Nabble - Bio.net - Btk-mca

Why is solubility phe>tyr ?

2009-04-25T18:55:55Z

I am also looking for answers for this type of question for a second year university lab report. I found your question online and was wondering what kind of answers you received if any. Thanks

Heather (New Zealand)

Get fit, feel better! All the help you need at Yahoo!Xtra Health
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kinetic constants in rabbit and mice

2009-04-22T09:06:27Z

Dear everybody,

I am working on a computational model on the metabolism in muscle cells based on
rabbit data. For two enzyme reactions though (Creatine kinase), I only fin\
d enzyme kinetic parameter values determined by experiments on mice.
The parameters are mainly binary and ternary dissociation constants, as well as
maximum reaction velocities.
What is the best way to deal with this? Does someone has an idea how I can
include those parameters "safely" into my model?

Thanks in advance,

hans

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Reminder, XIII ASMDA2009, Applied Stochastic Models and Data Analysis International Conference

2009-04-13T18:08:50Z

Dear Colleague,

This is just a reminder that there is still time to join to the
XIII ASMDA 2009 International Conference on Applied Stochastic Modeling and Data Analysis, June 30 -- July 3, 2009, Vilnius, Lithuania.

The conference website is at: http://www.mii.lt/asmda-2009/index.php?page,home.en

This is the XIII ASMDA event from 1981 when the first ASMDA Conference was held in Brussels.

Main Topics: Poisson, Markov, semi-Markov processes, Point processes, Martingales, Stochastic calculus, Random evolutions, Decision and Controlled Processes, Diffusion and Poisson approximations, Asymptotic models and Weak convergences, Statistical inference for Stochastic processes , Hidden Markov and semi-Markov processes, Fitting models for data, Reliability and survival analysis, Bayesian inference, Discriminant and Regression Analysis, Mixture model and Probabilistic approach to Clustering, Analysis of complex data (incomplete, censored, missing, spatio-temporal, imprecise, fuzzy,...), Theories of uncertainty, Graphical models and Bayesian networks, Multidimensional Scaling, Sensory Analysis, Classification and Documentation, Data and Text Mining, Chaotic and Stochastic processes, Analysis of Chaotic processes, Neural Networks, Genetic and Fuzzy Algorithms, Monte Carlo Methods and Chaotic Simulation.

If you like to submit an abstract/ paper/stream proposal please visit the conference website.

See the deadlines at: http://www.mii.lt/asmda-2009/index.php?page,deadlines.en

More information from the Conference Chair:

Prof. Leonidas Sakalauskas

Institute of Mathematics and Informatics

Akademijos 4

08663 Vilnius, Lithuania

Tel. +3705 2109323

Fax: +3705 2729209

e-mail: asmda2009@...

If you don't like to receive messages regarding the ASMDA2009 Conference, please click here: info@...

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JVMAH: CALL FOR PAPERS

2009-01-28T02:35:41Z

Journal of Veterinary Medicine and Animal Health

www.academicjournals.org/JVMAH

Dear Colleague,

Introducing ''Journal of Veterinary Medicine and Animal Health (JVMAH)"

The Journal of Veterinary Medicine and Animal Health is a multidisciplinary peer-reviewed journal published that will be monthly by Academic Journals (http://www.academicjournals.org/JVMAH). JVMAH is dedicated to increasing the depth of the subject across disciplines with the ultimate aim of expanding knowledge of the subject.

Editors and reviewers

JVMAH is seeking qualified researchers to join its editorial team as editors, subeditors or reviewers. Kindly send your resume to JVMAH@....

Call for Papers

JVMAH will cover all areas of the subject. The journal welcomes the submission of manuscripts that meet the general criteria of significance and scientific excellence, and will publish:

· Original articles in basic and applied research

· Case studies

· Critical reviews, surveys, opinions, commentaries and essays

We invite you to submit your manuscript(s) to JVMAH@... for publication in the Maiden Issue (May 2009). Our objective is to inform authors of the decision on their manuscript(s) within four weeks of submission. Following acceptance, a paper will normally be published in the next issue. Instruction for authors and other details are available on our website; http://www.academicjournals.org/JVMAH/Instruction.htm

JVMAH is an Open Access Journal

One key request of researchers across the world is unrestricted access to research publications. Open access gives a worldwide audience larger than that of any subscription-based journal and thus increases the visibility and impact of published works. It also enhances indexing, retrieval power and eliminates the need for permissions to reproduce and distribute content. JVMAH is fully committed to the Open Access Initiative and will provide free access to all articles as soon as they are published.

