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Request Genomic DNA of Burkholderia mallei


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8 replies to this topic

#1 Adrian K

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Posted 23 October 2009 - 03:42 PM

Dear All,

Recently I had developed a rapid and economic multiplex PCR system which able to differentiate between Burkholderia pseudomallei (B.ps) and Burkholderia thailandensis (B.t), and possible burkholderia mallei. However, I do not have the genomic material of burkholderia mallei and thus I am unable to make any comparison with it. I had tested with my B.ps clinical isolates (which I got plenty) and some environmental strains of B.t. All i need now is genomic DNA of B.mallei, even just 2 or 3 reference strain will do before I can write up and publish, or the worst case I might just publish without it.

I am looking for collaborators possible somewhere near Malaysia or Southeast Asia who can provide me B.m genomic material, or maybe can exchange with my B.pseudomallei cultures/genomic material. I understand that in some countries like USA where possession and transportation is strictly regulated but If you do have any permits to overcome the problem you are always welcome. I just need a non-infectious material (DNA) and not living culture but I not sure will it be categorized as BSL3 in your country.

Waiting for your good news.

Adrian (Malaysia)
Expecting the world to treat you fairly because you are a good person is like expecting the lion not to attack you because you are a vegetarian.

..."best of our knowledge, as far as we know this had never been reported before, though I can't possible read all the published journals on earth, but by perform thorough search in google, the keywords did not match any documents"...

"what doesn't kill you, makes you stronger"---Goddess Casandra reminds me to be strong

"It's all just DNA. Do it."---phage434

#2 Feelcontraire

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Posted 17 November 2009 - 02:14 PM

Dear All,

Recently I had developed a rapid and economic multiplex PCR system which able to differentiate between Burkholderia pseudomallei (B.ps) and Burkholderia thailandensis (B.t), and possible burkholderia mallei. However, I do not have the genomic material of burkholderia mallei and thus I am unable to make any comparison with it. I had tested with my B.ps clinical isolates (which I got plenty) and some environmental strains of B.t. All i need now is genomic DNA of B.mallei, even just 2 or 3 reference strain will do before I can write up and publish, or the worst case I might just publish without it.

I am looking for collaborators possible somewhere near Malaysia or Southeast Asia who can provide me B.m genomic material, or maybe can exchange with my B.pseudomallei cultures/genomic material. I understand that in some countries like USA where possession and transportation is strictly regulated but If you do have any permits to overcome the problem you are always welcome. I just need a non-infectious material (DNA) and not living culture but I not sure will it be categorized as BSL3 in your country.

Waiting for your good news.

Adrian (Malaysia)



I suppose that you have already tried but...have you offered colaboration to the authors of the last published papers in which P.mallei is used?

#3 Adrian K

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Posted 17 November 2009 - 07:25 PM

Hi, I Tried to contact a few but no respond yet...
:)
Expecting the world to treat you fairly because you are a good person is like expecting the lion not to attack you because you are a vegetarian.

..."best of our knowledge, as far as we know this had never been reported before, though I can't possible read all the published journals on earth, but by perform thorough search in google, the keywords did not match any documents"...

"what doesn't kill you, makes you stronger"---Goddess Casandra reminds me to be strong

"It's all just DNA. Do it."---phage434

#4 sanjiun

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Posted 17 November 2009 - 07:51 PM

Multiplex PCR system... hmm... interesting...

Adrian...
May I know from which institute you are from? Don't tell me you are from the same lab I used to work??? Are you someone I know? Collaborators/ from same group etc? :) (Obviously you already know where I come from...)

As far as I know, UM, UKM and USM has a big research groups in Burkholderia research.
Have you try VRI (Vet Research Institute)? As B. mallei is the causative agent for horse glanders, they might be able to get some B. mallei for you. Or you can try IMR (Institute of Medical Research). Our lab used to get few B.p. isolates from them (they isolated from clinical samples).


Bioforum is really a SMALL world...

Edited by sanjiun, 17 November 2009 - 08:00 PM.


#5 Adrian K

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Posted 19 November 2009 - 08:58 PM

Multiplex PCR system... hmm... interesting...

Adrian...
May I know from which institute you are from? Don't tell me you are from the same lab I used to work??? Are you someone I know? Collaborators/ from same group etc? :D (Obviously you already know where I come from...)

As far as I know, UM, UKM and USM has a big research groups in Burkholderia research.
Have you try VRI (Vet Research Institute)? As B. mallei is the causative agent for horse glanders, they might be able to get some B. mallei for you. Or you can try IMR (Institute of Medical Research). Our lab used to get few B.p. isolates from them (they isolated from clinical samples).


Bioforum is really a SMALL world...


Hi sanjiun,
We never met each other before but I do read in one of the old post saying that you are from UKM, and I'm not from your lab...i'm from one of the groups in UM. As far as I concern, none of our local universities have B. mallei. I haven't try VRI and IMR yet as I don't know have the contact. Do you have it?

BTW, right now which lab you are working with? :D
Expecting the world to treat you fairly because you are a good person is like expecting the lion not to attack you because you are a vegetarian.

..."best of our knowledge, as far as we know this had never been reported before, though I can't possible read all the published journals on earth, but by perform thorough search in google, the keywords did not match any documents"...

"what doesn't kill you, makes you stronger"---Goddess Casandra reminds me to be strong

"It's all just DNA. Do it."---phage434

#6 sanjiun

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Posted 20 November 2009 - 12:19 AM

Hi sanjiun,
We never met each other before but I do read in one of the old post saying that you are from UKM, and I'm not from your lab...i'm from one of the groups in UM. As far as I concern, none of our local universities have B. mallei. I haven't try VRI and IMR yet as I don't know have the contact. Do you have it?

