From owner-biophysics@net.bio.net Fri Jan 01 22:00:00 1999 Path: biosci!biosci!not-for-mail From: kottenhahn@icdd.com Newsgroups: bionet.biophysics,bionet.cellbiol,bionet.molbio.proteins Subject: 1999 Denver X-ray Conference Announcement Date: 2 Jan 1999 05:29:49 -0800 Organization: International Centre for Diffraction Data Lines: 30 Sender: daemon@net.bio.net Distribution: world Message-ID: <76dgvn$r3r$1@nnrp1.dejanews.com> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.biophysics:4695 bionet.cellbiol:11073 bionet.molbio.proteins:13756 1999 Denver X-ray Conference Announcement The 1999 Denver X-ray Conference will be held August 2-6 at the Sheraton Steamboat Resort, Steamboat Springs, Colorado, U.S.A. The Call for Papers includes information regarding the sessions and workshops that are scheduled for the '99 conference, abstract submission guidelines, and also hotel reservation information. You can find this information at http://www.dxcicdd.com If you would like to be added to the Denver X-ray Conference mailing list, or require additional information regarding the conference, please contact: Denise Flaherty, Conference Coordinator ICDD 12 Campus Blvd. Newtown Square, PA 19073 Phone: 610-325-9814 Fax: 610-325-9823 E-mail: flaherty@icdd.com -- 1999 Denver X-ray Conference International Centre for Diffraction Data www.icdd.com, www.dxcicdd.com, www.ixas.org webmaster@icdd.com -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-biophysics@net.bio.net Fri Jan 01 22:00:00 1999 From: "clive delmonte" Newsgroups: bionet.biophysics Subject: DNA Structure: Puzzle Number 14 Date: Sat, 2 Jan 1999 13:56:29 -0000 Lines: 63 X-Newsreader: Microsoft Outlook Express 4.71.1712.3 X-MimeOLE: Produced By Microsoft MimeOLE V4.71.1712.3 NNTP-Posting-Host: 195.7.225.152 Message-ID: <368e1078.0@news.netdirect.net.uk> X-Trace: 2 Jan 1999 12:26:32 GMT, 195.7.225.152 Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.tli.de!newsfeed.nacamar.de!ayres.ftech.net!news.ftech.net!peer.news.nildram.co.uk!news-peer.netdirect.net.uk!news.netdirect.net.uk!195.7.225.152 The Linking Number Paradox The topological geometry of double-helical DNA has been extensively explored. There remains a problem, however. Keller's electrophoretic gels (32) display quantised integer values of Tw in bands with a very clear background between bands. How would there be no blurring between bands, arising from different drag coefficients, if it were really true that the twist in a closed circular duplex DNA could take a continuum of values, through partitioning, determined by Tw=Lk - Wr ? The true side-by-side structure recorded by Lee et al. (Puzzle 1, ref. 1), for which Lk=0 in the relaxed state, would allow circular closure with only an identically integral number of positive or negative supercoils, for which Lk=Tw. The restrictive topological criteria set down by Crick et al. (33) and Bauer et al. (34), in their attempt to eliminate side-by-side models, did not apply to every side-by-side structural possibility, and do not apply to the structure found by Lee et al.: "...This proves that the linking number is not equal to zero (at least for the great majority of those (i.e., side-by-side molecules))." (33) and also their criteria apply only to such side-by-side models "...in which the two...chains do not coil around each other...but instead lie side by side over most of their length, having only a few helical turns." (34) The structure found by Lee et al. has Lk=0, identically, in the relaxed state over any and all lengths. When wound around nucleosomal cores in closed circular DNA, with -1.75 superhelical turns per nucleosome, subsequent removal of the core histones can introduce only identically -1 superhelical turn per nucleosome. Here is a straightforward, simple resolution of the Linking Number Paradox. 32 Determination of the Number of Superhelical Turns in SV40 DNA by Gel Electrophoresis; W. Keller; Proc. Nat. Acad. Sci. Vol 72 (1975) 4876 - 4880 33 Is DNA Really a Double Helix ? F.H.C. Crick, J.C. Wang & W.R. Bauer; J Mol Biol Vo, 129 (1979) 449 - 461 34 Supercoiled DNA; W.R. Bauer, F.H.C. Crick & J.H. White; Scientific American Vol 243 (1980) 100 - 113 -------------------------------------------------------------------- Clive Delmonte From owner-biophysics@net.bio.net Fri Jan 01 22:00:00 1999 Path: biosci!biosci!not-for-mail From: kottenhahn@icdd.com Newsgroups: bionet.biophysics,bionet.cellbiol,bionet.molbio.proteins Subject: Pharmaceutical Powder X-ray Diffraction Symposium Date: 2 Jan 1999 05:29:35 -0800 Organization: International Centre for Diffraction Data Lines: 29 Sender: daemon@net.bio.net Distribution: world Message-ID: <76df52$pji$1@nnrp1.dejanews.com> NNTP-Posting-Host: net.bio.net Xref: biosci bionet.biophysics:4694 bionet.cellbiol:11072 bionet.molbio.proteins:13755 Announcing PPXRD - Pharmaceutical Powder X-ray Diffraction Symposium September 27-29, 1999 Pennsylvania, U.S.A. Organized by the International Centre for Diffraction Data. Topics include: XRD Applications in Pre-Formulation and Formulation Non-ambient XRD Applications in Pharmaceuticals Crystallinity and Crystal Form Quantification Structure Determination, Indexing and Molecular Modeling Patents & Regulatory Issues. Questions/Comments/Suggestions? Contact: J. Ginsburg, ICDD, 12 Campus Blvd., Newtown Square, PA, 19073, U.S.A. FAX: 610-325-9823, E-mail:PPXRD@icdd.com Web site: www.icdd.com -- International Centre for Diffraction Data www.icdd.com, www.dxcicdd.com, www.ixas.org webmaster@icdd.com -----------== Posted via Deja News, The Discussion Network ==---------- http://www.dejanews.com/ Search, Read, Discuss, or Start Your Own From owner-biophysics@net.bio.net Sat Jan 02 22:00:00 1999 Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news.nero.net!newshub.tc.umn.edu!news1.tc.umn.edu!not-for-mail From: "Chris Gross" Newsgroups: bionet.biophysics Subject: 16th American Peptide Symposium Date: Sun, 03 Jan 1999 16:55:09 -0600 Organization: University of Minnesota Lines: 43 Message-ID: <76osah$k2$4@news1.tc.umn.edu> NNTP-Posting-Host: x162-77.chem.umn.edu Mime-Version: 1.0 Content-Type: text/plain; charset="US-ASCII" Content-Transfer-Encoding: 7bit X-Newsreader: Microsoft Outlook Express for Macintosh - 4.01 (295) Dear Colleagues, We would like to call to your attention the 16th American Peptide Symposium which will be held in Minneapolis from June 26-July 1, 1999. The "Call for Papers & Registration Information" was mailed to current members of the American Peptide Society just before Thanksgiving and should have been received by now. Requests for information should be sent via e-mail to 16aps@chem.umn.edu. In addition, please check our web site at www.chem.umn.edu/16aps, which contains all of the pertinent information and is now set up to accept both abstracts and registrations electronically. In setting as the theme for the meeting "Peptides for the New Millennium," we want to highlight how peptide science can play a role in fields as diverse as synthetic chemistry, pharmaceutical discovery, biomaterials, and proteomics, among the topics that will be featured. Subscribers to this forum may be particularly interested in our session on analytical and biophysical methods. We hope that you will consider attending, and perhaps submit one or more abstracts. Feel free to pass along your suggestions to us, and also to spread the news about the Symposium to others in your professional circle. With thanks and best wishes for a Happy New Year! GB and GF ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ George Barany Telephone: (612) 625-1028 Distinguished McKnight University Professor of Chemistry, Laboratory Medicine & Pathology Department of Chemistry FAX: (612) 626-7541 University of Minnesota e-mail: barany@tc.umn.edu 207 Pleasant Street S.E. web site: http://www.chem.umn.edu/ Minneapolis, MN 55455 groups/baranygp/barany.html Gregg B. Fields Telephone: (561) 297-2093 Professor of Chemistry & Biochemistry Center for Molecular Biology & Biotechnology FAX: (561) 297-2759 Florida Atlantic University e-mail: fieldsg@fau.edu 777 Glades Road web site: http://www.science.fau.edu/ Boca Raton, FL 33431-0991 chemistry/fields.htm From owner-biophysics@net.bio.net Sat Jan 02 22:00:00 1999 Path: biosci!agate!newsfeed.berkeley.edu!cyclone.swbell.net!nntp.giganews.com!news2.giganews.com.POSTED!not-for-mail From: "barry" Subject: Attn. European PI's Newsgroups: bionet.biophysics Message-ID: <01be36df$2af29360$a039a5d1@gout> X-Newsreader: Microsoft Internet News 4.70.1162 Lines: 15 NNTP-Posting-Date: Sun, 03 Jan 1999 00:06:43 CDT X-Trace: sv1-YD6tIcA37rZpv5x7rBw4OJYFqBjMrBaT9nJnaNS2FDnKbKuUU4sBQhq7TatMpJS9W9tvlVW/gt8/n2O!iNMhnwn8aNsg X-Complaints-To: abuse@GigaNews.Com X-Abuse-Info: Please be sure to forward a copy of ALL headers X-Abuse-Info: Otherwise we will be unable to process your complaint properly Date: Sun, 03 Jan 1999 06:06:43 GMT Hello, I am a twenty-seven year old graduate. I have been working in the area of molecular biology for a few years now and my greatest aspiration has been to work in Europe to learn a foreign language while working in my field. I speak some French and less German. I have investigated some job and student opportunities abroad but it seems that one needs to be an EU citizen. I have gotten to the point where I feel I must give up this dream of going to Europe or I should reconsider my career goals. If anyone out there knows of a program that could accommodate an American interested in going to France/Germany to study in the area of structural biology (X-ray cryst., NMR, etc.), please contact me or forward this message to a colleague. I will send a resume promptly. Thank you very much for your assistance. Sincerely, C.Barry From owner-biophysics@net.bio.net Sat Jan 02 22:00:00 1999 Path: biosci!OTTER.BIOCHEM.UBC.CA!mcintosh From: mcintosh@OTTER.BIOCHEM.UBC.CA (Lawrence McIntosh) Newsgroups: bionet.biophysics Subject: biophysics grad. program Date: 2 Jan 1999 17:45:51 -0800 Organization: ubc Lines: 60 Sender: daemon@net.bio.net Distribution: world Message-ID: <368ECBFC.39E2B9D3@otter.biochem.ubc.ca> Reply-To: mcintosh@otter.biochem.ubc.ca NNTP-Posting-Host: net.bio.net --------------6C2AA8EDC9C3B892F62D025E Content-Type: text/plain; charset=us-ascii Content-Transfer-Encoding: 7bit Hello: We are beginning to organize a graduate program in molecular biophysics / structural biology at the University of British Columbia. The program will likely bridge numerous departments / faculties and involve a common series of graduate level courses and seminars. If you are involved in a similar program, or know of one, I would greatly appreciate any information (e.g. brochures, websites) or practical advice describing its organization, requirements, courses, etc. With thanks, Lawrence McIntosh Department of Biochemistry 2146 Health Sciences Mall University of British Columbia Vancouver, BC, Canada V6T 1Z3 mcintosh@otter.biochem.ubc.ca --------------6C2AA8EDC9C3B892F62D025E Content-Type: text/html; charset=us-ascii Content-Transfer-Encoding: 7bit 

  Hello:


We are beginning to organize a graduate program in

molecular biophysics / structural biology at the

University of British Columbia. The program will likely

bridge numerous departments / faculties and involve

a common series of graduate level courses and seminars.


