Today's event

1. Help uncle Larry rip off the masking tape on the roof of the newly built Tzuchi office Hamilton branch.
2. Attend an "unofficial" graduation celebration for uncle Larry, Peter Hsieh, uncle Chen and Ryan.
3. Fix Gavin's computer - install Gavin's new network card ("crab card" from DSE) and solve the internet problem...temporarily.Still better to reinstall the whole system ASAP, otherwise that computer is damn crawling...

Test test 123...

TEST
Test
test
てすと
テスト
測試

Today's event

1. Record the result of PAE test of manuka honey (M115) on S.aureus (with and without catalysed) , E.faecalis and E.faecium

2. Have my hair cut

3. Have dinner with aunt Sanger, uncle Larry, Vincent, Jessica, Margarett and Ryan for celebrating Magarett's birthday.

Peter away

I'm told by Peter that he'll be away for holiday next week (precisely, the whole week) and will be back after 3 Jan.

Xmas is really coming there.

Today's event

Filming movie - of course, the filming company only interview Peter and Kerry, but this really has hampered my PAE work today, so I've got to postpone the work till tomorrow.

Weird blog - cont'd

I've just added up a few topics in my diary, and suddenly noticed that the layout of "Tzuchi anniversity" on 22/Oct now shows correct. -.-;

...but still, some recent posts have got weird layout...what the hell is this... :(

Ehh?! Weird blog

I haven't logged into blogger.com and was thinking of updating my diary now. Unexpectedly a notice board which says the blogger system has been upgrading to a new version and I was suggested to transfer my blog to the new beta version. It also says that the blog transferring will be executed automatically and the layout and format of my blog won't be changed. So I let blogger.com upgraded my blog.

The result, however, has proved to be a disaster. As one may find in this post and the one on 22/Oct, the paragraph layout looks odd - lines don't break where they're supposed to; some lines even exceed the width of the template whereas there's no option that I can do to this problem!! I've tried to change my template but still no joy. This never happen before... Even preview  doesn't reflect the layout it will reveals after uploading... I really shouldn't have done this troublesome upgrading... :(   Arghhhh...my blog now looks so ugly ...  :~~

Apparently other bloggers have also got heaps of problem as well. Unless blogger.com gets this problem sort out shortly, I suppose I'll switch to another blog site! :(

beta.Blogger.com, are you listening?

Campy work submitted

 Submit Campy work to Journal of Antimicrobial Chemotherapy (JAC) online today.

Fix computer

Another computer repairation today.

Aunti Sanger came to my place while I was away this afternoon. When I was back I was told by Vicky that aunti Sanger was looking for me, hence I rang her and knew that another Tzuchi member's (named "Star") computer has got weird internet, which hasn't been able to get online for ages and would like me to have a look on it.

After having dinner with Stars', we had a look on the problematic computer. It was quite slow - a common problem which can be seen on most computers. The main issue - the internet - was eventually found to be caused by the security suite (TrandMicro's product) installed in Star's computer. After uninstalling it, the internet came to alive. However it's surprising that he hasn't got any protection against spywares, virus and other attack (i.e. he's got the security suite but he's NEVER update them).

As it'd been a bit late, I just made a rough tuning up for Star so that the computer may run more smooth than before and came back with aunti Sanger and uncle Larry. Probably I'll have to go over there again in near future.

Flooding

Here the flooding doesn't mean that sort of environmental disaster or phenomenon, but refers to an artificial watering in a house - the 6 year-old baby has been extremely noughty and has made the whole bathroom, most part of the corridor, toilet, and half of our laundry flooding and still wouldn't get out of the bath. The water also gets into Gavin's room, and the carpet in children's room is also getting wet; probably the internet equipments (hub and adsl modem) on the floor are also gonna be dead. Pop has been called; Vicky in Auckland has been texted; insurance won't pay for anything damaged or infected. Fxxking bastard...!

Noise from the fan

The long time running of distributed computing may do some harm to the fan in a laptop, as I can hear some screaming from the fan in my one. I probably need to lubricate the fan sometime this weekend...

Tzuchi anniversary

I was asked to help Tzuchi foundation's anniversary 2 (or 3?) weeks ago, and today it's the day to work out.

As I'm not the member of the foundation, I don't know very well (nor want to know) about this society. I'm not a volunteer of them either, and also have got no plan to attend to be a member of them in future. What I've been doing with them these days is just give them a hand where they really need when I can, and actually there's nothing much I can do for them. Even today I felt I didn't do too much for them as well.

Well...this on the other hand might mean they've got really lots of member in this group.

OOo extends its competition

I've noticed on the mailing list of OOo that someone suggest extending the submission due date of Documentation Project Template/Clipart Competition as Oct 13 is just too rush for many people, and obviously the OOo has now extended the submission day, which is now from September 20, 2006 to October 31, 2006 at 23h59EDT (GMT-4). I believe this is a good new to every submitter (including me). I've got some ideas but was thinking the time was just too short, and now I've got a bit relief. :)

Helicobacter pylori gram's stain

It's strange that the Helicobacter pylori cells have got different formations when grown on different media, and even on the same plate they may also look different: I. Urea agar: Columbia blood agar base + 7% fetal bovin serum + HCl + urea + phenol red + antibiotics (vancomycin + amphotericin B + polymixin B) II. CHBHP: Columbia blood agar base + 10% horse blood + antibiotics (vancomycin + amphotericin B + polymixin B) They're all gram negative so this time gram positive cocci have been removed (or suppressed), but as they've got several looks and some of them look different from what I know about helicobacters, now I can't really make sure if they are exactly Helicobacter... :(

Typhi in the Waikato ?!

Rat disease hits (on Waikato Times) I remember there occationally are some mice running around in our house. Not quite sure if the fleas from rats would also be spread through mice...

Helicobacter contamination (still)

My helicobacter looks still contaminated by other cutlures; from the gram's stain, many gram positive cocci can be seen (I guess enterococci). Now I'm using urea agar (columbia agar + serum + HCl + urea + phenol red) and trying to get single colony for recovering helicobacter, but honestly I don't expect too much on it now... :( Ray told me that I could add vancomycin to get rid of enterococci. Actually this has been included in the urea agar plates, so give them a few more days and see what'll happen. If these stock cultures are still unrecoverable, I reckon I'll need to re-order another copy of helicobacter type strain from ESR. In the photo Ray said the faint pink organisms (the gram negative ones) should be helicobacters but I doubt it; they look too fat as helicobacter.

Medical examination

The (stupid) immigration had changed their rule of applying student visa last year, thus now I got to do full medical examination every 2 years (Geez...). Today is the day I have the examination. The medical centre: Victoria Centre (abbreviated as VC) Examed items: X-ray Blood Urine Eye-sight Height, weight Physical checks (?) Fee: ...expensive Waiting before proceeding examination: > 40 min Result: need 4 working days (i.e. Tuesday week)

Laptop batteries fire (...how many time is this anyway?)

Flaming LAX laptop was a ThinkPad (on CNET.com) Lenovo probes Sony laptop battery fire (on CNET.com) Lenovo...IBM...Sony... :( ...and here is a topic which may have something to do with Japan: Japanese fret that quality is in decline (on CNET.com)

Huh!! Laptop explodes!

Don't get me wrong...it's not mine. Dell battery explodes at Yahoo HQ, hundreds evacuate (on engadget.com) ...and the laptop looks disastrous: When Laptops Explode, side view It doesn't say where the battery is from, but I guess...sony again?

OpenOffice Template/Clipart Creation Contest

OpenOffice.org is holding the Documentation Project/Worldlabel Template/Clipart Competition recently. It's from September 13, 2006 to October 13, 2006. (Ouch! It's been running for 1 week) and the awards will be announced on November 1, 2006. It looks interesting, and also the prizes are quite attractive: PRIZES FOR TEMPLATES: 1st Prize USD750 2nd Prize USD300 3rd Prize USD250 4th and 5th Prizes USD200 100s of Tshirts and other Openoffice.org goodies for templates which will be part of the Documentation Project. PRIZES FOR CLIPART: 1st Prize USD750 2nd Prize USD300 3rd Prize USD250 4th and 5th Prizes USD200 100s of Tshirts and other Openoffice.org goodies for clipart submitted which will be part of the Documentation Project. I may try to submit some of my works. :)

Battery recall (again)

Toshiba recalls 340,000 Sony laptop batteries 340,000 batteries from Sony in Toshiba boxes...who's the next?