Best regards,

Michael Oruah

Editorial Assistant

Journal of Veterinary Medicine and Animal Health.

E-mail: JVMAH@...

http://www.academicjournals.org/JVMAH

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Muscle vs. fat catabolism?

2009-01-19T14:17:59Z

So, I am interested in the answer to your fabulous question “what biochemicals determine the relative catabolic rate of muscle versus fat under conditions of caloric intake deficits?”

Henry C Ecker Jr RN

Clinical Manager

MacNeal Home Care

708 783-2788

Hecker@...

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Seasonal Weight Changes Linked To Metabolic Syndrome

2008-12-14T22:00:19Z

Seasonal changes in weight increase the risk for metabolic syndrome, a
group of scientists from National Public Health Institute, Helsinki,
Finland.
This finding was based on analysis of 8,028 individuals,
representative of the general population aged over 30, who attended a
nationwide health examination survey.

According to the current study, individuals with metabolic syndrome
have more seasonal changes in their mood and behavior. The study
concludes that the seasonal changes in weight in particular are linked
to metabolic syndrome.

With people having the 'winter blues' the risk of metabolic syndrome
is heightened by 56 per cent. The negative effect of the seasonal
changes equals to the protective effect against metabolic syndrome
gained with regular physical exercise.

Because of easy assessment the scoring of seasonal changes in weight
might be taken as a routine part of health status examination in
persons being at risk of or currently having metabolic syndrome. If
there were these changes, treatment options including scheduled
exposures to light and regular physical exercise need to be
considered.

Tonny
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Re: bounds of fluxes of e.coli metabolism (JS)

2008-10-09T09:33:15Z

First off, is there any reason you're working with JR904? I ask because
there is a newer E. coli model, AF1260.

As for setting bounds on fluxes, you only really need to set bounds for
uptake reactions. In other words, if you're doing a simulation in which
glucose is your only carbon source, then you will need to determine the
glucose uptake rate for the experimental system you're interested in, use
this value as the uptake rate in the model, and then set bounds
accordingly. The lower bound should be zero, and the upper bound is
usually set to the uptake rate in rich medium. Obviously, you'll want to
use common sense too. If glucose is you're only carbon source, set uptake
rates for all other carbon sources to zero.

For internal fluxes, a good starting point is simply to set the lower
bound to -1000 and the upper bound to +1000 (this approximates -infinity
and +infinity) if the reaction is reversible. Otherwise, the lower bound
is 0 for irreversible. This works well because the uptake rates you set
will automatically constrain the internal fluxes in the system since the
system is mass balanced. Just be sure to check your simulation results
for values that do not make sense. This usually means there are internal
loops somewhere in your simulation such that mass is not flowing
throughout the entire system.

Hope this helps,
Pep

>
>
> Today's Topics:
>
> 1. bounds of fluxes of e.coli metabolism (JS)
>
>
> ----------------------------------------------------------------------
>
> Message: 1
> Date: Tue, 7 Oct 2008 12:56:30 -0700 (PDT)
> From: JS <lee.joosang@...>
> Subject: [Biothermokinetics] bounds of fluxes of e.coli metabolism
> To: bionet-metabolic-reg@...
> Message-ID:
> <314c2044-e1de-4ac2-8512-e68fe0811ef6@...>
> Content-Type: text/plain; charset=ISO-8859-1
>
> hello,
>
> I am looking for the upper and lower bounds the fluxes e. coli
> metabolic network. Does anybody happen to know of any reference which
> contains some information on the bounds of individual fluxes of e.coli
> metabolism? I am using JR904 model, but other models are also fine.
>
> best regards,
> JS
>
>
>
> ------------------------------
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> End of Btk-mca Digest, Vol 8, Issue 1
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bounds of fluxes of e.coli metabolism

2008-10-07T12:56:30Z

hello,

I am looking for the upper and lower bounds the fluxes e. coli
metabolic network. Does anybody happen to know of any reference which
contains some information on the bounds of individual fluxes of e.coli
metabolism? I am using JR904 model, but other models are also fine.

best regards,
JS

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Phtosynthesis and Global Warming

