, I don't buy the conspiracy theories, but at least Michael's sister La Toya Jackson is literally right, "He was worth more dead than alive."

Moving my 360 blog to wordpress

Yahoo 360. Once it was part and parcel of my life; Apart from serving as a diary which bears marks of the history of certain part of my life, I had 81 friends, a huge fan base and more than 22000 web visits. Unfortunately yahoo has decided to shut down its 360 service on 13th July 2009. Like most of the fans of this service, I'm utterly disappointed. But at the end, I'd no choice but migrate my blog to other platforms.

There were many options, at least according to Yahoo!

• Migrate to yahoo profile
• Migrate to wordpress, blogger or other platforms

Couple of google searches and I myself found following additional options:

• Import tool at My Opera
• Import tool at Multiply

Yahoo profile seems okay, the only problem is I couldn't find the comments! Besides no image, no html imports. Only texts being imported. Its disappointing. I tried with blogger, but failed due to absence of any sort of import option!

All of the rest three imported part of my blog!!!

• Wordpress imported without the images.
• My Opera imported only the comments.
• Multipy imported only the blogs, leaving the comments behind.

It felt like yahoo willingly ignored its 360 users! Considering all these facts, I opted for wordpress, manually added all the images (wasn't easy with 125 posts!) and tags. Now its in shape, at least to some extent.

The social networking face is missing from wordpress, but at least I've the blog!

I kept the weblink similar to my 360 one!

http://neelsky2000.wordpress.com/

How language shape our cognition

Apart from Molecular Biology, there are certain other subjects on which I've deep interest. Psychology, Cognitive Neuroscience (unlike some of my peers who are quite enthusiastic about the subject, I'm not a fan of general Neuroscience) as well as Linguistics. While going through my google reader updates from wordorigins, I ended up in this page on How does our language shape the way we think?

This is quite an informative review on the interface between human cognition and linguistics! Clearly described and well reviewed. Some facts discussed are indeed worth pondering.

Anyone interested in human language development and its effect on shaping our thoughts and emotions should give a look!

I've already hyperlinked to the web-page, in case you couldn't find, the link is given below:
How does our language shape the way we think?

Nature, Science and Michael...

It has been a long day :p Slept a lot, the only productive part of it was going through the current issues of Nature (Volume 459 Number 7250 pp1033-1160) and Science (Volume 324 Number 5935 pp1603-1754).

If you're reading Nature or Science, definitely you're going to find something interesting, no matter what is your taste or interest. Anyway, to me, current issues of both of the journal lacked the usual glamour, generally I cant pick my clear favourate. One article in Science really caught my attention, the group assayed DNA-Protein interaction of ~100 mice Transcription Factor (TF) DNA Binding Domain (DBD); Vol 324 p 1720. Another paper on formation of functional centromere by synthetic heterochromatin was worth mentioning; Vol 324, p 1716.

Nature was slightly better, there were three articles on science journalsim which I thought worth reading; Vol 459, pp 1054-1057. The research article on membrane fusion (p 1091) and correlation between transcription and DNA replicatio fidelity (p 1150) was quite interesting. But I thought the paper on role of mechanical force generated by the first cardiac pump in embryonic haematopoesis is a masterpiece (p 1131).

Last but not least, I woke up this morning and my brother gave me this bad news: The King of Pop Michael Jackson died of cardiac arrest. The news was really a saddening one, but we all have to die at some point of time.

Heal the world... Make it a better place... for you and for me and for the entire human race... RIP Michael.

Repairing XP Boot file

About an hour ago, my sister came to me complaining her XP doesn't start! It gives an error message which roughly says it can't find boot file at C:\Windows location. Right then I knew its a mess, definitely the boot.ini has been deleted. So I asked what happened? The initial story was, there was load shedding, when power supply resumed and the PC was tried to turn on, the message kept on appearing. Then she said, she wrote this code yesterday which deletes files and it deleted lots of files in C: drive and she thought its no big deal since the OS is installed in E: drive. By then I figured out whats wrong, I replied although the XP is installed in E: drive, the boot file is in C: drive and now the PC can't find the boot file, thus no start up.

Anyway, despite my initial thought this would be a tough task, it turned out to be an easy one! I used XP installation CD, selected repair option, then typed \help in the command prompt, there was help on command \bootcfg, I knew I was in the right place, I used the \rebuild command, I didn't understand some of the queries of the command, so googled and came up with this about.com article, a handy one, which solved my problem. Below is the link:

Repair or Replace boot.ini file in Windows XP

I thought I might share in case anyone faces similar problem.