Soulseek

Jesicca asked me to help sorting out her computer thing - to make a program called "soulseek" work on Vicky's computer. The problem she's got is that she couldn't get soulseek connect onto its server. After 2 or 3 times try, I decide to try on my computer as I suspect there're something wrong with Vicky's computer (I'm pretty sure the computer has got heaps of problem). By the way, Jessica said she wanted to download music with thie program and it was downloaded by Christle. As I know nothing about soulseek, I proceeded a few search before I really try it on my computer, and hell, I found some virus would spread through this P2P (peer-to-peer) program. Having some prevention work, I tried this program on my computer and found it did connect to its server flawlessly. Hm, looks like it's really got some problems with Vicky's computer. Of course, I deleted the program from my computer within a couple of minute (this includes installation, trying, and uninstallation). I've also told Jesicca and Gloria not to use this program anymore. It is always good to be paranoid when it comes to computer security. :)

Night sight-seeing

A party held on campus; everyone dressed very formal. I saw many of them also got mask on their faces. Masked dancing?

Arghhhhh~~~ My Helicobacter...!!

After a loooooong time incubation, I went over my lab and see how Helicobacter is going. As soon as the "HP castle" comes to my eyes, I nearly drop dead - the tape for sealing the "HP castle" flipped over and hence it's not air-tight any longer. Needless to say, those Helicobacters have been dead and I'll have to recover another copy of Helicobacter from -70C stock. Oohhhhhhh~~~~shocking... T_T

Peter is back and Kerry is gone

It's Kerry's time to go abroad - actually it's her long holiday. She'll have a big trip in Europe from 4 Sep to 7 Oct. By the way, she is not going to see Katherin although she might get through Germany.

Battery recalls

Sony is used to be thought as the first choice when purchasing IT products (audio, TV, laptop, etc) a few years ago, but apparently this has been a passed history. Recently a number of battery recalls have been announced; each of which are associated with the batteries manufactured by sony. DELL recalls 4.1 million batteries: Dell Announces Battery Recall (14/Aug/06, on DELL.com) Dell takes heat over battery recall (on CNET.com) A week later, iBook and PowerBook from Apple (1.8 million batteries)... Battery Exchange Program iBook G4 and PowerBook G4 (on Apple.com) Apple recalls 1.8 million batteries (on CNET.com) ...and now Sony VAIO from Sony itself: Laptop Bursts Into Flames - Owner Says Laptop Was Charging Looks like MIJ is not necessarily trustworthy any more.

Golf

Peter to abroad

Peter is going abroad to give presentation during the next 3 weeks (13 Sep till 31 Sep). The destinations would cover Japan, Hongkong, Malaysia and Taiwan. However he's a bit nervous about his powerpoint slides as the slides keeps breakinig as soon as he fixes the powerpoint file - the position of pictures moves away from where they are supposed to be, the size of text fonts varies, the animations behave oddly , and the most weird thing is that the powerpoint file size goes up to more than 200MB! I'll have a look on the file and see what the hell is the problem with it.

M$ Excel inadequates for statistical analysis

Key words: Excel, inadequate Using Excel for Statistical Data Analysis Report in 1999 (pdf) Spreadsheet Addiction Problems using Microsoft Excel for statistics (pdf) Is it practical to use Excel for stats? Statistical flaws in Excel (pdf)

Unknown contamination

The subcultured plate looks quite yuck: Apparently they've got capsule on them and they're also hemolytic (beta-hemolytic). Due to the capsule, the colonies are so sticky that I've got trouble with making slide smear from its single colony. The Gram stain of the "unknown contamination": Sticky colony, clogging cells. Looks like these Bacillus-like cells indeed have got capsules on their cells. Strangly, the thick capsule somehow can't be seen on some of them.

AMD + ATI

AMD has announced that the company and ATI will join together. Presumably ATI will no longer manufacture the chipset for Intel based products, but who knows? Anyway, I'm more curious about how they'd rename their new(?) company... "AT&A" ?!

2 days after subculturing Helicobacter pylori

The subcultured HP seems to have formed some visible colonies now, and since 5 days incubation looks too long for them (not quite sure though), I'll subculture them tomorrow (i.e. 3 days) again so that their colonies may not be too sticky.

Day 5

Unfortunately, after opening the microaerobic jar I noticed that some of the agars had been contaminated by other bacteria. I was using BHIYE agar (x2), BHIYE-chocolate agar (x 2) and CHBHP agar (x 2), among them BHIYE agars were heavily contaminated by unknown species. I'll check what they are with Gram's stain some time. Apparently I do need antibiotics for inhibiting those contaminants. I'll add vancomycin, polymyxin and trimethoprim into the agars next time.

Day 3

I can see some spots on CHBHP; must be Helicobacters. That's quicker that I've imagined!

Culturing Helicobacter pylori

As we've expected, my columbia agar plate and defibrinated horse blood arrive today, so now I can get onto work...but wait! How come the expiry date of the two bottles of horse blood are this weird?? "20/05/06" and "??/??/07" ...anyway, I'll check what the hell is wrong with this next week, but I just use one of them for making my CHBHPs, and inoculate the Helicobacter type strain and incubate them as soon as possible. I feel the colonies quite sticky, just like the feeling that I felt when Campys are dying...but I hope this won't be true...

Helicobacter pylori arrived

The one of the biggest challenging bacterium I'd manage finally arrived today. This extremely fastidious bug - Helicobacter pylori is such a fragile thing that anyone who handle it would need to spend more care on it: 1. Need highly nutritious media. Probably BHI (Brain Heart Infusion) or Columbia media is a choice. 2. Like other microaerobes, Helicobacters also need blood (or equivalent) to quench the damage from oxygen and its derivatives (free radicals, hydrogen peroxide, etc). So defibricated sheep blood or horse blood would be unavoidable. 3. Due to its slow growth, I'll have to incubate it much longer than other genus. Roughly 3-7 days. 4. During the long term incubation, contamination should be an issue; especially I'm also handling other enterbacters, which are major competant cultures of Helicobacters. Suitable antibiotics would also be required. 5. Last but not least, need to keep high humidity. It's reported that a water activity of at least 0.95 is required for its growth. Under such a high humidity, fungi would be a big concern. (So germicides have to take into account...) What I've decided to use for the media is Columbia Horse Blood HP (shortly CHBHP), which is reported to be superior for culturing Helicobacter pylori in Japan (fast growth, low contamination). The problem is... the columbia agar and horse blood we've ordered haven't arrived yet...(actually the HP culture was supposed to be arrive tomorrow, but who knows it arrives TODAY...) Now here is a big dillema. This afternoon I was told that the two stuff would arrive tomorrow. So, should I wait till tomorrow so that I can use the freshly-made CHBHP, or should I culture and freeze the cells today with BHI (Brain Heart Infusion) so that those cells wouldn't transform into coccoid form or even die? Eventually I decide to postpone one day and see if the reagents would arrive tomorrow.

Fixing DVD player

Vicky's DVD player is failed. The symptom is that the player shows "NO DISC" even if actually there's in it. Apparently the pick-up lens needs to be cleaned. So I took it apart and cleaned the lense with isopropanol, and also observed some other weired points: a few condensers had been leaking! ...but still, it came to alive after the cleaning, so now they don't have to use play station 2 for watching DVD now.

Enterobacter spp.

There're a few Enterobacter spp. in Vanessa's culture collection, but according to the record it's supposed to be in the chest freezer on the corridor whereas actually it wasn't. Eventually we found that theose cultures had been moved to PC2 lab. I'll recover Enterobacter aerogenes and Enterobacter cloacae this week.

