HDTenEightyP/NetNews huggingface dataset:
From: twarnow@cs.sandia.gov (Tandy Warnow)
Newsgroups: sci.bio
Subject: Tutorial and Workshop on Algorithms for Molecular Sequence Alignment
Summary: Nov. 5 and 6, 1992, in Albuquerque
Date: 16 Oct 92 17:49:56 GMT
Article-I.D.: cs.1992Oct16.174956.12242
Organization: Sandia National Laboratories, Albuquerque, NM


                      Tutorial and Workshop on
             Algorithms for Molecular Sequence Alignment


                         Nov. 5 - 6, 1992
              University of New Mexico, Albuquerque, NM

Sandia National Laboratories and the Computer Science Department at 
the University of New Mexico are pleased to announce a tutorial and 
workshop on {\em Algorithms for Molecular Sequence Alignment}, to be 
held on Nov. 5 and 6, 1992, at the University of New Mexico, in 
Albuquerque, NM.  The tutorial is designed to introduce the problem 
of molecular sequence alignment, while the workshop will focus on new 
algorithmic techniques for this fundamental problem in computational 
biology.  The tutorial and workshop will be free and open to the public.
Graduate students and postdocs are especially encouraged to attend.

Thursday, Nov. 5: Tutorial


       Topics to be covered include:
            biological background, optimal pairwise alignments,
            global and local alignment, suboptimal pairwise alignments,
            distance vs. similarity, scoring matrices, database searching, 
            and multiple alignment: trees and profiles.

 Instructor: Martin Vingron
             Department of Mathematics
             University of Southern California


Friday, Nov. 6:  Workshop

Lectures: 


"On Suboptimal Alignments of Biological Sequences" 
        Dalit Naor
        Department of Biochemistry
        Stanford University

"Multiple Alignment with Guaranteed Error Bounds" 
        Pavel Pevzner
        Department of Computer Science
        Pennsylvania State University

"Scoring Systems for Macromolecular Sequence Comparison"
        Stephen Altschul
        National Institute of Health

Title to be announced
        John Kececioglu
        Department of Computer Science
        University of California at Davis


"Analysis and Biological Evaluation of Parametric Sequence Alignments"
        Martin Vingron
        Department of Mathematics
        University of Southern California


"Dinucleotide Simple Sequence Repeats in Human DNA"
        David Torney
        Los Alamos National Laboratories

"3-D Profile Method and its Application in Protein Secondary Structure Prediction"
        Kam Zhang
        Molecular Biology Institute
        University of California at Los Angeles


For further information, please contact Tandy Warnow at (505) 845-7604
or by email at twarnow@cs.sandia.gov.
Xref: sparky sci.bio:3563 sci.environment:11952
From: jstravis@bass.bu.edu (John Travis)
Newsgroups: sci.bio,sci.environment
Subject: Another prize announcemnet
Date: 14 Oct 92 18:53:54 GMT
Article-I.D.: bu.98647
Reply-To: jstravis@bass.bu.edu (John Travis)
Followup-To: sci.bio
Organization: Boston University

Knut Scmidt-Nielsen of Duke University won Japan's International
Prize for Biology, which I guess is suppose to complement areas the Nobel
prizes tend to miss. His work was on the physiology of vertebrates, particul-
ary their adaptions to extreme environments. For example, i believe he
fisrt explained how camels and kangaroo rats save water in deserts by
having different metabolisms. Anyone out there know more about his
work and how influential it is?
Xref: sparky sci.bio:3501 bionet.neuroscience:441
From: mlevin@husc8.harvard.edu (Michael Levin)
Newsgroups: sci.bio,bionet.neuroscience
Subject: glia and dendritic spines
Date: 9 Oct 92 00:57:26 GMT
Distribution: usa
Organization: Harvard University Science Center


    Is there any known connection between glial cells and dendritic
spines? I.e., how do I get a person interested in dendritic spines to
be excited about some work with glia? All imaginative replies are
welcome. Is there any evidence that they interact, affect each other,
etc.? Please send replies (prefereably, but not necessarily, with
references) to mlevin@husc8.harvard.edu.

