Finish making!

Oh yeah! Finally succeed making OpenOffice2.o this time. It's really a big baby - it took my laptop ~8.5 hrs to bear (make) it!! Now I've got Office suite on my BSD box.

Make Openoffice2.0 - rechallenge

OpenOffice2.0 has had a minor updating and now it's 2.0.1. Would this make any difference or bring me any luck on Openoffice compile? # cd /usr/ports/editors/openoffice.org-2.0 # make -DWITHOUT_JAVA -DWITHOUT_MOZILLA install As OOo's source code is quite a big thing (>200MB!), I just leave it download its sourcecode and let it make over night.

Fonts gone??!!

I can realize if far-eastern fonts are not installed then those asian characters wouldn't be able to be shown correctly, but how to explain if the English interface of a software disappear??!! This exactly happens in front of my eyes!! This trouble happens on Linux-Opera, and all the interface which are supposed to be English characters are now all blank, and even the English websites also show nothing! Odd enough, it can show asian websites without any problems! Now I'm using FreeBSD native Opera to write this diary, but without Linux-Opera it's unconvenient to browse those Flash-powered websites... Need to find a way to go...

Fonts reappear

Just re-install the whole OS (I know I shouldn't have to do this, but in case), and now everything is back. I'm suspecting there might be something wrong with linux-fonts (such as...I deleted them accidently and unconsciously...I don't know)...but I wouldn't re-try it again.

Compile unsusceed...

The OpenOffice2.0 making procedure has failed when I come back in front of my laptop. /_\

Make OpenOffice2.0

I'm a bit curious how long it would take to compile OOo2.0 on my laptop, and thus start a crazy thing today - install OOo2.0 from ports rather than from packages. My environment: OS: FreeBSD-6.0-Release CPU: AMD Athlon XP-M 2400+ RAM:768 MB HD: Seagate 30G, sliced as follow: / - 500MB swap - 1536MB /home - 4 GB /var - 4 GB /usr - 18 GB As I don't like to install JDK as it'll pull my laptop's leg and makes it crawling, I compile OOo2.0 without Java enabled. That is, # cd /usr/ports/editors/openoffice.org-2.0 # make WITHOUT_JAVA=yes install clean

Nobody today

After all, today is boxing day and everyone has gone for their long holidays, and the whole building looks fairly quiet. Actually those staff come to work have also left before lunch time. As with my lab, we also turn off most of the equipment and power (except those which need to be run 24/7 such as fridge) and close the unit. #Complaint: 1. After a short lunch, I bring Sachiyo walking around the campus (well, she forced me to show her around...). 2. Yuuki said we'd see in front of cinema at 5pm; Charito said Burger King at 6pm; Andrew didn't show up until 6:10pm; Marivic said Subway at 6pm; and Yuuki didn't show up and eventually didn't come back home tonight.

Open the autoclave room~~~~!!

I was right - the autoclave room has been locked and thus I've got to leave the stuff there for the whole holidays. Who's that said "autoclave is gonna shutdown in the afternoon on Thursday"?! Actually it's far earlier than pm!

Met ray just now

He was just going to leave C block when I was trying to autoclave some dirty things. He said he'd show me the PCR after coming back (from holiday, of course). There was nobody at C block that time and, apparently Ray was going out for holiday as well (casual shirt and short jeans, carrying backpack)...isn't it still too early?! ...Wait! That means the autoclave room's also been locked and nobody would unlock the door for me this afternoon; how should I collect my autoclaved stuff this afternoon then?

Autoclave down

I got an email forwarded from Kerry and it said the autoclave in C block was going to shutdown late Thursday afternoon and would restart it on January 4. That means I have to stop my work 2 days before that.

Airmail

I received cards from old friends in Taiwan (Guo-Jun) and Japan (Masae). Apparently they've got my cards as well. Nice to hear from you, guys!

Bacterio-static or -cidal?

I notice that on subculturing plates of Campys there are different results under different temperatures. This is a test of examining bacterio-static or -cidal of Campys after treatment of honeys, and I found that on 42C plates the Campys don't grow yet they do on 37C. I read some papers pointed that it would be necessarily to incubate freeze or antibiotics damaged Campys under 37C rather than 42C to recover them (that is, in a relatively mild envoronment). Hm, so what does this result mean? Honey is suppressing or killing bugs?

That's a big (and awful) news between scientists

S Korea stem cell success 'faked' (from BBC News)

Taq arrive

This is HotMasterMix from Eppendorf. Now I still need oligos (still waiting).

Xmas card from parents

Receive a Xmas card from lovely parents in Taiwan when I came home. Somehow the Turners also got a Xmas card from Taiwan...and guess what! It's from my parents as well...! Andrew said they'd send back another card to my parents too. # Don't bother if my parents can read Andrew's handscript or not...:P

Agar dilution and microdilution test on Campy

Campy samples: Campy from yesterday's broth inocula (overnight incubation, in 3ml Muller-Hinton broth). Camp120-125 (except 122 - initial inoculum too few); ie 5 isolates. 1.Agar dilution: Agar: Campylobacter Selective Agar ("CSA"; charcoal agar) w/o antibiotics Honey final conc: 0%, 2.5%, 5%, 7.5% Inocula conc: 10^3, 10^6, 10^9 Temp: 37C and 42C 2. Microdilution Dilution broth: Muller-Hinton broth Honey conc: 15% honey serial dil'n Inocula conc: 10^6 Temp: 37C

Rough MIC test of Campy

The result shows that Campy only grow on plates with 0% honey; other plates (2.5%, 5%, 7.5% and 10% honey) reveal that Campy may not survive on them. The MIC could be < 2.5%. Looks like Campy are quite prone to honey. (this is merely a rough test though) Post-work: inoculate Camp 120-125 into Muller-Hinton broth (only 3ml each for in case) and incubate in 37C and 42C overnight to see if they grow in broth media.

Andrew back

After 3 weeks travelling, Andrew finally comes back from Australia this afternoon. I was with Budhism community at dinner time, and he'd been watching TV when I came home at 21:00. He looks good.

Fake manuka

Found a recent news about fake manuka honey: Fake Manuka Honey trader's second prosecution (on Scoop.co.nz)

Tubes ok, plate contaminated

Well, what can I say? Same work yet different results. I wouldn't like to consider that the plate itself may have been contaminated, but otherwise how can this result be explained...? A bit tired of serial dilution, I made up some fresh CSA (no antibiotics added) and something other for Campy's MIC test preparation. As it's impossible to incubate them in microplate reader or even to obtain its growth curve, I would have to modify my antiseptic protocol especialized to them. # Made up: 1. Single strength CSA w/o antibiotics --- 200 ml (~16 plates) 2. Double strength CSA w/o antibiotics --- 25 ml x4 (for agar dilution) 3. Serial diluted 0.5A Campy (79, 84, 89, 90). Serial diluted by 10-folds in Muller-Hinton broth => 0.5A, 10^-1, 10^-2, 10^-3, 10^-4, 10^-5, 10^-6. Duplicate, incubate in both 37C and 42C.

Synchronous MIC

Do MIC test of Salmonella spp today (both tubes and microplate). Unsurprisingly it took me much more time to prepare the serial diluted honey and cultures (roughly 2 hr longer than usual). Consequently today's lunch time is around 3:00(!). Just before running micrplate reader (the "icebox" one), the reader somehow doesn't response to its software. Consulting Kerry, she changed lamp in the reader and it came to alive again. Next time I can do it myself!

Kids visiting

As Peter'd told me yesterday, a group of students (and their teacher) come to our lab...at 12:20! As I was handling my Campys and to prevent from contamination, I was not able to talk or even open mouth, for in case (this is Peter's idea, though). And actually I was picking colonies from heaps of CSA, I could hardly pay attention on them. Probably owing to the CampyHouses on the bench behind me, Peter realized what I was doing and explained to them briefly (although they're not supposed to understand). They stayed in our lab about 10 min (I guess) and left E block at 13:30, which was my lunch time today. By the way, we took our 8-channel pipette apart, cleaned and lubricated it. It was a bit stiff before but now it's much better. And where is Katherine anyway? ...Her boyfriend is coming to NZ today and she's gone to Auckland to pick him up!

MIC (tube edition)

Actually I didn't expect too much on tube MIC test before I checked the result this morning, but the result somewhat relieve (and puzzled) me - the MIC result is apparently perfect. Not even a contamination! So there shouldn't be any problem with my operation. But what's the cause of the weird micplate result then...???

"Are you gonna do your labwork tomorrow?"