Subculture from high conc. of honey

Advice from Ray about subculturing from high conc of honey onto agar plate: 1. make buffered agar plate (e.g. Tris-buffered TS agar); or 2. centrifuge bacteria down and wash the cells with fresh media.

The effect of pH on honey

Have a meeting with Peter this morning and showed him the result of the work on the effect of acidity on the antibacterial activity of honey. As there're quite lots of data and I hadn't finished analysing them, it was a bit mess when I showed Peter those results (Ah~~ what a shame~~), but still Peter looks to be pleased with the result. :)

Yumiko got burgled

Coming back from badminton, Gavin told me that Vicky'd went to Yumiko's place as she'd got burgled. As usual police wouldn't come within a few days (which is totally useless), and as Yumiko and Tatsuya (Yumiko's 6 year boy) were scared, they're gonna stay with us for a couple of days. BTW, here is the list of their stolen stuff: laptop digital camera Tatsuya's school bag ...and something other

Trapped by toilet..

...for about 1/2 hr (I guess) before going out for badmintonat around 20:00. What a shame... -.-;;

WEB days

Today and tomorrow are WEB days which is for demonstrating to 13 year old students what DNA work would look like. My roster is from 9:00-10:00 and 14:00-15:00. What we (demonstrators) actually did are to see those students get kiwi fruit pulp and add salt and detergent, water bath for 15 min and precepitate the DNA with ice-cold methylated spirit (hell, I didn't know that the spirit can be used in this way before). Meanwhile we also showed them how to use dispenser and autopipettor, and also let them try to load DNA sample (actually it's just a blue dye) into agarose gel. Overall the process was seamless, except those students were somewhat unorganized and the process was also a bit in rush. Oh, and I found somebody had dumped the used kiwi pulp down the sink. I hope it wouldn't get blocked... -.-; (not my fault not my fault...)

R in NZ Herald

A bit old news but still worth a read. Local 'language' spreads worldwide (on NZ Herald)

A letter from court

Apparently Patrick - the damm hell Chinese student - has done some other troubles somewhere else. Today we got a letter from the Department of Judgement which is for Patrick, although he doesn't live in here any more. According to it, Patrick has sold a kiwi a computer 3D graphics card which is what Patrick claims "brand new" and sues $430 on an online auction. However the card didn't work on the kiwi's computer (actually, it makes the computer keep crashing). Besides, the kiwi also found that the card had been scratched, which is not supposed to be seen on a new computer part. Now the kiwi wants his money back and the court ordered Patrick to return his money back by the end of this month. Unfortunately that Dick doesn't live in here. What will happen next...? This Patrick is literally a trouble maker...no wonder Jesica wants to kill him. :(

Security issue - Skype

Skype URL Handling File Disclosure Vulnerability (on Secunia) SKYPE-SB/2006-001: Improper handling of URI arguments (on Skype official site)

Corridor information update

Got an email from our office which says the information board introducing the research topic of each grad/post-grad student on the corridor has been out-dated and needs to be renewed urgently, therefore the staff is asking if we could supply our information (research area, interest, etc) and personal photograph ASAP. Now they finally aware of the expiry of the information board... Nearly half a year has passed this year... :P

Dell provides AMD products

AMD Issues Statement On Dell Decision To Offer Customers Choice (on AMD official site) Dell opts for AMD's Opteron (on CNET News) Dell switch dents Intel shares (on CNET News) A big leap of AMD marketting! \(^o^)/

Crazy bill

Vicky's got telecom bill, which makes her really really really mad today - actually she almost kills her daughter Jesica. Well, how could a person calm down if he/she gets a bill with up to 600 dollars! Especially when it's because her daughter rang "a friend in HAWAII"?! (within 2 weeks?!!) Vicky got so upset that she pushed Jess down and grabbed her hair and shake her violently (literally!), threw her a rubbish bag and wanted her get out of this house with her stuff. Finally Vicky took Brandon (5 year old son) and Jess to their grandmother's SEMITRY (hey, it's been 8:30, at night) and say sorry to the grandmother. After that they went Pop(grandfather)'s home and tell him what Jess had done. Of course Pop got angry too, but at least his heartattack didn't come out. Vicky had been bankrupt before I came here - a Chinese student Patrick ruined Vicky's business van which worths 8000 dollars; he also ripped her off >700 dollars with her low-end computer and stupid adsl lines. Patrick and other chinese students had also messed up every thing in this house when Vicky moved into this house, and Vicky and Jesica had to cost a fortune to clean those mess up. Now Vicky's got 2 jobs and 1 night part-time job, but still they're in big debt (home loan, tax, whatever). And now they have to pay the telecom bill tomorrow. How can she pay $600 since she hasn't got any money to pay...? (I suppose she'll borrow some money from Pop)

Campy news

Quite a lot. Campylobacter found in most chicken (on TVNZ.com) Scientists study Campylobacter bacteria (on Dailyindia.com) Action must be taken against fouled chicken (on Scoop News) Searching for clues to NZ tummy trouble (on WaikatoTimes) "...New Zealand has the highest campylobacter rates in the world" ...my goodness... Virtually all chicken carries campylobacter bacteria (on RadioNZ) Production Practices Effect Antimicrobial Resistance in Poultry (on RxPG News) Zooming in on the Campylobacter That Would Resist Antibiotics (on Newswise.com) Campylobacter in poultry subject of two studies (on FoodProductionDaily-USA) Stress may help campylobacter infect broilers (on FarmersWeekly) Research projects map out food safety hotspots (on NutraIngredients.com)

Meeting with Peter

1. There were some news (or reports...whatever) last weekend about Campylobacters in NZ. Interesting. I'll find them out these days. 2. Get ready to submit the paper for my works on Campylobacter. I'm workiing on it now. 3. There're some strange data in the result of Campylobacter MIC test. Re-check them. 4. Compare the MIC and MBC of normal and catalased manuka honey against bacteria, so that if we can see any relationship between the MBC and hydrogen peroxide. Choose Staphylococcus to proceed it. 5. Enterococci are , compare with other bacteria, relatively resistant to hydrogen peroxide, which might be responsible for the result of long-time surviving in manuka honey solution. Put this hypothesis in my thesis...until the antibacterial mechanism of manuka honey is cleared one day :P

Blood and... EtBr?!

Kerry showed me the new sheep blood she ordered recently and... the Ethidium Bromide Kerry ordered for me before the Xmas last year!!? Even though EtBr is carcinogen, still it shouldn't have taken this long to get here! Where the hell has it been during these months ?!?!

Security

I personally reckon that the importance of security can't be over-emphasized, especially those who are using computers or touching the internet are not supposed to do anything without considereing this issue. Sadly, even major facilities usually ignore how critical this issue is. By security I don't mean merely virus, spywares or malware things, but also other minor things such as the overall structure of websites or even the basic maintainance of the OS everyone is using. Oddly, many big facilities, even educational institute miss out this point. Recently I found a university puts a commercial software like this on there server yet set no protection on it and, honestly, I could copy it if I'd like to... :(

FreeBSD 6.1 released

Here is the release note.

2 more Enterococcus spp. from Ray

Enterococcus faecalis Enterococcus faecium See if these enterococci have similar trend to Enteroccus faecalis 1106 when incubated in honey solution within different time...(Ha! One more 12-hours-time-effect test...)

OpenBSD 3.9 released!!

The security-oriented OpenBSD project has announced its new release this month. Keep working Puffy!! BTW, would the next release be 3.10 or 4.0?