DST from my perspective

The country is clearly another step ahead by using DST, Daylight Saving Time, from tonight. I wont go for justifications (one of my friend, Minhaz seriously doubts its any positive effect and he put forward lots of geographical explanations, lets not go to that.)

What I felt is the government failed to publicize it. Its now just a high class educated society clock time change phenomenon, rather than being an event of mass participation. I can give an example form my own life. The guard at our house today refused to open the gate at 7 am, he was insisting the gate will be opened at 7 but now its only 6 am. My brother, to his utter annoyance, failed to convince him that 7 is 7 and all the offices, schools, colleges and universities will start according to the new time schedule.

But the fact is, I'm not surprized at all, its the way things work in our beloved country. We have some highly talented individuals at the administration who execute their decisions without even the need of planning, let alone the concept of proper planning. Its ridiculous to start DST when technically we have already finished summer and on the brink of the longest day of the year (21st June, DST should be evenly distributed at the both side of the longest day, i.e. if DST is in operation for two months, one should be before the longest day, the rest should be after it).

Hail us and our leaders...


Image courtesy:
http://pakistaniat.com/images/Daylight-savings-Time.jpg

Catching Cold by reading New Scientist !!!

Theoritically right now I should not be writing blogs, I should have been checking different universities or taking rest :p

Anyway, couple of days back I was reading this article on Common Cold in New Scientist I brought from British Council. It was kind of interesting. Three suggestions were there if you want to avoid cold (don't sue me if you still catch cold):

1. Avoid direct contact with children, they are miserably efficient in transmitting viruses.
2. Avoid having cold feet, I'm not quite sure how this works, but I think the mechanism is if your feet is cold, the blood flow is directed to feet reducing the flow at the nose, thus reduced immunity! (No reference please, I'm not quite sure about the mechanism myself)
3. Finally, wash your hand regularly. In case you shake your hand with a person who has cold, you can also catch! Wash them, be safe :)

The funny thing is after reading the article, I wasn't feeling that much good! The very next day I caught cold! Is there any mechanism of catching cold by reading New Scientist article on Common Cold :p

Evolution of Anthocyanin pathway gene dihydroflavonol-4-reductases

I've started writing reviews of recent papers on GNOBB. I'll post my reviews here also. Below goes my first review, its on gene evolution through duplication, published online in Nature.

Gene duplication is one of the major ways of evolving genes with novel functions. There are two models on how gene duplications lead to new functions: 1) The NEO-F Model (Neo-functionalization) & 2) EAC (Escape of Adaptive Conflict) Model. In NEO-F model, new function is achieved after the event of duplication. On the contrary, in relatively unexplored EAC model genes acquire novel function which maintains its ancestral function also. This gene is constrained from improving either novel or ancestral function because of detrimental pleiotropic effects on the other function. But upon duplication, any of the copies can be selected for enhancement of the novel function. In a recent paper accepted in Nature Marias et al. explores the evolution of Anthocyanin pathway gene dihydroflavonol-4-reductases (DFR, EC number 1.1.1.219) in Eudicots with respect to both of these models. Their study suggests EAC as mode of evolutionary change of this gene. Besides they also conclude EAC may be far common mode of evolution than previously thought. One interesting conclusion of their study is that the evolution of novel function may sometimes be a byproduct of the evolution in enhanced ancestral activity.

Ref: Marais et al (2008). Escape from adaptive conflict after duplication in an anthocyanin pathway gene. doi:10.1038/nature07092.

Sequencing Beta-Globin

Yesterday our Thalassaemia research has crossed an important milestone, it may be a small step in our project yet it is the very first and utterly significant stride towards achieving our ultimate goal.

We have successfully sequenced a region of Beta-globin from a healthy individual. We don't yet have the sequence in our hand, expecting to have it in a while. I'm quite excited!!! Can't wait anymore....

DNA at last

Last few days had been quite hectic, starting from the 1st Day of 2008.

The objective was isolation and amplification of 587 bp region of Beta-globin. Started with isolation of buffy coat. I think this was the trickiest step, required lots of anticipations and assumptions. But I think we're very lucky, it didn't take much of our time. Then the DNA isolation and PCR. Today we've successfully completed PCR.