Mike Levin
Newsgroups: sci.bio
From: gordon@tramp.Colorado.EDU (GORDON ALLEN R)
Subject: Re: are there any toroidal cells?
Organization: University of Colorado, Boulder
Date: Fri, 16 Oct 1992 14:18:28 GMT

cohen@cumuli.vmsmail.ethz.ch (Mark Cohen) writes:

>I have a hole down the middle and so do many multicellular organisms
>the question is do you consider the gut as sufficient to classify me
>as toroidal or do the various sphincters make me spherical?

>Mark Cohen
>cohen@cumuli.vmsmail.ethz.ch


You qualify.  Topologically even with sphincters, you are a tube.

-- 
Allen Gordon 		         *If the folly of but one of us was changed to*
Research Associate         	 *intelligence, and divided amongst a thousand*
gordon@tramp.colorado.edu   	 *toads, each would be more intelligent than  *
				 *Aristotle				      *
From: jack@dcs.glasgow.ac.uk (Jack Campin)
Newsgroups: sci.bio
Subject: Re: are there any toroidal cells?
Date: 15 Oct 92 19:39:53 GMT
Reply-To: jack@dcs.glasgow.ac.uk (Jack Campin)
Organization: COMANDOS Project, Glesga Yoonie

jack@dcs.glasgow.ac.uk (Jack Campin) wrote:
> Idle question: are any cells topologically toroidal, either throughout
> their life or as a phase of significant duration?  If not, why not?

Perhaps I should explain what I was thinking of here.  There is a theorem
of topology - the Brouwer fixed point theorem - which says that a hairy
sphere must have a parting.  It doesn't apply to a toroid; unlike a
topological sphere (which all cells I know of are) a toroidal cell could
use scale-like plates to cover itself and have no chink to worry about, or
have a uniform coat of oriented cilia (with a choice of major-axis, minor-
axis, or helical orientation).

One kind of locomotion made possible by being toroidal is rolling your
membrane round through your hole; if your hole is small, the resistance
round the outside will exceed that on the inside and give a nett propulsion
along your axis of symmetry.  Or if you can break and relink yourself you
can form a chain with your fellow doughnuts.  Or you can stack yourselves
into a tube; nature finds it worthwhile to build tubes in much more complex
ways, so why not this one?  And you can have a higher surface/volume ratio
than your oblate-spheroid competitors and use contraction and dilatation as
an efficient mechanism for churning up the fluid around you.  And you can
just surround big rod-like organisms and throttle them without any of the
messy, antigen-prone and expensive chemical warfare that usually goes on
in fights between microorganisms.

So, if you're a cell, there are all sorts of advantages to being a
doughnut, with the only obvious costs being the extra rigidity and the
extra area of cell membrane; but as far as I know neither monocellular nor
multicellular organisms have taken up the offer.  Why is it so difficult?

-- 
--  Jack Campin    room G092, Computing Science Department, Glasgow University,
17 Lilybank Gardens, Glasgow G12 8RZ, Scotland   TEL: 041 339 8855 x6854 (work)
INTERNET: jack@dcs.glasgow.ac.uk or via nsfnet-relay.ac.uk    FAX: 041 330 4913
BANG!net: via mcsun and uknet     BITNET: via UKACRL    UUCP: jack@glasgow.uucp
Newsgroups: sci.bio
From: rambaut@castle.ed.ac.uk (A E Ram aut)
Newsgroups: sci.bio
Subject: Re: The old "are humans veggies or carnivores" thing
Date: 15 Oct 92 14:29:50 GMT
Organization: Edinburgh University

timi@mendel.berkeley.edu ( Tim Ikeda) writes:

>In article <1992Oct14.192253.8495@alw.nih.gov> singley@helix.nih.gov (Erick Sing
>ley) writes:
>>A minor addition, if we're going on body parts as a distintion: position of
>>eyes: most herbs have side-facing eyes (horse, rabbit, etc.) to watch for
>>preds; while preds have forward facing for better binc/depth (lion, dog).
>>Humans would fall under this latter catagory, yes?

>Yes, but maybe not to become better predators.  3-D vision is a 
>benefit for creatures that have to swing from branch to branch.

