[DIYbio] A beginners question about a medicinal plant

Hi everyone, i kind of stumbled onto the diy bio movement and it seems really interesting. I don't really know where to start so some recommended reading or tips would be really appreciated.

I got interested in this because there is a plant in my country that is supposed to have a positive effect on the immune system of someone who has a weakened immune system, for what ever reason. I saw it work on my mother when she had dengue fever a few months ago. Long story short, after the results from a blood analysis came back, it showed that her immune system wasn't doing too well, she came back home grounded the leaves and put them in water and drank it through a metal straw that we call "bombilla" that has a metal filter at the end. After which her immune system rebounded and got better, I've heard of other people doing this same thing and getting similar results.

So my question is, where can i start? i want to analyse this plant for it's medicinal properties and maybe turn it into some type of medicine. If what i've observed and heard is possible then many people could be benefited with this kind of medicine. And it's not the only one, many plants and the like are said to have medicinal properties around here, i've used some of them and they've been pretty effective. I would like to start testing and analysing them.

Btw im a Comp sci student, if i can make a good case i might be able to persuade my principal into getting the people in biotech and biology involved(my campus is about 200km from the main university campus where the dept. of science is located, which is why i haven't been able to go to them with this idea)


Thanks for taking the time to respond
-Cristian from Paraguay

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[DIYbio] Re: Zika Virus Detection

Found a primer sequence here...
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4016539/
(Table 3)

Forward primer = AARTACACATACCARAACAAAGTGGT
Reverse primer = TCCRCTCCCYCTYTGGTCTTG

Here's a good site for aligning virus sequence...
http://www.viprbrc.org/brc/home.spg?decorator=flavi_zika

So you'd need an extraction kit like QIAamp Viral RNA Mini Kit, a one-step RT-PCR kit, the primers, and a gel or spec for measuring amplification.  A bit expensive for a one-off test, but you can probably get samples if you shop around.


On Monday, March 28, 2016 at 2:53:34 AM UTC-7, Bryan Daniels wrote:
I am just back from Spring Break in Puerto Rico and have come down with a 103 F fever, sore eyes etc. CDC has classified PR as high risk Zika zone. Most likely I have influenza, but on the off-chance it is Zika, I thought it might be an interesting DIY bio project. (I am male and past pregnancy stages in our family. . .)

I have poked around on-line and there appear to be PCR based diagnostic tests, so there are clearly primers available. Also found this article: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4285245/

I'm wondering if anyone in DIY bio community has tried this test themselves (on the cheap). As I'm not feeling too well right now, so I am also interested in how to preserve samples (and what type of samples) for later use. Any straight-forward protocols, would be much appreciated.

I have a reasonably well equipped basic lab, but only ordinary PCR capabilities, I.e., no real-time OCR.

Thanks in advance.

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Required || PeopleSoft Developer- Data Conversion || Irvine, CA || GC / Citizen Only

Dear Partner

 

Hope you are doing great!!

 

Please add me on yahoo at arpittechwire and do share me your hotlist also at Arpit@tresourceinc.com.

 

Please go through the requirement and let me know if you have any consultant for the same position.

 

 

We got these roles today and have begun working on them. I am sending this out in advance. I will be working on these roles tomorrow

 

PeopleSoft Developer- Data

Irvine, CA
8+ Months

Phone Skype

 

·         Experience as a testing or Functional lead in large scale HCM implementation projects, preferably Workday.

·         Knowledge of testing cycles for HCM, integrations and payroll (including payroll parallel coordination)

·         Lead data validation track for data converted from PeopleSoft to Workday

·         App designer, App Engine, SQR, Oracle SQL, Knowledge and experience in PS-Workday conversion is a plus.

·         Build validation scripts to review data output from Workday after conversion is complete.

 

Thanks & Regards,

 

Arpit Arora | Assistant Team Lead-Recruitment

Technology Resource Group Inc. 
1700 Park St, Unit 212, and Naperville IL, 60563

Office:408-709-1760 Ext : 9961

Fax: 408-884-2409

Arpit@tresourceinc.com | www.tresourceinc.com

 

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Job Title: Technical Lead - Senior Java Software Engineer with MongoDB Must; San Jose, CA :: 6+ Months

HI,

 

Please find the below position and respond back to me at praveenk@xperttech.com  .