When Peter asked me this question, I was a bit puzzled why he asked this. Of course I'm. Then he told me there were a few children (Ouch! I hate this) gonna visit our campus and also would look around our lab so that they'd have some idea what Uni is like. They are said to be around 12-year-olds...that means they have completely no idea about security or danger of bacteria!! Goodness me...

MIC test with tubes

Not knowing what should be done to solve the mysteric contamination in microplate MIC test, I decide to change the test a bit - do the test with tubes rather than with microplate. Unlike microplate methods, I can't use 8-channel pipette and hence I have to add broth and honey, serial dilute the honey and inoculate cultures to each tube one by one with single pipette. It also use up much more honey and broth than microplate edition. It's indeed tiring, but whatelse can I do with MIC test?

Campys moving new house

My "CampyHouse" (a plastic candle jar) is gonna melt by the flame after a few weeks' usage, hence I need to find another substitution. It needs to be... 1. made of steel. 2. able to block air leakage. 3. large enough to contain more petri dishes than the current one, but small enough to fit in both 42C and 37C incubaters. I got another 25 cultures from Medlab (Campy x24, Salmonella x1), and I also suspect some factors such as antibiotics in media and temperatures may infect the groth of campys; therefore I went to the Warehouse near our campus and found 2 cake-alike stock pots which would meet my needs. Actually they look working perfectly. Their lids are made of transparant plastic(? maybe) and I just need to put them upside down so that the steel bodies come upward and won't have to be concerned about the candle flame. (so now they've got steel lids!). Furthermore, compare with the preceding candle jar, it's much easier to pack 24 petri dishes, which is more than 16 before! And don't forget they've got "transparant base" with them, so observing their groth without opening the container would also be possible as well (not quite sure yet though). With these merits, they cost just NZ$20 for both. It's really a bargain!! # New CampyHouses packed with... @42C: Charcoal selective agar ("CSA") plates from Medlab x6 (4 isolates/plate) Homemade CSA (with antibiotics added) x8 (3 isolates/plate) Homemade CSA (antibiotics not added) x8 (3 isolates/plate) @37C: Homemade CSA (with antibiotics added) x8 (3 isolates/plate) Homemade CSA (antibiotics not added) x8 (3 isolates/plate)

Fire alarm

I had a late lunch break today owing to my lovely Campys. Although those campys still not growing quite well, I have to inoculate them into Glycerol-TS broth (otherwise they're getting too old - 5 days incubation).As there are more than 40 isoates this week, it took me a bit longer to accomplish the task. It had been 13:00 when I was going to dump my lunch in my mouth. Unfortunately, fire alarm forced us to get out of the building and stay outside until firemen arrival and make sure everything is under control. So what should I do with my lunch box?! ...sit on the lawn and eat there. (Hey, I never imagine I'd have an outdoor meal today) Eventually it's been confirmed that a concrete cutter gets fire with dust and, fortunately, no disaster happened. I haven't even smelt the smoke!!

Muller Hinton broth...forgotten!!

Somehow I forgot to add Muller Hinton broth in the list sent to Kerry yesterday. Hence asked her to order the broth this afternoon.

PCR reagents

Sent Kerry the list of PCR reagents this morning. The results of Salmonella spp. MIC test are still strange - contaminated in fairly strange way. Even Peter and Kerry have no idea what cause the problem. Mmm... :(

Price of lab facilities

Recently I'm interested in the price of lab equipments and reagents, and have made some surveys. Here is the brief list. Biorad microplate reader ----- NZ$ 20,000 Labsystems microplate reader (the "icebox" one) ----- NZ$ 20,000 bMG microplate reader ----- NZ$ 60,000 => that is, its incubater function worths NZ$ 40,000 :P Fixing Zencom pipetter ----- NZ$ 350 Racked and sterilized 250 ul filter tips ----- NZ$ 150 $Racked tips ~ $Bulk tips x1.5 - x2 Disposable latex gloves ~ NZ$ 87(?)

New samples from Medlab

Receive: Campylobacter spp. x42(!!) Yersinia spp. x2 Salmonella spp. x5 # Salmonella typhimurium x2 # Salmonella mississippi x1 # Salmonella enteritidis x1 # Salmonella ??????????? x1

Fruits from Peter

Peter brings 2 bags of oranges to our lab today. He said he grew them up in his garden. It must take quite a long time to finish them up... :P

Andrew gonna travel

Andrew is going to Australia for about 3 weeks for holiday. He'll mainly move around Melbourne and Sydney, so there's a chance that he'll visit John (a Chinese student stay with us before) some day (not quite sure if they really will meet each other though).

Lab meeting

We had a lab meeting at 11am today. Each student were asked to give a very brief (about 1-2 minute) talk on their projects then Kerry (and Peter) went over some safety and security issues (theft, smuggling, bunsen burner burns student's lung, etc etc etc).

Microplate reader... with ice box?!

As the schedule of our bMG microplate reader is a bit crowded, I'm trying to use another plate reader machine which is much older than the bMG one. This old machine is somewhat odd: it's connected to Mac computer, put into a "simple" incubater (heated by a lamp...). What the most awkward is that it needs an ice box to cool down, otherwise its motor would overheat... So, since the ice box is for machine, it should be a special or an order-made model, right? Well, not really. It's just a normal water bottle wrapped in towel. That's it. Very strange cooling system eh? This is said to be Peter's idea... :P

Stupid mistake

In yesterday's "charcoal agar vs blood agar" test, there's no clony can be seen in the charcoal agar plate - not even a tiny spot; it's just tidy and clear... :( Calm down and think, I realize that I've made a really stupid mistake; I shouldn't have used the ordinary Campy Selective Agar - they all contain supplements, which are actually antibiotics for inhibiting other microbes' growth. Hehhh...so I'll have to make another batch of special charcoal agar without supplement...

Salmonella sunflower????

I wrote this Monday that my Campy didn't grow up (or merely tiny spots), but fortunately they look much better this morning. On the other hand, I noticed that one of the Salmonella cultures Medlab gave me last Friday, when I innoculated its culture media (10 ul) on blood agar and incubated overnight, its colonies formed like spreading-out-sunflower. Although some Salmonella do have flagella, it is of interest that they would migrate in this way.

Charcoal agar vs Blood agar

To test if charcoal would interfere antimicrobial activity in manuka honey, I innoculate Salmonella spp.(which is easier to raise) on both CSA and Blood agar and do well diffusion test (100ul, 40% honey into each well). Hopefully I'll be able to see if there're any differences between their size of inhibition rings.

Green light for PCR reagent purchasing

On Peter's replying email he says "the costs of the materials you need is low enough to not be a problem". Hmm..."low enough" to not be a problem...then what does "high price" mean in his mind??? Anyway, the price list I gave Peter was really a rough estimate, thus I'd have to find detail prices and their distributors next.

Rough price estimate

Here is the rough estimate of the cost of the PCR reagents. Some of them are converted from US dollar to NZ dollar. Primers and reference cultures are not included. HotMaster Mix (100 U) x 2 - NZ$ 63.3 x 2 = NZ$ 126.6 DNA marker (500 ul) - NZ$ 73.6 PCR 200ul tubes (1000 pcs) - NZ$ 98.05 Agarose (50 g) - NZ$ 117 TAE 10x buffer (1 L) - NZ$ 22.6 ---------------------------------------------------------------- Sub total - NZ$ 437.85 Bromophenol blue (5 g) - NZ$ 35 Ethidium Bromide (5 g) - NZ$ 109.2 I personally wouldn't order Bromophenol blue and Ethidium Bromide as 5 g is still too lots to use for long time, and especially I wouldn't store Ethidium Bromide in our lab for years (as I must not be able to run out of them). More than NZ$ 400... that's a bit big money. How'd Peter feel after seeing this? Hope he won't get heart shock...

Campylobacter culturing with Medlab's advice

I followed Chris' (Microbiology Manager of Medlab) advise to incubate the Campylobacter species in CO2 incubater (10% CO2 at 42C) last Friday. However, when I observed those Campys this morning (which have elapsed more than 48 hr), those colonies were much smaller than what they showed me before. I even doubt if those spots I saw are exactly the Campy colonies or merely the fiber of swabs. My incubating environment is as follow: 10% CO2 42C Campylobacter Selective Agar (Charcoal agar) with supplement (cefoperazone, amphotericin) added I have decided to give them another two days to go, but I really wonder what makes them grow so slow. Could it because I streaked the swabs too much? (but there is no problem with Salmonella spp.) What else could go wrong???

