Science

Awesome .. you are welcome to list your ad on labdonkey.com. 

Thanks John. You are absolutely right :-)

Labdonkey is a scientific skills marketplace connecting the "footloose scientific community" who are enthusiastic about doing  "the boring grunt work" for paying clients. I know money is a five letter word but ... it helps get things done.  

On Wednesday, August 29, 2012 10:30:28 AM UTC-4, John Griessen wrote:

On 08/28/2012 07:22 PM, Jonathan Cline wrote:
> Who's the donkey in this scenario and is that considered a good thing?

Whoever's lashed to the wheel of productivity :-)

He's just aiming the service at the normal "head in the clouds"
researcher with funds to spend on "the boring grunt work".  The donkey work.

Keep more footloose bio-engineer "donkeys" in beans with a
roof over their heads is the "good thing" of it.

I'll have to try a listing or two.

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On 08/28/2012 07:22 PM, Jonathan Cline wrote:
> Who's the donkey in this scenario and is that considered a good thing?

Whoever's lashed to the wheel of productivity :-)

He's just aiming the service at the normal "head in the clouds"
researcher with funds to spend on "the boring grunt work".  The donkey work.

Keep more footloose bio-engineer "donkeys" in beans with a
roof over their heads is the "good thing" of it.

I'll have to try a listing or two.

Hi Phillyj I work in Philly ... Biomed scientist 

On Monday, August 27, 2012 3:17:26 PM UTC-4, phillyj wrote:

On Tue, Aug 21, 2012 at 2:03 PM, Labdonkey <thela...@gmail.com> wrote:
> A microconsultancy website where science professionals can offer their
> services to general public or other science professionals. My hope is it
> will help the DIYers too ... it will be nice to see experts placing ads at
> labdonkey to offer microservices like "i will help your local microbrew
> group during weekends for $100 or offer plasmid prep lectures for $100" etc.
> What do you guys think?
>
Are you located in Philadelphia, PA?

Hi there. I have been reading a ton about SynBio and have become extremely interested. I have been trying to get research positions in the bioengineering department at my university to no avail, but I don't want to wait on a professor to get started with this incredible field. I'd really appreciate it if you guys and gals could point me in the right direction. If you would help me find out about equipment, techniques, good reading material, example experiments; any useful information at all, that would be fantastic. Hopefully, I will be able to contribute more and more to this forum and the field at large over time. Thanks for having me aboard!

On Friday, August 31, 2012 3:56:32 PM UTC-5, Gavin Scott wrote:

There's also This stuff (a Chlorhexidine Gluconate Oral Rinse) that my oral hygienist has me rinse my mouth out with before she starts scratching away. It's supposed to kill off 90-something percent of the bugs in your mouth and is prescribed for people with advanced periodontal disease I believe.

There's also This stuff (a Chlorhexidine Gluconate Oral Rinse) that my oral hygienist has me rinse my mouth out with before she starts scratching away. It's supposed to kill off 90-something percent of the bugs in your mouth and is prescribed for people with advanced periodontal disease I believe.

The xylitol will only be effective if you hold it in your mouth and do not swallow

http://www.volokh.com/2012/08/31/how-not-to-label-biotech-foods/

http://www.thenewatlantis.com/publications/how-not-to-label-biotech-foods

Sent from my iPhone

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http://www.xucker.de/xucker-xylit-xylitol-pulver/fein-grob-kombination/

This was the one I got.





Am Freitag, 23. September 2011 00:31:42 UTC+2 schrieb gobi:

At fist let me say, thats real cool and interessting stuff you are
doing!
Second: sorry for my bad english, I'm german.

I have a big problem : periodontosis
Dentists are telling me, there is nothing they can do, and my thees
have to been dranwn out. (!!)
Thats the same they did to my grandma in the same age - so no
progress???
Why there is now way to stop or better kill the bacterias sitting in
my jawbone?