 

Job Title: Technical Lead - Senior Java Software Engineer with MongoDB Must

Location: San Jose, CA

Duration: 6+ Months

 

INTERVIEW PROCESS: PHONE SCREEN AND IN-PERSON INTERVIEW - LOCAL CANDIDATES ONLY

 

EXPERIENCE SKILL MATRIX:

Total years of Experience in IT: years

Total years of US Experience: years

 

1. COMPLETE SKILL MATRIX (YEARS OF EXPERIENCE IN EACH SKILL):

1.       Technical Lead - Senior Java Software Engineer: years

2.       Core Java: years

3.       Spring: years

4.       GIT: years

5.       Backend services: years

6.       RESTful Web Services: years

7.       MongoDB: years

8.       PLUS - Cassandra: years

9.       PLUS - Kafka: years

10.   UI stack (HTML/JQuery/ Angular is a huge plus): years

 

Responsibilities:

1.       As a Tech Lead, Java Senior Software Engineer you should be able to drive end to end delivery of a Major rewrite of our backend components using Java with Spring and Mongo/NoSQL DB.

2.       The candidate must be hands on coder doing active development and lead an onsite/offshore team.

3.       He / She should possess excellent technical leadership skills, be a pro-active solution-oriented individual with strong written and verbal communication skills.

4.       At Apple, code quality and functional quality is always at the forefront and one of the keys measures of Success.

 

Qualifications:

1.       7+ years of Software development experience designing and building commercial/enterprise class backend platform/components.

2.       Expert level skills of Core Java + Spring.

3.       Strong problem solving skills.

4.       Good Oral and written English communication skills.

5.       Experience with GIT.

6.       Experience building highly performing and scalable backend components (a keen eye to performance/responsiveness of the backend services is a must for this role).

7.       Has demonstrated past experience of building scalable RESTful Web Services.

8.       Ability to wear multiple hats and a can-do attitude.

 

Education:

1.       B.S / M.S in Comp Sc engineering or equivalent.

 

Additional Requirements:

1.       Familiarity  with NoSQL DB's like Mongo.

2.       Cassandra is a huge plus.

3.       Familiarity with Kafka is a plus.

4.       Familiarity with UI stack (HTML/JQuery/ Angular is a huge plus).

 

 

Thanks/Regards,

 

Praveen Kumar

 

400 W Cummings Park

Suite#2850

Woburn, MA-01801

Email: praveenk@xperttech.com

Phone: 781-797-1042

Fax: 978-405-5040

www.xperttech.com

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Re: [DIYbio] Re: Zika Virus Detection

Identifying which particular disease you have is valuable information that many people even in developed countries have difficulty obtaining.

For instance,  I had the flu but have no idea which strain. My decision of whether or not to get a flue shot next year would change depending on if the one I had, and am now immune is included.  Rapid diagnosis in bacterial meningitis is crucial because it can kill so quickly and PCR  is fast. IIRC Eva Harris's book "PCR at Home" brought a then new technology to Central America to rapidly identify  dengue fever. This was, of course, used by by medical professionals. 

"Currently, the standard assay for Zika viral infection is a PCR test that probes for the presence of viral RNA in a sample. While it works well to detect the virus, the pathogen's RNA is only around for a short period of time. "By the time [patients] make it into the clinic, the virus is likely gone or it's at the tail end, beyond the limit of detection," said Vasilakis."

A urine test is better than blood according to this paper.
Detection of Zika Virus in Urine

I think many US hospitals underutilize  PCR as a diagnostic tool. If you can safely come up with a protocol to do it yourself it is a worthwhile endeavor that would lead to wider implementation of PCR diagnostics.  

On Mar 30, 2016, at 7:00 PM, Jake <jakestew@mail.com> wrote:

Quick note to amend my random comments earlier... Blood is always potentially hazardous.  I'm not volunteering to do anything with blood, just a poorly worded comment.

What I wanted to suggest is that he might take a sample, freeze it, and use his previously mentioned PCR capability to check for amplification.  If I were in his situation that's what I'd do out of curiosity.  It shouldn't be terribly difficult or expensive to do and would make an interesting project.


On Wednesday, March 30, 2016 at 6:20:31 PM UTC-7, Dakota wrote:
Let me preface my point with a story.