Oh?! Yaaayyy~~~ FreeBSD 6.0 released!!

After a long time waiting, FreeBSD 6.0 is released. Unlike 5.x, this 6.0 looks like much more stable and faster, which is quite attractive. Mmm...OpenBSD 3.8 and FreeBSD 6.0...which on earth should I choose...?? (^^);;

Idiot!!

I'm sure is not Guyfolk night is not today but tomorrow, yet some idiots are letting some fireworks now (actually from a couple days ago) and it's really annoying!! Bang! Bang!! Bang!!!

Hamilton Medlab

To collect some more culture samples for my research work, I went to Medlab not too far away from transport centre (~15 min walk). There, Chris (Microbiology Manager) gave me Campylobacter and Salmonella swabs and showed me what Campylobacter's (and Salmonella's) colonies look like She also pointed out how they incubated the cultures - CO2 incubater with 10% CO2 at 42C for 48 hr. Come back to HRU, I tried to raise the temperature and CO2 density on our CO2 incubater...but Alas!! It somehow started to beep - a fairly sharp and non-stopping beep. Trying and discussing with Kerry, we eventually found its solution - tuning the "temperature calibration knob" - well, its manual calls that but I personally wouldn't call it knob; this name is really misleading. Anyway, let's see what these Campylobacters'll look like next monday.

mPCR and reagents

To do multiplex PCR, many chemicals have to be prepared. Also, I was told by Ray that it'd be better to purchase my own reagents. That is... Taq (for hot-start) Taq buffer dNTP mix primers TAE/TBE (electrophoresis buffer) 200 ul PCR tubes Bromophenol blue (dye) Ethidium Bromide/SYBR Green DNA marker reference cultures (positive/negative controls) ...Huuhh...Even though Eppendorf company would be cheaper to purchase from, that must be still a big expense...:( How'd Peter feel...

Yaaay!! OpenBSD 3.8 released!!

...actually it was yesterday that is released. Anyhow, some updated news and discussions about it - 'Nightmare' drove desperate user to open source Re: Computerworld: Setting the story straight... OpenBSD 3.8 improves hardware support ...and Theo de Raadt's criticism of Linux: Open source rival attacks 'terrible' Linux

Health&Safety Seminar from 0900 to 1200

Well, that's quite a rushing seminar about laboratory safety...

Swabs Campylobacter...

...still not growing. Give them another 2 days to grow. # Apparantly the "Campylobacter" cultures I was trying are problematic - they grow unresonably fast; they even grow in AEROBIC ENVIRONMENT!! Ah, I didn't notice today is Halloween until I saw the board on our home's door "Sorry, no more lollies :( ". Hilary had gone out for collecting lollies when I came home.

BBQ

As usual, it's always noisy when it comes to BBQ - kids (Hilary and her pals) are dancing and singing and yelling and couldn't be louder. Actually, yesterday was Andrew and Marivic's marriage anniversary and this BBQ is a sort of celebration of them... # Campylobacter swabs of yesterday are not growing yet. # Salmonella typhimurium MIC result looks quite good.

Yuuki gonna be South Island

with 2-3 of his (Japanese) friends. They're gonna travel around there for the whole next week (backpack).

Sample from MedLab

Finally culture samples from MedLab arrived today (obtained by Kerry though). That means I'll get some more formal data other than Salmonella from now on. The cultures (this time, Campylobacter spp. and Salmonella spp.) are dipped in charcoal media with swabs in plastic tubes. Somehow one of the Salmonella spp. are put together in the same bag of Campylobacter spp.. Is this right...?

CampyPouch (cont'd)

All testing Campylobacters are growing quite well when I see them today. But there's something strange - they all grow oddly fast. For in case (of not been campylobacter but actually been contaminated by other organisms), I redo different conditions with new storage Campylobacter culture storage beads and see what'll happen. # Incubation temperature: same as yesterday # Incubation condition: basically same as yesterday, except of adding "normal incubater (i.e. aerobic condition)".

CampyPak CampyPouch

Sometime some wierd stuff can be found in the lab. Guess what I've found today - CampyPouch, which has expired in the year 1995 and 1999(?! How old...) As this sort of GasPak is quite expensive, Kerry has been keeping them until now even though not handling Campylobacter. And since it's expired (and out of my curiosity), I'd try if it really works (although they're not supposed to be still valid any more). # Incubation temperature: 37C and 42C. # Incubation condition: CampyPouch, candle jar and CO2 incubater.

Which PCR?

If I am right, when we want to isolate microbials, we normally have to streak mixed (and unknown) cultures on appropriate agar plates and pick single colonies, followed by streaking the single colonies on other agar plates/slants/broths and incubate them (and check if they are exactly pure cultures). However, as we've discussed with Ray and Peter before, I'll have to identify Campylobacter jejuni, C. coli and C. fetus from unknown Campylobacter spp. sent from MedLabs by means of PCR. Actually, there have been several variations of PCR tests for Campylobacter identification, such as multiplex PCR and PCR-RFLP. Here comes a problem - which of them should I use? mPCR can amplify several different DNA targets at once without seperating into tubes, and thus save lots of time and tubes if there're more than one candidate gene target. However it's not perfect. One of its downsides is the possibility of "primer dimer". To eliminate it, some preventions such as "hot start" should be taken. In order to preceed "hot start PCR", normally "AmpliTaq Gold" would be used rather than other normal Taq. AmpliTaq Gold itself is good but is also extremely expensive, which would be a big problem. Besides, I have a bad memory with it during my Master course before (nothing to do with its quality though). On the other hand, PCR-RFLP requires restriction enzyme, which is quite prone under unsuitable preserving condition. Although it can be completed with normal Taq and only one (or two) restriction enzyme and identify different species (as long as their restriction maps have been recognized), the unstable enzyme itself is quite problematic. According to Ray, he'd use multiplex PCR. Hmm...so, then, I'll have to search suitable primers for each of the species and optimal PCR condition. By the way, when it comes to disposing EtBr, some people say "just soak in bleach then throw away" yet I've also heard others said "that would inversely make it more carcinogenic". I used to place the used agarose gels under sunlight (as EtBr is light-sensitive), but I never quite sure what the proper treatment is. And I'm quite surprised when Ray told me that they normally DISPOSE OF EtBr DOWN THE SINK!!

Eating outside again

...and again, not with the Turners but with the Aunt. Unfortunately, Jason, a Taiwanese going to sit IELTS and asking me some advises, wasn't available today and didn't come together with us.

Labour Day, the national holiday

...and of course there's nobody at campus. Should be a good day to do research work, I thought. However, I was wrong - the door toward -70C freezer and Autoclave room is locked and my security card DOESN'T WORK ON IT, thus I couldn't get my sample and also couldn't sterilize media and broth!! Hence, there's nothing much I can do today... -.-;;

Eating outside for dinner

...but not with the Turners but with Aunt of Buddhism community.

Auckland Museum and lab

Went to Auckland Museum and Manukau with the Turners today, which is followed by going to lab this afternoon for collecting data and subculturing. The MIC result was quite terrible anyway... :(

Long weekend

Next Monday is Labour Day, a public holiday, and thus also public facilities such as bus and uni. are on holiday as well, which is not good for me - I can't go to lab without bus! (all staff at uni. and lab will also be on holiday though...)

Tailing-off curve? (and PCR)

This time the contamination issue is resolved. However, the growth curve reveals in another strange way - the curves are tailing off which they're supposed to be level off? What I can figure out in my mind is two possibility - not enough dilution or too short incubation time. Kerry and Peter think it may probably because Salmonella typhimurium are switching their nutrition requirment from protein or sugar to other component, so that they're still keep growing. By the way, Peter finally gave me a green light to prosecute PCR after discussion with Ray. Hmmm...but I didn't realize that the price of primers are the same as (or at least not too far away from) in Taiwan. It's just NZ$ 20...I'd been expecting that it'd be much more expensive in NZ... Anyway, now I'll have to find appropriate primer sequences for identify the species. Today's growth curve setting: 37C, 48 cycles (24 hrs), dilute from 10^-2.