I'm very excited about tomorrow's work!

HFE stands for Haemochromatosis

Actually I should have posted this blog at least four months earlier...

Our bioinformatics assignment had a part on Haemochromatosis gene, its nomenclature HFE appeared bit confusing, so I had searched for its origin. Well, there was no specific answer but I got something.

The actual reason behind naming this gene as HFE is not known, but FE might be for Iron, which is closely associated with the pathogenesis of this disease. Some scientific literature states this gene as HLA-H, eventhough there is a wide debate in designating this gene in the group of HLA (Human Leukocyte Antigen).

Reference:
Hemochromatosis gene nomenclature; American Journal of Medical Genetics 93:77 (2000)
www.genenames.org/activities/publications/PMID10861687.pdf

Scientific or Promotional!!!

Today a scientific conferance on Promotion of Biotechnology in Bangladesh: National and International Perspective has started at Sasaka Auditorium, ICDDR,B. The official URL for the conferance is

http://www.promotebiotechbd.net/index.htm

I was going through the conference schedule and related stuffs. My first reaction was, "Actually what is the purpose of arranging this conference?"

Its not a scientific conference. Most of the papers and posters going to be presented are already published stuffs!

A conference to promote biotechnology? Neither. In fact it will do even worse if this is the purpose. Only 300 restricted participants... inside a closed auditorium... no interaction with general people.

Another thing irked me. There is a cultural function session! Doesn't make any sense. To make things even worse Shuvro Dev has been paid Tk. 50000 to perform. Waste of invaluable money and time. You don't need cultural functions in scientific conference...

Bangladesh is a weird country with strange peoples! A conference has been arranged for the sake of arranging a conference... no goal, no objective...

Dream or Myth

BAS told not to disclose to anyone.

He thinks he knows someone who can cure cancer ... any type !!!

A dream or A myth!!!

Well, lets wait and see ;)

My 2nd Year Bioinfo Report

We have to write a report on Bioinformatics project each year.

Here goes my 2nd year bioinformatics report. (Course: GEB 207)

The Journey From Sequence to Structure.

Restriction Enzyme

Restriction enzymes are important tool for molecular biologists. As far as I know, these enzymes are solely found in Prokaryotic System... Is there any Eukaryotic Restriction Enzyme?

If you know any, please put the name and its source in the comment box.

Enjoy your time.

6/7 Hrs of VPg

6/7 hours (another 2/3 hrs in writing this entry) ... searching through net.... lots of research papers... At last, I've figured it out.

Yesterday, SRK was taking her lecture on plus strand RNA virus: Poliovirus and its life cycle.

The genome length of this novel (!!!) virus is 7500 b (According to SRK, but I think it varies. I've seen the range 7440 to 7700 b in different research papers.) Some features of Poliovirus genome are given below:

1. It has a covalently attached protein, VPg, at its 5' end. (¹)
2. Poly (A) tail at 3' end.
3. Three types of genes are present in this monocistronic genome: Structural, Protease (or proteinase) and RNA polymerase (from 5' to 3' respectively.) These genes are translated as single long polyprotein (~247 kD).









(right click and open in new window or tab to view enlarged image)

4. The proteinase has autosplicing capability. At first, it splices out itself, then it cleaves the polypeptide into different structural proteins and enzymes.

The list can be made much longer.

SRK said, poly (A) tail is required for infectivity, but VPg isn't. Later she said, RNA strand without covalently attached VPg can't be incorporated into viral capsid in maturation stage. I thought there was something missing... but I preferred not to ask. But this time Shammu was the person. She asked,"How can a RNA virus (or its RNA) be infective when it can't be inserted into viral capsid?" It was a good question, and I think I gave the answer in the class. But SRK didn't get my answer. Actually she didn't get the question either. She checked her lecture sheet and a book she brought with her (most probably Brock's Microbiology), then she dismissed one of her previous words. She thought it was her old book which is responsible. She told, "Forget about the sentence, "RNA with VPg can't be transcribed."...Well, Well, Well... this is another new statement. I don't think she told this before! May be I've missed.

So how to solve the puzzle. Remember none of her statements were wrong.

I've read some research papers published in different journals in between 1977 and 2006. The riddle is nearly solved ;)

VPg acts as a primer for new RNA strand synthesis (for both"+" and "-" strand synthesis.(^2,3)) It also stabilizes the RNA in cellular milieu. Recall cellular mRNAs are stabilized by 5'-cap. So VPg is necessary for replication of viral RNA. The RNA polymerase is coded by viral genome. RNA dependent RNA polymerase (RDR)... this enzyme requires primer, as far as I know other RNA polymerase don't require primer.