About 5 years ago or so I went to a Genome conference in Boston.  In between talks I was in the lobby and mingling with people, some around my own age at the time, early twenties.  I met a kid and we got to talking.  I said I was involved at a local community lab in Boston and did research stuff at home or at school on the side.  He asked what we did at the lab and I said we did GFP transformations, DNA barcoding, etc.  Basic molecular biology.

He said that was neat and all, but what he really wanted to do, and I'm not making this up was -- "I want to make like, a crazy virus, and put it on random door-handles"

I'll never forget that.

All of us in this community have a responsibility to ourselves, the world, the public, and each-other, to be exemplars of responsible citizen scientists.  There's a person on this group that waited years for a license just to be able to do a GFP transformation outside of a lab in an EU country.

We enjoy a lot more freedom in the US for at-home or extra curricular science and engineering.  No doubt though, garage and basement scientists are under scrutiny, whether it be from some invisible all-seeing government entity, the media, the general public, or even each-other.

I'm not saying don't go off the beaten path and be creative, inventive, or resourceful.  I applaud your enthusiasm and tenacity, get that shit done.

All I'm saying is each and every one of us could be in the spotlight, and we should maintain a certain level of care in what we do, for our own well being, our neighbors well being, and the community we're all a part of here.

I don't know your background, skills, your circumstances, or access to space.   You could be ultra-qualified to be processing blood samples and could be working in a university lab space you rent or are a part of where it's safe to handle these type of specimens.   

I'm not trying to put you on blast here, I'm just saying, would you want someone you don't know processing human blood contaminated with Zika virus in a salad spinner centrifuge and lightbulb PCR machine in the apartment next door, and throwing everything out in the trash?


On Wed, Mar 30, 2016 at 8:51 PM, Jake <jake...@mail.com> wrote:
I was under the impression that this was a matter of curiosity rather than a medical issue...  but yes, it is always better to outsource your medical needs to non-internet strangers, or internet based strangers that have paid their dues to the powers that be.

I would point out though that there's nothing wrong about drawing your own samples, every sample is mailed to a lab somewhere, and all blood products are considered potentially hazardous regardless of the source.

On Wednesday, March 30, 2016 at 5:18:15 PM UTC-7, Dakota wrote:

I'm all for affordable and accessible diagnostics, but you should probably go to the doctors and not send potentially hazardous infectious self-drawn blood samples to a stranger from the internet.

On Mar 30, 2016 8:06 PM, "Jake" <jake...@mail.com> wrote:
Haven't tried this as I'm not in a Zika zone or traveled through one.  I would think that as long as you have a thermocycler or are willing to do it manually... It should be simple enough.
Extract DNA, add primers and master mix, cycle, dye, and spec or run on gel.
I might be interested in trying this if I can get a presumed positive sample...  You did draw a vial of blood and freeze it right?

-Jake


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Re: [DIYbio] Re: Zika Virus Detection

Quick note to amend my random comments earlier... Blood is always potentially hazardous.  I'm not volunteering to do anything with blood, just a poorly worded comment.

What I wanted to suggest is that he might take a sample, freeze it, and use his previously mentioned PCR capability to check for amplification.  If I were in his situation that's what I'd do out of curiosity.  It shouldn't be terribly difficult or expensive to do and would make an interesting project.


On Wednesday, March 30, 2016 at 6:20:31 PM UTC-7, Dakota wrote:
Let me preface my point with a story.

About 5 years ago or so I went to a Genome conference in Boston.  In between talks I was in the lobby and mingling with people, some around my own age at the time, early twenties.  I met a kid and we got to talking.  I said I was involved at a local community lab in Boston and did research stuff at home or at school on the side.  He asked what we did at the lab and I said we did GFP transformations, DNA barcoding, etc.  Basic molecular biology.

He said that was neat and all, but what he really wanted to do, and I'm not making this up was -- "I want to make like, a crazy virus, and put it on random door-handles"

I'll never forget that.

All of us in this community have a responsibility to ourselves, the world, the public, and each-other, to be exemplars of responsible citizen scientists.  There's a person on this group that waited years for a license just to be able to do a GFP transformation outside of a lab in an EU country.