I have read a bit about "phags" (correct english translation?) , but
found verry less infos about this god idea... killing the bacterias
with a virus.
Any Suggestions?
I'm not a biologist! Searching for (german speaking would be verry
helpful) contacts , ideas, help

Gobi

Click Here and Watch Pakistan vs Australia Live Cricket Match on www.virtualians.pk
Regards

If you have an infection in your jaw, antibiotics would be the way to go!!

S. mutans is not going to be the bacteria causing periodontitus, it
would be something like P. gingivalis (a gram negative bacteria).
The best protection against S. mutans, besides

On the whole, for natural treatments against oral bacteria, perhaps
cranberry juice might be a good option? It has some natural sugars
that block colonization by bacteria, and was a treatment for GI
problems.

This treatment for S. mutans looks quite interesting:
http://adr.sagepub.com/content/24/2/94.full

Its a peptide that messes up the cytoplasmic membrane (specific to S.
mutans) and kills the cells quickly, but doesn't affect other microbes
so you could keep the other good bacteria around.

-Matt Larson

On Fri, Aug 31, 2012 at 11:29 AM, Mega <masterstorm123@gmail.com> wrote:
> If it were my teeth, I would use Xylitol.
>
> And in fact, I use it. Bought like 3 kg (1.5 kg * 2) for some Euros (it
> surely was affordable, don't remember. Maybe 25€ alltogether?) and it was
> many many month ago.
>
> I've been coonsuming one tea spoon of Xylitol a day for some month, and now
> for several month just every now and then (when I feel like it). And there
> is still some 0.5 kilogram left. You womn't run out of stuff ever :D
>
>
> Xylitiol is not only against cavities, it is said to be bacteriostatic in
> general.
>
>
> Summa sumarum, the few bucks it costs is absolutely worth that it may save
> one's teeth. And it tastes great too :D
>
>
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So Beautiful Doua of Today

So Beautifill Name of Allah

Do you agree Reality of Journalism..................????

Joke of The Day 

If it were my teeth, I would use Xylitol.

And in fact, I use it. Bought like 3 kg (1.5 kg * 2) for some Euros   (it surely was affordable, don't remember. Maybe 25€ alltogether?)  and it was many many month ago.

I've been coonsuming one tea spoon of Xylitol a day for some month, and now for several month just every now and then (when I feel like it). And there is still some 0.5 kilogram left. You womn't run out of stuff ever :D


Xylitiol is not only against cavities, it is said to be bacteriostatic in general.


Summa sumarum, the few bucks it costs is absolutely worth that it may save one's teeth. And it tastes great too :D

90 minutes exam:-p

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Posted By Sheroo to **Virtual University Of Pakistan**Student Cafe at 8/31/2012 07:29:00 AM

Xylitol maybe a good try, being also in chewing gum form (cowgummi) makes it seem less like treatment!

You might also consider another ayurvedic treatment called 'Dant manjan' by the company 'dabur', it's a red powder you put on your toothbrush and add a drop of water, instead of tooth paste

http://www.dabur.com/Products-Health%20Care-Red%20Tooth%20Powder

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When I posted my ideas what you could try, I missed xylitol (=xylit), preferably as chewing gum.
I have used it myself to control infections around the head. This is *practically an antibiotic you
can buy OTC, so prepare for bowel side effects if you use it heavily.

Sounds good enough to try for $6.06, I would if my teeth were at such risk

From that page, in case you thought it was spam: (P.S. it would be
cool if we could get a list of the latin names for the 'Ingredients')
"
G32 is a best remedy for Gingivitis, Spongy, Painful, Swollen,
Bleeding gums. It is best helpful in Painful, Shaky and Aching teeth.