Are you sure that humans evolved from brachiating ancestor?  Anyway, the
current idea is that all primated evolved from a small insectivorous
ancestor, and insects are not plants (what a perceptive statement).

Andrew
Xref: sparky sci.bio:3598 sci.environment:12037
From: ewartd@emu.insted.unimelb.edu.au
Newsgroups: sci.bio,sci.environment
Subject: Re: World Food Prize Awarded for Eco-Friendly War on Pests
Summary: All its cracked up to be?
Date: 16 Oct 92 13:41:47 GMT

In article <1992Oct14.165411.12660@aurora.com>, isaak@aurora.com (Mark Isaak) writes:
> In article <1992Oct13.090556.16359@samba.oit.unc.edu> Nigel.Allen@bbs.oit.unc.edu (Nigel Allen) writes:
>>
>>Here is a press release from The World Food Prize Foundation.
>>   DES MOINES, Iowa, Oct. 12  -- A technique developed more 
>>than 40 years ago is being used this fall to eradicate screwworm
>>from Mexico and the Medfly from California.
>>   Dr. Edward F. Knipling, 83, of Arlington, Va., and Dr. Raymond C.
>>Bushland, 82, of Kerrville, Texas, both retired entomologists from
>>the USDA Agricultural Research Service, received the award for . . .
>>Sterile Insect Technique (SIT) [which] uses no chemicals, leaves no
>>residues and has no effect on non-target species.
> 
> The Sterile Insect Technique has indeed had outstanding success
> against the screwworm fly, but it is far from a panacea.  Its
> potential for success depends a lot on the biology of the pest
> it's being used against.  (If I remember right, a big reason it
> is so successful against screwworms is that female screwworms
> only mate once.)  When the Sterile Insect Technique was tried
> against the Mediterranean fruit fly in the Santa Clara, CA area
> in the 1970's, the Medfly spread to five counties.
> 
> On a related subject...  Another article I saw about Knipling &
> Bushland's prize gave the impression that a recent screwworm
> infestation in Africa has now been eradicated.  Can anyone
> confirm or deny that?
> -- 
> Mark Isaak           "Every generation thinks it has the answers, and every
> isaak@aurora.com      generation is humbled by nature." - Philip Lubin

Sterile insect technique would only ever be able to "eradicate" small,
vulnerable populations - like on islands with little or no chance of
recruitment.

The bit that worries me is that x% of the zapped flies will not be sterile.
How large can x be before its an obviously dumb idea?  

There was an article a few years back correlating the published successes
of sterile fly release with the actual weather conditions at the time
(weather is a strong regulator of many insect species) which suggested that
perhaps the weather had caused the population reductions that had been
reported.  [I can dig out the reference if anybody wants]

While biological controls are infintely preferable to most broadscale biocide
treatment (eg Malathion on Medfly), it is not without risk to the environment.

Cheers

Don
Newsgroups: sci.bio,bionet.molbio.evolution,talk.origins
From: sbradley@scic.intel.com (Seth Bradley)
Subject: Re: What Genomes have been Sequenced?
Organization: Intel SCIC, Beaverton, OR
Date: Fri, 9 Oct 1992 23:30:31 GMT

In article <robison1.718663846@husc10> robison1@husc10.harvard.edu (Keith Robison) writes:
>sbradley@scic.intel.com (Seth Bradley) writes:
>>Two human chromosomes have been sequenced.  The Y and the smallest of the
>>remaining ones (can't remember its designation).

>Sigh.  If only it were true. Unfortunately, Y and 23q have only been
>mapped into a complete set of cloned DNA fragments.

I reread the article, and you're correct about the sets of DNA fragments.
However, it was Y and chromosome 21, not 23, if anyone cares :-).
From the October 3 issue of Science Digest.