We enjoy a lot more freedom in the US for at-home or extra curricular science and engineering.  No doubt though, garage and basement scientists are under scrutiny, whether it be from some invisible all-seeing government entity, the media, the general public, or even each-other.

I'm not saying don't go off the beaten path and be creative, inventive, or resourceful.  I applaud your enthusiasm and tenacity, get that shit done.

All I'm saying is each and every one of us could be in the spotlight, and we should maintain a certain level of care in what we do, for our own well being, our neighbors well being, and the community we're all a part of here.

I don't know your background, skills, your circumstances, or access to space.   You could be ultra-qualified to be processing blood samples and could be working in a university lab space you rent or are a part of where it's safe to handle these type of specimens.   

I'm not trying to put you on blast here, I'm just saying, would you want someone you don't know processing human blood contaminated with Zika virus in a salad spinner centrifuge and lightbulb PCR machine in the apartment next door, and throwing everything out in the trash?


On Wed, Mar 30, 2016 at 8:51 PM, Jake <jake...@mail.com> wrote:
I was under the impression that this was a matter of curiosity rather than a medical issue...  but yes, it is always better to outsource your medical needs to non-internet strangers, or internet based strangers that have paid their dues to the powers that be.

I would point out though that there's nothing wrong about drawing your own samples, every sample is mailed to a lab somewhere, and all blood products are considered potentially hazardous regardless of the source.

On Wednesday, March 30, 2016 at 5:18:15 PM UTC-7, Dakota wrote:

I'm all for affordable and accessible diagnostics, but you should probably go to the doctors and not send potentially hazardous infectious self-drawn blood samples to a stranger from the internet.

On Mar 30, 2016 8:06 PM, "Jake" <jake...@mail.com> wrote:
Haven't tried this as I'm not in a Zika zone or traveled through one.  I would think that as long as you have a thermocycler or are willing to do it manually... It should be simple enough.
Extract DNA, add primers and master mix, cycle, dye, and spec or run on gel.
I might be interested in trying this if I can get a presumed positive sample...  You did draw a vial of blood and freeze it right?

-Jake


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Re: [DIYbio] Re: Zika Virus Detection

Let me preface my point with a story.

About 5 years ago or so I went to a Genome conference in Boston.  In between talks I was in the lobby and mingling with people, some around my own age at the time, early twenties.  I met a kid and we got to talking.  I said I was involved at a local community lab in Boston and did research stuff at home or at school on the side.  He asked what we did at the lab and I said we did GFP transformations, DNA barcoding, etc.  Basic molecular biology.

He said that was neat and all, but what he really wanted to do, and I'm not making this up was -- "I want to make like, a crazy virus, and put it on random door-handles"

I'll never forget that.

All of us in this community have a responsibility to ourselves, the world, the public, and each-other, to be exemplars of responsible citizen scientists.  There's a person on this group that waited years for a license just to be able to do a GFP transformation outside of a lab in an EU country.

We enjoy a lot more freedom in the US for at-home or extra curricular science and engineering.  No doubt though, garage and basement scientists are under scrutiny, whether it be from some invisible all-seeing government entity, the media, the general public, or even each-other.

I'm not saying don't go off the beaten path and be creative, inventive, or resourceful.  I applaud your enthusiasm and tenacity, get that shit done.

All I'm saying is each and every one of us could be in the spotlight, and we should maintain a certain level of care in what we do, for our own well being, our neighbors well being, and the community we're all a part of here.

I don't know your background, skills, your circumstances, or access to space.   You could be ultra-qualified to be processing blood samples and could be working in a university lab space you rent or are a part of where it's safe to handle these type of specimens.   

I'm not trying to put you on blast here, I'm just saying, would you want someone you don't know processing human blood contaminated with Zika virus in a salad spinner centrifuge and lightbulb PCR machine in the apartment next door, and throwing everything out in the trash?


On Wed, Mar 30, 2016 at 8:51 PM, Jake <jakestew@mail.com> wrote:
I was under the impression that this was a matter of curiosity rather than a medical issue...  but yes, it is always better to outsource your medical needs to non-internet strangers, or internet based strangers that have paid their dues to the powers that be.

I would point out though that there's nothing wrong about drawing your own samples, every sample is mailed to a lab somewhere, and all blood products are considered potentially hazardous regardless of the source.

