Friday, April 30, 2010
New views at the nanoscale
New views at the nanoscale
"With MRFM, the sample to be examined is attached to the end of a tiny silicon cantilever (about 100 millionths of a meter long and 100 billionths of a meter wide). As a magnetic iron cobalt tip moves close to the sample, the atoms’ nuclear spins become attracted to it and generate a small force on the cantilever. The spins are then repeatedly flipped, causing the cantilever to gently sway back and forth in a synchronous motion. That displacement is measured with a laser beam to create a series of 2-D images of the sample, which are combined to generate a 3-D image."
"With MRFM, the sample to be examined is attached to the end of a tiny silicon cantilever (about 100 millionths of a meter long and 100 billionths of a meter wide). As a magnetic iron cobalt tip moves close to the sample, the atoms’ nuclear spins become attracted to it and generate a small force on the cantilever. The spins are then repeatedly flipped, causing the cantilever to gently sway back and forth in a synchronous motion. That displacement is measured with a laser beam to create a series of 2-D images of the sample, which are combined to generate a 3-D image."
Thursday, April 29, 2010
Wednesday, April 28, 2010
Tuesday, April 27, 2010
Monday, April 26, 2010
Sunday, April 25, 2010
Fwd: primer design guide
---------- Forwarded message ----------
From: John Cumbers <johncumbers@gmail.com>
Date: Sun, Apr 25, 2010 at 1:45 AM
Subject: Fwd: primer design guide
To: Mackenzie Cowell <macowell@gmail.com>, diybio@googlegroups.com
Hi Mac,
I've started using geneious for primer design, it uses primers3 but
with a nicer interface. I know you can make primers with the 30 day
free trial and maybe after that with the limited version. Genious is
a really nice tool in general for organizing and playing around with
sequences, although for high throughput stuff it is not the right
tool.
http://www.geneious.com/
Cheers,
John
---------- Forwarded message ----------
From: Nathan McCorkle <nmz787@gmail.com>
Date: Tue, Apr 20, 2010 at 8:17 PM
Subject: Re: primer design guide
To: Cory Tobin <cory.tobin@gmail.com>, diybio <diybio@googlegroups.com>
Thanks,
the square brackets fixed things as far as getting the coding sequence
inside the primers... now do you know if there is a way to tell it
specifically where to start and stop? or should I just remove the UTR
regions if I don't want to prime on them?
can you tell me if I need to be concerned with removing or chopping
the untranslated regions? What are their purposes? I am thinking of
ligating this cDNA into a vector that has a his-tag or a translocation
sequence (if I use it in yeast for secretion).
Again thanks a lot, great stuff to know (even though I could have got
it out of a prof in 5 minutes, its gonna stick with me now for sure)
-Nathan
On Tue, Apr 20, 2010 at 11:06 PM, Cory Tobin <cory.tobin@gmail.com> wrote:
>
> On Tue, Apr 20, 2010 at 7:06 PM, Nathan McCorkle <nmz787@gmail.com> wrote:
> > Still isn't working... ugh I did exactly what you said but it just keeps
> > pushing the start primer forward in the sequence, and the end primer is
> > getting pulled further into the sequence.... I'm really not sure why, this
> > system seems like it needs a redesign, or I'm just really missing something.
> > Any more help?
>
> Oh my bad, square brackets, not curly brackets.
>
> Yeah, the site isn't very web2.0ish. Pretty much the exact opposite.
> Although, they do a good job of describing what each of the parameters
> does (if you click on the links) and how to use them. It's just not
> blatantly obvious how everything works.
>
> Btw, the code is GPL so anyone can use it to make their own
> new-and-improved primer picker. I'm sure people have, I'm just not
> aware of them.
>
>
> -Cory
--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics
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From: John Cumbers <johncumbers@gmail.com>
Date: Sun, Apr 25, 2010 at 1:45 AM
Subject: Fwd: primer design guide
To: Mackenzie Cowell <macowell@gmail.com>, diybio@googlegroups.com
Hi Mac,
I've started using geneious for primer design, it uses primers3 but
with a nicer interface. I know you can make primers with the 30 day
free trial and maybe after that with the limited version. Genious is
a really nice tool in general for organizing and playing around with
sequences, although for high throughput stuff it is not the right
tool.
http://www.geneious.com/
Cheers,
John
---------- Forwarded message ----------
From: Nathan McCorkle <nmz787@gmail.com>
Date: Tue, Apr 20, 2010 at 8:17 PM
Subject: Re: primer design guide
To: Cory Tobin <cory.tobin@gmail.com>, diybio <diybio@googlegroups.com>
Thanks,
the square brackets fixed things as far as getting the coding sequence
inside the primers... now do you know if there is a way to tell it
specifically where to start and stop? or should I just remove the UTR
regions if I don't want to prime on them?
can you tell me if I need to be concerned with removing or chopping
the untranslated regions? What are their purposes? I am thinking of
ligating this cDNA into a vector that has a his-tag or a translocation
sequence (if I use it in yeast for secretion).
