Re: [DIYbio] Wood filter

here's the original article link:
http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0089934

TL;DR:

Xylem Structure and Rationale for ue of Conifer Xylem:
Angiosperms (flowering plants) have xylem conduits called vessels that
are derived from several cells arranged in a single file, having
diameters up to 0.5 mm and lengths ranging from a few millimeters to
several meters [7]. These parallel conduits have closed ends and are
connected to adjacent conduits via "pits" [8] (Figure 1d,e). The pits
have membranes with nanoscale pores that perform the critical function
of preventing bubbles from crossing over from one conduit to another.
The porosity of the pit membranes ranges in size from a few nanometers
to a few hundred nanometers, with pore sizes in the case of
angiosperms tending to be smaller than those in gymnosperms.

Construction of the Xylem Filter:
1 inch-long sections were cut from a branch with approximately 1 cm
diameter. The bark and cambium were peeled off, and the piece was
mounted at the end of a tube and sealed with epoxy. The filters were
flushed with 10 mL of deionized water before experiments. Care was
taken to avoid drying of the filter.
The xylem filter device was constructed by simply peeling off the bark
and cambium from a section of the pine branch and inserting it into a
tube (Figure 2a). Although a simple tube fastener could provide a
leak-tight seal between the tube and the xylem, we used epoxy to
ensure that there was no inadvertent leakage. When deionized water was
loaded into the tube above the xylem and subjected to pressure in the
0.5-5 psi (3.45 to 34.5 kPa) range, we found that water readily flowed
through the xylem. The flow rate was proportional to applied pressure

Conclusions:
Pigment filtration experiments revealed a size cutoff of about 100 nm,
with most of the filtration occurring within the first 2-3 mm of the
xylem filter. The xylem filter could effectively filter out bacteria
from water with rejection exceeding 99.9%.
Pit membranes were identified as the functional unit where actual
filtration of the bacteria occurred.
Flow rates of about 4 L/d were obtained through ~1 cm2 filter areas
at applied pressures of about 5 psi, which is sufficient to meet the
drinking water needs of one person.

The simple construction of xylem filters, combined with their
fabrication from an inexpensive, biodegradable, and disposable
material suggests that further research and development of xylem
filters could potentially lead to their widespread use and greatly
reduce the incidence of waterborne infectious disease in the world.


On Fri, Feb 28, 2014 at 9:54 AM, leaking pen <itsatrap@gmail.com> wrote:
> http://www.upi.com/Science_News/2014/02/27/MIT-scientists-show-tree-branch-to-be-effective-water-purifier/7811393531999/?spt=mps&or=1
>
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[DIYbio] Re: large dna extraction

A suggestion:
 
If you can reproduce the 15kb band, you can core out a section from the gel and use WGA (whole genome amplifcation kit)  to amplify it, then sequence the amplification product.  The presence of EtBr won't interfere with the amplification.
Stacy

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Fwd: Urgent Client Need: Java Developer; (Wellesley, MA; 1 Year

Please send your resumes at niranjan@datasoft-tech.com

 

Hi,


This is Niranjan from Datasoft; hope you are doing well.

Please go through below description and reply with your resume, contact details and current location, if you feel comfortable

 

Java Developer

Skills – Spring, Hibernate, Restful Webservices Java

Location – (Wellesley, MA)

Duration – 1 Year

 

Most Important – This is a financial client and they will need to do a background check through a security agency. The security agency checks about 7 years of background, both in the US and India or elsewhere.

 

Interview – 2 over the phone. If the candidate is local than 1 onsite might be needed.

 

Start Date – Immediately, after passing the interview and the security check (which takes about 1-3 days and they need to fill some paperwork and provide proper documents etc.

 

 

Thanks& Regards

Niranjan Kumar

https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcTED2K-ZSNrENGYfQqbsVsOHYM6siFiMXKNTNdUYfECQhH0owJ4hg

 

DataSoft Technologies, Inc.

11555 Medlock Bridge Rd Suite 100
Johns Creek, GA 30097
Contact No: 770-755-1713
Email: niranjan@datasoft-tech.com
Fax: 877-888-7207
www.datasoft-tech.com

 



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Urgent Client Need: Java Developer; (Wellesley, MA; 1 Year

Please send your resumes at niranjan@datasoft-tech.com

 

Hi,


This is Niranjan from Datasoft; hope you are doing well.