AMD Opteron notice

AMD Opteron x52 and x54 Processor Production Notice: CPU Frequency Margin Test Escape (from AMD official site) FAQ (from AMD official site) Opteron x52, x54...I think it's unafordable for individual users... :P

Joe's computer

I was asked to fix Joe's computer today as somehow his computer didn't boot up. From its beeps I realised it's caused by the video card or its cable. But apparently the problem is not that all. Some messages about SATA and RAID show up after booting up, and it also looks like some hardwares can hardly be detected. This is solely some mis-setting on BIOS. The biggest problem is that he wants to play online game (World of Warcraft) with this 3-year old machine, with which it's quite hard to play seamlessly. Actually even now the speed of the computer is quite bloody slow for daily use. What he can do is reinstall the whole Winblows Windows system for short term, or upgrade his hardwares for long term's viewpoint. The re-installation itself is not quite a hard task for me; the installation disk is the one Jou borrowed from his friend. As this is illegal version and the system can't be updated from M$'s website, the security issue is quite of concern to me. To play his game smoothly, it's unavailable for Jou to get some new parts and upgrade the spec of the computer (VGA, RAM, CPU, and hence motherboard as well). He said he'd buy new RAM module tomorrow morning. By the way. here is the current spec of Jou's computer (just in case): CPU: AMD Athlon 2100+ MB: Gigabyte 7VAXP Ultra RAM: 256 + 512 MB (I find the 512MB one is not working :P ) HD: Seagate 80G Audio: onboard NIC: onboard (RTL8139)

R 2.2.1 -> R 2.3.0

The R project has relesased the new version of R. As usual, tons of update and new functions have been added in this new release. Rock! CRAN!!

Kerry's got eye infection

This morning we got a phone call from Kerry and said she'd got eye infection and would be off today. I was asked to do her a favor: Collect all towels and lab coats, pop them down to the science store and get new towels, and also get a box of petri dish and niddle.

Earthquake

Quake rocks remote Russian region (on BBC News) 7.7 magnitude...that's much more violent than 921 quake hit Taiwan years ago eh...

Another donation to OpenBSD (OpenSSH) project

GoDaddy.com Donates $10K to Open Source Development Project (on The Hosting News) Another $10k for OpenBSD project (and, again, therefore OpenSSH projct as well). Anyway, when would Sun show their respect to OpenSSH project by way of donation? :P (Huh? I heard they said NEVER)

Discussion with Ray (and David...?)

As I've got some strange result in time-effect test when comparing with Enterococcus faecalis and Pseudomonas aeruginosa, I took those results down to Ray's place and had a small discussion. David was there as well. It looks like this result interested Ray and David, and they even thought this has to do with resistant gene and would like me to screen there genes. Not quite sure what resistnat genes may be responsible to this, Ray asked David which gene should be screened. Guess what David answered - 16S?! (Even Ray was surprised... :P ) Ray pointed out that the volume I'd been using (20ul) is too small and, I should use 100ul-1 ml instead. He also considered that the inoculum density of mine (100,000 CFU/ml) is too heavy and may reduce it down to thousands or even hundreds of CFU/ml. However, 20ul is what we've been using in our lab, and also 100,000 CFU/ml is the standard in CLSI (previously called NCCLS). Dillema...

Flight tonight ?!

Gloria got a message from Vicky, which says ask Pop to ring Vicky's cell phone. After that I knew that Robyn had told Pop to ring her a few minutes ago. Surprisingly, Vicky is gonna take tonight's flight to NZ - because Jessica has got sick. Is this another joke?

Empty email box

What can be more terrible than all emails are missing? Unfortunately this seems happened to Vicky a few hours ago. Is this is a joke?! There is one possibility I can figure out that may cause her emails disappear - when Vicky read them this morning, she (actually the computer she used this morning) had moved all emails FROM EMAIL SERVER to the computer she used this morning. In most case this is due to the setting of email agency (such as Outlook Express). I emailed her and told her if she still need those emails then she can send back those messages from the computer to her own email box - as long as those messages are still kept in that computer (and make sure her email box still got enough space to receive messages; I know her campus email box has been full...:P ). I hope she didn't check her emails in internet cafe this morning, or there could be no chance to rescue her mails back...

Vicky's response

After sending email to Vicky last week, she finally gives me a reponse. Apparently she's always been in a rush in the past days.

Go to Japan! ...Er...not me

Vickly will be abroad in the following 2 weeks; 2 days in Tahiti and the rest 10 days in Japan. It's quite a shame that they are so unorganized. They are supposed to get all luggages ready before today whereas actually they're still looking for something until nearly 9:00am, this morning ! Vickly even hasn't prepared her speech which will be given in Japan...

Mozilla Foundation Donates $10K to OpenSSH

After deRaadt's claiming that the OpenBSD project(and hence OpenSSH as well) is in difficult in their finance weeks ago, Mozilla foundation announces to donate $10K which is a big help to the project. Mozilla Foundation activities, week ending 2006/03/31 - Projects for the week Mozilla Foundation Donates $10K to OpenSSH Although they still need more funding, at least this is a good start.

The PhD game

This is really a funny one (and is also quite a sad one though). The PhD Game

Dorset Naga

I don't like hot or spicy things, but I have to admit I'm a bit of interested in this "super chili. Can Korean bear it? :P Farmers claim to grow hottest chili (on TMCnet.com News) (UPI Quirks in the News Via Thomson Dialog NewsEdge)Two farmers in England claim to grow the world's hottest chili -- the Dorset Naga, which registered a Scoville heat unit of 876,000. The most recent Guinness Book of Records says the Red Savina Habanero, with a rating of 577,000 is the hottest chili -- but Joy and Michael Michaud of West Bexington, England, say they will contact the Guinness Book of Records to claim the record, The Daily Telegraph reported Saturday. The U.S. laboratory that tested the chili -- developed from a variety which originated in Bangladesh -- found it was almost 60 percent hotter than the one listed in the Guinness Book of Records. The results were so surprising the laboratory did a second test, the Michauds said. They said they even have to wear gloves when they harvest the seeds. Most people don't cook with it; they just have it near to them when they eat, said Aktar Miha, of the Indis Bangladeshi restaurant in Bournemouth, England. If you don't know what you are doing it could blow your head off. The chilli so hot you need gloves (on TIMESONLINE) THE world’s hottest chilli pepper does not come from a tropical hot spot where the locals are impervious to its fiery heat but a smallholding in deepest Dorset. Some chillis are fierce enough to make your eyes water. Anyone foolhardy enough to eat a whole Dorset Naga would almost certainly require hospital treatment. The pepper, almost twice as hot as the previous record- holder, was grown by Joy and Michael Michaud in a poly- tunnel at their market garden. The couple run a business called Peppers by Post and spent four years developing the Dorset Naga. They knew the 2cm-long specimens were hot because they had to wear gloves and remove the seeds outdoors when preparing them for drying, but had no idea they had grown a record-breaker. Some customers complained the peppers were so fiery that even half a small one would make a curry too hot to eat. Others loved them and the Michauds sold a quarter of a million Dorset Nagas last year. At the end of last season Mrs Michaud sent a sample to a laboratory in America out of curiosity. The owner had never tested anything like it. According to Mrs Michaud, the hottest habañero peppers popular in chilli-eating competitions in the US generally measure about 100,000 units on the standard Scoville scale, named after its inventor, Wilbur Scoville, who developed it in 1912. At first the scale was a subjective taste test but it later developed into the measure of capsaicinoids present. The hottest chilli pepper in The Guinness Book of Records is a Red Savina habañero with a rating of 570,000 Scoville Heat Units (SHU). Mrs Michaud was stunned when the Dorset Naga gave a reading of nearly 900,000SHU. A fresh sample was sent to a lab in New York used by the American Spice Trade Association and recorded a mouth-numbing 923,000SHUs. Mrs Michaud said: “The man in the first lab was so excited — he’d never had one even half as hot as that. The second lab took a long time because they were checking it carefully as it was so outrageously high.” The Dorset Naga was grown from a plant that originated in Bangladesh. The Michauds bought their original plant in an oriental store in Bournemouth. Mrs Michaud said: “We weren’t even selecting the peppers for hotness but for shape and flavour. There is an element of machismo in peppers that we aren’t really interested in. When the results of the heat tests came back I was gobsmacked.” The couple are now seeking Plant Variety Protection from the Department for Environment, Food and Rural Affairs, which will mean that no one else can sell the seeds. Mrs Michaud, 48, has run the company with her husband at West Bexington, near Dorchester, for ten years. Mr Michaud, 56, has been a regular on the television chef Hugh Fearnley-Whittingstall’s River Cottage series, advising on vegetable growing. Anyone wanting to try the Dorset Naga will have to be patient as chillis are harvested only from July on. In Bangladesh the chillies grow in temperatures of well over 100F (38C) but in Dorset they thrive in polytunnels. Aktar Miha, from the Indus Bangladeshi restaurant in Bournemouth, said that even in its home country the naga chilli was treated with respect. “It is used in some cooking, mainly with fish curries, but most people don’t cook with it. They hold it by the stalk and just touch their food with it,” he said. “It has a refreshing smell and a very good taste but you don’t want too much of it. It is a killer chilli and you have to be careful and wash your hands and the cutting board. If you don’t know what you are doing it could blow your head off.”