Again thanks a lot, great stuff to know (even though I could have got
it out of a prof in 5 minutes, its gonna stick with me now for sure)
-Nathan
On Tue, Apr 20, 2010 at 11:06 PM, Cory Tobin <cory.tobin@gmail.com> wrote:
>
> On Tue, Apr 20, 2010 at 7:06 PM, Nathan McCorkle <nmz787@gmail.com> wrote:
> > Still isn't working... ugh I did exactly what you said but it just keeps
> > pushing the start primer forward in the sequence, and the end primer is
> > getting pulled further into the sequence.... I'm really not sure why, this
> > system seems like it needs a redesign, or I'm just really missing something.
> > Any more help?
>
> Oh my bad, square brackets, not curly brackets.
>
> Yeah, the site isn't very web2.0ish. Pretty much the exact opposite.
> Although, they do a good job of describing what each of the parameters
> does (if you click on the links) and how to use them. It's just not
> blatantly obvious how everything works.
>
> Btw, the code is GPL so anyone can use it to make their own
> new-and-improved primer picker. I'm sure people have, I'm just not
> aware of them.
>
>
> -Cory
--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics
--
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Saturday, April 24, 2010
Friday, April 23, 2010
Thursday, April 22, 2010
Wednesday, April 21, 2010
Facebook F8: One graph to rule them all | The Social - CNET News
Facebook F8: One graph to rule them all | The Social - CNET News:
"'The stream is ephemeral. You post something to the stream and people see it for a few hours and then it mostly floats away,'"
Which is why I harvest from facebook and post to blogger
"'The stream is ephemeral. You post something to the stream and people see it for a few hours and then it mostly floats away,'"
Which is why I harvest from facebook and post to blogger
Tuesday, April 20, 2010
Google releases tool to show government censorship requests | Technology | The Guardian
Google releases tool to show government censorship requests | Technology | The Guardian:
"'Chinese officials consider censorship demands as state secrets, so we cannot disclose that information at this time.'"
There should be no 'state secrets' in any country. Whatever they are hiding is probably wrong.
"'Chinese officials consider censorship demands as state secrets, so we cannot disclose that information at this time.'"
There should be no 'state secrets' in any country. Whatever they are hiding is probably wrong.
DARPA announces plans for self-piloted flying car
DARPA announces plans for self-piloted flying car:
"And it should be built and ready for testing by 2015."
The CAD files of all designs made with public money should be publicly posted throughout the development process.
"And it should be built and ready for testing by 2015."
The CAD files of all designs made with public money should be publicly posted throughout the development process.
Scientists track variant of gene-regulating protein in embryonic stem cells
Scientists track variant of gene-regulating protein in embryonic stem cells
Articles like this should be edited and gathered into an up to date online textbook.
Articles like this should be edited and gathered into an up to date online textbook.
The $1000 Genome: Coming Soon?
The $1000 Genome: Coming Soon?
“We intend to introduce another instrument in 2014 capable of sequencing an entire human genome in a matter of 15 minutes for $100,”
“We intend to introduce another instrument in 2014 capable of sequencing an entire human genome in a matter of 15 minutes for $100,”
Monday, April 19, 2010
Fwd: [Open Manufacturing] Fwd: [ssi_list] 3-D Printing Device Could Build Moon Base from Lunar Dust
---------- Forwarded message ----------
From: Bryan Bishop <kanzure@gmail.com>
Date: Fri, Apr 16, 2010 at 1:33 PM
Subject: [Open Manufacturing] Fwd: [ssi_list] 3-D Printing Device Could Build Moon Base from Lunar Dust
To: Open Manufacturing <openmanufacturing@googlegroups.com>, kanzure@gmail.com
--
- Bryan
http://heybryan.org/
1 512 203 0507
--
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From: Bryan Bishop <kanzure@gmail.com>
Date: Fri, Apr 16, 2010 at 1:33 PM
Subject: [Open Manufacturing] Fwd: [ssi_list] 3-D Printing Device Could Build Moon Base from Lunar Dust
To: Open Manufacturing <openmanufacturing@googlegroups.com>, kanzure@gmail.com
---------- Forwarded message ----------
From: markreiff <markreiff@earthlink.net>
Date: Fri, Apr 16, 2010 at 1:24 PM
Subject: [ssi_list] 3-D Printing Device Could Build Moon Base from Lunar Dust
To: ssi_list@yahoogroups.com
![Yahoo! Groups]()
![]()
From: markreiff <markreiff@earthlink.net>
Date: Fri, Apr 16, 2010 at 1:24 PM
Subject: [ssi_list] 3-D Printing Device Could Build Moon Base from Lunar Dust
To: ssi_list@yahoogroups.com
FYI,
"3-D Printing Device Could Build Moon Base from Lunar Dust"
Space.com
http://www.space.com/businesstechnology/3-d-printer-moon-base-100416.html
: Future astronauts might end up living in a moon base created
: largely from lunar dust and regolith, if a giant 3-D printing
: device can work on the lunar surface.