Please go through below description and reply with your resume, contact details and current location, if you feel comfortable

 

Java Developer

Skills – Spring, Hibernate, Restful Webservices Java

Location – (Wellesley, MA)

Duration – 1 Year

 

Most Important – This is a financial client and they will need to do a background check through a security agency. The security agency checks about 7 years of background, both in the US and India or elsewhere.

 

Interview – 2 over the phone. If the candidate is local than 1 onsite might be needed.

 

Start Date – Immediately, after passing the interview and the security check (which takes about 1-3 days and they need to fill some paperwork and provide proper documents etc.

 

 

Thanks& Regards

Niranjan Kumar

https://encrypted-tbn0.gstatic.com/images?q=tbn:ANd9GcTED2K-ZSNrENGYfQqbsVsOHYM6siFiMXKNTNdUYfECQhH0owJ4hg

 

DataSoft Technologies, Inc.

11555 Medlock Bridge Rd Suite 100
Johns Creek, GA 30097
Contact No: 770-755-1713
Email: niranjan@datasoft-tech.com
Fax: 877-888-7207
www.datasoft-tech.com

 

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Urgent requirement : Oracle DBA : Princeton, NJ.

Hello,
Hope you are doing well,

Please go through the following requirement and let me know on
Dhruv@riderconsultinginc.com if you have any available resources

 

 

Position:  Oracle DBA

 

 

Locations:  Princeton, NJ

 

 

Duration: 6+ month contract

 

 

Job Description :

Please do not send Junior candidates, I will not consider them.

3-5  10 + years experience as an Oracle Infrastructure DBA

·        Hands on experience building, configuring and regression testing Oracle RAC

·        Hands on experience with installing and configuring Oracle GRID control and monitoring and alarming

·        Hands on experience with Oracle ASO installation and wallet and encryption key management

·        Experienced with database backup, recovery, Rman (Data Domain or Avomar experience a plus)

·        Strong verbal and written communication skills

·        Must be able to work independently and effectively in a team environment

 

 

 

Thanks,
Dhruv Soni

Phone : 980-272-1261
Email :
Dhruv@riderconsultinginc.com
Gtalk :
dhruvsoni.rider@gmail.com

 

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[DIYbio] Wood filter

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[DIYbio] Re: Ultra-Cheap DNA Printing/Sequencing

Curiously, have you priced out the materials?  Not the materials to make the device, but the materials to run it, the enzymes and nucleotides?

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[DIYbio] Re: Any favorite safety videos?

The Zombie College Lab Safety film is a fun one.

http://www.youtube.com/watch?v=S6WARqVdWrE&list=PL4qaj9envIYnltGxkA_BUAxk0WbhypQIo&index=2

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Urgent requirement : Project Manager : Philadelphia, PA

Hello,
Hope you are doing well,

Please go through the following requirement and let me know on
Dhruv@riderconsultinginc.com if you have any available resources

 

 

Position:  Project Manager

 

Locations:  Philadelphia, PA

 

Skill Set:  Mobile - Objective C / iPhone

Duration: 18 months+

 

 

Job Description :

 

A Project Manager with regulatory experience would be a great fit.

 

Project Manager

Responsibilities include:

 

·         Plan, organize, monitor and control projects for the completion of procedural, infrastructure and/or software development to meet project specifications.

·         Identify and utilize appropriate skill levels to staff project teams, while providing development opportunities and mentoring for team members, as appropriate.

·         Understand and apply the Project Management Institute (PMI) Body of Knowledge (PMBOK).

 

Minimum Skills and Experience:

 

·         Three to Five years’ experience in project management

·         Experience managing projects with vendor activities

·         Demonstrated success as a project manager

·         Through understanding of Microsoft Project Professional, Project Web Access and Project Server, as well as, baseline management and change control.

·         PMI membership and/or PMI certification, a plus

·         Working knowledge of PMBOK principles.

 

 

Thanks,
Dhruv Soni

Phone : 980-272-1261
Email :
Dhruv@riderconsultinginc.com
Gtalk :
dhruvsoni.rider@gmail.com

 

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Re: [DIYbio] Re: dna purification (once more)

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I don't have much to add on chromosomal isolation, but:

> The smears on your miniprep gel are most likely from the supercoiling
> of the plasmid. This is easily remedied by a single digestion to
> linearize the plasmid.

Nope; supercoiling yields three bands. One for supercoiled DNA, one for
circular but relaxed (single-strand nick) and another for linearised
(double-stranded break). A smear indicates DNA degradation beyond nicks
or single-point breaks, or impure sample (as in, more than just DNA in
there).

