CADD

Its my third assignment, sharing what I've learned so far in CADD class.

1. MEROPS Database



Protein sequence
It provides catalogue and structure-based classification of peptidase. This is a large group of proteins that is important in medicine and biotechnology. MEROPS is a database of peptidases that are calssified into families and and then group into clans.In the class we select randomly some protein sequence and use BLAST from NCBI web to identify the similarity between them by having percentage (100% means it is similar). Besides, we can get their ID number.

2. PROTEIN DATA BANK (PDB)

PDB website

The Protein Data Bank (PDB) archive is the single worldwide repository of information about the 3D structures of large biological molecules, including proteins and nucleic acids.


2. ARTEMIS software


Artemis sequence

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation.

3. CLUSTALX

Loaded clp n lon sequence


To align multiple sequences and using Tree View to know their hierarchial view of information. Then, we can get their phylogenetics, the evolutionaryrelationship among variuos organisms.

4. RASWIN

1RR9 via Raswin


This is a software again people, even though sounds like Aswin right..huhu..just kidding..it can be used to view 3D structure of the protein (early in gz file, u have to convert it to pdb file in PDB web)....very cool when we can 'play' with the colour, rotate it 360..

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My banana flower

Scientific research is something very unexpected..For now, I have to stop my research due to some problems..TE infection is not successful...daym disappointed..might be due to the way we store the stock blood in liquid nitrogen or the problem with the liquid nitrogen itself..whatever it is..my moral is really down..no mood to even move...haha...

I dont want to say about it again..wanna hear my story other than fyp..

I met Sis Azizah who is PHD student in animal room..she is very nice, willing to share her research with me..She is doing research about banana flower or jantung pisang in Malay..effect to lactation in rat after delivery..She said to me that she heard some women eat jantung pisang to increase their milk for breast feeding..

the research is done and the result is amazing..it works..

and I am more shocked when I told mother about it, my mom said that she also eats jantung pisang and it is very effective...not to mention that my mon did breastfed all my 6 siblings...

now I really amazed..with their experience, we have to study what our parents, or grandparents practice..may be they just claim based on their own experience, but sometimes it can be proven by science..

I think science is really interesting...yeah..I want to study more about our Malay tradition la..

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FYP season 2

T. E could be easily identified between RBC and WBC...It will be stained purple due to nucleus possession..




It's certain now that I will study Trypanosoma evansi..it is usually found in cattle, horse, camels, and buffaloes..it is rarely causing disease in human..

Yesterday, I had injected all 12 mice with blood containing T.E..It's hard to inject them IP because sometimes I didn't really sure it goes to IP or IM..hopefully i did it right..

The stock we get from Parasitology lab UKM Bangi..Thanx to En. Nan who is really generous to give some of their experties and materials..we get Picric acid that meant to be a safe and long-lasting marker for mice..So, goodbye marker pen that we used to mark the tail..

But the bad thing is we left force-feed needle there..haha..it just really chaotic at first because it's very limited..thanx Allah we have 1 more..En. Nan will bring it on 26 Dec when he comes to Kuantan for wedding..Otherwise, we have to pay it which is cost us hundred bucks..haha..

this 3 days will be very crucial..Giemsa staining 12 slide..examination of parasitemia..treatment will start and continued until the mice died after 3 days (how dangerous this parasite, the mice only can last 3 days, can you imagine..)

till then, i pray for the best...Insya Allah..

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FYP: Full Yourself with Pressure

If my friend, Saifullah Arif defines FYP as For Your Pleasure, I have this kind of thought; FYP for me is ironically Full Yourself with Pressure..yes, FYP is hard time for everybody...with 4 months left to finish your research and complete the thesis, I notice all my friends are busy morning to nite...24 hours...7 days...that's including me...

my topic is changed now...from anthelminthic study to anti-malaria/ anti-trypanosoma..there are 2 choices, either I want to test my crude aqeous extract (CAE) of Avocado leaves against Plasmodium berghei (natural to mice) or Trypanosoma evansi (also natural cause in mice)..