: The print-on-demand technology, known as D-Shape, could save on
: launch and transportation costs for manned missions to the moon.
: But the concept must first prove itself in exploratory tests funded
: by the European Space Agency (ESA)
: "We will make very basic printing trials in a vacuum environment to
: verify if this is possible," said Enrico Dini, chairman of Monolite
: UK Ltd and creator of D-Shape.
: Dini's D-Shape has created full-size sandstone buildings on Earth
: by using a 3-D printing process similar to how inkjet printers
: work. It adds a special inorganic binder to sand so that it can
: build a structure from the bottom up, one layer at a time.
: The device raises its printer head by just 5 to 10 millimeters for
: each layer, moving from side to side on horizontal beams as well as
: up and down on four metal frame columns. Finished structures end
: made out of a marble-like material that's superior to certain types
: of cement. The buildings do not require iron reinforcing.
: Such a concept might help future lunar colonists live off the land,
: as well as provide thick-walled structures that protect against
: solar storms or micrometeorites.
: Space agencies have already begun testing other technologies meant
: to mine water and oxygen from the lunar regolith. NASA scientists
: have also played with possible recipes for a sort of lunar concrete
: based on moon dust.
: But D-Shape offers the added attraction of having a somewhat
: straightforward building process that does not require huge amounts
: of construction machinery or many robot laborers.
: Making the device work in a lunar environment may yet prove tricky.
: A first challenge involves making D-Shape function within the
: vacuum environment on a moon that lacks any meaningful atmospheric
: pressure. But Dini remains self-admittedly optimistic by nature.
: "I'm not a scientist and I'm not a technician — I'm an inventor,"
: Dini told SPACE.com. He spent five years "facing unexpected issues
: and finding unexpected solutions" when he first designed D-Shape,
: before heeding the call from ESA.
: Dini's Monolite has teamed up with an Italian aerospace firm called
: Alta, which has a large vacuum chamber in its Pisa facilities. They
: hope to build a small structure perhaps just 3 feet (1 meter) on
: each side during the vacuum trials.
: Other partners working on the ESA project include Foster+Partners,
: a UK architecture firm, and Scuola Superiore Sant'Anna Perceptual
: Robotics Laboratory, an Italian lab that specializes in robotics
: and automation.
: A second challenge comes from the cost of running D-Shape trials by
: using expensive lunar regolith simulant. Dini has tried developing
: a possible alternative to NASA's JSC-1 simulant that might work for
: his research. Structures built from such material will have to
: undergo resistance testing.
: Even a functional D-Shape that works with lunar regolith would
: still face building limitations based on the amount of binder that
: a rocket could carry to the moon. Yet success would mean
: transforming lunar dust into part of the solution, rather than just
: a problem for astronauts and robotic explorers.
: NASA researchers have experimented with a different type of on-site
: manufacturing device that could someday create spare parts or new
: materials for the International Space Station. D-Shape could also
: end up deploying beyond Earth for additional testing, if all goes
: well with the first phase.
: The most important trials will be done in outer space," Dini said.
Mark Reiff
__._,_.___
MARKETPLACE
.
__,_._,___
--
- Bryan
http://heybryan.org/
1 512 203 0507
--
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Sunday, April 18, 2010
Viruses harnessed to split water
Viruses harnessed to split water
2 years until a prototype?
Important technologies should be kept on a strict development track.
2 years until a prototype?
Important technologies should be kept on a strict development track.
Friday, April 16, 2010
Thursday, April 15, 2010
Fwd: [MakerBot] Re: New Firmware
---------- Forwarded message ----------
From: Nate True <natetrue@gmail.com>
Date: Thu, Apr 15, 2010 at 8:59 PM
Subject: [MakerBot] Re: New Firmware
To: MakerBot Operators <makerbot@googlegroups.com>
I loaded the new firmware and also had issues getting up to the right
temperature. My extruder was set to 230 but only ever got to 175, and
my platform was set to 100 but only got heated up to 75. Rolling back
to the previous extruder firmware returns my Makerbot to working
order. Anyone have any idea why the new firmware has these issues?