Growth curve on BMG plate reader

The result of growth curve is still terrible. However, look at the microplate carefully and I notice that inter-contamination between culture_wells and blank_wells can be seen. Apparently this is caused when the BioRad microplate reader shook the plate and the media in the wells splashed out and contaminated each other. Unfortunately this BioRad reader can't change its shaking speed, thus I need to try another microplate machine - BMG microplate reader. And also, for in case, I adjusted the total volume of each well to 125 ul, dilution facter 6 (can't dilute by 10-fold because we don't have suitable 8ch pipette in this case) and for rather in case, kept a fence_well between culture_wells and blank_wells. Microplate reader setting: 37C, rotate shaking, shaking diameter 3mm, 36 cycles (i.e. 18 hrs)

Growth curve 'n' Campylobacter

1. Growth curve Somehow the curves are still strange. How come even blank_wells also shows tailing-off growth curve?! Kerry suggested increasing my sample volume from 90ul to, say, 200 ul. => Repeat making growth curve. 2. Campylobacter On the other hand, some Campylobacters (well, actually only 1 in 15 on average) are forming quite big CFUs, which are the biggiest ones I've seen these days. Keep testing other isolates!

Faulty hardwares

Found couple of news about faulty hardwares - laptop batteries and digital cameras. 1. HP Mobile Battery Pack Replacement Program This claims that some models of battery packs would suffer short circuit and are advised to replace without paying any shipment or other fees. Basically the problematic models in this issues are those which barcode start with either "GC", "IA", "L0" or "L1". Although my laptop (Compaq Presario 2100 series) is in the list of suffered-model, I don't have to be concerned about it since my battery pack bar-code starts with "SS". However, the second news does annoying me. 2. Digital-camera makers to replace faulty image sensors What it says about the faulty digital cameras is that those problematic models would appear distorted virtically or even blank images owing to CCDs on them. The distort images look like this: (Pictures from Konica Minolta) The suffered models range from Sony, Canon, Konica Minolta, Fuji, Ricoh to Olympus, which is quite a long list. Unfortunately my one - Canon Powershot A70 - is also in the list and, what's more, I noticed that similar sympton has come out days ago. (But rather than virtical distort, mine one appears horizontally). It's good to see the companies would replace or fix them regardless of warranty status. The bad thing is - I haven't seen any announcement on Canon_NZ's website...

Nothing much today

As soon as seeing the result, I found the curves are strange. It seems even blank wells were also contaminated. Futhermore, somebody may had changed the setting of the computer connected to the BioRad microplate reader before I started my incubation yesterday, and so that the result wasn't printed out after I stopped the reading... :( Anyway, just redo what'd done yesterday again - adjust absorbance (A540 = 0.5), serial dilute, incubate and wait... till Monday and see what'll happen.

Rosamund's leaving

Rosamund is gonna leave Waikato next week, and this week could be the last chance to see her. Hence I've sent all folks of Lv7 CAEL this information and ask them to attend the farewell party held this afternoon. In the party, there are some unusual faces that I haven't seen for quite a long time. Besides Carol (the boss), Katherine, Kylie and also Meg (huh, really long time no see) came to join the party. Eventully, Tomoko, Suzana, Tina and Xaomin came to the party. Well, bettern than nothing. Today's exp.: Salmonella typhimurium serovar. DT104 dilution optimisation (building growth curve). Serial diluting the culture by a facter of 10 (90ul/well), incubate in Bio-Rad microplate reader (37C) and wait for 18 hrs.

Identify or not?

Peter thinks that Campylobacter is a kind of "difficult cultures" and wouldn't like me to spend too much effort (and budget) on isolation and identification of Campylobacter species. After all, isolation and identification of Campylobacter is not the point of my research work. (and also many medical papers just notify "Campylobacter spp" rather than specifically notify the species' name like "Campylobacter coli""Campylobacter jejuni" such and such) On the other hand, Ray - my another supervisor - thinks that to identify the species of Campylobacter is very important from medical point of view and suggested me to use PCR method rather than traditional biochemical methods to identify them (to his mind, PCR is cheaper than traditional biochemical tests). However, Peter thinks identify the species of Campylobacter with PCR would cost hundreds of thousands of dollars and take months of time to do, which is unaffordable and also unfavorable. Indeed, those molecular methods are normally expensive than traditional tests; and also Campylobacters are growing much slower than other bacteria (such Salmonella spp, E.coli etc.) and in most case they don't survive in -70C storage. Identify or not?...Mmm...it's really a dillema.

Testing vitality

As we have to clear out some more space in -70C freezer, I also start to check the vitality of Campylobacters in the freezer; if they're not growing then we may throw them away (not rubbish bin, of course). Consider the space in the candle jar, I inoculated 14 isolates (SC1 - SC14) onto 7 charcoal agar plates (i.e. 2 beads/plate). And also, some referable papers about "species-specific PCR" are founded. Looks like they are based on 16S rRNA, nested PCR, real-time RT-PCR or RFLP methods. Some Campylobacter-specific primers are also reported. This could be the way I can go.

Homestay meeting, Hamilton Lake Garden and night

After school time, we came back to the Turners and let my parents see them. Due to the time, we just had a short talk and faced toward Hamilton garden. Although I've been in NZ for over a year, I haven't walked around in the Garden yet. It is a maze-like green path and consists of Japan, Rome and whatever style parts. During the dinner (again, long dinner), I was asked by Aunt - one of Tzuchi members - to join Tzuchi's charity activity. What she hoped me to do is to translate some of their documents and formal e-communication. At this moment it's hard to say if this would influence my research, but here I just left my email to her.

Isolation method

As Medlab told Kerry that they couldn't identify what species the Campylobacters and Yersinia they're going to send are, I'll have to identify them by myself. As with this issue, I had a talk with Ray. According to Ray, commercial isolation systems (a.k.a. "kit") are not cost-friendly; traditional biochemical methods are time, effort and budget consuming. The latter is also hard to judge the results. To his mind, PCR would be the best choice (he said because he likes simple yes/no results). Hmm, PCR...that means I'll have to handle nucletide things again.

Meeting with Peter

One of the objectives my parents come to NZ is to see my superviser. Arriving at school and found the reserved car park (at first we're confused with Amy's idea...), we walked up to Peter's office. His office is obviously too small to pack all of his visitors (because both Peter and me didn't expect that Uncle Yeh and Amy would also come into the office... :( ) ...anyway, Dad seems to be very excited to see Peter. Before that we expected he'd just say hello to Peter, but in fact they talked quite a long time. Before out Peter's office, they exchenged their research papers each other (and Sun Cake from Dad...Peter, I think you've had enough sweet, haven't you?) After that, they visited HRU (Honey Research Unit) - my laboratory - for a short while then went to other place...Hey! They haven't walked around the campus?!

Parents arrival

In spite of the bad weather, some members of Tzuchi and I went to Auckland airport for picking my parents up this afternoon. Although the flight delayed a bit, they eventually arrived safely. Needless to say, we gave each other a big hug as soon as we got together. I see how excited my Dad was when he hugged me. However, we had to face Hamilton as soon as possible as Dad had to make a speech about health care. For this reason, I had been asked to bring my laptop as well, so that he could show several pictures to Tzuchi audiences after the speech. And, as having been expected, the questions were raised one after another and it looked like to be an endless activity. As the church where the speech was held could be lent out until 6 pm, Uncle Yeh had to stop the speech although others still would like to ask somthing to Dad. Tonight I didn't go back to the Turners but stay with parents in Aunt Liu's house. After shower, we had a loooooooooong dinner with some Tzuchi members (and some other audiences in the speech). This dinner lasted until 11 pm... -.-;;

Campylobacter 'n' other species

Campylobacter in 42C candle jar do grow much better than in 37C CO2 incubater. I'm not sure which facter matters the most; but anyway, things seem to be getting better. On the other hand, Kerry said Medlab told her that they couldn't identify what species the Campylobacter and Yersinia they're going to send me. That is, I'll have to identify what species they are. Mm...any good methods to identify Campylobacter jejuni, C. coli, C. fetus and Yersinia enterocolitica? Biochemical methods may be a way to go, as long as everything can go smooth if following Bergey's Manual of Determinative Bacteriology (the differentiation criteria look quite complicating though)

This appointment and that appointment

Checked with Peter and rang to Amy, the person made appointment with Peter, now the fact was made clear - the 10 am appointment was exactly made for my Dad ...by Amy. She is a member of Tzuchi and had been asked by Uncle Yeh to get contact with Peter... Knowing what on earch happens, the appointment was set to 9:30 am and the 10 am one was cancelled. Phew~~~~

Car park reservation and ...?!?!

Peter told me that he'll have an appointment at 10 am on next Monday, and asked me to ask my parents at what time they'd visit him. At Peter'd reserve a car parking place for us previously, I told him 9:30 am as my Dad would just say hello to him and wouldn't stay too long. However, I heard something embarrasing from Dad on telephone at night - Uncle Yeh had asked some members in Tzuchi to get contact with Peter for Dad and, what's more, the appointment was said to be 10 am ...!? I'm not quite sure, but I have a feeling...could the appointment Peter will have at 10 am on Monday be ...???