If you are involved in a similar program, or know of

one, I would greatly appreciate any information (e.g.

brochures, websites) or practical advice describing its

organization, requirements, courses, etc.


With thanks,


Lawrence McIntosh


Department of Biochemistry

2146 Health Sciences Mall

University of British Columbia

Vancouver, BC, Canada   V6T 1Z3

mcintosh@otter.biochem.ubc.ca

--------------6C2AA8EDC9C3B892F62D025E--


From owner-biophysics@net.bio.net Wed Jan 06 22:00:00 1999
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From: "charade" 
Subject: Neuroscience site
Newsgroups: bionet.biophysics
Followup-To: bionet.biophysics
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Date: Tue, 05 Jan 1999 16:03:00 GMT
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Hi,

I maintain a Neuroscience site at The Mining Co.  The site is designed
to be a useful resource for information on the internet that is related
to neuroscience and neurological issues.  It has original feature
articles on a wide range of topics and pages of annotated links to
other neuroscience-related sites on the net.

The site is located at:  http://neuroscience.miningco.com/


Rich Schuerger

_________________________________________________________________

Richard Schuerger
Northwestern University                      Voice: (312)503-9810
Dept. of Physiology M211                       FAX: (312)503-5101
303 E. Chicago Ave.,  Chicago, IL 60611
   http://neuroscience.miningco.com
   http://pubweb.acns.nwu.edu/~rjs979/useful.html

Today's Quote (#426)

Every great advance in science has issued from a new audacity of
imagination.
    - John Dewey, 1859-1952



--
Surf Usenet at home, on the road, and by email -- always at Talkway.
http://www.talkway.com



From owner-biophysics@net.bio.net Wed Jan 06 22:00:00 1999
Path: biosci!news.alaska.edu!newsfeed.acns.nwu.edu!newsfeed.berkeley.edu!newsfeed.cwix.com!158.43.192.17!rill.news.pipex.net!pipex!ams.news.uu.net!uunet!in5.uu.net!news.inter.net.il!not-for-mail
From: nir_21@internet-zahav.net (Nir Dagan)
Newsgroups: bionet.biophysics
Subject: rasmol
Date: Tue, 05 Jan 1999 22:49:10 GMT
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I am making an academic evaluation of the Rasmol program for graphic
visualisation of proteins and would appreciate any comments any of you
might have regarding the benefits, shortcomings and specially comments
for improvment. 

thanks,				Nir Dagan

       nir_21@internet-zahav.net

From owner-biophysics@net.bio.net Wed Jan 06 22:00:00 1999
From: "clive delmonte" 
Newsgroups: bionet.biophysics
Subject: DNA Structure: Puzzle Number 16
Date: Mon, 4 Jan 1999 22:27:09 -0000
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More Fun with Z-DNA

Chen (37) reported that methylated poly(dC.dG) x 2  existed in the Z forms
at both low and high salt concentrations, and that both of these forms were
interconvertible into a B form at intermediate salt concentrations.  A
rather similar sequence of interconversions, of Z to A and then on to a
further Z form was reported by Wu & Behe (38) as they raised the salt
concentration monotonically from low to high values in their study.

Are we to consider that all of these interconvertible transitions were of
left going to right and then back to left-handed forms as the salt
concentration was raised ?

In the previous Puzzle we saw how the proposition that Z, A and B forms had
the same helical handedness allowed an explanation of the results of fibre
transitions of B to Z, and also those of Miller et al. for the much
accelerated B to Z transition on nucleosomal cores.

For refs. 37 and 38 we can consider as a working hypothesis that there are
several Z forms (both based on Hoogsteen pairing), rather as there are
several forms (A & B) based on Watson-Crick pairing, and it is one of these
several Z forms which lie on each side of the B and A forms reported
respectively in refs. 37 and 38.


37        Conformational Lability of Poly(dG.5 methyl dC); Fu-Ming Chen;
Nucl Acids Res Vol 14 (1986) 5081 - 5097

38        Salt-induced Z-A-Z transition sequence in the mixed ribo-deoxyribo
copolymer poly (rG-dC); H.-Y. Wu & M.J. Behe; Proc Nat Acad Sci (USA) Vol 81
(1984) 7284 - 7287

--------------------------------------------------------------
Clive Delmonte




From owner-biophysics@net.bio.net Wed Jan 06 22:00:00 1999
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Message-ID: <3691348F.138E42D1@magellan.umontreal.ca>
From: Stefan Seefeld 
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Subject: Re: Kepplers Second Law
References: <368CC44A.BF5E6E34@emirates.net.ae>
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Juzer Gunja wrote:
> 
> Can anyone out there PROVE Kepplers Second Law????????

it is a geometrical statement of the conservation of
angular momentum, which follows from isotropy of space.

So once you accept isotropy of space ("there is no way
to distiguish a direction in space, all laws act equally
with respect to directional changes") you get conservation
of angular momentum. The exact mathematical formulation (in
it's integral form) IS Keplers second law.

Stefan

_______________________________________________________              
              
Stefan Seefeld
Departement de Physique
Universite de Montreal
email: seefelds@magellan.umontreal.ca

_______________________________________________________

      ...ich hab' noch einen Koffer in Berlin...

From owner-biophysics@net.bio.net Wed Jan 06 22:00:00 1999
From: "clive delmonte" 
Newsgroups: bionet.biophysics
Subject: DNA Structure: Puzzle Number 15
Date: Mon, 4 Jan 1999 14:01:25 -0000
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Z-DNA

Miller et al. (35) reported that, using duplex poly deoxy (Guanosine -
5-methyl-Cytosine), the B to Z transition took place an order of magnitude
faster when the polymer in the B form was fully wound round nucleosome cores
than when the B-DNA was free in solution.

How would a right to left helical transition in duplex DNA take place an
order of magnitude faster when wound around nucleosomal histones than when
free in solution?

There is a clue to a possible answer in the work of Sasisekharan &
Brahmachari, and others, (Puzzle 5, refs. 26 & 27) who suggest that B- and
Z-DNA have the same helical handedness since the B to Z transition is seen
by several groups to occur under very mild conditions inside a solid fibre.
(Such reasoning
had been advanced many years earlier as support for the proposition that the
A & B forms had the same handedness because of the same observation.)

Then the B to Z transition could be faster on nucleosomes because of the
highly ordered structure, and slower in solution because of the high degree
of folding and twisting of the duplex in solution.

We recall that there is actually no direct experimental evidence that Z-DNA
is left-handed.  Topological experiments predicated on its left-handedness
have failed, and none known to me have succeeded.  The X-ray diffraction
reports on Z-DNA structure (e.g., Puzzle 12, ref. 22) were based on fitting
the data to a model chosen by the workers themselves (e.g., Ref. 22 (Note
19) and ref.36 (page 4017, "..we should again attempt the method...using a
trial model of left-handed Z-DNA.))

On this basis, the fast B to Z transition observed by Miller et al. might
merely consist of Watson-Crick base pairs becoming Hoogsteen pairs, by a
fast purine flip, leading to CD inversion at certain frequencies, with both
B & Z forms being right-handed.   With a Hoogsteen base pair width of
0.88nm, a true side-by-side duplex has a major elliptical axis of some 1.76
nm and will just fit into certain reported, small unit cells such as that of
Arnott & Selsing (Puzzle 6, ref.9 (1.78nm)), for example, which is too small
to accommodate a Watson-Crick double helix.


35        Nucleosome-core Assembly on B & Z Forms of Duplex
Poly(d(G-5-methyl-C)); F.D. Miller, J.B. Rattner & J.H. van der Sande: Cold
Spring Harbor Symposia on Quantitative Biology Vol 47 (1983) 571-575

36        The tetramer d(CGCG) crystallises as a left-handed double helix;
J.L.Crawford et al.; Proc Nat Acad Sci (USA); Vol 77 (1980) 4016 - 4020
---------------------------------------------------------
Clive Delmonte




From owner-biophysics@net.bio.net Wed Jan 06 22:00:00 1999
From: "clive delmonte" 
Newsgroups: bionet.biophysics
Subject: DNA Structure: Puzzle Number 17
Date: Tue, 5 Jan 1999 19:00:09 -0000
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More on AFM & STM

A number of research groups have measured the heights of single stranded DNA
as being the same as duplex DNA, within experimental error (e.g., 39, giving
a diameter of 1 nm approx.)

This result is quite impossible for a DNA double helix when compared with a
single- stranded helix.   However, if we look again at the true side-by-side
DNA duplex recorded by Lee et al. (Puzzle 1, ref.1) it is evident that this
is the only possible outcome, namely, that single- and double-stranded DNA
would have the same height under AFM and STM.

Moreover, a helical diameter of around 1 nm accords with the results of the
studies recorded in Puzzles 1, 2, 3, 4 and 12.



39        Atomic force microscopy of single- and double-stranded DNA; H.G.
Hansma et al.; Nucl Acids Res Vol 20 (1992) 3585 - 3590

------------------------------------------------------------------
Clive Delmonte








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From: cathy168@yahoo.com
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I was wondering if anyone had any suggestions for reading material concerning
Sequence Analysis.  I am looking for books on Computer Algorithms.

I have "Computer Analysis of Sequence Data, Part I" (on loan from a
professor), but the copyright is 1994.  I was wondering if anyone knew of
anything more recent.

A quick search of amazon.com brings up a few items.  However, if anyone has
read what amazon brings up, commentary on those would be good to hear.

Any help would be appreciated.  Thanks in advance.

--dave
dkk@eden.rutgers.edu

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From owner-biophysics@net.bio.net Fri Jan 08 22:00:00 1999
From: "clive delmonte" 
Newsgroups: bionet.biophysics
Subject: DNA Structure: Puzzle Number 18
Date: Fri, 8 Jan 1999 19:35:00 -0000
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The Diameter of Tetraplexes under AFM

Vesenka and colleagues have measured the strand height of DNA tetraplexes.
Their guanine-rich tetraplexes were found to have a strand height, i.e.,
diameter of 2.1 to 2.5nm (40).

Curiously enough, this is the height which should be recorded for the DNA
double helix under AFM and STM, but no-one has ever found these values, or
anything approaching them, for duplex DNA.

It seems that this situation has caused Vesenka to reflect on the meaning of
the height measurements for duplex and tetraplex DNA (41).

Determined readers of these Puzzles will discern a different explanation
(42).  If two of the true side-by-side DNA duplexes caught on STM by Lee et
al. (Puzzle 1, ref. 1, Figure 3b (duplex height = 1.3 nm)) are laid one upon
the other, et voila! we have a true side-by-side tetraplex with a height
around 2.5 nm.

The implied pairing of base pairs into tetrads was described by Loewdin long
ago (43).

Equally important, and in accord with the structure of Lee et al., using
AFM, Vesenka's group reports "...no significant differences in duplex and
quadruplex DNA width." (44)


40        A new DNA nanostructure, the G-wire, imaged by scanning probe
microscopy; T.C. Marsh, J. Vesenka & E. Henderson; Nucl Acids Res Vol 23
(1995) 696 - 700

41        Atomic Force Microscopy of Duplex DNA Diameter Paradox; J.
Vesenka; Scanning Vol 18 (1996) 133 - 134

42        Advances in AFM & STM Applied to the Nucleic Acids; Clive Delmonte
(1997); ISBN 0 9512276 2 9; Chapter 8, Figure 8.1

43        Electronic Aspects of Biochemistry, Chapter by P.-O. Loewdin,
Editor: B. Pullman; Academic Press (1963)

44        The morphology of duplex and quadruplex DNA on mica; Tera Muir et
al.; Draft paper kindly supplied by James Vesenka prior to publication in J
Vac Sci & Tech. (1996)
--------------------------------------------------------------
Clive Delmonte












From owner-biophysics@net.bio.net Fri Jan 08 22:00:00 1999
Message-ID: <3696258F.139BA1C@guest.pf.wau.nl>
Date: Fri, 08 Jan 1999 16:34:39 +0100
From: "Paul W.J. van den Wijngaard" 
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Subject: source for heating filaments L/M pipette puller
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Could someone please give me a telephone or fax number to contact List
medical to order heating filaments for a L/M-3-P-A patch pipette puller.
When I try the numbers I have there is no answer.
If someone knows a different supplier of filaments that will fit my List
medical puller that would be great too.