On 27/02/14 17:49, W. Estell wrote:
> You can keep running the gel with your genomic DNA kit sample and cut
> out the chromosomal DNA. You can do a clean up of the DNA with
> protease instead of phenol/chloroform. There should be a protocol for
> the protease purification in this kit (
> http://sciencewiz.com/products/science_Books_Kits_DNA.php), or some
> other I saw for making DNA ink. Also, there is this video of a very
> simple DNA extraction (http://www.youtube.com/watch?v=uJI_Ti0N1Dk).
> You could do a Tide/ethanol extraction then gel purify your sample to
> get your plasmid and chromosomal DNA. I think this would be the
> cheapest way to do it. The Tide will work great if it isn't
> contaminated with DNA. The proteases in the detergent should (might)
> kill any nucleases.
>
> So, I would suggest trying the "protocol" from the video as a
> starting point for a cheap DNA prep. You are going to run the sample
> on a gel no mater what, so it wouldn't make much sense to purify
> before the gel when you can just cut out the bands.
>
> The smears on your miniprep gel are most likely from the supercoiling
> of the plasmid. This is easily remedied by a single digestion to
> linearize the plasmid.
>
> On Wednesday, February 26, 2014 1:00:47 PM UTC-8, phillyj wrote:
>>
>> Hi again, I'm going to start a new thread, with pics.
>>
>> So intro: gram positive bacteria, need to extract chromosomal dna
>> and its plasmid dna.
>>
>> Tried so far: [1] Modified qiagen miniprep (lysozyme treatment
>> before lysis). The results: Nanodrop concentration of 100ng/uL. The
>> gel image shows a smear. See attached image. [2] Used Life
>> Technologies chargeswitch genomic DNA kit.Got about 20ng/uL
>> consistently for 4 samples. Gel shows one band above 10kb (so maybe
>> 15-20kb?) and another band just on top in wells.
>>
>> What I need to do: [3] Since I have total dna, if I can just get
>> the plasmid dna out, I can then proceed to sequencing. I am not
>> sure why the plasmid extraction failed using the miniprep kit. It
>> also failed to purify the plasmid band on the gel using gel
>> extraction kit.
>>
>> I hate to keep spending money buying different kits. I want to find
>> out what exactly is going on.
>>
>

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Re: [DIYbio] About The Brainwave control:

I am willing to sell my emotiv eeg headset right now—never used. Software packages must be bought separately or hacked from the python library available online. Email privately if interested!


On Wed, Feb 26, 2014 at 11:13 AM, Jonathan BISSON <bjonnh-diybio@bjonnh.net> wrote:
Thomas Liu <qazcom3@gmail.com> writes:

> My name is Thomas Liu, i am Hong Kong Institute of Education student, i do
> my final project About use the Brainwave control to control phone calls
> switch , but i test the waveform is not stable, and i not have other brain
> wave to contrast, I am not currently have any clue, can give me some
> proposal?
>
You may have a look at hackaday, they often show some mind-reading
related projects.

Especially this one:
http://hackaday.com/2014/02/07/thumbs-down-songs-on-pandora-with-your-mind/

Which looks like you may be able to use it almost directly for your
project.


There are also more "complex" things:
http://hackaday.com/2013/05/23/herd-single-cell-organisms-with-your-mind/

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[DIYbio] Re: dna purification (once more)

Do you actually know that this bacteria has a plasmid in it? If so, do you know how big the plasmid is? Is it a naturally occurring plasmid? Do you know its copy number?
 
Naturally occurring plasmids typically exist at low copy number, often only 1-2 copies per cell. This contrasts with common plasmid vectors used for research in E. coli, which have been engineered to have much higher copy numbers, often several hundred per cell. Small, high copy number plasmids are easy to see on gels because they're small enough to survive cell lysis and purification without being broken up, and there's a lot of the plasmid.
 
In contrast, large, low copy number plasmids are usually difficult or impossible to see on gels. There's not as much total DNA (due to the low copy number), and their large size often means they get broken into random fragments during lysis/purification (just like the chromosomal DNA does).
 
Note that the band that you're seeing in the gdna.jpg image isn't necessarily a plasmid. Sometimes, depending on how you isolate the DNA and how you run the gel, the randomly fragmented chromosomal DNA will appear as a fairly discrete band, looking a lot like what you've shown. I'm not sure why, but I saw it fairly often as a grad student. It may partly be a tendency for the chromosomal DNA to break up into similarly sized pieces. Also, standard agarose gels aren't able to resolve DNA outside of a certain size range. So a given gel might easily separate plasmids that are 3K & 4K in size, but pieces of DNA that are 20K and 50K could all migrate in the same position.
 