-- 
Seth J. Bradley, Senior System Administrator, Intel SCIC
Internet: sbradley@scic.intel.com   UUCP: uunet!scic.intel.com!sbradley
----------------------------------------
"A system admin's life is a sorry one.  The only advantage he has over
Emergency Room doctors is that malpractice suits are rare.  On the other
hand, ER doctors never have to deal with patients installing new versions
of their own innards!"  -Michael O'Brien
Xref: sparky sci.bio:3556 bionet.sci-resources:205
Newsgroups: sci.bio,bionet.sci-resources
Subject: what do you use to look stuff up???
From: mlevin@husc8.harvard.edu (Michael Levin)
Date: 13 Oct 92 20:11:39 EDT
Distribution: usa
Organization: Harvard University Science Center


      I'm a first year grad student in developmental bio, and I am
wondering what people out there are using to look for papers on a
given topic (computerized searches, I mean). We have a link to Medline
here, but it seems that it is missing a lot of the non-medical (basic
research stuff), although it certainly has a lot too (i.e., I can't
figure out how they decide what to put in). Anyways, is there any
database that one can search that covers all the normal biology
journals? In addition, are there ones that specializes (or includes)
physics and computer science journals also? Please reply to
mlevin@husc8.harvard.edu. 

Mike Levin
Newsgroups: sci.bio
From: singley@helix.nih.gov (Erick Singley)
Subject: Re: quipazine, where to buy ?
Organization: (National Institutes of Health, Bethesda, MD)
Date: Thu, 15 Oct 1992 21:04:24 GMT

I searched through five catalogues, when my boss plops this one down on the way
through the door:

RBI (Research Biochemicals Incorporated) 1992-1993
One Strathmore Rd
Natick, MA 01760-2418 USA
800-736-3690 Orders
508-651-8151 Tech Info
508-655-1359 Fax (24 hr)

on pg 219 they list:
S-007 Quipazine dimaleate[2-(1-Piperazinyl)quinoline dimalate] serotonin agonist
   pg 220
Q-109 Quipazine, 6-Nitro-[6 Nitro 2-(1-Piperazinyl)quinoline] 'potent and
selective serotonin uptake inhibitor
Q-107 Quipazine, N-methyl-, dimaleate[ 2-[1-(4methyl-)Piperazinyl]quinoline
dimalate]

Disclamer: I pass this info along on net since I am unable to reach your Mail
site. I have no ties with said company nor knowledge of availablity of chemicals
or prices.

Hope thats what you needed- if not (maybe) they'll have better ideas?
Erick
--
singley@clinpharm.niaaa.nih.gov
Newsgroups: sci.bio,talk.environment,sci.environment,alt.activism,misc.rural
From: eduardo@porthos.cs.ua.edu (Eduardo Kortright)
Subject: Cypress Range Limits
Organization: Department of Computer Science, University of Alabama
Date: Wed, 14 Oct 1992 22:03:08 GMT

Hi there,

I am not a biologist, but my sister is having an interesting time
trying to do some research on the limits of cypress ranges, and I
promised I would help her by posting a query to this group.  The
cypress she is interested in is _Taxodium_distichum_, and as far as I
can make out, she is interested in finding out what research has been
done on why cypress grow only in the flat areas of the coastal plain,
and whether the beginning of hillier terrain corresponds to the end of
cypress growth.  She would especially like references or comments from
people who have done any kind of work on the conditions at the
transition between the areas where cypress grow, and the areas where
they don't.

If you have any relevant information, or can point me to other
appropriate newsgroups, I would greatly appreciate any e-mail sent to:

	eduardo@cs.ua.edu

If anyone else is interested, I can post a summary of information
received.

Thanks,

=-=-=-=
Eduardo Kortright
A graduate student at the University of Alabama Computer Science Dept.
-- 
     ._ 			    //  Eduardo Kortright
    /_  ._/ . .  ._   ._ ._/ ._	   //  Grad Student
   /__ /_/ /_/_ /_/_ /  /_/ /_/   //  University of Alabama at Tuscaloosa

Xref: sparky sci.bio:3516 bionet.molbio.evolution:359 talk.origins:12807
From: cherry@OPAL.MGH.HARVARD.EDU
Newsgroups: sci.bio,bionet.molbio.evolution,talk.origins
Subject: Re: What Genomes have been Sequenced?
Date: 9 Oct 92 12:47:41 GMT
Reply-To: cherry@OPAL.MGH.HARVARD.EDU
Organization: Molecular Biology - Mass Gen Hospital