On Apr 15, 3:02 pm, Lyndondr <lyndo...@gmail.com> wrote:
> Another thing I keep seeing with these pause and hang issues that on
> one tries is the R1 - 180 ohm resistor the wiki says
>
> "Optional Component: This is the termination resistor for the RS485
> comms. The motherboard is located on one end of the bus, and only one
> extruder at the end of the bus should also have a termination
> resistor. You can remove it or omit it if you have multiple extruders
> and at least one has this resistor in place. This component can be
> placed in any orientation. "
>
> The key line here is "at least one has this resistor in place". The
> link below seems to confirm my theory. If you have ever worked with
> the old coax network cables you had to have a resistor at each end for
> it to work I think this is a similar situation. If I ever have this
> issue this will be the first thing I try. One thing that does puzzle
> me is why is this problem not more wide spread.
>
> http://www.lafraze.net/nbernard/makerbot/index.html
>
> On Apr 14, 3:34 pm, Chorca <cho...@gmail.com> wrote:
>
>
>
> > Here's the full story:
>
> > Been running a MakerBot for about two weeks here.. Been making parts
> > for a mendel, and started having issues where the x/y would pause and
> > the extruder would keep extruding, resulting in blobs that ruined the
> > print. Tried everything listed in the makerbot FAQ including moving
> > the machine, turning off fluorescent lights, twisting stepper wires,
> > rewiring to keep stepper wires away from comm wires, new ethernet
> > cable for connection to extruder, removed optostop cables, tried
> > different ports, looked for solder issues, etc. Tried the newer
> > firmware that was out, found that 2.0 a1 caused axis inversion issues.
> > Moved back to 1.6 on the motherboard, and 2.0a1 on the extruder, which
> > seemed to mostly fix the problem. It would still pause occasionally,
> > but only for a second, then pick back up.
>
> > A few days ago the extruder started having issues during a print, the
> > filament was buckling in the extruder even though the nozzle was to
> > temp. Decided to rebuild the nozzle. Tore it apart, cleaned everything
> > perfectly, redid threads with a tap/die, installed new MakerGear
> > HeatCore, affixed thermistor to nozzle, installed new PEEK barrier,
> > etc. Restarted printing, worked fine. Installed a .01uf cap between
> > the motor terminals to try and lower EMI output from the motor.
>
> > Yesterday I found the new firmware was at release 0 now, Tried it,
> > axis inversion problems were fixed, but extruder now would not get up
> > to temp. Was getting up to 170 when set to 240. Went back to old 1.8
> > firmware, temps resumed normal operation. Tried to print, same
> > filament buckling issue happened again. Rebuilt extruder a second
> > time, cleaning everything. Reinstalled, and it was still having this
> > issue. After about 5 mins of testing after the second rebuild, I
> > noticed the extruder had turned the drive motor off, and the temps
> > were falling. I reset the board, rewrote the firmware, and tried it
> > again. This time, the motor only came on for about 5 seconds before
> > going off, and it seemed to reset, the way the temps began falling.
> > Tried it a third time, and it just blipped on for about 1/2sec before
> > shutting down again. Lost comm when this happened as well.
>
> > Every time though, it's able to get right up to temp with no problems.
> > Plastic oozes out of the tip, but i can't get the plastic through.
> > Extruder controller will not turn on the motor any longer. I don't
> > know what the issue might be with the controller.. not sure if an H
> > bridge is burned out, we have a bad solder joint or something else is
> > wrong. I'm going to be trying my extruder controller (techzone remix)
> > that I got for my mendel to see if that works properly. Worst case i
> > plan to mount up my Wade's extruder with the heatcore and run that
> > with the mendel extruder controller running makerbot software.
>
> > Any ideas are appreciated. I doubt it's the firmware as when it failed
> > the last time, it was back on 1.8 - heated platform support.
>
> > On Apr 14, 3:01 pm, Lyndondr <lyndo...@gmail.com> wrote:
>
> > > What version firmware were you using and what are you ate know. When
> > > you say your controller "Borked", you may have to get a little more
> > > technical or talk down to me what ever the case may be. If I were to
> > > guess your barrel is not heating, and that can be a few different
> > > things.
>
> > > On Apr 14, 12:03 pm, Chorca <cho...@gmail.com> wrote:
>
> > > > I loaded this up last night and had some issues before my extruder
> > > > controller board died. I don't believe the firmware did that, since
> > > > i've been having issues for some time now, but I was not able to get
> > > > the heater to get up to temp.. the PWM seemed to level off way too
> > > > soon.. i.e. I had the temp set to 240, and it would only get to 170.