2007-10-04T11:41:35Z

Once it is understood and accepted that the oxygen of photosynthesis can be only exothermic, that change a lot of theories.
As for Global Warming, it is believed that it is the concentration of CO2, which, enable the process of global warming. But if you do remove the vegetation, then no rising of the temperature is observed. So the concentration fo CO2 do act through photosynthesis. So more of the production of new molecules, more heat hence an observed rising of the temperature must be. Oxygen being exothermic, if true, is a new factor in the equation of the climate.
But it is not as simple as that. You have to consider the local production of new molecules via the overall production of the planet. A continuum of heat is built but its reparation is according to the relative strength of the patches (on a continental scale) of vegetation. So a region as Toronto may see its temperature lowered, while northern regions may know a rise of the temperature.
If Hurricane season do correspond to a minimum in the seasonal production of the total photosynthesis output products, then we have something akin of a glacial period. For a planet aging is as to lose its forests, forests that become deserts: a lowering of the total production of the photosynthesis.
Pierre Verville Jardinier forestier
Pierre-m.verville at hotmail.com
263 notre-dame ouest #6, Victoriaville, Qc, CANADA G6P1S1

Asking help for protocol to determine Glycerol-3-Phosphate Concentration

2007-08-22T19:30:21Z

I saw on internet and I'm writing to you.

I also would like to know the protocol and how to extract G3P.

If you have found out already, could you tell the protocol for me?

Thank you in advance.

Kaori Sugimoto

"EMF <COH.org>" made the following annotations.
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looking for lignin

2007-05-16T13:27:14Z

Did you ever find any - if so, where?

David Eustace

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C4P for the new special issue of EURASIP Journal on Bioinformatics and Systems Biology

2006-09-07T06:43:42Z

Information Theoretic Methods for Bioinformatics

Call for Papers
Information theoretic methods for modeling are at the center of the current
efforts to interpret bioinformatics data. The high pace at which new
technologies are developed for collecting genomic and proteomic data
requires a sustained effort to provide powerful methods for modeling the
data acquired. Recent advances in universal modeling and minimum
description length techniques have been shown to be well suited for
modeling and analyzing such data. This special issue calls for
contributions to modeling of data arising in bioinformatics and systems
biology by information theoretic means. Submissions should address
theoretical developments, computational aspects, or specific applications.
Suitable topics for this special issue include but are not limited to:

Normalized maximum-likelihood (NML) universal models
Minimum description length (MDL) techniques
Microarray data modeling
Denoising of genomic data
Pattern recognition
Data compression-based modeling
Authors should follow the EURASIP JBSB manuscript format described at the
journal site http://www.hindawi.com/GetJournal.aspx?journal=BSB.
Prospective authors should submit an electronic copy of their complete
manuscript through the EURASIP JBSB's Manuscript Tracking System at
http://www.hindawi.com/mts/, according to the following timetable:

Manuscript Due February 1, 2007
Acceptance Notification May 1, 2007
Final Manuscript Due July 1, 2007
Publication Date 3rd Quarter, 2007

Guest Editors:
Jorma Rissanen, Computer Learning Research Center, University of London,
Royal Holloway,TW20 0EX, UK

Peter Grünwald, Centrum voor Wiskunde en Informatica (CWI), National
Research Institute for Mathematics and Computer Science, P.O. Box 94079,
1090 GB Amsterdam, The Netherlands

Jukka Heikkonen, Laboratory of Computational Engineering, Helsinki
University of Technology, P.O. Box 9203, 02015 HUT, Finland

Petri Myllymäki, Department of Computer Science, University of Helsinki,
P.O. Box 68 (Gustaf Hällströmin katu 2b), 00014, Finland

Teemu Roos, Complex Systems Computation Group, Helsinki Institute for
Information Technology, University of Helsinki, P.O.Box 68, 00014, Finland

Juho Rousu, Department of Computer Science, University of Helsinki, P.O.
Box 68 (Gustaf Hällströmin katu 2b), 00014, Finland

For more information please contact
Dalia.hassanin@...

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Re: Kinetics of bacterial mixed cultures

2006-09-05T14:05:16Z

Hi all, hi Iraklis.

> I have cultivated anaerobic mixed cultures and I am trying to test their
> ability to decompose some organic compounds under different environmental
> conditions. Currently I am trying to start studying the appropriate
> bibliography about bacterial kinetics in order to stimulate their
> behaviour.

I am not sure what you mean by stimulate (or is this a nice typo, did
you mean "simulate"?).

> Is there any basic reading for bacterial kinetics that I have to start with?

I would read the following books in this order:

@BOOK{Cornish-Bowden2004,
title = {Fundamentals of Enzyme Kinetics},
publisher = {Portland Press},
year = {2004},
author = {Athel Cornish-Bowden},
edition = {3.},
note = {ISBN: 1855781581}
}

@BOOK{Fell1996,
title = {Understanding the Control of Metabolism},
publisher = {Ashgate Publishing},
year = {1996},
author = {David Fell},
note = {ISBN: 185578047X}
}

@BOOK{Heinrich1996,
title = {The Regulation Of Cellular Systems},
publisher = {Springer},
year = {1996},
author = {Reinhart Heinrich and Stefan Schuster},
edition = {1.},
note = {ISBN: 0412032619}
}

> Is there any basic reading of kinetic coefficients measurements in the lab?