Candle jar

Some essential conditions for Campylobacter to grow: 1. CO2 5-10% 2. O2 5-10% 3. 42C 4. Humidity 5. Relatively long time -.-;; As Kerry is also using the CO2 incubater as well (for Haemophilus influenza), I can't use 42C in CO2 incubater. Hence I have to consider candle jar. Find a suitable plastic container (actually it was Virkon's container...), put agar plates and lit a short candle (make its height as low as possible so that it won't melt the plastic lid down) then put in normal (but 42C) incubater. That's it!

Another fraud mail (from eBay)

Following the yeasterday's fanky mail, here it comes another spoof mail. ########## Begin of suspicious mail ########### Update Your Account Information Within 24 Hours Valued eBay Member, According to our site policy you will have to confirm that you are the real owner of the eBay account by completing the following form or else your account will be suspended within 24 hours for investigations. Never share your eBay password to anyone! Establish your proof of identity with ID Verify (free of charge) - an easy way to help others trust you as their trading partner. The process takes about 5 minutes to complete and involves updating your eBay information. When you're successfully verified, you will receive an ID Verify icon in your feedback profile. Currently, the service is only available to residents of the United States and U.S. territories (Puerto Rico, US Virgin Islands and Guam.) ########## End of suspicious mail ################ Again, this fraud mail is still not smart enough to fool me.

Fraud mail

Today I got 2 unusual emails, which are both from Paypal(?!). The content is as following: ######### Biginning of the suspicious mail 1 ############# Dear valued PayPal® member: Due to concerns, for the safety and integrity of the paypal account we have issued this warning message. It has come to our attention that your PayPal® account information needs to be updated as part of our continuing commitment to protect your account and to reduce the instance of fraud on our website. If you could please take 5-10 minutes out of your online experience and update your personal records you will not run into any future problems with the online service. However, failure to update your records will result in account suspension. Please update your records on or before October 05, 2005. Once you have updated your account records your paypal account service will not be interrupted and will continue as normal. To update your PayPal® records click on the following link: http://www.paypal.com/cgi-bin/webscr?cmd=_login-run Thank You. PayPal® UPDATE TEAM Accounts Management As outlined in our User Agreement, PayPal® will periodically send you information about site changes and enhancements. Visit our Privacy Policy and User Agreement if you have any questions. http://www.paypal.com/cgi-bin/webscr?cmd=p/gen/ua/policy_privacy-outside The HTML graphics in this message have been displayed. [Edit Preferences - What's This?] ######### End of suspicious mail 1 ############# ######### Begin of suspicious mail 2 ############ PayPal Security Measures! We are contacting you to remind you that: on 24 August 2005 our Account Review Team identified some unusual activity in your account, one or more attempts to log in to your PayPal account from a foreign IP address. IP Address Time Country 80.53.1.130 August 24, 2005 15:05:08 PDT Poland 80.53.255.174 August 24, 2005 15:07:58 PDT Poland 141.85.99.169 August 24, 2005 15:13:09 PDT Romania 141.85.99.169 August 24, 2005 21:28:08 PDT Romania 195.61.146.130 August 24, 2005 21:33:43 PDT Romania In accordance with PayPal's User Agreement and to ensure that your account has not been compromised, access to your account was limited. Your account access will remain limited until this issue has been resolved. To secure your account and quickly restore full access, we may require some additional information from you. To securely confirm your PayPal information please go directly to https://www.paypal.com/ log in to your PayPal account and perform the steps necessary to restore your account access as soon as possible or click bellow: To continue your verification procedure click here Thank you for using PayPal! The PayPal Team Please do not reply to this e-mail. Mail sent to this address cannot be answered. For assistance, log in to your PayPal account and choose the "Help" link in the footer of any page. To receive email notifications in plain text instead of HTML, update your preferences here. ######## End of suspicious email 2 ############ Briefly, both of them are claiming that there're some security problems with my paypal account, and ask me to check id or login through the link given in the mail blah blah blah ... Bah! Stupid and ridiculous fraud mail! Too many his sort of silly phishing mail mucking around these days (and also strangely enough, much more people DO believe in or are trapped by these stupid jokes...) Unfortunately, these silly mails don't work on me~~~~ You stupid fraud~~~~ ♪~♫♫~~♪~

What a coincidence!!

IMHO I should have informed everyone I've changed my email account, and I've expected that all the mail would be sent to my new one - now it looks like not quite true. At least, Peter, my professor, sent email to my ex-mailbox several days ago which I didn't check it until now. Anyway, I borrowed several books from campus library this week (Tuesday or Wednesday, I think) as a reference of my gastro-intestinal pathogens list. So what does this do with the email mentioned above? I checked my ex-mailbox just now (which is a once-a-week job) and realized that Peter had sent me an email, which informs me that "there is a new book 'Medical Microbiology' in the library that may be interest of you". In fact, this is exactly one of the books I borrowed JUST BEFORE Peter mailed me this book information, whereas I didn't know he'd sent the information about it until now!! That's definitely a coincidence eh!!

2 of 4 innoculums are growing

Campylobacter is exactly a sort of "difficult cultures". Not all of them are growing even innoculate on freshly-made and supplement-added agar plate. Seem I have to optimise their incubating condition such as temperature (37˚C -> 42˚C) and atmosphere (CO2 7.5% -> 10% or even 20%). You fastidious bugs...!!

Grow grow grow grow grow....

...not growing. It's very "clean" on the CSA (Campylobacter Selection Agar) plates. Not even a tiny colony. :( 2 days after incubation...

Growing...or not?

Those charcoal agar plates seem to be growing when I looked at them this morning, but somehow not all of them are growing. I cultured 4 strains of Campylobacter on both agar plates with/without supplement, and the result shows that the one with supplement seems to be more or less easier to survive. As the agar plates with supplement were made 1 year ago (which is quite old), I made another batch of charcoal agar plates with supplement, then subcultured those surviving colonies and also culture another 4 new Campylobacter beads on the new plates. Hopefully they'll grow better than last week...or will they?

My Campylobacter are not growing

...of course. They don't grow that fast....

Is this a joke ?!

Caught on camera but they got away - "A murderer and serial burglar escaped from Arohata Prison in Wellington despite being caught in the act by surveillance cameras – because guards did not know how to view the video". (on Waikato Times)

Campylobacter (and some others)

It seems like not many researches are done about Campylobacter due to its difficulty of culturization. Even if they do, there isn't too much information about the sensitivity of Campylobacter on honey. Since this is a multi-resistant bacteria, I think it is worth to try to examine its MIC thoroughly. Professor as well says that Campylobacter is in fact one of the most important entero-pathogens in NZ. Hence this may be my first material in near future. As a pre-test, I'm going to pick this difficult-culture up tomorrow. It'll be inoculated on CSM (Campylobacter Selective Media) which is in fact a kind of charcoal agar, and it is literally black (due to the charcoal). It looks yuck! Its stock cultures, unlike other normal bactria, should be stored in -70 ºC freezer. Its incubation also has to be carried out not in the normal incubator but in the CO2 one (also the gas condition may need some more modifications). It's somewhat troublesome. On the other hand, I found there are some "minor" bacteria classified into Enterobacteriacea family yet not be reported too often. For example, an opportunistic organism Kluyvera genus (Kluyvera ascorbata sp. and Kluyvera cryocrescens sp.) produce β-lactamase which also means they would resist to β-lactam antibiotics such as penicillins and cephalothins. Would it be worth to examine these kinds of minor bacteria as well? Maybe some more literature reviews are required.

Opera 8.50 released

According to Opera's press releases "Feel Free: Opera Eliminates Ad Banner and Licensing Fee", the add banner and license fee have been removed in this new version. Also some vulnerabilities have been fixed as well. I wonder why the company can achieve that. Could it be because they've got big profit on mobile browser's market?

Blizzard

A snow storm has hit South Island in NZ. Icy blanket swathes Canterbury (on NZ Herald) City of Gales rugs up (on NZ Herald) Snow moves north and shuts roads (on NZ Herald) Chill hits central NI (on Waikato Times) Waikato feels nature's lash (on Waikato Times) According to news, this week is fairly freezing. No wonder it was unexpectedly chilly yesterday although the blizzard is actually in South Island. (and the heavy shower makes the weather much more icy...!!)