G32 as Gum & Oral Cavity massage, Dentifrice, Rinse and Gargle. Gives
relief from symptoms in 2-3 applications. Remarkable improvement in
2-3 days.
Indications:
GUMS : Gingivitis, Spongy, Painful, Swollen, Bleeding gums
TEETH : Painful, Shaky, Aching, Hyper-sensitive, Removes external
stains, Non-maligant common oral mucosal lesions : Leukoplakia
Sub-mucous fibrosis etc. stomatitis, ptyalisim, Trench mouth,
pharyngitis, sore throat, Halitosis
Post Oral Surgery : Scaling, Curetting, Gingivectomy, Excision, Extraction etc
Oral Trauma : Pre and Post wearing of appliances, Denture sores, Fixed
Frame abrations, Broken teeth ulcerations etc.
Dosages:
Crush 1 to 3 tablets G32 to fine powder. Massage this powder over
gums, teeth and on the effected parts and inside the whole mouth
properly, with the help of finger tip. Keep it for minimum five
minutes for effective action. Then rinse with fresh water. Repeat two
or three times a day as necessary.
Follow up after surgical measures: G32 twice a day. In acute diseased
conditions: G32 three times a day.
To maintain good Oral - Hygiene in health and sickness - Use G32
regularly as above, morning and at bed time.
Results supported by clinical trials from all over India show:
Stops gum bleeding, reduces inflammation.
Restores normal orange peel appearance and texture of the gums
Helps healing process by Kertinization and Granulation
Improves Oral Hygiene
Gingivectomy can be avoided in stage I and II periodontitis by 3-4
weeks treatment with G32
Effective in non-malignant common oral mucosal lesions
Ingredients:
Bakul, Chok, Katha, Laving, Chikni Sopari, Fatakdi, Maiphala, Elaichi,
Sonageru, Jira, Majith, Pushanbhed, Vavading, Pipal Lakh, Samudraphen,
Vajradanti, Taj, Kali Mirch, Sajikhar, Kulinjana, Pipar, Kapur.
"



On Thu, Aug 30, 2012 at 11:22 PM, Vrgopal <vrgopal@gmail.com> wrote:
> There is a tablet which is crushed and used to clean the teeth with fingers
> in India. Name is G32
> http://www.lovenaturalremedies.com/Alarsin/Dental-Care/G32-for-Teeth-Gums.html
> see this link.It is made of Indian herbs. Very useful to protect your tooth
> loss
>
> V.Rajagopalan
>
> On Aug 31, 2012, at 5:43 AM, gobi <gobi2@emw-r35.de> wrote:
>
> thats exactly what I'm looking for, but how to find?
>
> Sorry, I didn't realised new posts here...
> Meanwhile , nearly a year later, I'm still doing the cleaning with hydrogen
> peroxide. It's helpfull, and if I miss it a few days, it's getting worser...
> Gum is still getting less and less, I'm wondering how far this could go??
>
> I lost one tooth, witch was allready verry loosely . The dentist showed it
> to me and it was full of plaque up to the root because of the gap betwenn
> tooth an bone... terrible.... no wonder that it made a big infection...
>
> But loosing one tooth is better than loosing all of them in the moment....
>
>
>>
> --
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thats exactly what I'm looking for, but how to find?

Sorry, I didn't realised new posts here...
Meanwhile , nearly a year later, I'm still doing  the cleaning with hydrogen peroxide. It's helpfull, and if I miss it a few days, it's getting worser...
Gum is still getting less and less, I'm wondering how far this could go??

I lost one tooth, witch was allready verry loosely . The dentist showed it to me and it was full of plaque up to the root because of the gap betwenn tooth an bone... terrible.... no wonder that it made a big infection...

But loosing one tooth is better than loosing all of them in the moment....

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It cost nothing since they could not synthesize it. If I want it I may just PCR it up and clone it the old fashioned way.

On Thursday, August 30, 2012 9:56:22 PM UTC-4, phillyj wrote:

I don't know much about how companies synthesize oligos so what was
the reason for the failure? Too high GC content and other stability
issues?

I know we did some custom synthesis by PCR for a client since they had
trouble getting the synthesis companies to create it. Maybe you have
to go down that road?

By the way, how much did it cost you for this promoter at Operon?