>In article <1992Oct9.005050.11581@s1.gov>, lip@s1.gov (Loren I. Petrich) writes:
>>	I presume that _Escherichia coli_ would be a good candidate
>>for being the first self-contained organism (that is, not a virus) to
>>be completely sequenced. Has it been done? And if not, how much of _E.
>>coli_'s genome has been sequenced or mapped?
>>
>>	I bring this up because of recent news of the complete
>>sequencing of a yeast chromosome, #3. This chromosome was found to
>>have almost no genes previously known, many of the with obscure
>>functions (deleting one of them had no effect, except when the yeast
>>cells were put in some hot acetic acid (or something)). The team
>>stated that the job for the others should be done late in this decade.
>>
>>	Anything on the favorite lab nematode (_Caenorhabditis
>>elegans_), or the fruit fly, or even the human genome?

There have been several viral genomes completely sequenced.

Sequencing of E. coli is about 50% done and C. elegans is about 1%
finished.

My understanding to the yeast chromosome III result was not quite the
same as yours. There are many genes identified that had great
similarity to other known genes. However there was also a large
percentage of the predicted coding regions that had no match with the
existing sequence databases. I believe the percentage of coding
regions with no similarity was around 40%. This is similar to the
percentage of EST sequences from human brain as well as C. elegans
that have no similarity to the sequence databases.

Mike Cherry
Xref: sparky sci.bio:3599 sci.engr.biomed:580 bionet.jobs:562 sci.research.careers:1313
From: tjfeue@bb1t.monsanto.com
Newsgroups: sci.bio,sci.engr.biomed,bionet.jobs,sci.research.careers
Subject: Biotech in Singapore?
Date: 15 Oct 92 13:44:51 CST
Organization: Monsanto Company, St. Louis, MO

Does anyone have a listing of biotechnology companies in Singapore?
An email address of anyone working at one there?

Thanks,
Ted Feuerbach - Scientific Systems Consultant
Disclaimer:  Monsanto didn't say this, I did.
From: rpgrant@vax.path.ox.ac.uk
Newsgroups: sci.bio
Subject: Re: Sleeping
Date: 9 Oct 92 15:19:42 GMT
Organization: Oxford University Molecular Biology Data Centre
Nntp-Posting-User: rpgrant

In article <92283.110837E65292@TRMETU.BITNET>, E65292@TRMETU.BITNET (Gokhan Tolun) writes:
> Which species never sleep ?
> 
> 
>                                                          E65292@TRMETU

My boss, as far as I can tell.....

Richard 
Newsgroups: sci.bio,sci.environment
From: isaak@aurora.com (Mark Isaak)
Subject: Re: World Food Prize Awarded for Eco-Friendly War on Pests
Reply-To: isaak@aurora.com (Mark Isaak)
Organization: The Aurora Group
Date: Wed, 14 Oct 92 16:54:11 GMT

In article <1992Oct13.090556.16359@samba.oit.unc.edu> Nigel.Allen@bbs.oit.unc.edu (Nigel Allen) writes:
>
>Here is a press release from The World Food Prize Foundation.
>   DES MOINES, Iowa, Oct. 12  -- A technique developed more 
>than 40 years ago is being used this fall to eradicate screwworm
>from Mexico and the Medfly from California.
>   Dr. Edward F. Knipling, 83, of Arlington, Va., and Dr. Raymond C.
>Bushland, 82, of Kerrville, Texas, both retired entomologists from
>the USDA Agricultural Research Service, received the award for . . .
>Sterile Insect Technique (SIT) [which] uses no chemicals, leaves no
>residues and has no effect on non-target species.

The Sterile Insect Technique has indeed had outstanding success
against the screwworm fly, but it is far from a panacea.  Its
potential for success depends a lot on the biology of the pest
it's being used against.  (If I remember right, a big reason it
is so successful against screwworms is that female screwworms
only mate once.)  When the Sterile Insect Technique was tried
against the Mediterranean fruit fly in the Santa Clara, CA area
in the 1970's, the Medfly spread to five counties.