In addition to the above-mentioned this may be a good resource if you
are looking for coefficients: http://www.brenda.uni-koeln.de/
An additional recommended reading focusing on wet lab methods? Don't
have one right now.

> Should I try to find a software to model their kinetics?

If you really want to try to build a kinetic model, I would suggest:
http://www.copasi.org/
or
http://sbw.sourceforge.net/

One warning: Before you start with the modeling process, I would rethink
the approach. A kinetic model may not be what you are searching for. The
modeling procedure should focus on the questions to be answered. What
exactly do you want to achieve with the model?

Kai

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Kinetics of bacterial mixed cultures

2006-09-05T07:20:13Z

Dear group,

I have cultivated anaerobic mixed cultures and I am trying to test their
ability to decompose some organic compounds under different environmental
conditions. Currently I am trying to start studying the appropriate
bibliography about bacterial kinetics in order to stimulate their
behaviour.

Is this possible for mixed cultures?
Is there any basic reading for bacterial kinetics that I have to start with?
Is there any basic reading of kinetic coefficients measurements in the lab?
Should I try to find a software to model their kinetics?

Any help would be valuable.
Thank you.

--

Iraklis Panagiotakis
PhD candidate
Department of Water Resources, Hydraulic & Maritime Engineering
Faculty of Civil Engineering
National Technical University of Athens
Iroon Polytechneiou 5
157 80 Zografou
tel. ++30 210 7721610

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Reducing agents for protein chemistry

2006-08-09T10:42:54Z

Hello,

I happened to run across your post on the Btk-mca mailing list looking for a listing of redox potentials for common reducing agents, way back in 1999. Did you ever happen to get a list, if so could you send me a link?

Thanks,

Natalie

-------------------------------------------------

Natalie Winblade Nairn, Ph.D.

Senior Scientist

Allozyne

1616 Eastlake Ave E

Seattle WA 98102

206-957-7324

nnairn@...

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Constructing a large model with few parameters

2006-08-08T02:16:08Z

Hi all.

First of all: The btk-mca newsgroups - the one on yahoogroups.com and
the one on bio.net - have been very inspiring. It is very unfortunate
that open discussions like these are hard to find. If anyone can hint me
to more material on the web with this quality, please write.

On topic:
I would like to build a bacterial model with ca. 200 reactions and as
few parameters as possible. I'm not interested in exact reproduction of
flux and concentration data, but the trends (rises & falls) would be
sufficient. Therefore, my first idea is to build a model with mass
action kinetics (which makes use of equilibrium constants and has only
one parameter left) and add only a few more detailed rate laws at
critical points.

Questions:
1. Does this make sense? What would be a better approach?
2. How do I identify these critical points (e.g. large equilibrium
constant, enzymes which are regulated by feedback inhibition, ...)?

Looking forward to your suggestions,

Kai

PS: Cross-posting is intended, please don't get offended.

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Photosynthesis: exothermic or endothermic?

2006-08-04T08:58:00Z

A new molecule have to be exoergic (exergonic ?). Because ortherwise it is
unstable ( a very short life).

In order to say endoergic you have to consider two molecules of water to
provide the four protons for the basic monomer. Is the oxygen of
photosynthesis endo or exo ... thermic. I propose exothermic.

For me exergonic is a term to be utilized in when it is related to biology
instead of chemistry. For photosynthesis I am not sure which to utilize. If
the oxygen is exo then when it is forming the former molecule was in a
liquid state to become what, with an exo potential of a reaction. ((an
exergonic reaction have more than heat, e.g. the position in the outer
shells as for P))

I would have had a lot more to tell about that question. I even found
something in the famous top review of chemistry of the u.s.a. . When I try
to begin a discussion with the staff of my university they panicked.

Up to now those who try to answer that say : endothermic, endergonic. And
they have a curious redox serie of reaction. A true redox reactions come at
once, not successively. There is not a wandering electron that make the
oxidized or reduced state, climbing the photosystems energy or so on. I
found the father of the expression also.

So as a student I have done a lot of research for that question. And I
desire to be evaluate officially. But I want to know what it entails and so
on.

Think about it. The earth is wandering in a very cold cosmos. If
photosynthesis is endo...... then photosynthesis is of no help in this
fight against the cosmos : the heat fight.

Waiting for an answer, sincerely yours pierre-m.verville@...

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