Overdue issue

The first task today is sorting out what happens on my record (of my enrolment and progress report). After showing Rou (the officer informed me that my enrolment had been confirmed) the letters, she got quite embarrased. She explained that their computer systems (and thus database systems as well) are being changed and apparently some parts of their data are being transfered. She said I can just ignor the 2 odd letters. As the progress reports form came along with the letters are also a bit different from each other, I also checked of which is the correct one (and again, she was embarrased again). Looks like their systems really need to be checked... -.-;;

Overdued progress report?!!

What else can be more annoying then this? I got 2 letters from uni when I came back; both of them are from the postgraduate studies office. The contents are basically the same; they mainly say I'm supposed to submit my 6-months-progress report of 30 Sep 2005 yet I haven't, and something would happen if I don't submit it asap. What a Dick!! I just submitted my full research plan at the end of Feb and my enrolment is just confirmed a couple of weeks ago, hence the first progress report submission shouldn't be acquired until the end of August this year; how can the uni send these rediculous letters?! There must be something wrong with the letters, or with the rule of research project. I should ask the office what the hell happen tomorrow morning.

Reply from ESR in Christchurch

Dr. On replied to my enquiry this afternoon. It's really amazing he's got a huge culture collection of up to 2700 species, which encompasses almost all known species of Campylobacter, Helicobacter and Arcobacter. He'd also like to know a little more about my research project within, if possible, 4 weeks as biocontrol of Campylobacter is a subject of considerable interest to him. As Prof. Murdoch noted, he is exactly keen to work on Campy. :)

Easter Egg in OpenOffice.org

1. create a new sheetin openoffice.org Calc (spreadsheet) 2. enter this formula in a cell : =game() and validate (validation button or enter) 3.the cell will display "say what?" 4. Enter this formula: =GAME("StarWars") 5. a new window will open with a little game star war game. 6. But if you type again this formula, the cell will return the display "oh no, not again!" XD 7. To be able to play again, we need to close the file, close openoffice.org and the QuickStarter, and then restart OpenOffice.org This is really a good egg!! XD

Prohibited exports

For some personal reasons, I'd like to send some honey products to TW recently; however I can't do this as easily as I've thought - due to import/export prohibition. I know lots of dairy products such as honey are not allowed to be imported into NZ, and so are not to be exported from NZ (according to Prohibited Exports on NZ Custom Service); but what about honey products such as soap or lip balm?? Unlike pure honeys, these products shouldn't be able to spread any diseases or something like that, but who knows what those authorities are thinking... I just send the authoroty an email and asked them if these honey products are allowed to send by parcel. Hope they'll give me a reply tomorrow, 'coz it's a bit in a hurry...

Another specialist

Prof. Murdoch introduced me another researcher - Dr. On in ESR, Christchurch, who has a longstanding interest in Campylobacter. Prof. Murdoch also noted that Dr. On has got quite a collection of Campylobacter. Unfortunately an auto-response mail comes bake right after I send an email to Dr. On. It looks like he's away these days.

Cyclone Wati

Vicky says there's a cyclone going to hit NZ this week. What's more, it's gonna hit the North island. It sounds it would be a quite strong gale. But according to this updated news, it would cause too much devastation - I think. At least that wouldn't cause running mountain like in TW. :P

IE vulnerability

Microsoft Internet Explorer "createTextRange()" Code Execution (on Secunia.com) "...The vulnerability has been confirmed on a fully patched system with Internet Explorer 6.0 and Microsoft Windows XP SP2. The vulnerability has also been confirmed in Internet Explorer 7 Beta 2 Preview (January edition). Other versions may also be affected... " ...what's this SP2 for then... Useless! :P

The last mPCR

With the last Campy swab samples from the Medlab, I proceded the last multiplex pcr today to type what species they are. Results: All Campylobacter jejuni. Somewhat disappointing. Keep waiting the C. fetus isolates from Christchurch then.

Response from Christchurch

I received replying from Christchurch today. The head said they'd got only 2 isoloates of C. fetus, and was asking me if I'm interested in. Of course I am. Hopefully those isolates will arrive next week (or the week after).

Joe's birthday today

...How come there're so many birthdays these days?

Campy with MicroAeroPak

Looks like this combination is not too bad. All campy samples grow on all plates and broths... don't know if the MicroAeroPak or my optimization matters the most though. # Today's work: Pick those pin-point-alike single colonies from plates and multiply them, so that they are exactly pure culture. Incubate another 2 days (till Friday).

Birthday meal

Last night aunt Sangar asked me to attend a birthday party of uncle Yeh, uncle Larry and another kiwi friend of them today. She said they'll pick me up at Gate 8 at 18:45, but actually they're late... :( The place we had the dinner is called "Katayya ?????? ??????" (can't remember this awkward name). Pope is also invited by them. Vicky? Because she is allergic to gluten, she can't join us. I have to say this meal is a bit boring to me; most of the time they're just talking - introducing Tzuchi foundation to the kiwi friends. Aunt Sangar promised me last night that the meal wouldn't be too long, but actually it lasted till 21:00+, and after the dinner they also spent some time on Karaoke... I reckon this is really a waste of time to me. :(

OpenBSD finances

According to OpenBSD Journal, OpenBSD's finance is not in a good condition; actually they've had a loss of approximately $40K USD total. What a shame! Considering their works on security such as OpenSSH and cryptography, that MUST BE a big loss for IT area if they cease their hackathon. :(

The last Campy swabs (I hope)

As I haven't got any response from Christchurch, I asked Medlab if they could collect some Campy swabs for me. This week I get 7 isolates. At the same time, I also want to try the efficiency of MicroAeroPak from MGC company. So I streaked the swabs on plates and also soaked in 10 ml BHIYE broths (with 0.025% FBP supplement) and incubate them in polycarbonate jar with 2 sachets of MicroAeroPak in it. The humudity in the jar is also tried to be maintained by way of placing 2 glass dishes of water with cottons soaked in them. These are what I can do to optimize the growth condition of Campy by far. Hope the result won't make me too disappointed.

Big cleaning

Today we have a big exercise cleaning (and moving). As those stuff in my room(-to-be) is finally cleared out, I can move into my new room. It took me less than 30 min to move my stuff from my "camping tent" to my new room. Since I move into my new room, my old "camping tent" is also cleaned and lots of boxes are unpacked (Vicky's stuff...). Actually this room is supposed to be a guest room, therefore we've tried hard to make it looks different from what it looks like before. Actually there's also another spare room left at upstairs and we thought it'd be a good idea to make it to be another guest room as well. After moving out unwanted sofa, boxes, sofa, stuff, quilts and sheets (huh, quite lots eh?), assembling banks (bunks?) and bed, vacuum cleaning and finally these two guest rooms make us feel like we're in motel! :) By the way, we're gonna have "Boil-Up" for dinner. Vicky said this is Maori food and they eat boil-up only on Saturday. I really look forward to it~~ :D~~

Enrolment confirmation

Just received an email informing the confirmation of my enrolment just now. In the past 6 months I was a conditional student, but now my enrolment is confirmed. And that also means now that your enrolment has been confirmed, I'm required to submit regular progress reports every 6 months. Monday week I can finally renew my ID card (the words "Expires 28 Feb 2006" look really yuck).