> > > > Other than that, it seemed to work in concert with the new mobo
> > > > firmware well, though I couldn't really test it as my extruder
> > > > controller borked shortly after.
>
> > > > On Apr 13, 11:39 pm, Lyndondr <lyndo...@gmail.com> wrote:
>
> > > > > Here is a link to all the firmware stuff.
>
> > > > > http://github.com/makerbot/G3Firmware
>
> > > > > On Apr 13, 7:26 pm, Jarek <supersonik...@gmail.com> wrote:
>
> > > > > > Downloaded and updated the firmware on my cupcake, but I'm really
> > > > > > curious as to what it does. Does anyone know a website where I can
> > > > > > view a changelog of the firmwares?
--
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From: Nate True <natetrue@gmail.com>
Date: Thu, Apr 15, 2010 at 8:59 PM
Subject: [MakerBot] Re: New Firmware
To: MakerBot Operators <makerbot@googlegroups.com>
I loaded the new firmware and also had issues getting up to the right
temperature. My extruder was set to 230 but only ever got to 175, and
my platform was set to 100 but only got heated up to 75. Rolling back
to the previous extruder firmware returns my Makerbot to working
order. Anyone have any idea why the new firmware has these issues?
On Apr 15, 3:02 pm, Lyndondr <lyndo...@gmail.com> wrote:
> Another thing I keep seeing with these pause and hang issues that on
> one tries is the R1 - 180 ohm resistor the wiki says
>
> "Optional Component: This is the termination resistor for the RS485
> comms. The motherboard is located on one end of the bus, and only one
> extruder at the end of the bus should also have a termination
> resistor. You can remove it or omit it if you have multiple extruders
> and at least one has this resistor in place. This component can be
> placed in any orientation. "
>
> The key line here is "at least one has this resistor in place". The
> link below seems to confirm my theory. If you have ever worked with
> the old coax network cables you had to have a resistor at each end for
> it to work I think this is a similar situation. If I ever have this
> issue this will be the first thing I try. One thing that does puzzle
> me is why is this problem not more wide spread.
>
> http://www.lafraze.net/nbernard/makerbot/index.html
>
> On Apr 14, 3:34 pm, Chorca <cho...@gmail.com> wrote:
>
>
>
> > Here's the full story:
>
> > Been running a MakerBot for about two weeks here.. Been making parts
> > for a mendel, and started having issues where the x/y would pause and
> > the extruder would keep extruding, resulting in blobs that ruined the
> > print. Tried everything listed in the makerbot FAQ including moving
> > the machine, turning off fluorescent lights, twisting stepper wires,
> > rewiring to keep stepper wires away from comm wires, new ethernet
> > cable for connection to extruder, removed optostop cables, tried
> > different ports, looked for solder issues, etc. Tried the newer
> > firmware that was out, found that 2.0 a1 caused axis inversion issues.
> > Moved back to 1.6 on the motherboard, and 2.0a1 on the extruder, which
> > seemed to mostly fix the problem. It would still pause occasionally,
> > but only for a second, then pick back up.
>
> > A few days ago the extruder started having issues during a print, the
> > filament was buckling in the extruder even though the nozzle was to
> > temp. Decided to rebuild the nozzle. Tore it apart, cleaned everything
> > perfectly, redid threads with a tap/die, installed new MakerGear
> > HeatCore, affixed thermistor to nozzle, installed new PEEK barrier,
> > etc. Restarted printing, worked fine. Installed a .01uf cap between
> > the motor terminals to try and lower EMI output from the motor.
>
> > Yesterday I found the new firmware was at release 0 now, Tried it,
> > axis inversion problems were fixed, but extruder now would not get up
> > to temp. Was getting up to 170 when set to 240. Went back to old 1.8
> > firmware, temps resumed normal operation. Tried to print, same
> > filament buckling issue happened again. Rebuilt extruder a second
> > time, cleaning everything. Reinstalled, and it was still having this
> > issue. After about 5 mins of testing after the second rebuild, I
> > noticed the extruder had turned the drive motor off, and the temps
> > were falling. I reset the board, rewrote the firmware, and tried it
> > again. This time, the motor only came on for about 5 seconds before
> > going off, and it seemed to reset, the way the temps began falling.
> > Tried it a third time, and it just blipped on for about 1/2sec before
> > shutting down again. Lost comm when this happened as well.
>
> > Every time though, it's able to get right up to temp with no problems.
> > Plastic oozes out of the tip, but i can't get the plastic through.