On Thu, Aug 30, 2012 at 4:29 PM, Tom Randall <tara...@gmail.com> wrote:
>
>
> On Thursday, August 30, 2012 3:46:48 PM UTC-4, Dakota wrote:
>>
>> This is pretty neat, if I remember you are the one that payed to get the
>> Neurospora genome sequenced for your own data?
>>
>>
>> How did you go about chosing these 1014 bps for your synthetic promoter?
>> I imagine there are multiple promoter sequences, what about an entirely new
>> one?
>>
>>
>> http://www.broadinstitute.org/annotation/genome/neurospora/GeneDetails.html?sp=S7000006085103696
>>
>>
>> http://www.broadinstitute.org/annotation/genome/neurospora/GeneNeighborhoodPage.html?sp=kGene%2F7000006085103696
>>
>> I was just messing around looking at the H1 gene, but I get so lost in
>> genome software and usually quit from frustration.  I just want to see the
>> ssDNA sequence upstream and downstream of that gene but can't figure out
>> how.
>>
>> Out of curiosity, why are those repeat homopolymers needed?  The cytosine
>> run of 11 bp's in the already rich GC area seems to be something they had
>> trouble with.
>>
>> Unfortunately I do not have experience with this to offer any help, but it
>> is a pretty sweet project!
>
>
> I just picked that sequence since somebody else had used it in a construct
> as a promoter and it was sufficient to drive expression, cant remember the
> reference offhand. I dont know why those repeats are needed, or if any
> detailed promoter bashing of this sequence has been done, likely not. Why
> they are there? Either they are needed or an evolutionary accident I
> suppose.
>
> The Broad display of this genome is a bit clunky, but I find it easier to
> use that the version at Ensembl Genomes, and the UCSC Browser people do not
> do much support of micro-organisms.
>
> Funny you should ask about the genome, I just put up the current status of
> that project in a different post, the link is below.
>
> http://www.roningenetics.org/Sequencing.html
>
>
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>

I don't know much about how companies synthesize oligos so what was
the reason for the failure? Too high GC content and other stability
issues?

I know we did some custom synthesis by PCR for a client since they had
trouble getting the synthesis companies to create it. Maybe you have
to go down that road?

By the way, how much did it cost you for this promoter at Operon?

On Thu, Aug 30, 2012 at 4:29 PM, Tom Randall <tarandall@gmail.com> wrote:
>
>
> On Thursday, August 30, 2012 3:46:48 PM UTC-4, Dakota wrote:
>>
>> This is pretty neat, if I remember you are the one that payed to get the
>> Neurospora genome sequenced for your own data?
>>
>>
>> How did you go about chosing these 1014 bps for your synthetic promoter?
>> I imagine there are multiple promoter sequences, what about an entirely new
>> one?
>>
>>
>> http://www.broadinstitute.org/annotation/genome/neurospora/GeneDetails.html?sp=S7000006085103696
>>
>>
>> http://www.broadinstitute.org/annotation/genome/neurospora/GeneNeighborhoodPage.html?sp=kGene%2F7000006085103696
>>
>> I was just messing around looking at the H1 gene, but I get so lost in
>> genome software and usually quit from frustration. I just want to see the
>> ssDNA sequence upstream and downstream of that gene but can't figure out
>> how.
>>
>> Out of curiosity, why are those repeat homopolymers needed? The cytosine
>> run of 11 bp's in the already rich GC area seems to be something they had
>> trouble with.
>>
>> Unfortunately I do not have experience with this to offer any help, but it
>> is a pretty sweet project!
>
>
> I just picked that sequence since somebody else had used it in a construct
> as a promoter and it was sufficient to drive expression, cant remember the
> reference offhand. I dont know why those repeats are needed, or if any
> detailed promoter bashing of this sequence has been done, likely not. Why
> they are there? Either they are needed or an evolutionary accident I
> suppose.
>
> The Broad display of this genome is a bit clunky, but I find it easier to
> use that the version at Ensembl Genomes, and the UCSC Browser people do not
> do much support of micro-organisms.
>
> Funny you should ask about the genome, I just put up the current status of
> that project in a different post, the link is below.
>
> http://www.roningenetics.org/Sequencing.html
>
>
> --
> You received this message because you are subscribed to the Google Groups
> "DIYbio" group.
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maybe this

http://www.questdiagnostics.com/testcenter/BUOrderInfo.action?tc=16406X&labCode=QTE&fromPage=BUOrderinfo&fromPageKeyword=Antibiotic%20Microbial%20Assay

