molecular biology laboratory from scratch RE: Methods Digest, Vol 40, Issue 17

Utsugi, Heidi K via methods%40net.bio.net (by hutsugi from fhcrc.org)
Tue Sep 23 12:50:34 EST 2008


One the most important Mol. Bio. Lab. tool that I tell my graduating Lab Managers (PI newbies) is SPACE FOR A SECURED -80C.  Buy a freezer, plug it into a 'dedicated outlet with alarm phone notification' and never, never give any shelf space away.  Fill the freezer with empty boxes to give the illusion that it is all in use.  You'll use it eventually.
 
Heidi

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Sent: Tue 9/23/2008 10:05 AM
To: methods from magpie.bio.indiana.edu
Subject: Methods Digest, Vol 40, Issue 17



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Today's Topics:

   1. Setting up a new mole biol laboratory (yoginee budhkar)
   2. About PEG (darshini.prasanna from gmail.com)
   3. neural networks (darshini.prasanna from gmail.com)
   4. Re: Setting up a new mole biol laboratory (WS)
   5. Re: neural networks (WS)
   6. RACE (Scott Brown)


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Message: 1
Date: Mon, 22 Sep 2008 10:35:48 +0530
From: "yoginee budhkar" <eenigoy from gmail.com>
Subject: Setting up a new mole biol laboratory
To: methods from magpie.bio.indiana.edu
Message-ID:
        <77ddf6c70809212205m6b8e8c71t545f237191342316 from mail.gmail.com>
Content-Type: text/plain; charset=ISO-8859-1

Dear Friends,

We are planning to set up a molecular biology laboratory from scratch. I am
required to make a list of equipments required for regular use in the
laboratory. We have already shortlisted major equipment like

chemidoc system, RT PCR, 2D gel electrophoresis system, laminar air flow,
 etc

with smaller equipments like submarine gel electrophoresis units, PAGE
units, western and southern blot apparatus, speed vac, hand held uv torch,
uv transilluminator, tabletop centrifuge, autoclave,

and other everyday use apparetus like waterbath, pH meter, magnetic
stirrers, vortex, incubator, oven, digital balance and the freezers of -20
and -70 degrees Celsius etc

I need some inputs on whether there is anything crucial from the point of
view of a mole biol lab that I may have missed out... Any and all
suggestions are welcome!

Regards,
--Yg


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Message: 2
Date: Mon, 22 Sep 2008 02:50:37 -0700 (PDT)
From: darshini.prasanna from gmail.com
Subject: About PEG
To: methods from net.bio.net
Message-ID:
        <09d6802f-2298-4947-bde8-1dc1db7c802a from p31g2000prf.googlegroups.com>
Content-Type: text/plain; charset=ISO-8859-1

Hi does anyone know how PEG can be used for cell lysis.? whats the
mechanism of cell lysis by PEG?


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Message: 3
Date: Mon, 22 Sep 2008 02:56:55 -0700 (PDT)
From: darshini.prasanna from gmail.com
Subject: neural networks
To: methods from net.bio.net
Message-ID:
        <811b5d78-dfcc-4bdd-9a26-b7cdf69a8727 from n33g2000pri.googlegroups.com>
Content-Type: text/plain; charset=ISO-8859-1

hi can anyone help me how to use neural network in matlab? like how to
give inputs,weights,targets.?


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Message: 4
Date: Mon, 22 Sep 2008 14:39:14 -0700 (PDT)
From: WS <novalidaddress from nurfuerspam.de>
Subject: Re: Setting up a new mole biol laboratory
To: methods from net.bio.net
Message-ID:
        <9292eb86-dbbc-4842-a497-76ac7a6f5bcd from l42g2000hsc.googlegroups.com>
Content-Type: text/plain; charset=ISO-8859-1

Dear Yg,

basically, you already have mentioned all you need.

It might be a good thing to think of the regulations for work with
GMOs (which standards to follow to please administration and
government) and to apply for necessary permits before you start,
however.

Another point is to set up a system for tracking plasmids, primers and
GMOs (a small homebrew database with eg. Filemaker or something
similar should do it).

The most important ingredient might be a senior postdoc or technician
who is really familiar with molecular biology, knows all the nasty
tricks and how to avoid overpriced nice looking boxes containing
'super duper' kits for things that may be achieved much cheaper and
faster with homebrew methods and reagents (you might browse our
archives here and ask the wise guys of this NG any time).

One thing you maybe have omitted in your list is a well assorted set
of basic enyzmes and chemicals. Some vendors have special offers for
starting labs, so it might be worth to ask your favorite supplier for
a decent discount on that what you need. Also access to a source of
crushed ice and a quantitative realtime cycler (depending on your
scientific tasks) might be a plus. Also do not forget a household
microwave oven to boil agarose. A laminar flow actually is not really
necessary at all, at least as long as you do not need to protect
yourself from your bugs or work in an environment full of molds and
dust.
If you should want to perform sensitive PCRs or even diagnostics,
strongly consider separate rooms for assembling PCRs and running/
analyzing them.

Regarding geldocs systems, a cheap digital camera, equipped with an
orange filter should and a close-up lens do the job as well. For
cloning purposes, instead of a UV transilluminator, you better use a
blue LED light source. UV nicely kills DNA almost instantly. You may
get a small one for quite cheap together with a box of pre-cast
agarose gels in an orange plastic box which makes up a perfect filter
for EtBr an CyBrgreen (when cut in pieces. Thinking of Cambrex, now
part of Lonza). As an alternative to a water bath, thermocyclers so
nicely may be "abused" as programmable incubators...

What you won't need is a 2D gel system (at least for ordinary cloning
etc.)

Best of luck and happy cloning!

Wolfgang


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Message: 5
Date: Mon, 22 Sep 2008 14:58:49 -0700 (PDT)
From: WS <novalidaddress from nurfuerspam.de>
Subject: Re: neural networks
To: methods from net.bio.net
Message-ID:
        <7dca9ac8-1eec-4838-a45c-5550e70f38c2 from 79g2000hsk.googlegroups.com>
Content-Type: text/plain; charset=ISO-8859-1

Dear Darshini,

better post this question in the appropriate forum from Mathworks or
Octave (a free Matlab clone).
https://www-old.cae.wisc.edu/mailman/listinfo/help-octave

Enjoy!

Wo


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Message: 6
Date: Tue, 23 Sep 2008 08:58:19 +1000
From: "Scott Brown" <SBrown from ccia.unsw.edu.au>
Subject: RACE
To: <methods from magpie.bio.indiana.edu>
Message-ID:
        <2A67EA781EC7F949A2AB0A0D07A86C6A04C54F8B from mail01.ccia.local>
Content-Type: text/plain;       charset="us-ascii"


Dpes anyone know why the annealing temperatures for 3'RACE are always
much higher than normal?

S


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