H. influenza

Unlike what we've felt about influenza (say, hard to cure), this bacteria seems to be quite vulnerable - no bacteria was growing even if no honey was added into the agar ...

Another bacteria

Besides Clostridium difficile, we handled another microorganism today. Its name is ..... Haemophilus influenza. Did I say any respiratory diseases? :P

Election results

Labour 50 seats, National 49 seats. It's amazingly 50-50. That's definitely a neck and neck competition; and good on them, there's no protest or lawsuit after that. (Those from TW must know what I mean eh?)

NZ election

Today is NZ's voting day. Marivic and Andrew went to vote at a school near our house this morning. It looks like Marivic Charito and Alan support Labour party, and Andrew follows them (though actually he doesn't like both Labor and National party). Me? I say, "who cares!" :P

Ohoooo~~~ finally...

Finally my passport comes back today, and that also means my student permit is renewed as well. (more than 1 month...where have you been??) However, there is no label placed in my passport...? Somehow, NZIS leaves a note with the passport and it says: "Please note that NO student permit label has been placed in your passport. Your permit is recorded electronically and will have exactly the same conditions as your student visa label." ...I really can't understand NZIS eh... (-.-);;

Racism in NZ

Asians in NZ subjected to racism, study finds (on NZ Herald) Agree. Although many NZers I've met are normally friendly, but some others exactly have given me that sort of feeling...

Big mistake

Today Kerry and me both made a stupid mistake, and that made all of what we'd done today should be re-done tomorrow. When I was serial-diluting honey and Kerry was preparing bacteria, she shouted suddenly. We BOTH forgot to dilute the honey previously, hence its concentration was too high and it's impossible to get any result the next day if we kept doing today. Strictly speaking this should be my fault as I'm serial-diluting the honey and should have noticed something wrong before this had happened...Sorry Kerry... T_T

Rediculously large file

Last night I noticed that the loading time of Opera was oddly long. It kept accessing harddisk for a while, which is unusual. So I checked my harddisk and guess what... This is just weird !! Almost no more space in my harddisk ?! Searching any possible large files in the drive, I found the reason. It's in the folder of Folding@Home: Cracking me!! A text log over 20GB?! The Fahlog-Prev.txt had eaten up all space in my harddisk. Hmm...I wonder why. Normally a text file couldn't grow up to such a huge size. Furthermore, like UD, I've been using Folding@Home for awhile and this never happened before. Surfing on the forum, found that this rarely occured before (and not knowing why. could be some sort of bug). Luckly this huge thing can be deleted without causing any problems. What's in this text file? Who knows. It's nearly impossible to open it with GUI editor coz' of the size. I should be able to open it with command line such as type Fahlog-prev.txt | more or more < Fahlog-prev.txt ...it's been too late when these method came up to my mind as I'd already deleted it. Never mind. I'll try it next time I come accross with it again.

This really drives me nuts

Having acquired the so-called "offer of place from Uni" and faxed it to the Immigration and confirm with them if they'd received it, now they said IT'S NOT WHAT THEY WANTED !! Rather than that, they said they wanted "evidence of tuition payment" ?! The thing is getting crazy now! So now I get to apply another document at finance and FAX again ! I'm pretty sure I've also submitted the payment evidence along with my passport!! I really would blame at the Immigration - why didn't you SAY THAT CLEARLY in the email, you stupid NZIS !!!! ...and WHAT HAVE YOU DONE with my passport in this 1 month !!!!

So, what's this time?!

There was a phone call for me when I was still at school. Although the voice from the answering machine was so POOR that we hardly could tell who that call was made from. At last we got the idea - the IMMIGRATION, and they're asking me to call them back. Why the Immigration?? I had a bad feeling. I've handed my passport to the Immigration for about 1 month, and there's still no response from them. Does the phone call mean there're some problem with my application? How could it be!! It seems the Immigration also sent an email to me and ...ask me to submit "offer of place" something from Waikato University?! All documents are supposed to have been submitted, I think? ...Anyway, I'll apply another one copy at Uni and FAX them. PS: Somehow the email from the Immigration had been dumped into rubbish bin when I found it. Hehehe, apparantly my email box as well dislikes them... XD

Blood agar n pipette

As the cultures (Cl. difficile) show some strange result, we redo what we did yesterday. We also make some more sheep blood agar. Basically just adding a certain amount of sheep blood into autoclaved agar and pour into petri-dishes. What really surprised me is that all pipetmans were never released after used. After the work I tried to release them and found some of which seem to had been under the condition of reform fatigue for a long time. I might be wrong but as far as I know, all pipetemans must be released after using. I personally reckon any equipments require maintainance; no matter it's gadget, computer, or even laboratory things. After all, in this case, a pipetman to a reseacher is like a firearm to a soldier. I'm also wondering if the O-rings, seals and pistons have rusted or been damaged...

Autoclave

The autoclave here is automated. There is not handle or bar on it; instead, we press the buttons on LCD monitor. It's touchscreen. We can attach trolly (?) onto the autoclave so that materials can be sent into or pull out from the clave (imagine train on rail). The only thing I feel odd is the FLOPPY DRIVE attached on it. Even Kerry can't figure out why it is burried into the autoclave. It really doesn't make sense. ================================================ Today's culture: Clostridium difficile Today's agar: Sheep Blood Agar

Everything different

I have to say almost everything here is different from my ex-lab. I mean the facilities. 1. Lab There're 2 labs in Honey Research Unit (shortly "HRU"). Biological lab and chemical lab is separated. In biological lab there's another small room for manipulating non-NZ honey so that NZ and non-NZ honey wouldn't contaminate each other. 2. Cabinet Unlike my "laminar-flow-desk" in my ex-lab, this is the real biosafety cabinet. Clean air blows up from its surface so that no bacterial would flow out of the cabinet. As safety functions, its pane would fix on certain location that it prevents bacteria from leakage yet wouldn't be too difficult for operators to manipulate their microorganisms. As there is air flow, we can't use bunsen burner to sterilize our inoculating loop and needles. Instead, we use disposible ones. They are made of coloured plastic (blue for loop and orange for needle) and look like lollies more than experimental instruments! How cute!! 3. Storage Chemicals, agars, NZ honey and non-NZ honey are all stored in separated place. 4. Safety The biggest difference between my ex-lab and HRU. As we have seen in Cabinet and Storage, they have placed much attention on their safety. Lab coat, glove, gas handles, extinguishers and water hose, eye wash and body shower, etc etc etc. I used to sit at an old laminar-flow-desk located beside a noisy dry oven and containers of HPLC (or whatsoever) solvent waste in a small over-crowded room... 5. Documents Kerry has collected lots of useful documents and those were sorted in several folders, namely MSDS (Mechanicals Safety Data Sheet). I knew before that there're compatability issue between chemicals and gloves, but now I can find all these information in MSDS anytime. 6. Many other things There must be some more undiscovered things here. Now I wonder if my ex-lab can really be called a lab. ============================================== Anyway, I'll be practicing (and revising) some techniques in the following weeks. Today's task is serial dilution of manuka honey and bacteria culture. Here we use E. coli and S. aureus (not MRSA, by the way) as our "sacrice" and culture them on chocolate agar (they've got a sweet tooth eh?). The UMF of the manuka honey we use is 10+. The whole processes, including serial dilution, culturing and streaking, were not that difficult; except... (1) Picking (or alternatively, "fishing") the culture beads from small vials (2) Weighting the manuka honey - I never know that the "real" honey is so sticky that it's just like peanut jam!!

Portfolios ≠ real looks

Today I finally met Dr. Cursons - another supervisor of mine. I'd read his introductions and seen his portfolio before, but frankly speaking, I was amazed when I just met him. The feeling of his appearance looks so different from that of in the portfolio and I wonder if they were not the same person...

Something unusual after dinner

We met a guy who was quite mad this evening. It was when we finished our dinner and was going to walk our from Burger King. A guy opened the door with his two arms. Actually, somehow this guy also said hello to Andrew when we're enjoying our meal. I asked Andrew if they knew each other. Andrew said no (?!) I just say thank you to the young guy when he opened the door, but it seems he didn't hear that. Rather, he started banging the door violently. Now we realized what the matter was, and kept walking and tried not to bother what happened behind us It's drug...