"
ANTIMICROB COMB,CF PANEL

Test Code
16406X

CPT Code(s)
87181 (x34)

Includes
Piperacillin and Tobramycin; Tobramycin and Meropenem; Tobramycin and
Ceftazidime; Tobramycin and Ticar/Clav; Tobramycin and Imipenem;
Tobramycin and Aztreonam; Meropenem and Amikacin; Imipenem and
Ciprofloxacin; Ceftazidime and Amikacin; Meropenem and Ciprofloxacin;
Piperacillin and Ciprofloxacin; Cefepime and Tobramycin

Preferred Specimen(s)
SEE INDIVIDUAL TEST COMPONENTS BELOW

Methodology
Antibiotic Gradient

Reference Range(s)
See Medical Report

Clinical Significance
The use of antimicrobial combinations for the treatment of infectious
diseases has become more common due to several factors including: more
severe infections, development of organism resistance, and infection
with multiple organisms. Antimicrobial combinations may help to expand
the spectrum of coverage, minimize drug toxicity, minimize development
of resistance, and may lead to antimicrobial combination synergy.
"

by using google translate and searching
antimikrobielle Panel assay site:.de
I found this company, who've I've seen before, their tests are a bit
expensive, but I think worth it for your health
http://www.biomerieux.de/servlet/srt/bio/germany/home

it's hard for me to read the results quickly to know if they're labs
or junk results... find yourself a medical laboratory through the
local hospital, call them and ask for this

On Thu, Aug 30, 2012 at 5:43 PM, gobi <gobi2@emw-r35.de> wrote:
> thats exactly what I'm looking for, but how to find?
>
> Sorry, I didn't realised new posts here...
> Meanwhile , nearly a year later, I'm still doing the cleaning with hydrogen
> peroxide. It's helpfull, and if I miss it a few days, it's getting worser...
> Gum is still getting less and less, I'm wondering how far this could go??
>
> I lost one tooth, witch was allready verry loosely . The dentist showed it
> to me and it was full of plaque up to the root because of the gap betwenn
> tooth an bone... terrible.... no wonder that it made a big infection...
>
> But loosing one tooth is better than loosing all of them in the moment....
>
>
>
>>
> --
> You received this message because you are subscribed to the Google Groups
> "DIYbio" group.
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>



--
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Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

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thats exactly what I'm looking for, but how to find?

Sorry, I didn't realised new posts here...
Meanwhile , nearly a year later, I'm still doing  the cleaning with hydrogen peroxide. It's helpfull, and if I miss it a few days, it's getting worser...
Gum is still getting less and less, I'm wondering how far this could go??

I lost one tooth, witch was allready verry loosely . The dentist showed it to me and it was full of plaque up to the root because of the gap betwenn tooth an bone... terrible.... no wonder that it made a big infection...

But loosing one tooth is better than loosing all of them in the moment....

http://cen.acs.org/articles/90/i26/Drugs-Never-Used.html

"
Cleveland BioLabs has been trying to move its lead candidate, CBLB502,
along this development path. The drug is an injectable recombinant
derivative of a bacterial protein flagellin that activates signaling
pathways and suppresses apoptotic cell death in hematopoietic and GI
cells. The firm also is exploring CBLB502 as a radioprotectant in
medical procedures. It has completed animal efficacy and human safety
studies, and it has regulatory-compliant manufacturing.
"

seems like you'd want radiation-damaged cells to apoptose, rather than
continue and possibly mutate into a cancer. CONSPIRACY THEORY: if this
actually got approved, people would think it was great, but it could
in reality just keep them coming back.

