National Institute for Research and Development

of Isotopic and Molecular Technologies

ROMANA

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Project Name:	IDEI
Project Type:	Proiecte de cercetare exploratorie
Project Code:	PN II IDEI cod ID_32

Organisation of the coding sequence of the microbian genome; autoregresive modelation

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• Abstract
• Objectives
• Activities
• Results
• Team members
• Publications
• Impact

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Director of Project: C.S.I. Dr. Ioan Turcu
E-mail:     Ioan.Turcu@itim-cj.ro

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Abstract:

Objective: Supramolecular organization of coding sequences in bacterial genome. Simulation is done with autoregressive models. It is shown that DNA organization is based on weak interaction between terms (the lengths of coding sequences). This type of organization is one of short-distance and not long-distance (or fractal).

New ideas brought by the project are the following:
- The type of DNA organization (length of coding sequences) is characterization by correlation proprieties at short distance.
- Pointing out the confusion at a big scale in literature by which structures and phenomena with spatial and temporal organization at short distance are confused with fractal structures, and also the best method to be used to avoid this confusion.
- Organization of bacterial genome is described by first and higher order autoregressive models, where the fundamental parameter is the interaction factor among the series terms.
- Phenomena can be categorized in structures (phenomena) with weak interaction (the case of microbial DNA), with strong interaction (proteins) or with medium interaction (other systems outside of the project interest).
- MATLAB programs are used to describe some structures and phenomena with autoregressive models.

It is estimated that these project results will be published in ISI journals (Physical Review E, Fluctuation and Noise Letters, Modern Physics Letters, Journal of Statistical Mechanics Theory and Experiment).

Utility of research: building a new evaluation methodology for comparing the type of organization of DNA and proteins, with impact in molecular biophysics, molecular biology, genomics, etc.

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Objectives:

1. – 2007: Generarea de modele autoregressive si caracterizarea spectrala a seriilor de date

2. – 2008: Caracteristici de corelare ale modelelor autoregresive; Caracterizarea spectrala a seriilor de date privind secventele de codare pentru organisme bacteriene model

3. – 2009: Modelarea spectrelor seriilor secventelor de codare din genomul bacterian prin modele autoregresive de ordin superior; Cercetari privind organizarea si modelarea genomului bacterian la diverse specii

4. – 2010: Diseminare si raport final

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Activities:

1. – 2007: Programare in MATLAB. Analiza spectrala a serilor de date autoregressive; redactare articol pentru revista cotata ISI

2. – 2008: Analiza prin metoda “Detrended fluctuation analysis” a serilor de date; redactare articol pentru revista cotata ISI; Programare in MATLAB; extragerea tendintei din serile de date; medierea spectrelor; fitare cu modelul autoregresiv de ordin 1.

3. – 2009: Programare MATLAB; verificare pe serii de date provenite din genomul bacterian al unor cazuri model; Analiza spectrala si identificare modelului autoregresiv optim pentru specii bacteriene selectate; redactare articol pentru revista cotata ISI

4. – 2010: Redactari de lucrari si comunicari

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Results:

• PHASE 1 / December, 2007:

• A comparative analysis of the fluctuating series was realised to establish the similarities between the two methods: Detrended Fluctuation Analysis and, respectively, the spectral analysis.
• A MATLAB code was elaborated to to generate the theoretical power spectra for the autoregressive models of any order.
• A numerical method was developed to analyse the periodicities in the power spectra of the autoregressive processes.

Annexes

• PHASE 2 / 2008:

• The short range character of the correlations which exist in the lengths series of the bacterial genome coding sequences was demonstrated.
• A MATLAB code was designed and realised which identifies and quantitatively characterises the correlation in the numerical series of the autoregressive processes of the 1-st order (AR 1)
• The series of the coding sequences lengths of the „B.subtilis” bacteria was investigated by means of two complementary methods: the spectral analysis and, respectively, the autoregressive modelling of AR 1 type.