Thanks very much,

Paul W. J. van den Wijngaard
laboratory of Plant Physiology
Wageningen Agricultural University
Wageningen, The Netherlands
paul.vandenwijngaard@guest.pf.wau.nl


From owner-biophysics@net.bio.net Sun Jan 10 22:00:00 1999
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From: "barry" 
Subject: Re: Attn. European PI's
Newsgroups: bionet.biophysics
References: <01be36df$2af29360$a039a5d1@gout>
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Thank you very much to everyone that responded. I would just like everyone
to note that I am not a Ph.D. yet, so I can not do a post-doc untill I am.
I am a highly motivated graduate with work experience. So if you know of
any European studentships for an American gradute, please keep sending me
contact information. Thanks in advance.


Chris

From owner-biophysics@net.bio.net Sun Jan 10 22:00:00 1999
Path: biosci!SENTURY.COM!Directmarketing
From: Directmarketing@SENTURY.COM
Newsgroups: bionet.biophysics
Subject: FREE! Download! URL Submission Software! Over 700+ Search Engines & Links (Growing Monthly!)
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From owner-biophysics@net.bio.net Mon Jan 11 22:00:00 1999
Path: biosci!news.stanford.edu!newsfeed.berkeley.edu!nntp2.dejanews.com!nnrp1.dejanews.com!not-for-mail
From: stourville@ibcusa.com
Newsgroups: bionet.biophysics
Subject: fluorescence and molecular probes
Date: Tue, 12 Jan 1999 22:06:46 GMT
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I am looking for any new information (6-8 Months) on fluorescence and/or
molecular probe technologies, particularly applications in drug discovery and
clinical diagnostics.

If you have any new information please forward a summary of the work to my
attention.

Thank you.

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From owner-biophysics@net.bio.net Tue Jan 12 22:00:00 1999
Path: biosci!news.stanford.edu!logbridge.uoregon.edu!newshub.nntp.mr.net!solomon.io.com!news.tamu.edu!not-for-mail
From: Ernie Maynard 
Newsgroups: bionet.biophysics
Subject: Re: Enzyme activity units?
Date: Tue, 12 Jan 1999 19:11:01 -0600
Organization: Texas A&M University, College Station, Texas
Lines: 12
Message-ID: <369BF2A5.BF9377D1@chemvx.tamu.edu>
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I believe it is generally held that 1 unit of enzymatic activity is equal to 1
micromole of product formed per minute. The specific activity of an enzyme is
defined in terms of units per mg.
--Ernie

JLaigle wrote:

> Can anyone tell me what units are used to measure enzyme activity? I am
> translating a doct from Spanish on food enzymes and came across an entry
> "enzyme activity" and the listing 10,000 NPU/g and 55,000 BAA/g. Are these
> international abbreviations or the Spanish equivalents of them?


From owner-biophysics@net.bio.net Tue Jan 12 22:00:00 1999
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From: "Wizard" 
Newsgroups: bionet.biophysics,nkz.fido.ru.biology
Subject: ðÏÍÏÇÉÔÅ ÒÅÛÉÔØ ÚÁÄÁÞËÕ ÐÏ ÂÉÏÆÉÚÉËÅ! çÏÒÀ!
Date: Wed, 13 Jan 1999 13:32:20 +0700
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éÔÁË ÓÁÍÁ ÚÁÄÁÞÁ:

þÅÍÕ ÒÁ×ÎÏ ÉÚÍÅÎÅÎÉÅ Ó×ÏÂÏÄÎÏÊ ÜÎÅÒÇÉÉ çÉÂÂÓÁ ÐÒÉ ÄÏÓÔÉÖÅÎÉÉ ÒÁ×ÎÏ×ÅÓÉÑ ×
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ÔÅÍÐÅÒÁÔÕÒÁ 37 ÇÒÁÄÕÓÏ× ãÅÌØÓÉÑ.

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< kvp@aero.altai.su > ÉÌÉ < vicpav@chat.ru >
ÉÌÉ ÏÔÐÒÁ×ÌÑÔØ × ËÏÎÆÅÒÅÎÃÉÀ.

éÚ×ÉÎÉÔÅ ÚÁ ×ÏÐÒÏÓ ÎÅ × ÓÔÒÏÞËÕ.

÷ÉËÔÏÒ ëÕÚÎÅÃÏ×.



From owner-biophysics@net.bio.net Thu Jan 14 22:00:00 1999
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From: fluorescence@hello.to
Newsgroups: bionet.biophysics
Subject: Re: fluorescence and molecular probes
Date: Fri, 15 Jan 1999 20:21:23 GMT
Organization: Deja News - The Leader in Internet Discussion
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In article <77gh1b$6sl$1@nnrp1.dejanews.com>,
  stourville@ibcusa.com wrote:
> I am looking for any new information (6-8 Months) on fluorescence and/or
> molecular probe technologies, particularly applications in drug discovery and
> clinical diagnostics.
>
> If you have any new information please forward a summary of the work to my
> attention.
>
> Thank you.

You should read the new updated section Journals and Books at
http://hello.to/fluorescence

There is a new book available containing a summary and a lot of news given on:
-Methods and Trends in Fluorescence Spectroscopy
-Analytical Fluorescence Probes
-Fluorescence Probes in Polymers
-Applications of Fluorescence Spectroscopy in Biology
-Fluorescence Techniques in Medicine - a Challenge for the Future.

In addition to this you should contact people listed in the work group
directory, members of the Society of Fluorescence or the Sof-webmaster.

Does this information helping you?

Best Regards
TW


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From owner-biophysics@net.bio.net Thu Jan 14 22:00:00 1999
Path: biosci!1STCONNECT.COM!temptingtearouts
From: temptingtearouts@1STCONNECT.COM (Tempting Tear-Outs)
Newsgroups: bionet.biophysics
Subject: ===>> reply via email for more info:   FREE 1 yr USA Magazine Sub
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To be removed from our mailing list, please send email to:
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From owner-biophysics@net.bio.net Fri Jan 15 22:00:00 1999
Path: biosci!pravda.ucr.edu!ihnp4.ucsd.edu!newsfeed.berkeley.edu!newsfeed.cwix.com!204.210.0.20!news.san.rr.com!not-for-mail
From: "Bruce Tedeschi" 
Newsgroups: bionet.biophysics
Subject: Informational Site
Lines: 3
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Organization: TWC Road Runner, San Diego, CA

www.sanbio.com  Pretty good...



From owner-biophysics@net.bio.net Sat Jan 16 22:00:00 1999
Path: biosci!rutgers!rockyd.rockefeller.edu!newsfeed.nyu.edu!newshub.northeast.verio.net!news-feeds.jump.net!solomon.io.com!outfeed1.news.cais.net!in1.nntp.cais.net!world2.bellatlantic.net!news
From: "Douglas Nicoll" 
Newsgroups: alt.bio.technology,alt.bio.technology.misc,bionet,bionet.biology,bionet.biophysics,bionet.cellbiol
Subject: Human Tissues, Organs and DNA from Families for Medical Research
Date: Sun, 17 Jan 1999 11:24:18 -0000
Organization: Bell Atlantic Internet Solutions
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Xref: biosci bionet.biophysics:4727 bionet.cellbiol:11131

See www.ndri.com for access to human tissues and organs for medical
researchers

See www.hbdi.org for information about family collections containing DNA and
immortalized cells - over 600 families - for medical and genetic researchers












From owner-biophysics@net.bio.net Sat Jan 16 22:00:00 1999
Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.enteract.com!cyclone.i1.net!uunet!in5.uu.net!news.inter.net.il!not-for-mail
From: "Barak Akabayov" 
Newsgroups: bionet.biophysics
Subject: Thermodynamics&Biology
Date: Sun, 17 Jan 1999 15:11:49 +0200
Organization: Internet Gold, ISRAEL
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Hi,
I need central concepts in Biological Application of Thermodynamics.
Thank you.
Ak_barak@internet-zahav.net




From owner-biophysics@net.bio.net Sat Jan 16 22:00:00 1999
Path: biosci!internet!biosci!not-for-mail
From: biohelp (BIOSCI Administrator)
Newsgroups: bionet.biophysics
Subject: BIOSCI/bionet miniFAQ & Fundraiser
Date: 17 Jan 1999 02:00:10 -0800
Organization: BIOSCI International Newsgroups for Molecular Biology
Lines: 233
Sender: daemon@net.bio.net
Distribution: world
Message-ID: <199901171000.CAA28336@net.bio.net>
NNTP-Posting-Host: net.bio.net

(LAST REVISION: 30-JUL-95)

This BIOSCI "miniFAQ" is designed to answer the questions that come up
the *most frequently*.  The main BIOSCI FAQ (Frequently Asked
Questions) is accessible on the World Wide Web at URL
http://www.bio.net/.

If you can not find an answer to your question in this or other
documentation, the BIOSCI technical support staff answers e-mail
queries sent to

		       biosci-help@net.bio.net

We can only answer questions about the use of the newsgroups and
mailing lists.  We unfortunately do not have the staff to do Internet
information searches or answer scientific questions.  Please post
those to the appropriate BIOSCI/bionet newsgroups.


	Contents:
	--------
	0) BIOSCI NEEDS YOUR SUPPORT!!

	1) Using the WWW to access the BIOSCI/bionet newsgroups.

	2) What to do about "spams," i.e., junk mail, ads, etc.

	3) Examples of subscribing and unsubscribing to the mailing lists.

	4) The BIOSCI user address and research interest directory.


0) BIOSCI NEEDS YOUR SUPPORT!!
------------------------------
BIOSCI's government funding has been expended, and we are now
operating solely from advertising revenue that we have raised from our
Web site at http://www.bio.net/.  We need just a few minutes of your
time to help us serve you.

You can do two important things which will take very little time for
you individually and will immensely help us continue to help you.

First, please use our WWW system at http://www.bio.net/ to access the
archives.  You can post or reply to messages via your Web browser as
described in item #1 below.  Your usage helps attract sponsors. If you
contact any of our sponsors, please be sure to thank them for
supporting BIOSCI. It is critical for them to get this feedback if
they are to continue their sponsorship for the long term.

Second, if you work for a company or organization that provides
products or services of interest to the biology community, please pass
this message on to your marketing or marketing communications
department or other appropriate group.  Please ask them to help
support BIOSCI by sponsoring our Web site and explain the uses and
benefits of the system to the biology community. If they are
interested, they can then contact us for further information at our
tech support address, biosci-help@net.bio.net.


1) Using the WWW to access the BIOSCI/bionet newsgroups.
--------------------------------------------------------
As of 10 December 1995, all BIOSCI/bionet full newsgroups are
accessible through the World Wide Web (WWW) at URL http://www.bio.net.
One can read and reply publicly or privately to both recent postings
and archived messages through one's Web browser if it is configured
properly to send e-mail.  Each newsgroup is equipped with its own WAIS
index.  The main BIOSCI home page also has access to the BIO-JOURNALS
Table of Contents database WAIS index and the BIOSCI user address
database described in another item further below.