So what about translation? Before translation, VPg is cleaved by cellular enzymes. RNAs attached to VPg can't be translated. The reason isn't still known, but it is thought that VPg interferes with some steps in translation. (²) 3D folded structure, Cis-acting Replication Element (cre) which along with Internal Ribosome Entry Site (IRES) plays vital role in initiation of translation... I am not sure whether cre and IRES are the same sequences or two different sequences... I'll update when I know.


Update: cre isn't necessary for translation, rather it is required for replication. cre is located within IRES but mutation in conserved cre region (AAACA motif) doesn't effect the rate of translation. (⁴)



Hurray! The dilemma is solved at last. Polio RNA without VPg is infectious since it can carry out penetration, translation, synthesize new VPg protein which can act as primer for new RNA synthesis by RDR. So infection continues... but this RNA can't be incorporated in Capsid in maturation phase! Who cares that? It is creating effective progeny, it is infecting its host, effectively stopping host translation... Fantastic Job! But the poor RNA itself dies with its host. An altruist.

Image Courtesy:
Poliovirus:
http://users.wfu.edu/banklm3/cell/index.html
Translation in Poliovirus:
http://pathmicro.med.sc.edu/book/virol-sta.htm

References:

1. Yuan Fon Lee et al., A Protein Covalently Linked to Poliovirus Genome RNA, 1977;74;59-63 PNAS oi:10.1073/pnas.74.1.59.

2. Akio Nomoto et al., The 5'-terminal Structures of Poliovirion RNA and Poliovirus mRNA Differ Only in the Genome-Linked Protein VPg, Proc. Natl. Acad. Sci. USA, Vol. 74, No. 12, pp. 5345-5349, December 1977.

3. Timothy J.R. Harris et al. Nucleic Acids Research, Vol. 8, No. 6, 1980.

4. Mason et al., Identificationand Characterizationofa cis-Acting Replication Element (cre) Adjacent to the Internal Ribosome Entry Site of Foot-and-Mouth Disease Virus, JOURNAL OF VIROLOGY, Oct. 2002, p. 9686–9694

12 hours and your cancer is cured!

Sometimes life is really tough. This entry was supposed to be in last Monday or Tuesday...

It's BAS. (Baizid Alam Shibib)

Last Monday, he came to the class and started day dreaming ;)

He was asking,"If someone from Bangladesh invents a drug which cures any type of cancer within 12 hours, will s/he get Nobel Prize?" I said,"Not once..."

How can a biochemist have such fantasy? When I told Tanaeem, he laughed and said,"This joker has no idea. Complications like cancer; curing in 12 hour! It is not a disease. You can't go and kill the pathogens! It's your cells dividing uncontrollably and bringing back the control requires hack of a time!!! At least couple of months, in fact years."

He could have increased his credibility! He could have said any particular cancer, may be in a month or 6 months... that would have made lot sense. All cancer! He has no idea how cancer forms. There are at least millions of ways: activation of oncogene, inactivation of tumor suppressor genes... non-functional cell signaling... mutation ... I don't think the list will ever end. And if someone says, he wants to treat all these with one and only drug (when I can't even list them in single sentence), then I guess he has problem in grasping the difference between cancer and other diseases... funny thing is he teaches Human Physiology in Department of Biochemistry. To add to the surprise list, Biochemistry students think he is the moving encyclopedia!!! Ha Ha Ha!

May be he meant Astrology's Cancer ;)

The Job of A Teacher

It was in DJ's class and I was bit confused about Physical Map of chromosome. Even though she didn't ask... it came up in my mind and I wanted to use this term. Yet I restrained. I had logics behind my idea. But I knew she wouldn't accept unless I'm right. Of course she is right in saying that I'm wrong. But not before hearing my explanations.

What's the job of a teacher? Is it just going to the class and deliver a pre-written speech like our President? I don't think so. Teaching is an interacting profession where your students are more important than you yourself. The most important part of teaching is developing your student's the quality of being critical to something, some ideas, concepts and developments. It's not like you go to your students, ask a question and reply, "Oh .... You are at the same place as yesterday."

I hate this rubbish educational system.

Image Courtesy: www.nature.com