> > Extruder controller will not turn on the motor any longer. I don't
> > know what the issue might be with the controller.. not sure if an H
> > bridge is burned out, we have a bad solder joint or something else is
> > wrong. I'm going to be trying my extruder controller (techzone remix)
> > that I got for my mendel to see if that works properly. Worst case i
> > plan to mount up my Wade's extruder with the heatcore and run that
> > with the mendel extruder controller running makerbot software.
>
> > Any ideas are appreciated. I doubt it's the firmware as when it failed
> > the last time, it was back on 1.8 - heated platform support.
>
> > On Apr 14, 3:01 pm, Lyndondr <lyndo...@gmail.com> wrote:
>
> > > What version firmware were you using and what are you ate know. When
> > > you say your controller "Borked", you may have to get a little more
> > > technical or talk down to me what ever the case may be. If I were to
> > > guess your barrel is not heating, and that can be a few different
> > > things.
>
> > > On Apr 14, 12:03 pm, Chorca <cho...@gmail.com> wrote:
>
> > > > I loaded this up last night and had some issues before my extruder
> > > > controller board died. I don't believe the firmware did that, since
> > > > i've been having issues for some time now, but I was not able to get
> > > > the heater to get up to temp.. the PWM seemed to level off way too
> > > > soon.. i.e. I had the temp set to 240, and it would only get to 170.
> > > > Other than that, it seemed to work in concert with the new mobo
> > > > firmware well, though I couldn't really test it as my extruder
> > > > controller borked shortly after.
>
> > > > On Apr 13, 11:39 pm, Lyndondr <lyndo...@gmail.com> wrote:
>
> > > > > Here is a link to all the firmware stuff.
>
> > > > > http://github.com/makerbot/G3Firmware
>
> > > > > On Apr 13, 7:26 pm, Jarek <supersonik...@gmail.com> wrote:
>
> > > > > > Downloaded and updated the firmware on my cupcake, but I'm really
> > > > > > curious as to what it does. Does anyone know a website where I can
> > > > > > view a changelog of the firmwares?
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Fwd: What kits do people prefer for cDNA synth, and why?
---------- Forwarded message ----------
From: Nathan McCorkle <nmz787@gmail.com>
Date: Thu, Apr 15, 2010 at 1:35 PM
Subject: Re: What kits do people prefer for cDNA synth, and why?
To: diybio@googlegroups.com
The kit I used this morning included AMV reverse transcriptase, which has higher functioning temp which is better for denaturing secondary RNA structures... not sure how big a problem that is with mRNA.
From: Nathan McCorkle <nmz787@gmail.com>
Date: Thu, Apr 15, 2010 at 1:35 PM
Subject: Re: What kits do people prefer for cDNA synth, and why?
To: diybio@googlegroups.com
The kit I used this morning included AMV reverse transcriptase, which has higher functioning temp which is better for denaturing secondary RNA structures... not sure how big a problem that is with mRNA.
It doesn't seem like RNase H activity is much of a problem since I'm looking to amplify only a certain mRNA, rather than make a library... does that make sense, or is RNase H activity just bad/useless ?
--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics
On Thu, Apr 15, 2010 at 2:07 PM, Stanley Han <zhan528@gmail.com> wrote:
NEB kit doesn't seem to be robust. I don't know whay. Invitrogen has a Rt enzyme that has no endo H activity so that yo get more cDNA.Clontech seems to be good too. They are all more expensive.
On Thu, Apr 15, 2010 at 12:19 PM, Nathan McCorkle <nmz787@gmail.com> wrote:
--I am looking for cDNA synth kits and settled on this one at $4.33 a reaction:I was settled actually, until I used a promega kit this morning after doing a trizol-chloroform RNA extraction. My professor said that trizol is cheap and yields high amounts of RNA, and said that he uses the promega kit because our school prefers to order through VWR... I am still waiting to hear if we get a discount through VWR or not.If anyone has opinions about the kit I posted through NEB, or has a better recommendation please send quickly, as I'm trying to purchase stuff tomorrow, or at least have money set aside for its purchase.
--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/BioinformaticsYou received this message because you are subscribed to the Google Groups "DIYbio" group.
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--
Nathan McCorkle
Rochester Institute of Technology
College of Science, Biotechnology/Bioinformatics
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Fwd: Sequencer update
---------- Forwarded message ----------
From: TS Nowlan <apokruphos@gmail.com>
Date: Thu, Apr 15, 2010 at 1:20 PM
Subject: Re: Sequencer update
To: diybio@googlegroups.com
We have an ABI PRISM 310, an older model single-capillary sequencer. There is an electrical fault somewhere, which we are still in the process of hunting down / fixing. I'm not personally familiar with its materials (I'm used to just working with the data afterwards), but once we have it up and running I'm sure we'd happy to help test out your kit however we can.