2) What to do about "spams," i.e., junk mail, ads, etc.
-------------------------------------------------------
BIOSCI is a set of parallel USENET newsgroups (the "bionet" groups),
mailing lists, and a hypermail archive at URL http://www.bio.net/.
The same postings are distributed on all media (except for a small
number of mailing-list-only groups at net.bio.net).  Unfortunately it
is becoming a despicable practice on the Internet (by a few people out
to make a fast buck) to do automated mass postings to thousands of
newsgroups and mailing lists.  These attempts to grab free advertising
are refered to as "spams" in the usual, somewhat boneheaded, net
terminology.  USENET is more susceptible to this practice, and many
spams originate on the USENET groups and then are passed on to the
mailing lists.  However, spammers also get lists of mailing addresses
and hit these too, so neither medium is immune.

What should you do personally if you get junk mail?
---------------------------------------------------
Just delete it and move on without reading it further.  Filing a
protest is becoming increasingly useless because spammers are often
disguising the addresses where the messages are sent from.  Unless you
really understand Internet mail systems, your attempt at protest by
sending replies to the message will often end up being sent to the
address of an innocent person that the spammer is victimizing.

What can BIOSCI/bionet do to protect its newsgroups?
----------------------------------------------------
The only solution currently available is to moderate the newsgroup.
If this newsgroup is already moderated, then you are in good shape.
Moderation protects the USENET distribution from about 95% of the
spams that are being sent to date and protects the mailing lists
completely.  Moderation means, however, that someone has to take the
time to review each message before it goes out.  We have set up
software here that simply allows the moderator to forward to an
address at net.bio.net messages that (s)he wishes to have distributed.
This takes no more time than that needed to read the message and pass
it on, say about 1 min. per message.

Most newsgroups currently have a discussion leader who is responsible
for their newsgroup.  The discussions leaders and their e-mail
addresses are listed in the BIOSCI Information Sheet which is
available on the Web at http://www.bio.net/.  If a newsgroup is being
hit with too many junk postings, please contact the discussion leader
for that group and see if there is interest in moderating the group.
Please do not assume that by simply posting a complaint to the
newsgroup itself, anyone on the BIOSCI staff will act on your
complaint.  With close to 100 newsgroups to run, the BIOSCI staff has
to rely on the discussion leaders of each newsgroup to report problems
directly to us at biosci-help@net.bio.net.

We will moderate any of our newsgroups if the discussion leader tells
us that the readership of the group wishes to do so and if a moderator
is willing to do the work.  For most BIOSCI/bionet groups, this
entails only a few minutes of work each day.

Moderating a newsgroup will resolve probably 95% of the junk postings
on the USENET distribution.  Unfortunately there are easy ways for
determined spammers to override the moderation mechanism on USENET,
but we can protect our e-mail subscribers from unwanted postings if
the newsgroup is moderated.  You can also access our newsgroups over
the WWW at URL http://www.bio.net.  While this Web interface will not
stop spammers from trying to post to the groups, this will give you
yet another way, besides using USENET news, to keep the junk out of
your personal mail files.  For those of you with local USENET news
systems, the Web interface will also give you faster access to new
newsgroups and recent postings.


3) Examples of subscribing and unsubscribing to the mailing lists.
------------------------------------------------------------------
PLEASE NOTE: The BIOSCI management does NOT act on
subscription/unsubscription requests that are posted improperly to the
newsgroups and mailing lists.  People who do this only bother everyone
on the lists to no avail.  Please be sure to follow the proper
procedures below.

Gory details are in the BIOSCI Information sheets on the Web at
http://www.bio.net.  Below we give an example utilizing the
METHODS-AND-REAGENTS list at both of our two BIOSCI sites:

Users in the Americas and Pacific Rim countries who use the BIOSCI
------------------------------------------------------------------
node at computer net.bio.net:
----------------------------

A) Determine the "listname" which is the <=8 character mail address
                                         ^^^^^^^^^^^^^
   for the group.  These can be found in the BIOSCI Info. Sheet.  For
   the METHODS-AND-REAGENTS group the mailing address is
   methods@net.bio.net.  The listname is the portion of the address to
   the left of the @ sign, i.e., "methods".  The listname is used with
   the "subscribe" and "unsubscribe" commands illustrated below.

B) Mail all commands in the body of a mail message addressed to
   biosci-server@net.bio.net.  Do NOT send commands to the newsgroup
   posting addresses!  Leave the Subject: line blank, any text on it
   will be ignored.

C) In the body of your message put one or more of the following
   commands with an "end" command on the last line, e.g.,

   subscribe methods
   unsubscribe methods
   end

   Do NOT put your e-mail address or other text on these lines.  The
   server only allows you to cancel your subscription if the address
   on your mail header matches the address on our mailing list.
   Please ask for help at biosci-help@net.bio.net if your address has
   changed, e.g., if you know you are on the list but the server tells
   you that you are not a member.


Users in Europe, Africa, and Central Asia who use the BIOSCI node at
--------------------------------------------------------------------
computer daresbury.ac.uk (also known as dl.ac.uk):
-------------------------------------------------

To subscribe and unsubscribe to/from the BIOSCI lists, you need to
specify the full USENET newsgroup name with "bionet-news." prepended.
The USENET newsgroup names are listed in the BIOSCI Information sheet
on the Web at http://www.bio.net/.  For the METHODS-AND-REAGENTS list
the USENET newsgroup name is bionet.molbio.methds-reagnts, thus the
appropriate commands are

    sub bionet-news.bionet.molbio.methds-reagnts

    unsub bionet-news.bionet.molbio.methds-reagnts

These commands are included in a message addressed to mxt@dl.ac.uk,
NOT to the newsgroup mailing addresses.  As usual, include the text in
the body of the message as text on the Subject: line is ignored.

To unsubscribe from all the lists at the UK node, use

    unsub bionet-news

Please note that if the address in the list is different than the one
in your mail message header, you will not be able to unsubscribe by
this method. If you have problems, please mail biosci@daresbury.ac.uk.


4) The BIOSCI user address and research interest directory.
-----------------------------------------------------------
Please take this opportunity to add your name, address, and research
interest information to the BIOSCI User Address Database if you have
not already done so.

You can fill out the address form directly through our Web page at URL
http://www.bio.net/adrform.html.

The address database is reindexed nightly for WWW access (the URL is
http://www.bio.net/).  If you are not directly on the Internet but can
reach it by e-mail, please use our waismail server to access the user
directory.  waismail use is described above.  You can also request a
user address form by e-mail from biosci-help@net.bio.net.

Please check your database entry from time-to-time to see if your
address information is still up-to-date.  Because of our limited
personnel resources, we ask that you resubmit a *complete* form to
revise your entry; we only replace complete entries and do not have
resources to edit old forms.


From owner-biophysics@net.bio.net Sat Jan 16 22:00:00 1999
Path: biosci!rutgers!rockyd.rockefeller.edu!news-nysernet-5.sprintlink.net!news-east1.sprintlink.net!news-peer1.sprintlink.net!news.sprintlink.net!howland.erols.net!cpk-news-hub1.bbnplanet.com!news.gtei.net!firehose.mindspring.com!not-for-mail
From: rkduncan@atlanticinteractive.com (Rick Duncan)
Newsgroups: bionet.biophysics
Subject: Echo-Web Online Medical Education
Date: Sun, 17 Jan 1999 17:35:48 GMT
Organization: Echo-Web: A Resource for Echocardiographers
Lines: 33
Message-ID: <36a81f54.8947728@news.mindspring.com>
NNTP-Posting-Host: d1.56.01.2f
Mime-Version: 1.0
Content-Type: text/plain; charset=us-ascii
Content-Transfer-Encoding: 7bit
X-Server-Date: 17 Jan 1999 17:32:58 GMT
X-Newsreader: Forte Agent 1.5/32.451

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From owner-biophysics@net.bio.net Sat Jan 16 22:00:00 1999
Path: biosci!cc.UManitoba.CA!gordonr
From: gordonr@cc.UManitoba.CA (Richard Gordon)
Newsgroups: bionet.biophysics
Subject: Biological Application of Thermodynamics
Date: 17 Jan 1999 11:33:34 -0800
Organization: BIOSCI International Newsgroups for Molecular Biology
Lines: 98
Sender: daemon@net.bio.net
Distribution: world
Message-ID: 
NNTP-Posting-Host: net.bio.net

To: biophys@net.bio.net
From: "Barak Akabayov" 
Subject: Thermodynamics&Biology
Date: Sun, 17 Jan 1999 15:11:49 +0200

Hi,
I need central concepts in Biological Application of Thermodynamics.
Thank you.
Ak_barak@internet-zahav.net

Dear Barak,
In regard to thermodynamics and evolution, see the refernces listed below
Yours, -Dick Gordon

Brooks, D.R., D.D. Cumming & P.H. LeBlond (1988). Dollo's law and the
second law of thermodynamics: analogy or extension. In: B.H. Weber, D.J.
Depew & J.D. Smith (eds.), Entropy, Information, and Evolution, Cambridge,
MA: The MIT Press, Bradford Books, p. 189-226.

Campbell, J.H. (1988). Evolution as nonequilibrium thermodynamics: halfway
there? In: B.H. Weber, D.J. Depew & J.D. Smith (eds.), Entropy,
Information, and Evolution, Cambridge, MA: MIT Press, Bradford Books, p.
275-284.

Conrad, M. (1974). Thermodynamic correlates of evolution. BioSystems  6(1),
1-15.

Depew, D.J. (1986). Nonequilibrium thermodynamics and evolution: a
philosophical perspective. Philosophica  37, 27-58.

Depew, D.J. & B.H. Weber (1988). Consequences of nonequlibrium
thermodynamics for the Darwinian tradition. In: B.H. Weber, D.J. Depew &
J.D. Smith (eds.), Entropy, Information, and Evolution, Cambridge, MA: MIT
Press, Bradford Books, p. 317-354.

Gladyshev, G.P. (1997). Thermodynamic Theory of the Evolution of Living
Beings. Moscow: N.N. Semenov Institute of Chemical Physics, Russian Academy
of Sciences.

Gladyshev, G.P. (1997). Thermodynamic Theory of the Evolution of Living
Beings. New York: NOVA Scientific Publishers.

Johnson, L. (1988). The thermodynamic origin of ecosystems: a tale of
broken symmetry. In: B.H. Weber, D.J. Depew & J.D. Smith (eds.), Entropy,
Information, and Evolution: New Perspectives on Physical and Biological
Evolution, Cambridge: MIT Press, p. 75-105.

Meléndez-Hevia, E., T.G. Waddell & M. Cascante (1996 Sep). The puzzle of
the Krebs citric acid cycle: assembling the pieces of chemically feasible
reactions, and opportunism in the design of metabolic pathways during
evolution. J Mol Evol  43(3), 293-303.

Meléndez-Hevia, E., T.G. Waddell, R. Heinrich & F. Montero (1997 Mar 1).
Theoretical approaches to the evolutionary optimization of glycolysis--
chemical analysis. Eur J Biochem  244(2), 527-43.

Schneider, E.D. (1988). Thermodynamics, ecological succession, and natural
selection: a common thread. In: B.H. Weber, D.J. Depew & J.D. Smith (eds.),
Entropy, Information, and Evolution: New Perspectives on Physical and
Biological Evolution, Cambridge: MIT Press, p. 106-138.

Shakhnovich, E.I. & A.M. Gutin (1990). Implications of thermodynamics of
protein folding for evolution of primary sequences. Nature  346, 773-775.

Weber, B.H., D.J. Depew, C. Dyke, S.N. Salthe, E.D. Schneider, R.E.
Ulanowicz & J.S. Wicken (1989). Evolution in thermodynamic perspective: an
ecological approach. Biol. Phil.  4, 373-405.

Wicken, J.S. (1979). The generation of complexity in evolution: a
thermodynamic and information-theoretical discussion. J. Theor. Biol.  77,
349-365.

Wicken, J.S. (1980). A thermodynamic theory of evolution. J. Theor. Biol.
87, 9-23.

Wicken, J.S. (1987). Evolution, Thermodynamics, and Information: Extending
the Darwinian Program. New York: Oxford University Press.