On Wednesday, March 30, 2016 at 5:18:15 PM UTC-7, Dakota wrote:

I'm all for affordable and accessible diagnostics, but you should probably go to the doctors and not send potentially hazardous infectious self-drawn blood samples to a stranger from the internet.

On Mar 30, 2016 8:06 PM, "Jake" <jake...@mail.com> wrote:
Haven't tried this as I'm not in a Zika zone or traveled through one.  I would think that as long as you have a thermocycler or are willing to do it manually... It should be simple enough.
Extract DNA, add primers and master mix, cycle, dye, and spec or run on gel.
I might be interested in trying this if I can get a presumed positive sample...  You did draw a vial of blood and freeze it right?

-Jake


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Re: [DIYbio] Re: Zika Virus Detection

I was under the impression that this was a matter of curiosity rather than a medical issue...  but yes, it is always better to outsource your medical needs to non-internet strangers, or internet based strangers that have paid their dues to the powers that be.

I would point out though that there's nothing wrong about drawing your own samples, every sample is mailed to a lab somewhere, and all blood products are considered potentially hazardous regardless of the source.

On Wednesday, March 30, 2016 at 5:18:15 PM UTC-7, Dakota wrote:

I'm all for affordable and accessible diagnostics, but you should probably go to the doctors and not send potentially hazardous infectious self-drawn blood samples to a stranger from the internet.

On Mar 30, 2016 8:06 PM, "Jake" <jake...@mail.com> wrote:
Haven't tried this as I'm not in a Zika zone or traveled through one.  I would think that as long as you have a thermocycler or are willing to do it manually... It should be simple enough.
Extract DNA, add primers and master mix, cycle, dye, and spec or run on gel.
I might be interested in trying this if I can get a presumed positive sample...  You did draw a vial of blood and freeze it right?

-Jake


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[DIYbio] Re: Mosquito

Glad to see the consensus here seems to be that all disease vector mosquitoes could be eliminated with a negligible negative effect on the environment.

Didn't really follow the patent discussion though.  When human lives are on the line are we really worried about a potential patent suit down the road on something we made little to no money from?

I'm not sure what the motivation for the infringement suit would be if there is no money to be had.  I don't doubt that in some other circumstances you might be the subject of a punitive action, but it doesn't seem like that would be the case in this instance.

Supposing a small non-profit corporation accidentally infringed on a patent or was unable to obtain suitable licensing terms and pursued a course that invited an infringement suit... what would the ramifications be?  Would mega-corp sue a humanitarian organization just to make it fold and intimidate others with no hope of a profitable judgement?


-Jake

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Re: [DIYbio] Re: Zika Virus Detection

I'm all for affordable and accessible diagnostics, but you should probably go to the doctors and not send potentially hazardous infectious self-drawn blood samples to a stranger from the internet.

On Mar 30, 2016 8:06 PM, "Jake" <jakestew@mail.com> wrote:
Haven't tried this as I'm not in a Zika zone or traveled through one.  I would think that as long as you have a thermocycler or are willing to do it manually... It should be simple enough.
Extract DNA, add primers and master mix, cycle, dye, and spec or run on gel.
I might be interested in trying this if I can get a presumed positive sample...  You did draw a vial of blood and freeze it right?

-Jake


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[DIYbio] Re: Zika Virus Detection

Haven't tried this as I'm not in a Zika zone or traveled through one.  I would think that as long as you have a thermocycler or are willing to do it manually... It should be simple enough.
Extract DNA, add primers and master mix, cycle, dye, and spec or run on gel.
I might be interested in trying this if I can get a presumed positive sample...  You did draw a vial of blood and freeze it right?

-Jake


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Re: [DIYbio] Need help in San Francisco (Burlingame)!

It needs to be shipped to Moscow, Idaho.  Basically the unit just needs to be picked up and delivered to the UPS store 5 min away.  If you can box the unit that would be wonderful, but I believe the UPS store can handle that if needed.  I already contacted the nearest UPS store and it does not seem to be a problem to supply payment info via email to have it shipped.

Please shoot me a text or email and I'll send the pickup number and shipping info.  PayPal will be the easiest way to pay you for your time, but WU can be arranged also!

-Jake

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[DIYbio] Transgenic Vector Control vs. Zika Virus...