-Tor
--
From: TS Nowlan <apokruphos@gmail.com>
Date: Thu, Apr 15, 2010 at 1:20 PM
Subject: Re: Sequencer update
To: diybio@googlegroups.com
We have an ABI PRISM 310, an older model single-capillary sequencer. There is an electrical fault somewhere, which we are still in the process of hunting down / fixing. I'm not personally familiar with its materials (I'm used to just working with the data afterwards), but once we have it up and running I'm sure we'd happy to help test out your kit however we can.
-Tor
On Thu, Apr 15, 2010 at 11:12 AM, Stanley Han <zhan528@gmail.com> wrote:
What type of ABI instrument do you have? I wonder if you will be interested in testing my dye removal kit with your instrument if you use capillery sequencer---PureSEQ?
On Thu, Apr 15, 2010 at 2:10 PM, Stanley Han <zhan528@gmail.com> wrote:
You need a enzyme that incorporate ddNTP efficiently for sequencing not regular Taq. Bigdye use this kind of Taq.
On Wed, Apr 14, 2010 at 7:39 PM, Mackenzie Cowell <mac@diybio.org> wrote:
I'm organizing a PCR genotyping workshop next weekend and have been looking for a diybio-friendly sanger sequencing provider (haven't actually made accounts or taked to anyone at any companies or sequencing centers yet, though). It would be extra cool to do some of the sequencing with diybio! If I got reagents, could you guys do some sequencing on one or two samples?Also, a general question about sanger sequencing: I'm probably going to use Taq, but I might purchase a higher-fidelity / higher-processivity polymerase. What sort of read lengths could I typically get from a commercial sanger sequencing provider? Like, 700-1000 bp? I would be interested in amplifying like 5kb, if possible.Cheers,Mac--
On Wed, Apr 14, 2010 at 7:23 PM, Bryan Bishop <kanzure@gmail.com> wrote:
---------- Forwarded message ----------
From: TS Nowlan <apokruphos@gmail.com>
Date: Wed, Apr 14, 2010 at 6:14 PM
Subject: Sequencer update
To: socal-diybio@googlegroups.com
Hey folks,
Things are moving slowly forward with our lovely sequencer, but I
thought it good to put all the docs and whatnot we've managed to find
together in one place. I've found a protocol for using it, a Windows
installer for ABI sequence analysis software (good to convert it into
a non-proprietary format for us to work with) and user's manuals for
the diagnostics system and the sequencer overall. I added links to all
that to the Lab Protocol wiki page, though I imagine it should have
its own page at some point. I'll likely be adding more this afternoon
as I find it.
Here's the link again for those that may have forgotten, or not made
accounts yet:
http://omegahelm.com/diybio/tiki-index.php?page=Lab+Protocols
And of course feel free to edit and add more stuff as you like.
-Tor
--
"And if ye cannot be saints of knowledge, then be at least its warriors."
-- Friedrich Nietzsche
--
- Bryan
http://heybryan.org/
1 512 203 0507
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+1.231.313.9062 / mac@diybio.org / @100ideas--
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-- Friedrich Nietzsche
--
-- Friedrich Nietzsche
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Wednesday, April 14, 2010
Fwd: MEMS-talk Digest, Vol 90, Issue 9
---------- Forwarded message ----------
From: <mems-talk-request@memsnet.org>
Date: Tue, Apr 13, 2010 at 11:00 AM
Subject: MEMS-talk Digest, Vol 90, Issue 9
To: mems-talk@memsnet.org
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mems-talk@memsnet.org
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Today's Topics:
1. wet chemical silicon etch with photoresist mask (10um)
(Robert MacDonald)
---------- Forwarded message ----------
From: Robert MacDonald <robm@shearwaterscientific.com>
To: mems-talk@memsnet.org
Date: Mon, 12 Apr 2010 00:09:49 -0800
Subject: [mems-talk] wet chemical silicon etch with photoresist mask (10um)
Does anyone know of a reliable wet chemical silicon etch (isotropic or anisotropic) which can be masked by photo resist? I need to etch down 10um.
Rob MacDonald
Hosted by the MEMS and Nanotechnology Exchange, the country's leading
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From: <mems-talk-request@memsnet.org>
Date: Tue, Apr 13, 2010 at 11:00 AM
Subject: MEMS-talk Digest, Vol 90, Issue 9
To: mems-talk@memsnet.org
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mems-talk@memsnet.org
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Today's Topics:
1. wet chemical silicon etch with photoresist mask (10um)
(Robert MacDonald)
---------- Forwarded message ----------
From: Robert MacDonald <robm@shearwaterscientific.com>
To: mems-talk@memsnet.org
Date: Mon, 12 Apr 2010 00:09:49 -0800
Subject: [mems-talk] wet chemical silicon etch with photoresist mask (10um)
Does anyone know of a reliable wet chemical silicon etch (isotropic or anisotropic) which can be masked by photo resist? I need to etch down 10um.