The lab

Getting familiar with the new environment is, needless to say, my first task before I start everything. Yetsterday, I was handed two booklets about safety from Lisa - a staff in the department office - and was told to sign by next week to show that I've exactly read them. According to the booklets, I noticed that many rules - actually almost all - are rather different and also strict than what I've ever learned. After asking Kerry some questions on the booklets, she oriented me some facilities in our lab briefly. To ensure that I could familiar with the environment, she assigned a small game and let me identify some facilities by myself (namely "treasure hunting game"). Including the mini-game and some documents reading, I would have to return back them within 2 weeks. That shouldn't be any problem. To sum up what I've learnt from and told by prof. and Kerry so far: 1. Security is extremely essential. Unauthorized persons and visitors are not allowed to come into the department building. Watchout strangers. There used to be thieves and have stolen a couple of equipments from the building. 2. Lab should be locked as long as there's no authorized person in the lab. Similar to the point 1. There're 3 rooms in our lab, and even students are in one of the rooms, the other 2 rooms still should be locked. 3. Chemicals will be purchased by technician. This is different from my MSc era. We had to order from chemical company by ourselves. 4. Materials such as bacteria and honey will be sent to the lab, hence we don't have to carry them from hospitals or suppliers. Also these will be contacted to suppliers by technician. We had to do all of these by ourselves in TW before... 5. There's no so-called group meeting every week. Can't agree more. According to professor, as everyone is working on different topic, it is no sence to spend extra time to show each other's result and discuss on them. Since discussion can be done anytime anywhere privately, and also it's hard to find time for everyone to get together, why waste extra time on preparing slides or powerpoint and meeting? Frequent meeting is totally waste of time and efficiency. 6. Attending seminars or presentations is not necessary. Basically similar to point 5, but also traffic is a reason. Moving from one city to another would spend lots of time and money, yet the school wouldn't support the expense. Besides, car is not a good choice since petrolium is getting rediculously expensive. 7. Submitting our works to academic journals is encouraged but not compulsory. That is, it is not necessary to submit to journals in order to graduate (although the submitting itself is a chance of reviewing our works, which is not a bad idea). 8. It's possible that we would see each other only for once a long time. As everyone has got their things to do, some of them wouldn't come to the lab every day (many of them are part-time students). 9. As there has been too many visitors and tasks, prof. Molan would stay at home so that he may keep away from those visitors and concentrate on his tasks. However, don't feel hesitate to call him if I get problem with my research; that is, my research is prior to anything else. Too many visitors and phone calls...poor professor...

Orientation

Finally my course at the University of Waikato starts today. Where should I go and what should I do first? Nobody knows. -.-;; Unlike those Bachelor or Master course, there's no orientation for PhD course. I even didn't know where my lab was. I walked in the department building and looked around for awhile. Those staff in this building might have noticed there's a stranger mucking around, eh? Afterall, there're some noticeboard says - "AUTHORIZED STAFF ONLY". Apparently unauthorized person, or visitors, are not allowed in this building. It's quite understandable since there're microbiology lab, isotope lab and that sort of things that security concern is extremely essential. Not knowing what to do, I went to the office of the department and asked for help. Fortunately, this was the way to go. There I filled some documents, got a key for my lab, led to the lap, met a technician (Kerry) and then received a security card. Came back to the lab, I was privided a desk. Frankly speaking, I was so impressed when I got my own desk - finally I have my own desk in the lab!! PS: I didn't have my own one during my Master course in TW. Instead, an old laminar flow cabinet was my "desk". I could turn on the fan when it getting hot, turn on the light when dark, and turn on the UV light if I get injured and need to sterilize the cut...(hey, of course the last one is a joke!!) I had a short introduction and chatting with Kerry and Haylie - a MSc student - and a Japanese girl Yuko who is merely staying in this lab temporary. But where's prof. Molan anyway? He's really a busy gentleman. He was having a meeting in the Waikato Hospital and didn't showup until afternoon. Prof just came back to our lab when I and Yuko came back from tea time. After that, we had a not-too-short talk in the lab. What really surprised (or I would say, amazed) me was that prof. Molan just pulled a chair and sit beside me rather than told me to move to his office!! This is absolutely unimaginable in my MSc (Master of Science) lab in TW!! Oh, professor, I really admire you and love you~~~!!

Empty tutorial

Wednesday again. Last wednesday there was only one audience attended the Wednesday Tutorial. Yes, that's me. How's this week then? The same. Well, not exactly - even the tutor didn't show up this week. Could it be due to the 2 weeks vacation in the campus? Not knowing what to do, I went to the couputer lab, take a look on their facilities (for the near future and partly for killing time) then came home early. By the way, I met Rosamund, Tomoko and new group of Japanese students. They're excactly new students, yet are also quite old - most of them are 75 or 80 years old. Good on them.

IELTS review ?!

I never imagined that I'd have to review IELTS things several months after the test. A relative of my relatives is introduced to me for asking about the IELTS things this afternoon. He said he'd taken some language course in TW and in NZ for a while yet none of them are specialize on IELTS preparation, thus was considering to transfer to the Waikato University Language Institute recently. Unfortunately, I've sorted out almost all documents about IELTS recently - just one or two weeks before he contacted me. Now what I can do for him is just provide some advice through email or online chatting or so. He really should have contacted me a bit earlier...

The yesterday's "photographer" is...

...Ketherine. I told Christina - the only coordinator of orientation - what had happened yesterday, and she explained that they're surveying each homestay if their students were living in good condition. As there're hundreds of students at the Language Institute and certainly she couldn't do that just by herself, she'd asked someone else to help her doing this job. Besides Kethirine, also Carol and Rosamund are helping doing the servey. Hmmm...it's good of them to make records of their students. Yet I still hope they can inform their students previously; it is their private after all. ...Eh? Their could be a chance that they have informed the Turners, but the Turners had forgotten to told me...

Co-ordinator with black hair??

The Turners told me that there was a teacher or the Language Institute came to visit them this afternoon and took my room's picture. As they'd forgotten her name, I could just guess from their description of her looks. 1. She once taught me before. => I've been taught by many teachers. 2. Young kiwi female with black hair. => Could be Kethrine, Jenifer, or Kylie. 3. She said she's a co-ordinator => ???? None of them match this one... Now I doubt who on earth that was. Actually, I'm a bit upset because nobody told me previously that someone would come and take photos of my room. :(

I'm the only one...

There is a tutorial for international students in my department...well, there should have been. In fact, I was the only one audience today. What a shame. Alison and Nikki were somewhat embarrased as there was no audience today (except me). However, I'm glad that I went to the tutorial hall as Nikki, the tutor of today, used to be Prof. Molan's student. Hence, rather than the tutorial, I got some information about the lab, Prof Molan (chief supervisor) and Prof Cursons (another supervisor). Althogh not much, at least it's a good start of my PhD study.

Tangi

It's unusual that Andrew was still home when I left this morning. Instead, he dressed in black. Actually there was a funeral for his Maori coworker today. The black suite shows respect in this situation. Nobody knows why his coworker passed away at Sunday (or Monday?) night. All he's known is that the Maori's eyes was moving strangely. Since it's Tangi ("funeral" in Maori language), they might sing Po Atarau as well... Po atarau ♪~♪~♫~~ (3-1-23--) E moea iho nei ♫~♫~♫~~ (33-24-7.1--) E haere ana ♪~♪~♫~♪~ (1-2-2#3-1-) Koe ki pamamao ♪~♫~♫~♪~ (2-17.-12-2#-) Haere ra ♪~♪~♫~~ (3-1-23-) Ka hoki mai ano ♫~♫~♫~~ (33-24-7.1--) Ki i nga tau ♪~♪~♫~ (1-2-2#3-) E tangi atu nei ♫~♫~♪~♪~ (14-36.-7.-1-)

Cold

I've never been home so early like today since I came to NZ. Actually I came home reall early today - 12:00. Of course I have to - I'm sick. I was well this morning - until arrive at school . There're many "patients" in the library at school, and I reckon I've been infected by them. AAAaaa~~~~CCCHHHOOOoooooo~~~~~~

Another tutorial mail

Following last Wednesday's tutorial informing mail, today I got another one. Basically it says there're only 3 students attended last week's tutorial, and is encouraging more other students to join the every Wednesday's tutorial. Mmm...Hmm...it's quite understandable that there're only 3 since, in my case, the inform letter wasn't received until that night. Anyway I'll see what's on the tutorial this week.