BTW, right now which lab you are working with? <_<


Oh... so you are with UM group. Prof Jamuna's (hope i don't spell her name wrongly.. ;)) group?
I used to work in Prof Sheila's lab. Mainly working on B. pseudomallei. I left few months ago and ended up in cancer research now.
I do not have VRI or IMR's contact as I wasn't the one who collected the samples from them. My seniors did. So I am also not too sure if the person they got in touch is still there now.
Maybe you can ask your PI to write to them or call their bacteriology department?
http://www.jphvri.go...=...3&Itemid=88
http://www.imr.gov.my/org/bacti.htm


Another option: why not buy from ATCC?
We used to buy B. thailandensis from ATCC too. But i guess it would be easier to import B.thai rather then B. mallei due to the biosafety regulation thing.

#7 Adrian K

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Posted 20 November 2009 - 09:24 AM

Hi Sanjiun,

Wow, you from Prof Sheila's lab. :lol: your lab is very active.

Haha, I'm from Prof SDP's group (you should know her full name, else i just PM you), not Prof Jamuna. We got one ATCC, strain for both B.thai and B.ps. We didn't have B.m. And because of this biosafety regulation, my prof doesn't want to go through all these troubles and responsibilities. The reason I want it is because I had 100 % confident my multiplex can differentiate this 3 species in one go, rapid and economic. I just need to prove it, thats all.

For B.ps we have hundreds here. I myself had stock at least 90+, some even weird weird and have different antimicrobial and enzymatic profiles, different morphology (morphology for 60+ isolates so far i had done) etc...thus the best option is through genomic aspect for best identification and differentiation. i can't reveal too much here because most of our result is still pending and waiting for publication.

p/s: I had come across your article title "Burkholderia pseudomallei animal and human isolates from Malaysia exhibit different phenotypic characteristics"...you got any more publications so that i might can use and cite in my references?
Expecting the world to treat you fairly because you are a good person is like expecting the lion not to attack you because you are a vegetarian.

..."best of our knowledge, as far as we know this had never been reported before, though I can't possible read all the published journals on earth, but by perform thorough search in google, the keywords did not match any documents"...

"what doesn't kill you, makes you stronger"---Goddess Casandra reminds me to be strong

"It's all just DNA. Do it."---phage434

#8 sanjiun

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Posted 22 November 2009 - 06:09 AM

Ya, Prof S lab is very active lately esp she now involved in using C.elegans for model to study Burkholderia's host-pathogen interaction. But i am no longer working in her lab (but she is really really a nice person), and work in cancer research (a huge transition from infectious disease to cancer).

Morphology of B. ps... it is really something fascinating. Same isolate can even change it's morphology after you use it to infect an animal and reculture from animal's organ. We too find it hard to screen their phenotype. One of them even fail to grow in Ashdown plates coz it fail to grow in Gentamicin. And most importantly, colonies look sooooo pretty on Ashdown like a flower but also DEADLY at the same time! LOL!

I guess there will be more publications in the near future as many of our paper is still in the process of getting reviewed etc. The one you mentioned is the paper we published 2 years ago after screening for the isolates we have collected in our lab. Previously our lab's publication only target single gene which might be potential essential gene in B.p, to kill it or as a drug target.... Only lately we moved towards a more general picture on the host-pathogen interaction, instead of the bacteria alone.

Edited by sanjiun, 22 November 2009 - 06:11 AM.


#9 Adrian K

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Posted 22 November 2009 - 06:25 PM

Hi Sanjiun,

Yes, true indeed. I do have few gentamicin sensitive strains and unable to grow in BPSA agar as well. Even when growth concurrently compare with LB agar, their morphology is different. Some looks like flower, some like spaghetti, some even like pizza. You eat it, you die...lol :D Thus, the common detection method where medical laboratories used to "look" on the morphology is not good enough in identify B.p. Also, Chromobacterium also can grow on these media, and chromo species is not always in purple colour. Furthermore API20NE which was used in medical diagnostics is also reported poorly performed by some of the researchers. Serology and agglutination test is not available in most lab unless they had pre-prepare it and usually in Malaysia they will just send their sample to IMR or UMMC or other hospital where the test is available (takes time). The cross-reactivity of serology by Bps, Bm and Bt could be happen. This is exactly the reason I was thinking we should target to genomic identification, which is rapid, accurate and sensitive. So the most promising way which everybody could be use is by using PCR, unless they don't have the machine that would be another story. Primers synthesis is also faster than antibody production for use of serology. I had optimized the condition for the PCR by using plate cultures. Right now I was thinking optimized it to be more sensitive in detection and shorter in time (less than 30 minutes PCR time, and the preliminary result is promising). As we know in diagnosis of melioidosis, time is not only money, but time is life! Late detection will cause fatality.

I do heard one of your junior (Malay Girl, forget her name) in MSMBB conference told me about Prof S using C.elegans as model. In fact, I also had thought of using this model in my study but in different approaches, but due to lack of funding and technical knowledge, I had put the thought aside.

Nice to hear from you. I wish you good luck in your cancer research. Keep in touch. :huh:

Sincerely,
Adrian

Edited by adrian kohsf, 22 November 2009 - 06:33 PM.

Expecting the world to treat you fairly because you are a good person is like expecting the lion not to attack you because you are a vegetarian.

..."best of our knowledge, as far as we know this had never been reported before, though I can't possible read all the published journals on earth, but by perform thorough search in google, the keywords did not match any documents"...

"what doesn't kill you, makes you stronger"---Goddess Casandra reminds me to be strong

"It's all just DNA. Do it."---phage434




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