Dear Colleagues,

Witnessing daily the tragedy and human suffering caused by the Zika virus outbreak, and expecting the news to only get worse as mosquito season approaches and the true human cost is revealed, I feel compelled to devote time and effort into a solution.  As my non-profit and I have a moderately well equipped molecular biology lab, we will be working to develop a vector control solution.

Oxitec has done a lot of work with repressable dominant lethal genes and produced two promising transgenic strains, a sterile male phenotype and a flightless female line.  However, I'm of the opinion that large, publicly traded biotech corporations aren't the best vehicle in which to secure community involvement and are not necessarily oriented towards a permanent solution.

I'd like to develop a strategy for the development of a transforming vector, and then make it available to labs around the world for the actual transformation.  Sort of a crowd sourced strategy to cover the labor involved in microinjection and create a large number of lines from diverse local populations.

To this end, it would be good to exploit positional effects to generate many lines with some variation.  On the other hand, a more permanent solution would be to develop a gene drive system that could more effectively crash the population.  Some good work has been done recently on CRISPR and TALEN based gene drive systems.

Any thoughts or ideas would be welcome...

Female-specific flightless phenotype for mosquito control
http://www.pnas.org/content/107/10/4550

-Jake

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2 Positions : BiZtalk Lead (AND) BizTalk Developer with SSIS; Philadelphia, PA :: 12+ Months

Hi,

 

Please find the below position and respond back to me at praveenk@xperttech.com

 

Job title 1: BizTalk Lead

Job Title 2 : BizTalk Developer with SSIS

Location: Philadelphia, PA

Duration: 12+ Months

 

Description:

1.       10+ years of .Net experience.

2.       Strong Object Oriented design/coding skills in C#, .NET.

3.       Experience with ASP.NET/ASP.NET MVC/Web API.

4.       Experience with REST,WCF, SOAP and related web service protocols.

5.       Experience with Entity Framework/LINQ SQL Server 2008-2012.

6.       Basic knowledge of HTML/CSS/JavaScript and popular Web UI libraries (JQuery) etc.

7.       knowledge / familiarity with applying design patterns.

8.       Experience with SSIS and possessing basic knowledge of SSRS.

9.       Excellent troubleshooting and debugging skills on SQL Server Stored Procedures and SSIS packages.

10.   Very good hands-on over migrating DTS packages into SSIS 2012 Packages.

11.   Familiar with DBA activities such as Backup and Restore, although not mandatory.

12.   At least 4+ years of experience in BizTalk development and its artifacts (like Maps, orchestrations, pipelines, custom pipelines, adapters).

13.   Experience creating BizTalk solutions using BizTalk design patterns and practices.

14.   Development, deployment, configuration and debugging of orchestration, transformations, messaging components, pipeline, and adapters

15.   Ability to communicate cross-functionally and negotiate with key stakeholders.

 

 

Thanks/Regards,

 

Praveen Kumar

 

400 W Cummings Park

Suite#2850

Woburn, MA-01801

Email: praveenk@xperttech.com

Phone: 781-797-1042

Fax: 978-405-5040

www.xperttech.com

 

 

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Re: [DIYbio] Need help in San Francisco (Burlingame)!

Jake,

Do you need it shipped somewhere or delivered? Where are you located
that the unit needs to be?

Maria

On Wed, Mar 30, 2016 at 11:31 AM, Jake <jakestew@mail.com> wrote:
> So I bought a pipette puller on ebay, and it turns out to be local pickup
> only. The unit weighs approx. 30 lbs, and they won't ship it to me. I'm
> hoping someone here might be willing to pick it up at 1576 Rollins Rd in
> Burlingame, CA. Looks like it's right off the 101.
>
> This unit is for my non-profit's efforts to create a transgenic mosquito for
> vector control in relation to the Zika virus. We'd be hoping to pay around
> $30 and/or a tax-deductible donation receipt to cover time and expense.
> We'd also handle the shipping cost of course.
>
> Sorry if this message would be better on Craigslist, but I tried there
> already and I think I'm just getting scammers replying. If you can help us
> out please contact me ASAP via text/phone/email, as they are charging
> storage fees by the day.
>
> Jake Stewart
> World Justice Action Co.
> Two Zero Eight 310 2562
> jakestew at mail dot com
>
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