Yuki(and other)'s birthday

Today is Yuki's birthday, but amazingly it is also one day before Emi and Emma's birthday. That's why there is a big flag(?) in the Turners' house and therere Yuki, Emi and Emma's name on it.

C. fetus request

As I haven't found any C. fetus from Medlab isolates, I decide to contact some other research institutes which are doing C. fetus. There're several facilities handling C. fetus in NZ, but somehow I couldn't find their contact, and eventually I can just contact with the one in Christchurch. After sending email to the facility in Christchurch this morning, I got a response at lunch time. Unfortunately it seems the one I sent to is not the representative of that unit, and he suggested that I may ask their head. Therefore I sent another enquiry to the head of the Christchurch facility if they could provide us some C. fetus isolates.

Manuka basket

Last week I was quite unhappy about those movie makers and photographer from somewhere (I knew afterward that they took those stuff for Comvita), but I have to say I may have to forgive thank them. Katherine and me, both of us, got a basket of Comvita's products today. Lets's see what's in there: Royal Jelly Hand & Body Lotion x1 Propolis Lip Balm x1 Bee Polen x1 Royal Jelly Soap with Manuka Honey and Apricot x1 Manuka honey (UMF10) x1 Kiwifruit & Honey x1 Pohutukawa Honey x1 ???? Soap x1 Skintensive Cream x1 Fortacold Throat Lozenges x1 ...and a lovely small bee ♫

A not so cold fridge

This afternoon Katherine noticed that one of our fridge is no cold. Look at its temperature gage and alas! 20C ?! When we were wondering why is this, we once thought that the fridge might have been out of action. Then I suddenly noticed another shocking matter – the power point for that fridge had been turned off!! Who the hell did this!!?? Those stuff such as blood agar plates, chocolate agar plates, honey samples and other chemicals in the fridge may have been off!! Kerry was also stunned when I told her some idiots had turned the fridge off. Well, we've had some idea who may have done this though... # Fortunately I'd moved all my charcoal agar plate into another fridge before...:P

A new comer

A stranger comes to our lab with Peter this morning. “She is from France and will be staying here for the next six months”, Peter said. Sounds like another Katherine.

No Internet yet :(

The internet in this new house is supposed to be get through on Friday, but apparently the internet company (Slingshot) hasn't connected it. Vicky, you should give them a yell on Monday (I mean, a BIG bloody yell).

Film making

When Peter told us we were going to be photographed by somebody, Katherine and me didn't realize what it exactly means, what the scale would be, and what it would exactly look like; and today, they finally gave us the answer. By the way, I'm not doing too many lab works this week as I'm focusing on my full research plan which should be submitted by the end of this month. What I'm doing for my lab work is no more than checking the purity and vitality of my Campys – a kind of routine task, and shouldn't take too much time to finish it. Anyway, those people are supposed to arrive at 3:00pm, but actually they didn't show up until 3:30pm. When they came into our Honey Research Unit, I was stunned by the scale – there are roughly 6-7 camera workers, technicians and assistants (?) and come along with several huge bags with their cameras and RAILS in them. As soon as they came in, some of them started to set the rail on the floor and others turned off the light or talked to Peter WHAT we were going to do and WHERE we should be located at – a typical film making. One of them wanted to lit my Bunsen burner but never succeed. After litting it up for him, he asked me if I can get more orange part of the flame and get it closer to me and Peter – he must have mistaken Bunsen burner is not for LIGHTING... They also wanted Katherine to sit at biosafety cabinet, me at bench top and Peter to stand beside us, and to pretend that we.were working while the camera was moving around us. Hey, Sir! Don't you know the Bunsen burner is very hot? But before that... How would you take responsibility of my Campys for staying in air for such a long time!! Finally the film making finished, but it's not all – we are asked to stay for “a few minutes” to take still pictures. Actually I felt this took us longer time than the film making did. The photographer tried several times to tune the angle and light of the scene, and asked us to move some stuff (Bunsen burner closer, oxygen generator and microscope away...), face my agar place toward the photographer, and even wanted Peter to lower down his body...!! As with Katherine, she had to hold 8-ch pipette with left hand and pretend working on serial dilution.-.-;; Finally (yeah, this time it's real final) the work finished. We all were showed how the still pictures look like. Hm...it's not too bad but how come the main point – the persons – are not in the center in those pictures?? Anyway, after all of them left away, I got my Campys into “CampyHouse” (candle jar) as soon as possible, incubate them and went home. They are really killing my Campys, really. I actually have a feeling that my Campys had been dead... Peter said they'd send us the film we took today within DVD. Who knows...

Move

Having had some hassles, I finally move to a new place which is closer to campus. To move to new place, I need someone to give me a hand to move my stuff, and Allan and Yuki did help moving them to the new place.(Thanks, guys!) The new host, Vicky, is a Maori, and they're having a BBQ party when we arrived there. It's quite surprising there're so many friends (and their kids as well) came to join the party. Roughly 20 people, I guess. By the way, it's really stupid of me to leave my laptop in Allan's car and didn't notice that until they'd left! :P Anyway, I met lots of Vicky's friends tonight.

M$ vs Symantec?

Microsoft Anti-Spyware Deleting Norton Anti-Virus (on WashingtonPost.com) Looks like M$ considers Symantec is odd as well... :P

Trees have something to do with greenhouse?

Scientists question trees' role in global warming (on ABC Online) Plants revealed as methane source (on BBC News) Quite a shocking information...I hope there won't be some sort of odd groups claim that cutting forest would help reducing global warming...

Looking for new accomodation

There're 2-3 boards still renting, and one of them is quite close to our building, which might be convenient for me to be there. Unfortunately the host seems to be out when I rang the number on the advertisement. He/she might be on out for holiday. I took a few minutes to walk around the area. It is exactly close - actually just in front of our lab and would take just 5-10 minutes to move between the area and our building...but there is a quite steep slope on the road. I would have to go up this big slope to work - Hmm...a good warming up exercise before start working huh? I have no idea how about the other 2 houses at this moment, but it's really time to make decision since Jason's host is unwilling to have a long-periond student to stay with them (she's gonna back to America soon, after all)

Identify more Campy

I met Peter unexpectedly when I was going to get autoclaved stuff this afternoon. I told him that the Campy's results are quite disappointing - most of the Campy samples are NOT exactly Campys. Take those unsurviving Campys into account, my samples have reduced from more than 100 (149, I think) to merely 36! The species variety is also limited - most of them are Campylobacter jejuni (more than 2/3) and followed by C. coli. No C. fetus or other species are detected. Peter advised me that I may do PCR with Sarah's (a student before) Campy samples and see what species they exactly are. ...Hence I'll have to do some more Campy samples in the following weeks...I hope I may finish Campys THIS MONTH~~~~!!

Campy mPCR (x46 isolates...!)

1. Looks like most of them are Campylobacter jejuni which is followed by C. coli, and there are rare of C. fetus. I may have killed all of C. fetus "unconciously" (when I raised the temperature up to 42C). 2. The high concentration of primers cause primer dimers. 3. The 23S bands don't show in each well => may not correlate with Campy very well 4. A few of "suspected Campys" are actually not campys. Although they grow on selective agar and in microaerobic condition, they're unlikely to be Campys from genetics viewpoint. (no wonder I felt they grow unusually faster than they're supposed to be)

mPCR result discussion

Ray came to our lab and ask for some sheep blood, and also asked if the mPCR result is right as being expected. As the result shows that the swabs MedLab gave me were NOT pure-cultured and there were several different species in one swab, I wondered why Ray told me I didn't need to isolate another pure culture. However, Ray said those non-pure-cultured swabs were "understandable"?! What the earth does he mean??

Holiday

Today is Auckland anniversary (nothing to do with hamilton though) and is off.