Wicken, J.S. (1988). Thermodynamics, evolution, and emergence: ingredients
for a new synthesis. In: B.H. Weber, D.J. Depew & J.D. Smith (eds.),
Entropy, Information, and Evolution, Cambridge: MIT Press, Bradford Books,
p. 139-172.

Wiley, E.O. & D.R. Brooks (1983). Nonequilibrium thermodynamics and
evolution:  a response to Løvtrup. Syst. Zool.  32, 209-219.

Yockey, H.P. (1995b). Comments on "Let there be life; Thermodynamic
reflections on biogenesis and evolution" by Avshalom C. Elitzur. J. Theor.
Biol  176, 349-355.

++++++++++++++++++++++++++++++++
Dr. Richard Gordon, Department of Radiology
University of Manitoba, Health Sciences Centre
820 Sherbrook Street, Winnipeg, MB R3A 1R9 Canada
Phone: (204) 789-3828,  Fax: (204) 787-2080,  E-mail: GordonR@cc.UManitoba.ca
The Hierarchical Genome and Differentiation Waves: Novel Unification of
Development, Genetics and Evolution:
http://www.wspc.com.sg/books/lifesci/2755.html

From owner-biophysics@net.bio.net Mon Jan 18 22:00:00 1999
Path: biosci!news.stanford.edu!logbridge.uoregon.edu!news-peer.gip.net!news-lond.gip.net!nntp.news.xara.net!xara.net!server6.netnews.ja.net!daresbury!not-for-mail
From: DOBBIE2ME@aol.com
Newsgroups: bionet.biophysics
Subject: The Perfect "Hands Off" Home Business!!
Date: 19 Jan 1999 02:39:58 -0000
Organization: Daresbury Laboratory, Warrington, U.K.
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From owner-biophysics@net.bio.net Mon Jan 18 22:00:00 1999
Path: biosci!news.stanford.edu!logbridge.uoregon.edu!nntp.teleport.com!news1.teleport.com!kaym
From: kaym@el-o.com (KayM)
Newsgroups: bionet.biophysics
Subject: Medical Search Engines - 1000 databases
Message-ID: 
Organization: Elite Living
Mime-Version: 1.0
Content-Type: text/plain; charset=ISO-8859-1
Content-transfer-encoding: 8bit
X-Newsreader: Yet Another NewsWatcher 2.2.0b13
Lines: 118
Date: Tue, 19 Jan 1999 06:08:48 -0800
NNTP-Posting-Host: 216.26.14.235
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X-Trace: news1.teleport.com 916754916 216.26.14.235 (Tue, 19 Jan 1999 06:08:36 PDT)
NNTP-Posting-Date: Tue, 19 Jan 1999 06:08:36 PDT

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From owner-biophysics@net.bio.net Wed Jan 20 22:00:00 1999
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From: "Southern Zhen Guan Agencies Pte Ltd" 
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Subject: ThinkQUest
Date: 21 Jan 1999 12:05:44 GMT
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Hello, my friend and I are from Singapore. We're doing a project on
circulatory system. If u're interested in the sub., pls give me a reply.
Thank you


From owner-biophysics@net.bio.net Thu Jan 21 22:00:00 1999
From: "Iris Delmonte" 
Newsgroups: bionet.biophysics
Subject: DNA Structure: Puzzle Number 19
Date: Fri, 22 Jan 1999 12:24:56 -0000
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The Microprobe Experiment of Mou et al.

Mou et al. (Ref.45) measured the height of duplex DNA when densely packed on
cationic lipid bilayers on a mica surface.   They found the height to be
some 2+ nm.  This result reminds us of that of James & Mazia (Puzzle 3,
Ref.4) who also measured the film height of duplex DNA under compression in
1953 and found a value of 2.1 - 2.2 nm.

Isolated duplexes, not under compression, using AFM & STM mostly have a
maximum measured height of some 1.3 nm, or so, and this has led Muir et al.
to suggest that "...duplex DNA may have an elliptical cross section when in
contact with mica."  (Puzzle 18, Ref. 44)

Wilkins and co-workers had suggested that DNA had an elliptical section in
1953 (Puzzle 12, Ref.20), and the results of James & Mazia, 2.1 - 2.2 nm x
1.2 nm, agree with this.


Even in very recent work (46, page 542) the apparent height of
two-dimensional sheets of DNA is reported as 1.35 - 1.45 nm using AFM.


Consequently, the work of Wilkins et al., James & Mazia, Muir et al., and
many others, would all suggest an elliptical cross section for dupex DNA of
approximately 2.1 - 2.2 nm x 1.2 - 1.4 nm.


45        J. Mou et al.; FEBS Lett Vol 371 (1995) 279

46        Design & self-assembly of two-dimensional DNA crystals; E. Winfree
et al.; NATURE Vol 394 (1998) 539-544
----------------------------------------------------------------
Clive Delmonte






From owner-biophysics@net.bio.net Thu Jan 21 22:00:00 1999
From: "Iris Delmonte" 
Newsgroups: bionet.biophysics
Subject: DNA Structure: Puzzle Number 20
Date: Fri, 22 Jan 1999 12:37:25 -0000
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Enhanced Rates of Cleavage of Duplex DNA

Sakonju & Brown (47) reported on the contacts made by a 40,000
daltontranscription factor, tf IIIA, which protected its substrate from the
actionof deoxyribonuclease 1 (RMM 31,000) between bases 44 to 90.   Within
that protected region, relative to bare duplex DNA, there is strong
enhancement of cleavage at 60 & 61, and marked enhancement also at bases 74,
75 & 76, that is, 1.5 double helical turns away from 60 & 61.

Since the two sites enjoy enhanced cleavage rates compared to bare DNA they
must both be more accessible than is bare DNA, even in the middle of
theprotected region, and even though tf III A must have some 2500 C,N,O
atoms and the nuclease must have some 2000 C,N,O atoms.


More specifically, site 60 & 61, if facing the nuclease, would leave site
74-76 on the opposite double helical face away from the nuclease, though
both sites experience enhanced rates of cleavage compared to bare DNA and
are only some 4.5 nm apart.

Drew & Travers (48) record their frustration with this situation:

"Many eukaryotic transcription factors, notably tf III A ... , protect up to
50 bp of DNA from enzymatic cleavage, yet somehow manage to induce regions
of enhanced cleavage within their binding sites..."

With the true side-by-side model (Puzzle 1, Ref.1) we can discern a possible
explanation of these results. Tf III A may bind largely to the rear face
where phosphates predominate, though, being a substantial protein, there may
be some obstuction of the other face where the base pairs are stacked upon
each other.

This allows deoxyribonuclease 1 access to the stacked base pairs at both
positions 60 - 61 and 1.5 turns away at 74 - 76, where both sites face way
from tf III A, and the rates of cleavage are enhanced compared to bare DNA
because the DNA bound onto tf III A is immobilised and entirely unfolded
compared to its situation alone with the
nuclease.

No explanation of enhanced rates of cutting within zones of protection has
ever been advanced based upon the double helical model of duplex DNA.

47        Contact Points between a Positive Transcription Factor and the
Xenopus 5S RNA Gene; S. Sakonju & D.D. Brown; Cell Vol 31 (1982) 395 - 405

48        DNA Bending and its Relation to Nucleosome Positioning; H.R. Drew
& A.A. Travers; J Mol Biol Vol 186 (1985) 773 - 790
---------------------------------------------------------------
Clive Delmonte






From owner-biophysics@net.bio.net Sun Jan 24 22:00:00 1999
From: "Clive Delmonte" 
Newsgroups: bionet.biophysics,bionet.xtallography
Subject: DNA Structure: An Age of Refinement Part 1 of 6
Date: Mon, 25 Jan 1999 13:23:22 -0000
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Xref: biosci bionet.biophysics:4739 bionet.xtallography:4563

Refining DNA Structures with a Paucity of X-ray Reflections

All DNA and oligonucleotide crystallographers have made extensive use of
refinement strategies in deducing structures from their diffraction studies.
In discussing the refinement of DNA and oligonucleotide structures, it seems
logical to start from the beginning, with high polymer DNA.

In the sixties, with the rise of powerful computers, came algorithms
intended to accelerate the deduction of structures from x-ray diffraction
from DNA fibres.

Among the better known was that of Arnott & Wonacott (49, 50, 59, 60) on
LALS (Linked Atom Least Squares). This still very widely used refinement
technique, e.g., 51, is known to utilise preliminary calculated phases which
are insensitive to the initial model (52) and which, by defining idealised
nucleotide coordinates within the model, seems to incorporate an implied
double helix within the algorithm (50, 53, 54).

The Limitations of Such Algorithms

However, Arnott et al.(55) and Marvin et al.(56) for example, had already
acknowledged that the mode of calculation of the structure factors of the
chosen model of the nucleic acids was such as to predispose a result
favourable to the chosen model:

"....Since Fourier syntheses are inevitably biased towards the structural
model from which the phases are derived...."  and

"This method has the disadvantage that the data are weighted so that the
synthesis tends to correspond to the model.....Moreover, the procedure is
justifiable if one assumes that the model is substantially correct and one
is interested in refining it...."

The work of Wonacott (50, page 70), Arnott et al. (57, page 2195 ), Hukins
(53, page 116) and Rich's group (58, Note 19) makes it clear that, in
their natural desire to minimise the number of unknowns to be determined
from the paucity of reflections, all these researchers have assumed that the
structure of the nucleic acids was a double helix.

The double helix has a highly symmetrical disposition of base pairs within a
helix of circular section.

Now, were the nucleic acids alleged to have a highly idiosyncratic,
asymmetric structure by Watson and Crick which the use of computer
optimisation of the structure factors of a suitable model was able to match
well with diffraction photographs, this would constitute impressive evidence
that the structure of the nucleic acids had been incontrovertibly
elucidated.

The true situation, though, is very different.   We are faced with:

1   the predisposition of the calculations towards favouring the double
helix by the use of phases actually deduced from the model whose structure
is supposedly being established,

2   a process of calculation which involves cylindrical averaging of
diffraction data when the current paradigm for the structure of the nucleic
acids, the double helix, is itself already cylindrical,

3   the use of optimisation techniques which assume that the paradigm is
true (for example, LALS) against a background in which Marvin et al.(56)
and Arnott et al.(52, 55), at least, acknowledge that the calculation
procedure is biased towards confirming the chosen model as the correct one,
and

4   the routine, explicit use of trial models of high polymer DNA which are
taken self-evidently to be double helices as starting points for structure
refinement algorithms now being deployed to "solve" the structure of
oligonucleotides in true crystals.

As Sir Peter Medawar reminds us in his "Advice to a Young Scientist":

"The intensity of a conviction that a hypothesis is true has no bearing over
whether it is true or not."

We now have the benefit of some 45 years of research in fields such as
biophysics and molecular biology, outside DNA & oligonucleotide
crystallography, and we are able to see that the double helix does not offer
us an explanation of the twenty DNA Structure Puzzles I have selected for
posting to newsgroups.