Annexes

• PHASE 3 / 2009:

• The analysis of the averaged periodograms of the data series including the coding sequences lengths for various bacteria and archaea species evidences significant correlation effects.
• A new method was developed destined for the analysis of the genome coding sequences ordering which is based on the application of some detrending techniques of the data series fluctuations followed by autoregressive modelling.
• In view of the implementation of the new method a MATLAB code was developed and its applicability was validated on several bacterial genomes.
• The autoregressive modelling of the 1-st order is generally adequate for the analysis of the averaged spectra (periodograms).
• The autoregressive models of higher order fit much better the periodogram but the offered information is essentially the same as that obtained from fitting with AR 1. When analysing the genome coding sequences it is necessary to separate data on the two helixes.
• The relationship between the correlation spectral exponent and the interaction factor is linear for the two helixes (dominant and recessive)
• When investigating the whole genome the relationship is no longer linear because the two helixes action one upon each other.

Annexes

• PHASE 4 / 2010 :

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Team Members:

Nr.	Prename and Name	Birthdays	Didactical and Scientific title *	Doctorates
1	Turcu Ioan	1955	CSI	Yes
2	Morariu V. Vasile	1943	CSI	Yes
3	Neamtu Silvia	1956	CSIII	Ph.D.
4	Buimaga-Iarinca Luiza	1981	Researcher assistant	Ph.D.
5	Hossu Mihaela	1979	Researcher assistant	Yes

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Publications:

1. Oana Zainea , V. Morariu, The length of coding sequences in a bacterial genome: evidence for short-range correlation, Fluctuation and Noise Letters, vol 7 No 4, 2007 L501-L506(2007)
2. V. Morariu, Distribution and correlation of the coding sequence lenghts in bacterial genome Rev. Chim. 59, 11, 1201-1204 (2008)
3. L. Buimaga-Iarinca, V. Morariu, Short range correlation of the erythrocyte membrane fluctuations, JPCS Volume, 182, (2009), 012005
4. V. Morariu, L. Buimaga-Iarinca, Autoregressive modeling of coding sequence lengths in bacterial genome, Fluctuation and Noise Letters, 9(1), L47-L59 (2010).
5. V. Morariu, C. Vamos, A. Pop, S. Soltuz, L. Buimaga-Iarinca, Autoregressive modeling of light emission from a galaxy - Rom. Journ. Phys 55, (7-8), (2010).
6. V. Morariu, C. Vamos, A. Pop, S. Soltuz, L. Buimaga-Iarinca, O. Zainea, Autoregressive modeling of biological phenomena, Biophys. Rev. Lett. 5(3), 1-20, (2010).
7. V. Morariu, L. Buimaga-Iarinca, Autoregressive modeling of coding sequence lengths in bacterial genome, Fluct. Noise Lett., 9(1), L47-L59 (2010).
8. Buimaga-Iarinca Luiza, Vasile V. Morariu, Noises and trends in autoregressive modeling, send to Modern Physics Letters B

Conference papers

1. C. Morari, D. Bogdan and I. Turcu, Towards rapid DNA sequencing - ab-initio study of nucleotide sandwiched between Au(111) plates, the 7th European Biophysics Congress Genoa, Italy, July 11-15 (2009)
2. C. Morari, D. Bogdan and I. Turcu, Electronic structure of DNA's base pairs in-between noble metal plate:“ab initio” study, XXth International Symposium on Bioelectrochemistry and Bioenergetics, Sibiu, Romania, 10-14 May (2009)
3. Diana Bogdan, I. Turcu and C. Morari, Ab-initio study of DNA nucleotides squeezed between Au(111) electrodes: applications to DNA sequencing technology, X-th National Conference of Biophysics (CNB 2009) 1-3 October 2009, Cluj-Napoca, Romania.
4. L Buimaga-Iarinca, V. Morariu, Short range correlation of the erythrocyte membrane fluctuations, PIM 2009, 24-26 September 2009, Cluj-Napoca, Romania.
5. Luiza Buimaga-Iarinca, Noise and trend influences in autoregressive modeling, Exploratory workshop: New tendencies in computational biophysics, 4-6 June 2009, West University, Timisoara, Romania
6. L. Buimaga-Iarinca, V Morariu, Short range correlation of the erythrocyte membrane fluctuations, National Conference of Biophysics, 1-3 October 2009, Cluj-Napoca, Romania

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Impact:

Impactul principal consta in cunoasterea organizarii genomului bacterian la nivel de secvente coding – lungimea lor si localizarea in genom. Anticipand rezultatele, caracteristica principala este neuniformitatea structurii si complementaritatea celor doua fire de AND ce alcatuiesc molecula de AND. Rezultatele se vor concretiaza in principal prin lucrari ISI.

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