Cost cut in a lab

Equipments and chemicals in a lab are normally expensive. Actually one can't find any exception on earth. Thus lab-workers may have to figure out their own way to cut cost as much as possible. I think re-using tips and buffers may be one of the most common manners in each lab. Here I find some interesting examples of know-how (from The Scientist, Volume20, Issue 1, Page 55): 1. Stay away from the latest technical developments, and make do with the previous generation of equipment. 2. Make your own reagents. # This is why I make my own TBE(10x), TE(10x) buffers instead of purchasing new ones for my pcr. I see some people even make their own Taq and markers as well!! (amazing! How do they do that?!) 3. Grow your own cells. 4. Ask for free samples. # Like the GoTaq from Promega...but actually it's been too late; Kerry'd ordered Eppendorf HotMasterMix before the in vitro sales came to us. Anyway, can GoTaq perform hotstart? 5. Buy fusion antibodies. 6. Avoid top-shelf reagents. # So I don't need Taq from Qiagen. Also we may extract nucleic acid with traditional method (phenol/chloroform method) which is much less expensive than DNA/RNA prep kits (e.g. spin column). 7. Scale down recipes. # We usually do this one. 8. Reuse antibodies. # I did this when I was performing Western blotting in ex-lab. 9. Avoid chamber slides. 10. Autoclave, don't filter. # ...but filter sterilization is still needed when autoclave is unsuitable (e.g. enzymes). 11. Split the use and the cost of research animals. 12. Reuse, reuse, reuse. # Hah! This is gold-standard method for budget saving!! Reuse agarose gel, electrophoresis buffer and tips, etc. 13. Buy plastic bagged instead of racked. # Can anybody suggest where we can purchase plastic BAGGED filter tips?? 14. Use sterile items only for sterile techniques. 15. Get biotech company leftovers. 16. Create the equipment you want. # In other words, "order-made".

SB buffer

Last time when I wanna make agarose gel and run electrophoresis, Ray didn't use TAE or TBE buffer but SB buffer. He said TAE/TBE is expensive. After that I did some brief search about SB buffer and find something below: 1. Tris is the expensive part of TAE/TBE and on the other hand SB is relatively cheaper than those buffers contain Tris. 2. With SB the electrophoresis time can be cut down to 1/3 with high voltage (275V, which is 3-5x of Tris gels!) yet low heat generation than ordinary Tris-based gels. I see some guys run gels at 200V for 0.5hr with the same resolution and separation as 2 hours at 50V in TBE. 3. DNA bands with SB would be sharper than with Tris-based gels.

Tris gel (110V)	SB gel (275V)

4. SB wouldn't salt-out like high concentration TBE normally does. 5. The recipe of SB: NaOH (10mM) pH adjusted to 8.5 with boric acid (works out at ~2.6g/L). That's cheap! # SB is first reported in: Brody JR, Kern SE.(2004).Sodium boric acid: a Tris-free, cooler conductive medium for DNA electrophoresis.36(2):214-6. Erratum in: Biotechniques. 2005 Jan;38(1):60

New host visiting

Just come back from new host visiting now. It is Jason's host at the moment - may until February. Basically it's a small (at least to my mind it's smaller than the Turners) yet lovely house. The host is a fairly talkative American lady and her English is quite easy to understand. I find her a bit naughty as well. :P By the way, to move to this new host or not has nothing to do with my parents and Tzuchi foundation's "pursuation". This is MY DECISION.

Fake stem cells 2

Hwang Woo-suk's news on CNN: Cloning scientist: Forgive me Cloning scientist asks forgiveness Stem cell fakery called 'criminal act in academia' School sorry over stem cell fraud School: Human stem cell work faked School: Human stem cell work faked In S. Korea, 'no' gets failing grade Panel: No data for stem cell claim Panel says stem cell work faked Panel says stem cell work faked Stem cell expert: Work is not fake 'Long road' for stem cell research

Fake stem cells

The following news about Hwang Woo-suk are all from BBC News: Korea cloning expert questioned S Korea probes stem cell trials Korea cloning researchers quizzed Journal retracts Hwang research Hwang apologises to South Koreans S Korea cloning research was fake Korea's national shock at scandal Science takes stock after clone row The fall of a scientific 'rock star' Science will stick with peer review South Korea's cloning controversy

I have a dream

I usually make strange dreams at night. I didn't plan about content of dream before sleep, but somehow the contents usually have something to do with my real life in some ways. These are some of them: 1. Doing resesarch work in my ex-lab (forgot its content) 2. I was on a fisherman's boat with its owner (he is one of the fishermans work at our harbour when I was serving as a CGA member. I've forgotten his name though). I wasn't a CGA member in that dream but just sitting on the boat and the fisherman was sailing his boat on a river - like Yellow River in China. As I was sitting at the edge of the boat, the edge crashed suddenly and needless to say I fell down into the water as well. Fortunately the water was not deep. 3. This one could be one of strangest dreams. It was in a barrak somewhere and there were a row of soldiers standing in front of me - their chief. I saw I was blaming at one of them. I couldn't see his face but I can still remember his voice. I: ~!@#$%^&*(!!! He: You can't talk me like this! @#$%^&*... I: Fxxx!! I've been standing you for long time but you still ~!@#$%^&*(^$...!!! I saw this dream just after I entered CGA but hadn't met those guys standing in front of me and didn't concern about it too much; and amazingly they eventually were in my barrack months later. When one of the guys came to my barrack, I had a feeling this was not the first time to see him but actually we never see each other before and I couldn't figure out why I had that feeling that time. ...and one day the situation came to true - almost the same. I was almost going to blame at that guy, and at the same time this dream came up to my mind and realized - it's him!! No wonder I felt I'd seen him before we exactly meet each other!! (Wow! I'm a fortune teller!!) 4. I've forgotten the detail of another one, but I can still remember Peter (my honoured boss) was also in that dream as well!! ...and last night Yuki showed up in my dream. I was gonna leave somewhere (?! a bit similar to my real situation) and somehow he knew one of my secret - a true secret in the real world that I've been keeping from him! Dream is really amazing. Anybody can explain these phenomena?

Metabolic pathways and others

Find a useful (yet quite large-sized) biochemical Metabolic Pathways Map on Sigma's website accidently. There're also some useful tutoring animations of biochemical reactions (e.g. TCA cycle, glycolysis, etc). PS: How to print them?? ^.^;;

Re-make oligo

Kerry showed me an email from Sigma which says some of their recent oligos may not meet their quality control and, unfortunately, one of my oligo primers is concerned as well (primer CFF) and asking me if I'd like them to re-make the issued oligo. Have a look on my mPCR results yesterday, I can't see any problem with the C. fetus band. Regardless of this, I still decide to re-make it (it should pay nothing, after all) :P The new oligo is supposed to arrive Wednesday next week.

Multiplex PCR

I've done PCR before (Er...I mean 4-5 years ago), but this is my first time to do multiplex one. Actually their principles are quite similar - except the number of primer pairs). The result shows that of 14 Campylobacter isolates (plus 1 negative control), most of them are C. jejuni which is followed by C. fetus and then C. coli; no other species (such as C. upsaliensis and C. lari). # It looks like the samples from Medlab are not necessarily pure cultures... :( # Method n Material: DNA extraction: boiling method with chloroform purification Taq: Eppendorf HotMaster Mix Thermocycler: MJR PTC-100 Electrophoresis system: ????? Electrophoresis gel: agarose dissolve in SB buffer (with Ethidium Bromide dissolved) Electrophoresis buffer: SB buffer (not TAE or TBE buffer!?) Gel imaging system: ??????

Centrifuge and absorbance ratio

Ethanol precipitation with Ray's centrifuge today. I reckon Ray's protocols are somewhat strange than normal ones. Yesterday I also had a feeling he might not check nucleotide purity (absorbance ratio test) after DNA extraction. ...and I'm right - they don't. "That's textbook!" said Ray. ...I can see what he means, but at the same time I still feel odd without doing QC...