Let us now proceed to Part 2 to analyse the algorithm "CORELS".
-----------------------------------------------------------
49        The Refinement of of the Crystal and Molecular Structure of
Polymers Using X-ray Data and Stereochemical Constraints; S. Arnott &
A.J. Wonacott; Polymer Vol 7 (1966) 157 - 166

50         Computational Techniques For Adjusting Molecular Models of
Long-chain Molecules Occurring in Biological and Other Systems to Agree
with the X-ray Diffraction Data; A.J. Wonacott; PhD Thesis, London
University, 1966

51        Sequence-Dependent Conformational Variations in the B-DNA
Double-Helix of Poly d(AATT). Poly d(AATT); R. Chandrasekaran et al.; J
Biomol Struct & Dyn Vol 11 (1994) 741 - 766

52           FIBER DIFFRACTION ANALYSIS OF BIOPOLYMER MOLECULES; S. Arnott;
Trans. Am. Cryst. Assoc. Proceedings of Symposium on 'Biophysical
Applications of Crystallographic Techniques' at University of Florida, Jan
14-18, 1973; 9 (1973) 31-56

53        Molecular Conformations of Nucleic Acids & Polynucleotides from
X-ray Diffraction Data: D.W.L. Hukins, PhD Thesis, London University 1972

54       LALS: A Linked-Atom Least-Squares Reciprocal-Space Refinement
System Incorporating Stereochemical Restraints to Supplement Sparse
Diffraction
Data; P.J. Campbell Smith & S. Arnott; Acta Cryst. A34 (1978) 3-11

55          Fourier Synthesis Studies of Lithium DNA. Part III:  Hoogsteen
Models; S. Arnott, M.H.F. Wilkins, L.D. Hamilton & R. Langridge; J. Mol.
Biol., 11 (1965) 391-402

56        Application of Fourier Synthesis  Technique to Low-resolution
Fibre Diffraction Data: Preliminary Study of Deoxyribonucleic Acid; D.A.
Marvin,
M.H.F. Wilkins & L.D. Hamilton; Acta Cryst., 20 (1966) 663-669

57       Least-squares Refinement of the Crystal and Molecular Structures of
DNA & RNA from X-ray Data and Standard Bond Lengths & Angles; S. Arnott,
S.D. Dover & A.J. Wonacott; Acta Cryst., B25 (1969) 2192-2206

58        Left-handed Double Helical DNA: Variations in the Backbone
Conformation; A.H.-J. Wang et al.; Science Vol 211 (1981) 171 - 176

59         Rigid-body least-squares refinement of nucleic acids; S. Arnott &
C.L. Coulter; Paper S1.27 of Sixth International Congress & Symposia of the
International Union of Crystallography, Rome (1963); Abstracts of the
Communications (Suppl. Acta Cryst. 16 (1963) page A175)

60       Least-Squares Refinement of the Crystal & Molecular Structures
of DNA & RNA from X-ray Data & Standard Bond Lengths & Angles; S. Arnott,
S.D. Dover & A.J. Wonacott; Acta Cryst. B25 (1969) 2192-2206

61     Refinement of the Structure of B-DNA & Implications for the Analysis
of X-ray Diffraction Data from the Fibers of Biopolymers; S. Arnott & D.W.L.
Hukins; J. Mol. Biol. 81 (1973) 93-105
-------------------------------------------------------------------
Clive Delmonte







From owner-biophysics@net.bio.net Mon Jan 25 22:00:00 1999
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From: "Simon Dobbs" 
Newsgroups: bionet.biophysics
Subject: Re: DNA Structure: Puzzle Number 20
Date: Tue, 26 Jan 1999 23:49:33 +0000
Organization: dobbs research
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On Fri, 22 Jan 1999 12:37:25 +0000, Iris Delmonte wrote
(in message <36a86b4e.0@news.netdirect.net.uk>):
> 
> 
> Enhanced Rates of Cleavage of Duplex DNA 
> 
> Sakonju & Brown (47) reported on the contacts made by a 40,000 
> daltontranscription factor, tf IIIA, which protected its substrate from the 
> actionof deoxyribonuclease 1 (RMM 31,000) between bases 44 to 90.   Within 
> that protected region, relative to bare duplex DNA, there is strong 
> enhancement of cleavage at 60 & 61, and marked enhancement also at bases 
> 74, 75 & 76, that is, 1.5 double helical turns away from 60 & 61. 
> 
> Since the two sites enjoy enhanced cleavage rates compared to bare DNA they 
> must both be more accessible than is bare DNA, even in the middle of 
> theprotected region, and even though tf III A must have some 2500 C,N,O 
> atoms and the nuclease must have some 2000 C,N,O atoms. 
> 
> 
> More specifically, site 60 & 61, if facing the nuclease, would leave site 
> 74-76 on the opposite double helical face away from the nuclease, though 
> both sites experience enhanced rates of cleavage compared to bare DNA and 
> are only some 4.5 nm apart. 
> 
> Drew & Travers (48) record their frustration with this situation: 
> 
> "Many eukaryotic transcription factors, notably tf III A ... , protect up 
> to 50 bp of DNA from enzymatic cleavage, yet somehow manage to induce 
> regions of enhanced cleavage within their binding sites..." 
> 
> With the true side-by-side model (Puzzle 1, Ref.1) we can discern a 
> possible explanation of these results. Tf III A may bind largely to the rear 
> face where phosphates predominate, though, being a substantial protein, 
> there may be some obstuction of the other face where the base pairs are 
> stacked upon each other. 
> 
> This allows deoxyribonuclease 1 access to the stacked base pairs at both 
> positions 60 - 61 and 1.5 turns away at 74 - 76, where both sites face way 
> from tf III A, and the rates of cleavage are enhanced compared to bare DNA 
> because the DNA bound onto tf III A is immobilised and entirely unfolded 
> compared to its situation alone with the nuclease. 
> 
> No explanation of enhanced rates of cutting within zones of protection has 
> ever been advanced based upon the double helical model of duplex DNA. 
> 
> 47        Contact Points between a Positive Transcription Factor and the 
> Xenopus 5S RNA Gene; S. Sakonju & D.D. Brown; Cell Vol 31 (1982) 395 - 405 
> 
> 48        DNA Bending and its Relation to Nucleosome Positioning; H.R. Drew 
> & A.A. Travers; J Mol Biol Vol 186 (1985) 773 - 790 
> --------------------------------------------------------------- Clive 
> Delmonte 
> 
> 
> 
> 
surely there is a philosophical difficulty in using our hazily understood model 
of one situation, viz the interaction of proteins with DNA, to criticise 
another model, the structure of DNA. Until we understand the former to a much 
greater degree, it is wrong to use this understanding to form another 
hypothesis. For instance, why is it not possible for a region of DNA to 'spool 
out' from the protein complex in such a way that a small region of DNA is 
accessible to attack- indead much more accesible than the surrounding region 
which is in intimate contact with the protein; it is therefore subject to 
enhanced cleavage relative to surrounding regions (it is also constrained in 
its position and may be strained due to its highly curved topology such that it 
is readiy cleaved). this 'hypothesis' may well  be bunkum, but until 
considered, can the presence of readily cleaved areas in a DNA-protein complex 
really be used as evidence for or against a particular model for the structure 
of DNA?  


From owner-biophysics@net.bio.net Mon Jan 25 22:00:00 1999
From: "Clive Delmonte" 
Newsgroups: bionet.biophysics,bionet.xtallography
Subject: DNA Structure: An Age of Refinement Part 2 of 6
Date: Tue, 26 Jan 1999 13:15:02 -0000
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Xref: biosci bionet.biophysics:4741 bionet.xtallography:4564

DNA Structure Refinement using Constrained & Restrained Least Squares
(CORELS)

We saw that in Part 1 that a natural desire to maximise the information that
could be extracted from sparse diffraction data from DNA and oligonucleotide
studies inevitably has led to the incorporation of double-helical features
into the LALS algorithm.   Structures refined using this algorithm have
informed the subsequent work in very many studies, often being used as
models based upon which new structures are refined.

A similar rationale seems to underpin the mode of application of the CORELS
approach to nucleic acid structure refinement (62, 63):

"We have used this method for idealizing a nucleic acid model..."   (62,
page 801), and

"The structure of this fragment (d(GGTATACC)) of DNA was determined ...  It
incorporated..... calculations assuming models of both B and A types of
DNA."  (63, page 229)

It was this structure which was then refined with CORELS.   We also see in
this latter quotation, as in the work of other research groups, the
assumption that the
crystallisation of short oligonucleotides gives rise to the same structure
in vitro as that formed by proteins when they synthesise and assemble high
polymer DNA in vivo, even though this proposition has never been proved.

In the years since 1953, a growing body of experimental results, illustrated
by the twenty DNA Structure Puzzles I selected for citation recently in
these newsgroups, has become impossible to explain using the DNA double
helical paradigm.

These days biophysics and molecular biology is increasingly constrained by a
model of duplex DNA which no longer offers helpful structural insights in a
wide range of situations and many researchers find themselves reporting
results in the literature without being able to offer any structural or
mechanistic insights to explain those results.  A wide-ranging review of
such literature reports up to 1990 has been published (64).

We find ourselves increasingly in a situation which calls to mind a remark
of Sir Lawrence Bragg:

"The important thing in Science is not so much to obtain new facts, as to
obtain new ways of thinking about them."

Oligonucleotide structures deduced by assuming duplex DNA to double helical
at any stage in the process are therefore likely to be compromised and can
only be used with caution, if at all, to explain experimental results in the
wider field outside oligonucleotide crystallography.


An entirely new possibility for duplex DNA has been described (64) and
visualised experimentally in STM (65, Figure 3b)

In An Age of Refinement Part 3 we shall consider the algorithm NUCLSQ.
-------------------------------------------------------------------------
62       A Structure-Factor Least-Squares Refinement Procedure for
Macromolecular Structures using Constrained and Restrained Parameters; J.L.
Sussman, S.R. Holbrook, G.M. Church & Sung-Hou Kim; Acta Cryst. A33 (1977)
800-804

63       APPLICATION OF REFINEMENT CONSTRAINTS AND RESTRAINTS TO PROTEINS
AND NUCLEIC ACIDS; J.L. Sussman; pages 206-237 in Methods & applications in
crystallographic computing; Ed. S.R. Hall & T. Ashida; Clarendon Press,
Oxford, 1984 (ISBN 0-19-855190-8)

64        "Towards a New Structural Molecular Biology" by Clive Delmonte,
ISBN 0 9512276 0 2  (1991)


65        Scanning Tunnelling Microscopy of Nucleic Acids: G. Lee et al.;
SCIENCE Vol 244 (1989) 475 - 477
-------------------------------------------------------------------------
Clive Delmonte





From owner-biophysics@net.bio.net Wed Jan 27 22:00:00 1999
From: "Clive Delmonte" 
Newsgroups: bionet.biophysics
Subject: DNA Structure: Puzzle Number 20 (Discussion)
Date: Thu, 28 Jan 1999 11:59:01 -0000
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In response to Puzzle 20, Simon Dobbs writes:

"Surely there is a philosophical difficulty in using our hazily understood
model
of one situation, viz the interaction of proteins with DNA, to criticise
another model, the structure of DNA. Until we understand the former to a
much greater degree, it is wrong to use this understanding to form another
hypothesis. For instance, why is it not possible for a region of DNA to
'spool out' from the protein complex in such a way that a small region of
DNA is accessible to attack- indeed much more accessible than the
surrounding region which is in intimate contact with the protein; it is
therefore subject to enhanced cleavage relative to surrounding regions (it
is also constrained in its position and may be strained due to its highly
curved topology such that it is readily cleaved).  This 'hypothesis' may
well  be bunkum, but until considered, can the presence of readily cleaved
areas in a DNA-protein complex really be used as evidence for or against a
particular model for the structure of DNA? "


I would be glad to agree with Simon's remarks as stated but would wish to
keep in mind that:

1    Puzzle 20, taken in isolation could not establish the structure of
duplex DNA.  The point about Puzzle 20 to my mind is that much of the
difficulty about enhanced cutting rates disappears at the very outset with a
true side-by-side model of DNA (Puzzle 1, ref.1) in which the Watson-Crick
base pairs would be stacked on the same side of the two right-handed
antiparallel chains across which they are held at the glycosidic links.
With such a model all the base pairs could face away from a protein core,
such as nucleosomal histones for example, giving very easy access to the
target sequences of incoming restriction endonucleases, polymerases, etc.,
and to general endonucleases like DNAase 1 (though not micrococcal nuclease
which I believe operates on the reverse face of duplex DNA.)