On a related subject...  Another article I saw about Knipling &
Bushland's prize gave the impression that a recent screwworm
infestation in Africa has now been eradicated.  Can anyone
confirm or deny that?
-- 
Mark Isaak           "Every generation thinks it has the answers, and every
isaak@aurora.com      generation is humbled by nature." - Philip Lubin
Newsgroups: sci.bio
From: eb3@world.std.com (Edwin Barkdoll)
Subject: Re: The old "are humans veggies or carnivores" thing
Organization: The World Public Access UNIX, Brookline, MA
Date: Fri, 16 Oct 1992 00:56:46 GMT

In article <4370003@hpcc01.corp.hp.com> loftis@hpcc01.corp.hp.com (Kirk Loftis) writes:
>	One thing I would like to add, wolves and dogs can eat other
>foods beside meats.  They can be oppurtunists and eat most everything
>humans eat.  Note: look at dog food contents - Rice and Lamb, Corn Meal,
>etc.  I am not saying that they are grazers like a cow or a horse or
>that they seek out those foods.  

	Our 2 dogs graze with the best of them...

>	I am not sure if a cow or a horse would even eat meat if it was
>presented to them.

	Actually common food additives for cattle include fish, bone,
meat and blood meals.

	And (are you out there MR?) certain ungulates suffering from
nutritional deficiencies (Ca or P) have been observed to eat the legs
of fledglings.  Strange but true.


-- 
Edwin Barkdoll
eb3@world.std.com
Newsgroups: sci.bio
From: lecl@quads.uchicago.edu (elizabeth e. leclair)
Subject: Cold/Hot Heads  
Reply-To: lecl@midway.uchicago.edu
Organization: University of Chicago Computing Organizations
Date: Tue, 6 Oct 1992 21:51:38 GMT

Newsgrou
>chmoris@techunix.technion.ac.il (Dr. Moris S.Eisen)
>
>
>
>
>
>
>


  For the person interested in the air-conditioned motorcycle helmet
  venture  (I lost your e-mail address, but here goes): 

  The average human being puts out a total of 80-100 watts (joules/sec).
  (Yes, the human body is a light bulb!)  About 15% of that is dissipated
  by the subcutaneous vascular tissues in the head.  So the average amount
  of energy lost through the head is about 10-15 watts.  Depends on skin
  hair, and level of activity, etc., but this is a ballpark figure that
  you might find useful.

   Do you think AC motorcycle helmets will encourage people to actually
  *wear* them??

   :-)  -a smiling biomechanist

 
-- 
~~~~~~~~~~~~~~ Elizabeth E. LeClair  (lecl@midway.uchicago.edu)~~~~~~~~~~~~~
           Committee on Evolutionary Biology, University of Chicago
"Sex is two wavy lines and the United States of America is a trapezoid." L.M.
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
From: skaamjm@ucl.ac.uk (Matthew Moore)
Newsgroups: sci.bio
Subject: Re: Origin of Life-DNA
Date: 12 Oct 92 15:59:46 GMT
Organization: Bloomsbury Computing Consortium

ssaf+@andrew.cmu.edu (Sreyas Srinivasan) writes:


>Pittsburgh. I happen to be very, very interested in evolutionary science
>and the origins of life. My bio book only gives a brief description of
>how DNA may have come into being (in reverse, from an RNA template). Are
>there any other theories out there about how it may have happened?


Two books which between them give an excellent review of current
theory, as well as describe a new(ish) theory (life originated in clay
minerals) are 'Seven Clues to the Origin of Life' and 'Genetic
Takeover', both by Cairns-Smith. (Member of the Chemistry Dept,
University of Glasgow).
From: P.C.Walker@bradford.ac.uk (Paul Walker)
Newsgroups: sci.bio
Subject: Appendix
Date: 9 Oct 92 09:36:24 GMT
Organization: University of Bradford, UK
Originator: 91657715@mail

I'm undergoing a project which involves a talk about the appendix as part
of the lymphoid system. I would like to be able to colour postscript a 
picture of the anatomy of the appendix, but as of yet, haven't been able to
find any GIF or other graphic files anywhere. I would appreciate it, if anyone
could send me a list of FTP sites which do such pictures, or send me a GIF file
of the appendix.

Thanks

Paul


p.c.walker@uk.ac.bradford