For the start, now I'm giving my first group of mice (pre-infection) with CAE extract everyday (12 noon)..I forgot to tell you these are 5 groups:

1) Pre-infection-3 mice
2) Right after infection-3 mice
3) Post-infection-3 mice
4) Positive control-Chloroquine (gold standard treatment for malaria)
5) Negative control- distilled water

Yesterday (Friday-11 Dec 2009), my lovely supervisor Madam Norazsida Ramli invited her senior in UKM who are now a microbiologist in Kulliyyah of Allied Health Sciene, IIUM to share his vast experiences in handling mice-model experiment..his name is Bro Syukri, wow, he is very expert in dealing with these tiny creature..

He taught us how the correct technique in these 3 basic yet crucial skill in my research:

1) Force feeding-giving the mice CAE extract
2) Intra-peritoneal injection
3) Blood withdraw from the tail


Alhamdulillah, this 3 hour session is benefial and I'm grateful to be shown the techniques from the expert..It is indeed my gratitude to Madam Norazsida and Bro Syukri for sharing their knowledge...Now, it's not that hard for me to give force feeding unlike before..it takes me just 1 hour to patiently give them the extract litle by litle..Now it's just seconds...How an achievement!

Next agenda in my schedule on Monday 14 Dec, heading to UKM Bangi to give the mice the infection..oh, how unfortunate their life will end...huhu..

till then...FYP, it is really full of pressure but pleasure at the end of your research when we are successfully prove something..it doesnt matter the treatment works or not...it just prove that matters..

Wassalam..

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Chapter 1: Journey of my life

First entry for new blog, in new sem with new energy, now I'm coming to share my journey of life..nothing much to write because now I dont really in the mood of story-telling..but here we go, I try to share a bit about my education background..

1. Sek Ren Kebangsaan Batu Lapan (now SK Fakih Abdul Samad)

1993-1995, I studied in this school only for 3 years..this is quite an old school in front of Taman Tas..here I was appointed as a prefect in Year 2 n 3...

2. Sek Ren Islam Al-Irsyad

1995-1998, I moved to this Islamic school just to learn more about religious knowledge..this is a private school with monthly fees..the nuance of this school is so serene, being located in Kg Kurnia Batu 3, just perfect although there was no field for sports..just a dessert..here students are taught to call themselves with arabic term..Ana-me, Anta/Anti-You, Muallim/Muallimah-Teacher..till now I'm still using all this terms when speaking to my ex-classmates or with my teachers there..

3. Sek Men Agama Al-Ihsan

1999-2003, I studied for 5 years in this school...I chose this school by having their interview and I passed it...located near fisherman village of Tanjung Api, you can smell fresh fish in your class especially at noon..here I was a prefect for 4 years...the school is not really well-equipped but I love it so much...now I manage a blog for my batch alumni and we had successfully organized twice Reunion in Vistana Hotel-2004 and Teluk Chempedak 2008..

4. Matriculation center of IIUM (now CENFOS)

2004-2005, for higher education, I chose MCIIIUM because it was my dream after all to be an IIUM student...at first, I was taking engineering course in first sem, but later on I appealed to convert to Science Bio...located in Petaling Jaya, so much fun studying here..first, it just takes 10 minutes for you to go to KL..and this is my first experience study in outside Kuantan..haha..it's true...I never had any thought of study far from my hometown because I dont want to stay at hostel..haha..but MCIIUM changed my mind...now I love the experiences there..

5. IIUM Gombak

July 2006-November 2006-I registered in Gombak with uncertainty with the rumours that Kulliyyah of Science will be moving to Kuantan campus..but I dont really care..it's near with my home...home sweet home..I love Taaruf Week in Gombak..it was tiring but fun..especiallly when we did I-robic at stadium..and my mahallah also very far from Kulliyyah building..believe me, it takes you almost 20 minutes from mahallah Talhah to KOS...thus, I decided to discipline myself to follow bus schedule..sometimes, I missed the bus, n my fren's motorcycle were all fully-booked...so, with all sweaty face, i had to walk....I hate those experience because it is tiring just to reach KOS building near KOE..

6. IIUM Kuantan

Disember 2006-we had to move to our new brand KOS building..we had all the problems at first to adjust ourselves with this "empty" campus, unlike joyful-Gombak campus..I had so many things to tell you about my experience here..but may be later on...I survived until my last sem now..Alhamdulillah...till we meet again...Adios...

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