Rob MacDonald
Hosted by the MEMS and Nanotechnology Exchange, the country's leading
provider of MEMS and Nanotechnology design and fabrication services.
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Fwd: MEMS-talk Digest, Vol 90, Issue 10
---------- Forwarded message ----------
From: <mems-talk-request@memsnet.org>
Date: Wed, Apr 14, 2010 at 11:00 AM
Subject: MEMS-talk Digest, Vol 90, Issue 10
To: mems-talk@memsnet.org
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mems-talk@memsnet.org
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than "Re: Contents of MEMS-talk digest..."
Today's Topics:
1. Remove TDTS cover from wafer? (Lukas Bogunovic)
---------- Forwarded message ----------
From: Lukas Bogunovic <bogunovic@physik.uni-bielefeld.de>
To: mems-talk@memsnet.org
Date: Wed, 14 Apr 2010 12:43:21 +0200
Subject: [mems-talk] Remove TDTS cover from wafer?
Hi folks,
i have a question concerning
Tridecafluor-1,1,2,2-tetra-hydrooctyl-trichlorosilane (TDTS).
Before we do softlithography with PDMS, our wafers are covered with
vapour of this chemical. Sometimes, there are wafers that are not needed
anymore. without the tdts the su-8 structures on it can be easyly
removed with Caro's acid. That doesn't work for TDTS covered wafers -
they are highly resistant. Does anyone know how to remove this silane,
so that the wafer can be reused?
Thanks in advance!
Lukas Bogunovic
Bielefeld University - Biophysics and applied Nanoscience
Germany
bogunovic@physik.uni-bielefeld.de
Hosted by the MEMS and Nanotechnology Exchange, the country's leading
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From: <mems-talk-request@memsnet.org>
Date: Wed, Apr 14, 2010 at 11:00 AM
Subject: MEMS-talk Digest, Vol 90, Issue 10
To: mems-talk@memsnet.org
Send MEMS-talk mailing list submissions to
mems-talk@memsnet.org
To subscribe or unsubscribe via the World Wide Web, visit
http://mail.mems-exchange.org/mailman/listinfo/mems-talk
or, via email, send a message with subject or body 'help' to
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You can reach the person managing the list at
mems-talk-owner@memsnet.org
When replying, please edit your Subject line so it is more specific
than "Re: Contents of MEMS-talk digest..."
Today's Topics:
1. Remove TDTS cover from wafer? (Lukas Bogunovic)
---------- Forwarded message ----------
From: Lukas Bogunovic <bogunovic@physik.uni-bielefeld.de>
To: mems-talk@memsnet.org
Date: Wed, 14 Apr 2010 12:43:21 +0200
Subject: [mems-talk] Remove TDTS cover from wafer?
Hi folks,
i have a question concerning
Tridecafluor-1,1,2,2-tetra-hydrooctyl-trichlorosilane (TDTS).
Before we do softlithography with PDMS, our wafers are covered with
vapour of this chemical. Sometimes, there are wafers that are not needed
anymore. without the tdts the su-8 structures on it can be easyly
removed with Caro's acid. That doesn't work for TDTS covered wafers -
they are highly resistant. Does anyone know how to remove this silane,
so that the wafer can be reused?
Thanks in advance!
Lukas Bogunovic
Bielefeld University - Biophysics and applied Nanoscience
Germany
bogunovic@physik.uni-bielefeld.de
Hosted by the MEMS and Nanotechnology Exchange, the country's leading
provider of MEMS and Nanotechnology design and fabrication services.
Visit us at http://www.mems-exchange.org
Want to advertise to this community? See http://www.memsnet.org
To unsubscribe:
http://mail.mems-exchange.org/mailman/listinfo/mems-talk
Fwd: You can now 3D print in glass with Shapeways
---------- Forwarded message ----------
From: Shapeways <Shapeways@mail.vresp.com>
Date: Wed, Apr 14, 2010 at 9:33 AM
Subject: You can now 3D print in glass with Shapeways
To: technologiclee@gmail.com
From: Shapeways <Shapeways@mail.vresp.com>
Date: Wed, Apr 14, 2010 at 9:33 AM
Subject: You can now 3D print in glass with Shapeways
To: technologiclee@gmail.com
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