2    Enhanced rates of cutting by DNAase 1 have been reported in many
studies.  That of Ford et al.(1), for example, involved a relatively small
porphyrin, without a protective protein present at all.  On the other hand,
Rhodes (2), working with a complex of nucleosomes with tf III A and DNAase 1
also found enhanced cutting rates.  With the new side-by-side model, no
unwinding is necessary and all the bases could hardly be more accessible
when facing away from the core.  It is the greater structural simplicity of
the new model that commends itself here, rather than an assertion that these
experiments could establish a particular structure for DNA.

3    Then there is the totality of the Puzzles to consider.  I have
attempted to develop themes in the Puzzles; to set out reasoning bearing on
the crystallography in Puzzles 2, 4, 5, 6, 9, 12, 15 and 16; reasoning based
on protein-related studies in Puzzles 7, 8, 10, and 11; AFM & STM in Puzzles
1, 17, 18 and 19; on the topology in Puzzle 14, and the very important study
in general chemistry in Puzzle 3.

I would wish to take an overview of the Puzzles as a whole, seeing Puzzle 20
within this context. Then I could suggest that a true side-by-side duplex
model for B-DNA, of elliptical section 1.3nm x 2.2nm, or so, can offer a
coherent, self-consistent, simplifying account of all the phenomena reported
in the molecular biology of duplex DNA.

What other model presently offers this ?
----------------------------------------------------------------------------
-
1       DNA Sequence Preferences for an Intercalating Porphyrin Compound
Revealed by Footprinting; K. Ford, K.R. Fox, S. Neidle & M.J. Waring; Nucl.
Acids Res. 15 (1987) 2221-2234

2       Structural Analysis of a Triple Complex between the Histone Octamer,
a Xenopus Gene for 5S RNA and Transcription Factor III A; D. Rhodes; The
EMBO J. 4 (1985) 3473-3482
----------------------------------------------------------------------------
-
Clive Delmonte




From owner-biophysics@net.bio.net Thu Jan 28 22:00:00 1999
Path: biosci!agate!newsfeed.berkeley.edu!newsfeed.xcom.net!news.shore.net!uunet!ffx.uu.net!in1.uu.net!server-b.cs.interbusiness.it!not-for-mail
From: Antonio 
Newsgroups: bionet.biophysics
Subject: Leucodistrofia
Date: Fri, 29 Jan 1999 09:39:26 +0100
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--------------D70C2851A941788D65EA94E8
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I've just received this help message.
If somebody knows LEUCODISTROFIA, please read the attached message.

The message is in italian.

Thank You

--------------D70C2851A941788D65EA94E8
Content-Type: text/plain; charset=us-ascii; name="marco.txt"
Content-Transfer-Encoding: 7bit
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English | Espagnol | Francaise | German | Nederlands | Svedish | Arab | 
Portuguese | Greek 
AIUTAMI A VIVERE
            
            
            Mi chiamo GianMarco, ho 3 anni e da un anno circa soffro di 
            LEUCODISTROFIA. I medici hanno detto ai miei genitori che la 
            LEUCODISTROFIA e' una malattia difficile da curare e da quel che mi 
            e' sembrato capire tra non molto raggiungero' la mia sorellina in 
            paradiso. Io voglio molto bene alla mia sorellina, ma voglio anche 
            bene a mamma e papa', e desidero stare con loro ancora per molto. I 
            miei genitori sono ormai disperati, io pero'.... penso che qualcosa 
            ancora si puo' fare. Tu che stai leggendo questa mia letterina, 
            aiutami a trovare un buon medico che possa salvarmi. Traducila in 
            tutte le lingue e mandala in giro per tutto il mondo. Forse solo 
            cosi' riusciro' a trovare un buon medico o una buona medicina che 
            possa salvarmi dalla morte.
            
            
            (Gian Marco)
            
            
            
    
    



Chiediamo che questo messaggio sia fatto circolare in tutte le reti


telematiche, inserito nei Web e tradotto in quante piu' lingue e' possibile


(inviando una copia della traduzione ad a.marescotti@peacelink.it); 

per chi volesse contattare la famiglia ecco il


telefono: 099 4775675 (famiglia Coniglio, Taranto).


email:opaco@tin.it




Due parole ancora...


La mamma di Gian Marco quando e' venuta da noi ci ha detto: "Non chiedo


soldi, chiedo solo che l'informazione venga diffusa su Internet per trovare


informazioni nel mondo su casi simili".


Dalle informazioni che abbiamo raccolto, Gian Marco - che gia' non riesce a


reggersi in piedi - rischia di morire entro quest'anno, anche se il decorso


della malattia (che porta alla perdita dell'uso di tutti gli arti ed ora


genera crisi di epilessia) non e' prevedibile con precisione e del resto ci


auguriamo che rimanga il tempo per fare ancora qualcosa. La leucodistrofia


ha diverse varianti e quella di Gian Marco e' una variante sconosciuta o


semisconosciuta per cui sarebbe utile avere notizie su altri casi simili nel


mondo e su centri che si occupino della leucodistrofia, magari collegati ad


Internet.





Abbiamo fatto delle ricerche con i classici motori di ricerca Internet ma le


difficolta' sono notevoli, in particolare occorrerebbe creare uno staff di


persone che conoscano l'inglese e la medicina, oltre che l'uso dei motori di


ricerca. Sarebbe poi auspicabile un lancio del caso di Gian Marco sui


newsgroup medici, cercando altri utenti che nel mondo abbiano esperienza di


ricerca in questo campo.





Invitiamo tutti coloro che possono aiutare Gian Marco a:


- diffondere queste informazioni sulle riviste e sui giornali collegati alla


rete;


- collegarsi all'area "VOCE A CHI NON HA VOCE" della rete telematica


PeaceLink; per chi viene da Internet occorre iscriversi alla mailing list


inviando un messaggio a LISTSERV@PEACELINK.IT senza soggetto e nel cui corpo


sia inserito


  subscribe voce


e per inviare messaggi alla mailing list occorre scrivere a


  voce@peacelink.it





Per chi, come noi, ha avuto la possibilita' di giocare e sorridere a questo


stupendo bambino, la fiducia non puo' aver limiti e nessuna rassegnazione


puo' bloccare il tentativo di un ulteriore ricerca.








Un grazie di cuore a chiunque aiutera' Gian Marco.





                               PEACELINK


                               ASSOCIAZIONE DI VOLONTARIATO TELEMATICO











e-mail to Alessandro Marescotti                               


                      portavoce 








e-mail to Giovanni Pugliese


                      segretario                





:::::::::::::::::::::::::::::::::::::::::::


Alessandro Marescotti


E-mail:    a.marescotti@peacelink.it


Fidonet:   2:335/703.20


PeaceLink, c.p. 2009, 74100 Taranto (Italy)


:::::::::::::::::::::::::::::::::::::::::::








Vai su PeaceLink Home Page





    
    
    
    





NEUROLOGIA PEDIATRICA


Istituto di Clinica Pediatrica


Universita' di Bologna





RELAZIONE CLINICA DI CONIGLIO GIAN MARCO





Il piccolo Gian Marco e' nato a termine il 28/01/1993 da 


gravidanza fisiologica e parto eutocico.





Peso alla nascita Kg 3,500.





I primi atti fisiologici sono riferiti nella norma.


All'anamnesi familiare risultano genitori in apparente buona 


salute, una sorella


di 13 anni in apparente buona salute, un fratello di 12 anni in 


apparente buona


salute, una sorellina deceduta all'eta' di 4 anni per 





LEUCODISTROFIA di n.n.d., diagnosticata all'eta' di 2 anni.





Il piccolo ha goduto buona salute fino all'eta' di 11 mesi quando 


e' comparso un episodio comiziale in iperpiressia della durata di circa 3 e 1/2 


ore e caratterizzato da revulsione dei bulbi oculari, ipertono diffuso, trisma, 


scialorrea e risoltosi dopo somministrazione di Valium e Rivotril.





La T.C. cerebrale eseguita in tale occasione e' risultata nella 


norma.





Nel primo tracciato EEG, registrato a 24 ore dall'episodio 


critico, viene riferita la presenza di anomalie subcontinue


localizzate prevalentemente a  sinistra, a tipo


Stato di Male.  Pertanto ha iniziato terapia con Luminalette.


Nell'ottobre 1994 e' comparso un secondo episodio comiziale in 


iperpiressia durato


circa 45 minuti con la stessa semeiologia del precedente e 


risoltosi con la somministrazione


di Valium.


La mamma riferisce che il tracciato EEG risulto' nella norma.


Gian Marco e' giunto, per la prima volta, alla nostra osservazione 


lo scorso gennaio ed e' stato sottoposto a RMN


cerebrale in cui sono risultate 


chiare note di leucodistrofia.





Altre indagini eseguite:


Fundus oculi: nella norma


VCM nervo peroneo ds. nella norma


EEG nella norma


ECG nella norma


BAEPs: tempo di conduzione Au.sn ritardato a livello centrale


ERG nella norma.


PVS apparente ritardo di conduzione in o. sn.


SSEP: aparente simmetrici e regolari.


Aminoacidi su sangue e urine: n. n.


dosaggio Carnitina: n. n.


Acidi organici su sangue e urina: n. n.


Oligosaccaridi urinari: n. n.


DNA  mitocondriale: n. n.


Precursore dell'Arilsulfatasi A ed Arilsulfatasi A: n. n.


Acidi grassi a catena molto lunga: n. n.


Dosaggio dell'enzima Galattocerebrosidasi su coltura di 


fibroblasti. n. n.


Enzima beta-galattosidasi, enzima beta-esosaminidasi, risultati 


nella norma.





Il piccolo giunge ora alla nostra osservazione per un 


peggioramento della situazione


clinica in quanto, 2 giorni fa, in seguito ad una caduta 


accidentale, ha presentato


monoparesi all'arto inferiore sinistro e impaccio motorio all'arto 


superiore destro.


Dagli esami finora eseguiti abbiamo escluso i deficit enzimatici 


finora conosciuti e che provocano un quadro di leucodistrofia.


Ci riserviamo di eseguire, il giorno 3/11/95, una spettro - RMN 


cerebrale, per cercare di ottenere ulteriori dati utili


al raggiungimento della diagnosi.


--------------D70C2851A941788D65EA94E8--


From owner-biophysics@net.bio.net Thu Jan 28 22:00:00 1999
From: "Clive Delmonte" 
Newsgroups: bionet.biophysics,bionet.xtallography
Subject: DNA Structure: An Age of Refinement Part 3 of 6
Date: Fri, 29 Jan 1999 11:23:49 -0000
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Xref: biosci bionet.biophysics:4746 bionet.xtallography:4571

Stereochemically Restrained Crystallographic Least-Squares Refinement of
Macromolecular Structures


Readers may recall that the DNA Structure Puzzles focussed attention upon
those published, experimental results for which a plectonaemically wound DNA
duplex would not seem to offer an explanation.

Aside from the adoption by Watson & Crick of Pauling & Corey's first use of
plectonaemic winding in DNA (and in many other biological macromolecules
also) (66,67), there is the complex question of the precise computational
origin of the proposed plectonaemic winding deduced from the deconvoluted
structure factors derived from the x-ray diffraction from true crystals of
short, synthetic oligonucleotides.

The well-known paper of Hendrickson & Konnert (68) has been adapted to serve
the specific needs of oligonucleotide refinement by at least two groups
(69a,b). For example, Westhof et al. (69a) report

"The adaptation of the restrained least-squares program for nucleic
acids..."      and

"...we developed an extended version of restrained least-squares programs
specifically for the refinement of nucleic acids (NUCLIN and NUCLSQ)." (Page
120)

It would not seem to be explicit in this paper whether or not plectonaemic
winding of the strands was incorporated as part of the "adaptation".
However, bond lengths, bond angles, torsion angles and other data were
incorporated as restraints, and, inasmuch as this data may have been taken,
at least in part, "from small molecule crystallography" (page 121) which
could have included studies of short oligonucleotides, the data may carry
within it the implication of plectonaemic winding.

