See what I have Blasted...

Just now, I helped my friend to blast her ~500 bp sequence of 16s rRNA gene of an unknown bacteria collected from soil.

Guess what is the result? [click to enlarge]

The E-value is low (in fact, it is so low it is zero). Low E value means it is highly possible that particular organism is the one you are looking for. In this case, it is Bacillus anthracis. OH... MY... GOD.................

Although it only says a partial sequence, a 500 bp out of the total 1400 bp 16S rRNA gene and with a score of 900+ and E value = 0, it has a good chance to be right! Then and again, a full-length gene is needed for a 100% identity. Sigh, too bad it is not a full length one.

WBLE trouble

Ok. Here is a shortcut to register your subjects.

1. Access WBLE
2. Select FES 201001 from the left sidebar
3. You will see a list of courses. Ignore it. Search "Bioinformatics" on the search field.
4. You should see 3 options, if I remembered correctly. Select the Dr Alan's one and make sure the year is 201001 for that subject.
5. Then click yes when a pop up is displayed.
6. Now, click on the "Participants" link on the left sidebar.
7. Search either Chua Chee Shin's, Mok, or Tan Chor Siong's name. If cannot, search mine la.
8. Then you click on their name.
9. You should see a list of subjects on one of the details. Click all of them ONE BY ONE. Every time you click, a pop up will ask you to enrol/register the subject. Just click yes. Anything just ask me.

Short Notice

1. Dr Haresh confirmed no lessons on CNY week (Week 5)

2. Replacement classes for Dr Haresh: Thursdays (3 times), 9-10 am, SE108
(I hope nobody takes holidays onwards by Week 4, no right? If too many ppl take "Pre-CNY Week Holiday" on Week 4, we need MORE replacement classes.)

3. As for Ms Charanjit's "Saturday presentation" issue, I am still waiting for her reply. So be patient ya...

4. Schedule for phototaking session:

5th of March, 2010
2.30 - 3.30 = Group 1*
3.30 - 4.30 = Group 2*
4.30 - 5.30 = Group 3*

*Groups are NOT the same as the tutorial groups. Make sure you check which group are you in when you get the name list later. The name list is the one that ask for you whether you want to attend the workshop, the tea session and the convo dinner.

There 3 sheets of paper for the name list. The first sheet is Group 1 and so on. As for the photo taking session. to be safe, EVERYBODY please come by 2 pm. Just in case if anything happens. Pass around the news.



Regards,
Your *still breathing, still alive* course rep... anything just ask me...

Short Announcement

1. The schedule of FYP sessions and the thesis format are found in our course email.

2. There is an FYP briefing on the 22nd(postponed to) 29th of January, 2010 at DK1, from 2 to 4 pm. This is because Dr Say is taking his students to the hospital for a visitation. Dr Hii and Dr Loo are present for the briefing.

3. No Fermentation Technology lab AND no Bioinfo lab on Week 1.


^[New!]4. Lab for MMP begins on Week 1.

5. Will keep you guys updated if there is anything new. Oh wait, I almost forgot, please get ready RM 5 - RM 10 (will decide on the exact amount later after we get to know how many notes are passed down by our dearest lecturers) for class fund.

At your service,
Your Course Rep (who wants needs more holidays...) and love you guys the most.

Ami17

Hehe... What a clean image...

Ok, enough for gel image... I will capture some lab images next week... Who want to be my models... Wahaha...

FYP spree

Well, since Mokky had post up some interesting pictures, why not I add on some onto the gallery while trying not to divulge my progress, hehe...

Okay, first of all, we get do some sampling around the Kampar campus area - the ex-tin mining secondary habitat. It is an extremely interesting area for research and sight-seeing, especially the extra-large servings of "cake", aka cow dung/牛粪.

One of our sampling sites is a home for a immensely huge Mimosa species, not the ordinary M. pudica/含羞草. Let the pictures do the talking (photos credits to Mike):

The size of this plant is about knee-height. No kidding. Like the normal M. pudica, the leaves close up upon touch. It is called the Mimosa pigra.

This is a closed-up view. See the menacing thorns? Much longer and more compared to ordinary "shy grass".

This "tree" is taller than me. It is also the plant shown before - M. pigra. Huge leh. Even Dr Choo was in aghast when he witnessed this unreal plant.


Now, the other sampling site:

We were sampling around the bushes until we saw this hole. This is not the only hole, mind you. There are no less than 10 holes around the bushy mound. The guards told us sightings of monitor lizards and pythons and cobras... we were like WTFREAK?!?! The hole is one of the entrance of a nest - probably a reptilian, a monitor lizard perhaps?, due to the leathery egg shells we found near the hole as shown in the next photo:

Nah, the eggshell.

This is the flower of the bush on the nest.

These are some gel images taken during the course of my FYP, no description is given since it is "highly classified", hihi.

FYI, before doing FYP, we only do once or twice of gels, and barely once PCR. Now, we do almost 2 PCRs per day, run about 2-3 gels per day, do DNA extraction about 2-3 times per week (regardless of gel extraction or soil DNA extraction). Now we feel nauseous whenever we hear the word "gel" and "PCR". God bless all FYP students...

Note: The gel images above were taken using a gel visualizer which is equipped with an EXPENSIVE camera. Too bad it was stolen last week. Wish the culprit would be apprehended and the camera returned. The photos taken by it were of high quality. Now we are resorted to another slightly inferior gel visualizer, Mike, don't get all fired up when you read this coz I know you abhor that thing a lot. lol. Till then...

Ami203

Hehe... another gel image...

The image is good, why?? Coz the ladder is very clear and good, haha... (from my senior, most FYP students will come to run gel with ladders only... haha)

Other bands seem very faint... Why?? Lane 2 actually use same sample as previous two gels, but they seem different... Why??

Anyone can answer me?? Hehe...