This just seems like shrewd marketing by pharma... to keep themselves
in business, the old 'it looks good in short-term, but keeps patients
coming back'



--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics

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On Thursday, August 30, 2012 3:46:48 PM UTC-4, Dakota wrote:

This is pretty neat, if I remember you are the one that payed to get the Neurospora genome sequenced for your own data?

How did you go about chosing these 1014 bps for your synthetic promoter?  I imagine there are multiple promoter sequences, what about an entirely new one?

http://www.broadinstitute.org/annotation/genome/neurospora/GeneDetails.html?sp=S7000006085103696

http://www.broadinstitute.org/annotation/genome/neurospora/GeneNeighborhoodPage.html?sp=kGene%2F7000006085103696

I was just messing around looking at the H1 gene, but I get so lost in genome software and usually quit from frustration.  I just want to see the ssDNA sequence upstream and downstream of that gene but can't figure out how.

Out of curiosity, why are those repeat homopolymers needed?  The cytosine run of 11 bp's in the already rich GC area seems to be something they had trouble with.

Unfortunately I do not have experience with this to offer any help, but it is a pretty sweet project! 

This is pretty neat, if I remember you are the one that payed to get the Neurospora genome sequenced for your own data?

On Sunday, April 1, 2012 1:30:11 PM UTC-4, Tom Randall wrote:

(1) Is anyone actually doing DIY work on synthetic biology?  What makes it DIY (e.g. taking place in a community lab)?  What makes it synbio (and not just biology or molecular biology)?

Thanks,

Jason

I have a lab at home and will likely soon be doing something that loosely might be considered synbio, but only because I intend on ordering a sequence from one of the companies like Blue Heron.
Specifically the project is that I have a morphological mutant in my organism of interest, an ascomycete fungus Neurospora crassa. I am interested in determining the gene responsible for the phenotype of this mutation. It has been genetically mapped so I know within 20-40 kb where it is. I have in the past done Sanger sequencing on a candidate gene, which found no mutation in or around that particular gene so decided to simply get the whole genome sequenced. Hopefully then I can compare that sequence to reference and find a SNP/indel responsible. If that is possible, I intend to order a sequence of ~ 1 kb around this mutation, including the candidate mutant allele, and transform this into a strain with the wild type allele of this candidate gene in order to generate a replacement of the wt allele with the mutant allele by homologous recombination in order to re-create the original phenotype and thus confirm (or not) the genetic lesion that resulted in the original mutant allele. I have sent the DNA from this mutant strain to Operon, but only last week so the sequencing is still is in progress. I would say this is only loosely synbio because I am simply going to be using a synthetic construct as a convenient  tool in the context of what is really a molecular genetics/bioinformatics project.

On Thu, Aug 30, 2012 at 7:33 AM, Ali Tarek <alitarek345@hotmail.com> wrote:
> I am a senior Pharmacy and Biotechnology student at the German University In
> Cairo,i am very interested in this Initiative and would like to know what is
> required from degrees ,experience and resources to start a local DIYbio
> community here in Egypt, i have been part of several community and global
> initiatives here but not scientific ones.

Ali, I recommend starting with reading the FAQ.

http://diyhpl.us/wiki/diybio/faq

For starting groups with shared labs, I think the most invaluable
resource is from the hackerspace community.

http://hackerspaces.org/wiki/Documentation
https://labitat.dk/wiki/How_to_start_a_hackerspace
http://hackspace.org.uk/view/Starting_a_Hackerspace

Also check if you have nearby groups:

http://diyhpl.us/wiki/diybio/groups
http://hackerspaces.org/wiki/List_of_Hacker_Spaces
http://hackerspaces.org/wiki/List_of_ALL_Hacker_Spaces

You don't need to create a shared lab space of course, perhaps you
just want to know people in your area to collaborate on projects
in-person, etc.

- Bryan
http://heybryan.org/
1 512 203 0507

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