While that of itself could be perfectly satisfactory, we may wish to keep in
mind that there has never been a direct demonstration of any kind to show
that oligonucleotide structures formed in vitro by low polymers, and then
determined by crystallography, are actually the same as those to be found in
high polymer DNA formed by proteins in vivo.

There would be, therefore, a philosophical distinction between, on the one
hand, arriving at a satisfactory small oligonucleotide structure through
crystallography, and, on the other, to merely suppose that data taken from
such short chain structures, such as torsion angles, sugar puckers and
pseudorotation angles, for example, can be properly incorporated into the
proposed structures of high polymer nucleic acids found in vivo.

Moreover, there is a further level of ambiguity to be considered.  Some of
the earlier reports on dinucleotide crystal structures are the synopses of
the work of Seeman et al. and Rosenberg et al. (70, 71).   The synopses
respectively contain the phrases "...The best fit to a double helix.." and
"...The best double helical fit..."   These phrases might mean that the data
had been fitted to a double helix by the investigators, or they might mean
that the deconvoluted data fell out naturally of itself into a good fit to a
double helical structure.


Evidently, if it transpires that the investigators in refs. 70 & 71
themselves fitted the data to a double helix, the consequent determinations
of bond angles, torsion angles, rotation angles, etc., could have been
carried forward into the libraries upon which later studies were based.

In Part 4 of 6, we shall reflect on the context of the use of the refinement
program ULTIMA.
------------------------------------------------------------------

66        Structure of the Nucleic Acids; L. Pauling & R. Corey; Nature Vol
171 (1953) 346

67        L. Pauling & R. Corey in Proc Nat Acad Sci Vol 37 (1951) 235 - 271
(Helical Configuration of Polypeptide Chains, The Pleated Sheet, Feather
Rachis Keratin, Hair, Muscle & Related Proteins)

68        Stereochemically Restrained Crystallographic Least-Squares
Refinement of Macromolecule Structures by W.A. Hendrickson & J.H. Konnert,
pages 43 - 82 in Biomolecular Structure, Conformation, Function and
Evolution, Volume 1, Editor: R. Srinivasan, Pergamon Press, 1981, ISBN
0-08-023187-X

69a        Crystallographic Refinement of Yeast Aspartic Acid Transfer RNA;
E. Westhof, P. Dumas & D. Moras; J Mol Biol Vol 184 (1985) 119 - 145


69b        Structural analysis of spermine and magnesium ion binding to
yeast phenylalanine transfer RNA; G.J. Quigley, M.M. Teeter & A. Rich; Proc
Nat Acad Sci Vol 75 (1978) 64 - 68

70        The Double Helix at Atomic Resolution I (ApU); N.C. Seeman et al.;
Amer. Cryst. Assoc. Meeting, Vol 1, Ser 2, C6 (1973) 130

71        The Double Helix at Atomic Resolution II (GpC); J.M. Rosenberg et
al.; ibid, C7 (1973) 130
---------------------------------------------------------------------
Clive Delmonte




From owner-biophysics@net.bio.net Thu Jan 28 22:00:00 1999
From: "NDRI/HBDI" 
Newsgroups: alt.bio.technology,alt.bio.technology.misc,bionet,bionet.biology,bionet.biophysics,bionet.cellbiol
Subject: Autopsy, Surgical Discard and Transplantation Tissues for Now Available for Research
Date: Fri, 29 Jan 1999 10:16:56 -0500
Organization: IDT (Best News In The World)
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Xref: biosci bionet.biophysics:4747 bionet.cellbiol:11213

See www.ndri.com for access to human tissues and organs for medical
researchers

See www.hbdi.org for information about family collections containing DNA and
immortalized cells - over 600 families - for medical and genetic researchers


NDRI and HBDI are non-profit organizations aiding medical research and the
search for disease genes.






From owner-biophysics@net.bio.net Fri Jan 29 22:00:00 1999
Path: biosci!news.stanford.edu!su-news-feed2.bbnplanet.com!su-news-hub1.bbnplanet.com!cam-news-feed2.bbnplanet.com!news.gtei.net!news.shore.net!news-spur1.maxwell.syr.edu!news.maxwell.syr.edu!isdnet!grolier!club-internet!not-for-mail
From: "François PINCE" 
Newsgroups: bionet.biophysics
Subject: vends livres de physique rares
Date: Sat, 30 Jan 1999 12:45:45 +0100
Organization: Club-Internet (France)
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Bonjour, je vends des livres de physique
Henri Bouasse 1966 -1953 (PHYSIQUE)
BSIP pour Bibliothèque Scientifique de l'Ingénieur et du Physicien
GRANDS IN-OCTAVO

* Hydrostatique, manomètres, baromètres, pompes, équilibre des corps
flottants
cartonné, 1923 -BSIP
1 000 FRF

* Hydrodynamique générale, fluides parfaits et visqueux, ailes d'avion
relié, 1928 -BSIP
1 000 FRF

* Jets, tubes et canaux
relié, 1923 -BSIP
500 FRF

* Diffraction
cartonné, 1923 -BSIP
1 000 FRF

* Acoustique, instruments à cordes et à membranes
cartonné, 1926 -BSIP
1 500 FRF

* Propagation de la lumière, théorie de la réflexion vitreuse et métallique
cartonné, 1925 -BSIP
1 000 FRF

* Résistance des fluides, vol des avions et des oiseaux,
hélices et moulins à vent, manoeuvre des navires
relié, 1928 -BSIP
1 000 FRF

* Théorie de l'élasticité, résistance des matériaux
cartonné, 1947 -BSIP
500 FRF

* Capillarité, phénomènes superficiels
relié, 1924 -BSIP
1 000 FRF

* Séismes et sismographes
relié, 1927 -BSIP
1 000 FRF

* Théorie des vecteurs, cinématique, mécanismes
cartonné, 1921 -BSIP
1 000 FRF

* Dynamique générale
cartonné, 1923 -BSIP
1 000 FRF

* Compléments de dynamique des fluides et d'acoustique, oeuvres inédites
(TOME 1)
broché, 1962
500 FRF
* Tourbillons, forces acoustique, circulations diverses
(TOME 2)
relié, 1932 -BSIP

* Gyroscopes et projectiles
cartonné, 1923 -BSIP
1 500 FRF

* Optique cristalline, polarisation rotatoire, états mésomorphes
broché, 1925 -BSIP
1 000 FRF

* Optique et photométrie dites géométriques
broché, 1947 -BSIP
500 FRF

* Thermodynamique générale, Gaz et vapeurs
broché, 1938 -BSIP
500 FRF

* Houle , rides, seiches et marées
relié, 1924 -BSIP
500 FRF

* Statique graphique, machines simples, bascules et balances,
frottement, freins, graissage
relié, 1920 -BSIP
1 500 FRF

* Interférences
cartonné, 1923 -BSIP
1 000 FRF

* Cours de Physique (TOME 1)
Mécanique physique
relié
500 FRF

* Cours de Physique (TOME 3)
Cours de magnétisme et d'électricité, Etude du champ électrique,
électricité statique, diélectrique, forces électromotrices, piles, ions
gazeux et électrons
500 FRF

* Cours de Physique (TOME 4)
Optique, étude des instruments
relié
500 FRF

* Cours de Physique (TOME 5)
Electroptique, ondes hertziennes
relié
500 FRF

* Cours de Physique (TOME 6)
Etude des symétries
relié
500 FRF

François PINCE45 rue du Taur31 000 ToulouseFRANCEpincef@club-internet.fr




From owner-biophysics@net.bio.net Sun Jan 31 22:00:00 1999
From: "Clive Delmonte" 
Newsgroups: bionet.biophysics,bionet.xtallography
Subject: DNA Structure: An Age of Refinement Part 4 of 6
Date: Mon, 1 Feb 1999 09:47:23 -0000
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Xref: biosci bionet.biophysics:4749 bionet.xtallography:4573

ULTIMA - An Approach by Rabinovich & Shakked (72)

ULTIMA is presented as a computer program which, inter alia, can be used in
a manner so as to solve the structures of crystallised oligonucleotides ab
initio.

While this very obviously represents excellent current practice, some
detailed scrutiny might be warranted in the light of earlier Parts in this
series.

First, the process seems to have been influenced by knowledge of the double
helix model, whose conformation seems to have informed the distances apart
chosen by the researchers for the phosphate, sugar and base components (72,
page
197).  Partly refined (double helical) structures were the result, an
outcome perhaps predetermined by the conformational library.

Next, during the refinement process, the partly refined structures from
ULTIMA were compared with idealised structures for high polymer DNA
published by Arnott & Hukins (73) which are informed by prior knowledge and
acceptance of the
double helix. Rabinovich & Shakked seem to have selected the ULTIMA
structure having the best fit to the Arnott & Hukins model and then refined
it further using CORELS (Part 3 of 6).

As with many other studies, a further, more general difficulty may relate to
the choice of unit cell dimensions, when there is a choice, since the cell
dimensions in (72) accord well with those chosen earlier by other workers
who knew they had to accommodate the Watson-Crick double helix in their unit
cells.  The choice of unit cell dimensions, where there is discretion, will
determine, of course, the axial scales in Patterson and other maps and may
force algorithms to move towards a double-helical diameter to fill the
chosen unit cell.

The literature contains many examples of x-ray diffraction from true
oligonucleotide crystals where the reported patterns of systematic absences,
sometimes plus weak presences, would have allowed the original researchers
to have chosen a smaller unit cell, for example, 74 (A-DNA), 75 (B-DNA), 76
(B-DNA), 77 (Z-DNA) & 78, into which reduced unit cells a double helix would
not fit.

Systematic weak presences are supposed to arise from distortions of the
(large) unit cell which diminish the intensities otherwise to be expected.
However, their very existence could arise from distortions of a small unit
cell from whose diffraction patterns they would otherwise not have been
observed at all.

Crystallographers rarely discuss in detail the patterns of systematic
absence plus any systematic weak presences to be seen in their structure
factors, and the Brookhaven oligonucleotide structure factor files on
deposit often reveal patterns which would seem to warrant further close
analysis.

For the DNA double helix, such is "the intensity of (our) conviction that
(the) hypothesis is true", to use Sir Peter Medawar's phrase, that we may be
able to agree with John Stuart Mill:

"When has there been a dominion which has not appeared natural to them that
possess it?"
---------------------------------------------------------------------------
72             A New Approach to Structure Determination of Large
Molecules by Multi-dimensional Search Methods; D. Rabinovich & Z. Shakked;
Acta Cryst. Vol A40 (1984) 195 - 200

73        S. Arnott & D. Hukins; Biochem. Biophys. Res. Commun. Vol
47 (1972) 1504 - 1509

74        Molecular Structure of d(GTGTACAC) in the spermine-bound
tetragonal and the spermine-free hexagonal crystal forms; Sanjeev Jain, PhD
Thesis; University of Wisconsin at Madison (1990)

75        Double helix conformation, groove dimensions & ligand binding
potential of a G/C stretch in B-DNA; Udo Heinemann, Claudia Alings & Manju
Bansal; The EMBO J Vol 11 (1992) 1931 - 1939


76        Unusual helical packing in crystals of DNA bearing a mutation hot
spot; Y Timsit et al.; Nature Vol 341 (1989) 459 - 462

77           A Salt-induced Conformational Change in Crystals of the
Synthetic Tetramer d(CGCG); H.R. Drew, R.E. Dickerson & K. Itakura; J Mol
Biol Vol 125 (1978) 535 - 543

78