Professor on news

~~~ On BBC News ~~~ Harnessing honey's healing power ========================================= ~~~ On The NZ Herald ~~~ NZ's healing honey under microscope Taste of honey no ulcer cure Manuka honey doesn't cure pepctic ulcer...at this moment. This news might somewhat disappoint some medical persons. Philippa Stevenson: Time for honey's day in the sun Philippa Stevenson: The secret of Christmas pies revealed This one does nothing with manuka honey but with professor's Christmas mince pies. Anyone wanna make it as well?

Several manuka news

~~~ On BBC News ~~~ Honey 'weapon against superbugs' Honey scare sparks shortage Honey from China is banned because it includes antibiotics...I personally am not surprised by the fact. ======================================== ~~~ On The NZ Herald ~~~ British hospitals want honey dressings Mauka honey used in hospitals. It looks like the law in Britain finally admits the use of honey in medical ways (I might be wrong). Honey team claims medical first Medical grade manuka honey values 10 times as much as traditional uses do. How's the price range, Sir? Honey NZ signs lucrative export deal The HNZ (see the previous news) also exports their honey not only to the US but to Japan. Price sting in honey shortage Suffer from bad climate and varroa mites, the production of honey in NZ dropped dramatically - by approximate half in 2002. Manuka deal looks promising Looks like the yield in 2003 was recovering. But who knows - it was just the beginning of the year. It was a good start though. NZ's healing honey under microscope Another news about the Professor :) Beehives destroyed near Nelson It's somewhat surprising that there is vandalism in NZ as well. ...and some problems around manuka honey such as fraud, fake, labelling, advertising, law and government (yes, stupid government again) : Manuka honey buyers 'often ripped off' Your manuka honey may not be pure Honey producer pooh-poohs rivals Mr. Bray (in the previous news) again. Honey puffs stung by advertising rules Healing honey runs foul of act over label Honey firm stung over false labels NZ$ 35,000 for fake labelling is somewhat a big money. Hope the fine for fake (or fraud) in my country can also be as hish as this level (otherwise the fine in TW never works).

Rosetta finishing

According to yesterday's forum on Grid.org, the Rosetta jobs (Human Proteome Folding Project) having been running on worldwide computer (including mine ^o^y ) have been finishing much more quickly than we had expected. That means following Smallpox Research Grid Project and Anthrax Research Project, another grid task is finally going to be completed. That's really good. Now then I will let my laptop concentrates on United Devices Cancer Research Project.

Somewhat odd tutorial mail

There's a mail sent from my department just now. Yes, just now. It says "there'll be a tutorial at the of science and engineering for international students, at 1:00 pm on this Wednesday." ...I wonder why they sent this information now since it's been night

Professor away oversea

Just received a mail from professor. It says he'll be in Australia and Hong Kong for the next one week. That could be for some conferences there. Don't work too hard, professor.

Culture shock - ear wax

Somehow Andrew's listening ability is worse than mine today. It seems like because there'is wax stuck in his ear. To my mind, we all have to tidy our ears up with cotton tips regularly (say weekly or, if longer, monthly). I wonder when was the last time he cleaned his ears. "About 10 years ago." Andrew said. Cracking me! How could he stand so long?! According to him, the Turners don't use qtips to pick their wax out; instead, they'd see doctors and suck or flush (?!) the wax out. Actually, he'd made appointment with doctor and would tidy his ears up on Wednesday. But why not qtips? He said because he considered qtips were not good for ears (such as... it would push the wax into the ear rather than pick it out). Well...I can't take it.

Anatomy of laptop

The cleaning work was once interrupted by the battery issue (I hadn't even started yet though :P) Yesterday I bought another set of batteries,and this time the batteries can be packed into the cleaner.

This time they can be packed into it.

Pray to Jusus and Budha make myself calm down, a big work is going to start~~~!! 1.Battery, HD and cables Before every thing goes start, check the laptop's battery, HD and cables (power cable, head phone, mouse, etc) has been removed. Also make sure to touch some metal things (such as door knob) frequently during the whole process lest static charge should ruin the laptop.

	Seagate 30G harddisk...
	...and its other side.

2. Top cover First of all, I have to remove 2 screws on the rear side of the top cover (otherwise I can't remove the cover). Then start to pry the top cover from right, middle, to left with flat-blade driver carefully.

	Pry from the right...
	...to the middle...
	...then to the left.
	Pry up!
	This side as well.
	Top cover front side.
	Top cover back side.

3. Speakers

Under the top cover

There are two small black speakers on both side. Here we can see the speakers are covered with dust.

Dirty speaker...

It looks much different after cleaning with vacuum cleaner.

Much better after cleaning. :)

4. Keyboard Removing the 4 screws beyond keyboard, I can flip the keyboard toward me and then find its cable. Unlike normal keyboard and cable, this one is so thin that any strain would damage it. (I personally would call it plastic sheet rather than cable). The cable is fixtated with a knotch underneath the main cover. Carefully lift up the knotch, the cable will (literally) “pop out”.

	Flip the keyboard.
	What a thin cable...
	Keyboard removed.

5.Speakers and Switch board Unfortunately the speakers on my laptop can't be removed as their cables seems to have been stuck onto the hooks by glue (or that sort of things). Deliberately pull them out will split them into segments and the speakers will never work again. Although leaving them will make my work a bit harder, here I just keep them intact.

These cables (and thus speakers) can't be removed.

Unplug 2 cables on switch board carefully (again, they're really thin and delicate), the switch board can be lifted and its cable can be found underneath. Unplug it and the switch board can be removed.

	Switch board front side.
	Switch board back side.

6.Monitor The monitor is fixed on right and left stand, each of which have 3 screws. Note that there is a land wire on one of the left screws.

	LCD screws (left).
	LCD screw (right).

Here the monitor cable is a big problem as the cable is thicker than the ditch which the cable is in, and also the cable slot is too close to remove the cable from it. Of course it can't be pulled out forcefully, hence this is a bit tricky and need some technique to make it “slide” out of there.

	Taking out this wire can be a bit tricky.
	LCD cable.
	LCD cable.

7.DVD-ROM drive Actually at the point I remove the keyboard, I'd been able to take DVD drive out. There are 2 screws in the hole denoted with the red circle. Unscrew them, stretch finger into the hole and push toward the right, the DVD drive will pop out from the bay. Watch out that the edge of the hole is somewhat sharp and don't get injured.

	Can you see where the DVD is?
	Put finger into the hole and push DVD drive out.
	DVD drive for laptop. Much different from those for desktops.

8. Main cover By main cover I mean the part on which I put my hand and arm. Touch pad is also on it. Here I have to remove nearly 20 screws from the main cover and also the bottom of the laptop.

So many screws...

Since I've removed those screws, I can now remove the main cover, right? But wait then. Lift the cover slowly, we can notice that there's a cable connecting to underneath.

	The white cable is connected to the touchpad and the power signal lights.
	Touchpad cable.
	Another viewpoint.

This is similar with keyboard's cable, except that this one is much narrower than the previous one. Again, lift the knotch, release the cable and finally the main cover is removed and we can see the mainboard, heatsink module, heaps of chips and others.

	Another thin plastic layer.
	Finally reach the motherboard.
	The other side of the main cover.
	VGA chip "ATi IGP320M"

Now we can see how dirty in this laptop is. (compare with cpu fan, these can still be called “clean” though...)

	The bottom of the speaker.
	Floppy drive bay (there's no floppy drive on this laptop, by the way).
	HD drive bay.
	Battery bay. It's amazing that never short even like this...
	Thermal pad.

9.Heatsink module The heatsink module (including cpu fan) is fixated with 3 tiny screws. Unplug the fan cable before removing the module.

	CPU fan. Made in Taiwan.
	Fan module (front).
	Fan module (rear).

Also the cpu fan is fixated with another 4 tiny screws. Unscrew them and see how it is inside...

	Erh! What a filthy...!
	Oh! Yuck!!
	...No wonder there's no airflow.

Errr~~~ it's yuck isn't it! What I can say other than dirty is still dirty. And this is where those cleaning kit is really needed.

	Dirt on the qtip...
	...and dirt in the dust bag of vacuum cleaner.
	After cleaning.
	After cleaning.

The cpu is AMD Atholon XP-M, and like other Thoroughbred-B core, there's no heat-spreader on it. Clean the surface of the cpu and heatsink carefully with lint-free paper (with isopropanol on it) and spread a thin layer of thermal compound on it with a plastic card.

Athlon XP-M with thin and smooth layer thermal compound.

10. Reassemble Lastly, reassemble all parts and reboot it to check if anything goes wrong. Fortunately nothing wrong and the temperature also decreases significantly even if cpu is full loaded. The airflow is also much stronger than before. That's all of it (well, not exactly). It's somewhat a big work, but I suppose it worths the effort. “Sam~~~! Dinner.” Marivic is calling me. Meal after an exhausting big work ...it must be particularly yummy~~~