Finally, I respectfully disagree with W. Estell that the smearing on the plasmid.jpg image could be due to supercoiling. Under some conditions, variation in supercoiling could show up as a bit of fuzziness in a plasmid band, but nothing approaching the size of the smear you're seeing. That's clearly due to getting a broad range of different size DNA fragments, almost certainly from fragmentation of the chromosome during lysis & purification. That can easily happen during qiagen-type procedures if you shake or mix things too vigorously after cell lysis.

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Re: [DIYbio] Re: dna purification (once more)

I would argue that the smearing is degradation and not supercoiling. I have not seen supercoiling run as a smear in the many gels I have run but this is still a possibility.


On Thu, Feb 27, 2014 at 9:49 AM, W. Estell <william.estell@gmail.com> wrote:
You can keep running the gel with your genomic DNA kit sample and cut out the chromosomal DNA. You can do a clean up of the DNA with protease instead of phenol/chloroform. There should be a protocol for the protease purification in this kit (http://sciencewiz.com/products/science_Books_Kits_DNA.php), or some other I saw for making DNA ink. Also, there is this video of a very simple DNA extraction (http://www.youtube.com/watch?v=uJI_Ti0N1Dk). You could do a Tide/ethanol extraction then gel purify your sample to get your plasmid and chromosomal DNA. I think this would be the cheapest way to do it. The Tide will work great if it isn't contaminated with DNA. The proteases in the detergent should (might) kill any nucleases.

So, I would suggest trying the "protocol" from the video as a starting point for a cheap DNA prep. You are going to run the sample on a gel no mater what, so it wouldn't make much sense to purify before the gel when you can just cut out the bands.

The smears on your miniprep gel are most likely from the supercoiling of the plasmid. This is easily remedied by a single digestion to linearize the plasmid.

On Wednesday, February 26, 2014 1:00:47 PM UTC-8, phillyj wrote:
Hi again, I'm going to start a new thread, with pics.

So intro: gram positive bacteria, need to extract chromosomal dna and
its plasmid dna.

Tried so far:
[1] Modified qiagen miniprep (lysozyme treatment before lysis). The
results: Nanodrop concentration of 100ng/uL. The gel image shows a
smear. See attached image.
[2] Used Life Technologies chargeswitch genomic DNA kit.Got about
20ng/uL consistently for 4 samples. Gel shows one band above 10kb (so
maybe 15-20kb?) and another band just on top in wells.

What I need to do:
[3] Since I have total dna, if I can just get the plasmid dna out, I
can then proceed to sequencing. I  am not sure why the plasmid
extraction failed using the miniprep kit. It also failed to purify the
plasmid band on the gel using gel extraction kit.

I hate to keep spending money buying different kits. I want to find
out what exactly is going on.

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[DIYbio] Re: dna purification (once more)

You can keep running the gel with your genomic DNA kit sample and cut out the chromosomal DNA. You can do a clean up of the DNA with protease instead of phenol/chloroform. There should be a protocol for the protease purification in this kit (http://sciencewiz.com/products/science_Books_Kits_DNA.php), or some other I saw for making DNA ink. Also, there is this video of a very simple DNA extraction (http://www.youtube.com/watch?v=uJI_Ti0N1Dk). You could do a Tide/ethanol extraction then gel purify your sample to get your plasmid and chromosomal DNA. I think this would be the cheapest way to do it. The Tide will work great if it isn't contaminated with DNA. The proteases in the detergent should (might) kill any nucleases.

So, I would suggest trying the "protocol" from the video as a starting point for a cheap DNA prep. You are going to run the sample on a gel no mater what, so it wouldn't make much sense to purify before the gel when you can just cut out the bands.

The smears on your miniprep gel are most likely from the supercoiling of the plasmid. This is easily remedied by a single digestion to linearize the plasmid.

On Wednesday, February 26, 2014 1:00:47 PM UTC-8, phillyj wrote:
Hi again, I'm going to start a new thread, with pics.

So intro: gram positive bacteria, need to extract chromosomal dna and
its plasmid dna.

Tried so far:
[1] Modified qiagen miniprep (lysozyme treatment before lysis). The
results: Nanodrop concentration of 100ng/uL. The gel image shows a
smear. See attached image.
[2] Used Life Technologies chargeswitch genomic DNA kit.Got about
20ng/uL consistently for 4 samples. Gel shows one band above 10kb (so
maybe 15-20kb?) and another band just on top in wells.