DNA extraction

To do PCR, DNA extraction is unavoidable, and thus I have to extract that of Campylobacter isolates. As I'm not using these DNA for SEQUENCING or CLONING but just differentiate what species they are, I wouldn't spend too much time on extraction and purification, hence I choose one of the simplest ways - boiling method - to do my work today. (Lysis method requires some more chemicals and that would increase my expense) 1. Boil Campys Normally I have to boil bacteria 10 min and suddenly chill on ice for another 10 min, but unfortunately the lids of eppendorf tubes pop out as the air heated up and I tried hardly to tie them up with celotapes (don't work) and sterilize tapes (more or less work) 2. Chloroform purification Unfortunately our chloroform has run out at the moment and Kerry borrowed a small bottle of chloroform (~80mL) from another lab. As this is a corrosive material, I'll have to record how much I use and write down on a track sheet, and collect the waste into another empty 2.5L winchester bottle. Eventually I used 2.8mL. Only 2.8mL chloroform in a big 2.5L winchester bottle... Looks stupid... -.-;; 3. Add NaOAc and Ethanol precipitate DNA Here's really a problem. I've got 1mL of ethanol and DNA sample in each eppendorf tube and have to centrifuge 5min - with the horizontal centrifuge in our lab. Oddly, the lid pop out and my samples almost flow out! Concerning my sample, I asked Kerry to change the roter into a "normal" one and, for in case, I tried to centrifuge some tubes with water to see if it's there's any problem. But alas! After testing 5 min centrifuge with water, the water gets warm and the roter is shockingly hot - actually it's untouchable! What would happen if ethanol is heated in capped tubes? (you can imagine how dangerous it is). This centrifuge is said to be around 15 years old... As this is unusable, I'd have to go down to Ray's lab and centrifuge my samples there... 4. Ethanol precipitation not needed?! In Ray's place, he told me I just need to use chloroform and then run pcr - ethanol not needed! This really surprised shocked me. Now I see his protocols are somehow different from normal ones...

Sales

I'm not handling genetics things too much in my research work, but a presentative from a chemical company still comes to see me and have a short meeting. Vanessa - the female PR - is from in vitro company and asked me if I could tell her what my work is about. We also talk about PCR and, somehow, Promega. She said she'd send me a catalogue of Promega for the year 2006 and GoTaq as a sample. She then went to Raywen's lab after that.

Andrew quits job again

As we'd suspected, the pay is exactly too low. Andrew said the job is too stiff and he wouldn't do it again and, as usual, starts complaining about his job. It is definitely better than equivalent to nothing. I wouldn't be too surprise to see Andrew changes his mind within only one day work; however I'm quite surprised when everyone feels the pay is too low whereas he still says it's better than nothing! :(

MIC with McFarland standard

Quite surprisingly, this time the result is quite consistant. Although the MICs are still slightly higher than with agar dilution method, it's now within an acceptable range. And also, this modified method has saved me quite a lots of effort and thus I may speed up my work on campys (decrease my working time from 4-5 days to only 2-3 days for each test!) Cool!!

Andrew's new job - picking onions ?!

Andrew has found a new job last Friday, and today is his first day to go. Needless to say, it's hard. Workers are supposed to pick onions under a beating sunshine and it is said to be paid by meters (not by hours?!) Andrew has went 77 meters today and when he came back home, he's almost been covered by dust (and so is our bathroom...) Andrew guess the pay might be 35 cents per meter, and of course all of us are surprised of its low pay. 35 cents!! Is this a joke?! Whereas he says it's better than nothing, but I'd say it's equivalent to nothing!! We asked him to ask his company how much the pay exactly is tomorrow.

McFarland standard <-> Optical Density

I've been having some difficulties on determining inoculum density as there's no golden standard for Campy. As the inioculu density may vary the final result of MIC significantly, we are supposed to control it consistently (and reasonably). Normally we can do "Total Count" to evaluate the total number of our bacteria in absorbance adjusted (0.5 absorbance at 540nm wavelength) and dilute it to particular concentration which is followed by loading 5-10 ul of it (triplex) on agar plate to see how many CFU there are. Here are two problems with my Campys. First, some of my Campys migrate on agar plates. This really make total count hard to achieve as several colonies might combine each other and it's impossible to count them. To overcome this I dilute the inoculum several more times so that there wouldn't be too many colonies on each observing unit (thus reduce the chance of merge). Second, and also the most annoying one, as Campys grow much slower than other cultures, I got to incubate quite a long time (2-3 days) to make the cell quantity achieves 0.5 absorbance. That really takes too long!! So, this time I modify my method: 1. Adjust inoculum concentration to 0.5 McFarland standard (~ 0.08 absorbance at 625nm wavelength) 2. Consider the antibacterial activity might reduce faster within aquatic condition (broth dilution method) than in semisolid condition (agar dilution), the incubation time is reduced to 1 day.

Before IELTS

Jason is gonna sit IELTS test tomorrow and gets me a phone call tonight. Apparently he's nervous, and it's a bit surprising that there're something he still doesn't know about, such as the stationary rule (examinees are not allowed to use their own ones) and the flow the whole test. Anyway, I reckon I've written most of my know-how on the tips.pdf I sent him before. All I can do is just tell him to have a quick review on the tips, take a shower and hit the sack. All the best to you, Jason.

Interloan

To find out what the standard method for Campylobacter is, I need to refer to NCCLS (National Committee for Clinical Laboratory Standards). Due to unavilibility of this item either in our library or online, I've issued an interloan request today. The item is: NCCLS (2002) Performance Standards for Antimicrobial Disk and Dilution Susceptibility Tests for Bacteria Isolated from Animals: Approved Standard M31-A2, 2nd edn. Wayne, PA: National Committee for Clinical Laboratory Standards. Since the average wait for an Interloan request is 2-3 weeks, it's supposed to be here by the end of this month.

2 more WMF vulnerabilities

Two New Windows Metafile Bugs Found (on PCWorld.com) Microsoft Windows GRE WMF Format Multiple Unauthorized Memory Access Vulnerabilities (on BugTraq) Broken windows... :P

Home sweet

Finally come back home after heaps of hassle yesterday... but that was not all. Alan Charito almost lost her camcorder bag and digital camera, which were put on the top of our car when we were in Napier!! Hum, she almost can buy another new one. :P

To Napier...!

Lots of hassle happened today - come across drunk driving, 8 hrs driving (which is supposed to take only 4-5 hrs), small SplashPlanet, looking for motel (all of them had been NO VACANCY) and glumpy Hilary... :(

Stream-cast online!

Possibly because of the age(?), my portable radio is getting under performace. It usually lose its tune so that eventually can't hear any sound but noise. Even if I re-tune it, it lost its sound again as soon as my hand leaves from it. It's useless! I'm picking it's getting sensitive to surrounding noise (any kinds of noise - including light!) Here I have an idea - why not switch to online streaming broadcast since we've got broadband? So that's why I turn my laptop into a "DJ box". Here's the how-to: OS: FreeBSD6.0 Realease Package: xmms-1.2.10_4 (/audio/xmms) Plug-in: xmms-liveice (/audio/xmms-liveice) 1. Install programs # cd /usr/ports/audio/xmms; make install clean # cd /usr/ports/audio/xmms-liveice; make install clean 2. xmms and plugin setting Launch xmms, press Ctr-p and a plug-ins list window shows up. In the tab "Effects Plugins" (I though it would be in "Audio I/O Plugins" but actually it's not) there should be a line says "Liveice 1.0.0 [libliveice.so]" if nothing goes wrong. Now everything's almost ready. 3. Choose channels Here I choose Shoutcast and select some casting servers (click on the "Tune in" buttons) and download their playlists. Their playlists are all uniformly named "shoutcast-playlist.pls", hence I have to rename them into other names so that they wouldn't be overwritten by any others. 4. Enjoy it! Everything's got ready. Now what I have to do is just add those downloaded (and renamed) playlists into xmms playlist and play them as normal musics. Yeah! It rocks!! No more radio disturbance!

5...4...3...

...2...1...Happy New Year to everyone!!! Welcome to the year 2006~~~!!!!