What I need to do:
[3] Since I have total dna, if I can just get the plasmid dna out, I
can then proceed to sequencing. I  am not sure why the plasmid
extraction failed using the miniprep kit. It also failed to purify the
plasmid band on the gel using gel extraction kit.

I hate to keep spending money buying different kits. I want to find
out what exactly is going on.

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[DIYbio] Re: free 3d printers for hackerspaces?

Free 1.000.000€!  ...if you win.

Am Donnerstag, 27. Februar 2014 12:53:11 UTC+1 schrieb jem:

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[DIYbio] free 3d printers for hackerspaces?

http://www.3ders.org/articles/20140225-lulzbot-giving-away-taz-3d-printers-to-hackerspaces.html


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[DIYbio] IndieFreeB - Submit your ideas for a chance to win a free IndieBB kit

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See here for details:
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The gist of this: If you can't afford IndieBB but want to get a kit, go
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best
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Re: [DIYbio] dna purification (once more)

There's hardly any difference between large plasmids and chromosomes. Both is just DNA. So I guess the genomic DNA kit will also co-purify plasmids.

Though, PCR purification kits usually have a mechanism to remove fragments <20 bp IIRC.

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Re: [DIYbio] dna purification (once more)

On Wed, Feb 26, 2014 at 8:43 PM, Josiah Zayner <josiah.zayner@gmail.com> wrote:
>
> Are you sample limited?
> If not why not try and grow up one culture for genomic DNA purification and
> another for plasmid purification.
>

Not really sample limited. I have a few grams of pelleted cells. These
can't be easily grown, they need some special media. It's a WT
bacteria, probably isolated from a sample.

> Are you sure that band is a plasmid? Have you tried retransforming it and.or
> cleaving it with restriction enzymes or PCR?
>
I am going to guess that it is not a common bacteria. I was not told
anything more about its sequence or features. It needs to be
sequenced, so maybe it is novel? I will have to find out more though.
If it is not plasmid, what else could it be?

> Do you have a spectrophotometer.nanodrop to check the concentration of the
> DNA that was purified?
>
Yes. Miniprep results gave me 100ng/uL. gDNA results show around 20ng/uL.


By the way, when a kit says it purifies genomic dna from bacteria, is
it just chromosomal dna or will it also have plasmid in it?

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Re: [DIYbio] dna purification (once more)

Google has many PDF versions, it's also on the wiki
http://diyhpl.us/wiki/diybio/faq/books/

On Wed, Feb 26, 2014 at 3:24 PM, Jeswin <phillyj101@gmail.com> wrote:
> On Wed, Feb 26, 2014 at 5:42 PM, Nathan McCorkle <nmz787@gmail.com> wrote:
>> Did you try the tried and true methods from sambrook? They're quite cheap
>> and easy and not size dependent.
>>
> No, I haven't looked into it yet. I don't have the book, so is there a
> place I can see those protocols? Or at least give me names of the
> methods so I can google it.
>
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Re: [DIYbio] dna purification (once more)


Are you sample limited?
If not why not try and grow up one culture for genomic DNA purification and another for plasmid purification.

Are you sure that band is a plasmid? Have you tried retransforming it and.or cleaving it with restriction enzymes or PCR?

Do you have a spectrophotometer.nanodrop to check the concentration of the DNA that was purified?

If you have access to Phenol, Chloroform and Ethanol you can do a Phenol chloroform purification. Lots of protoocols for this online.



On Wednesday, February 26, 2014 3:24:16 PM UTC-8, phillyj wrote:
On Wed, Feb 26, 2014 at 5:42 PM, Nathan McCorkle <nmz...@gmail.com> wrote:
> Did you try the tried and true methods from sambrook? They're quite cheap
> and easy and not size dependent.
>
No, I haven't looked into it yet. I don't have the book, so is there a
place I can see those protocols? Or at least give me names of the
methods so I can google it.

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Re: [DIYbio] dna purification (once more)

phillyj, I just send you a message about it

El jueves, 27 de febrero de 2014 10:24:16 UTC+11, phillyj escribió:
On Wed, Feb 26, 2014 at 5:42 PM, Nathan McCorkle <nmz...@gmail.com> wrote:
> Did you try the tried and true methods from sambrook? They're quite cheap
> and easy and not size dependent.
>
No, I haven't looked into it yet. I don't have the book, so is there a
place I can see those protocols? Or at least give me names of the
methods so I can google it.

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