Yuri Kalambet - Profile on Academia.edu (original) (raw)
Papers by Yuri Kalambet
A study of the reversibility of helix-coil transition in DNA
Nucleic Acids Research, 1981
The reversibility of DNA melting has been thoroughly investigated at different ionic strengths. W... more The reversibility of DNA melting has been thoroughly investigated at different ionic strengths. We concentrated on those stages of the process that do not involve a complete separation of the strands of the double helix. The differential melting curves of pBR 322 DNA and a fragment of T7 phage DNA in a buffer containing 0.02M Na+ have been shown to differ substantially from the differential curves of renaturation. Electron-microscopic mapping of pBR 322 DNA at different degrees of unwinding (by a previously elaborated technique) has shown that the irreversibility of melting under real experimental conditions is connected with the stage of forming new helical regions during renaturation. In a buffer containing 0.2M Na+ the melting curves of the DNAs used (pBR322, a fragment of T7 phage DNA, a fragment of phage Lambda DNA, a fragment of phiX174 phage DNA) coincide with the renaturation curves, i.e. the process is equilibrium. We have carried out a semi-quantitative analysis of the emergence of irreversibility in the melting of a double helix. The problem of comparing theoretical and experimental melting curves is discussed.
Noise filtering: the ultimate solution?
ABSTRACT
Computer Analysis of Genetic Texts
ABSTRACT
[Transcription of the riboflavin operon in Bacillus subtilis]
Doklady Akademii nauk SSSR
Factor analysis is widely used [1] for separation of incompletely separated chromatographic peaks... more Factor analysis is widely used [1] for separation of incompletely separated chromatographic peaks. We combined this technique with an analysis of the angle derivative of the multi-channel chromatogram to get a better choice of basic spectra. Improvement in the algorithm is demonstrated through examples. The technique used facilitates doubling the peak capacity of the column, as baseline separation requirement is replaced with requirement to separate peaks so, that for every component there is a time point, where it elutes pure.
The Exponentially Modified Gaussian (EMG) peak shape [1] is widely used for peak approximation in... more The Exponentially Modified Gaussian (EMG) peak shape [1] is widely used for peak approximation in chromatography. We constructed the EMG peak deconvolution routine for chromatography, using a combination of two EMG formulas [1,2] and linear optimization methods. This routine accounts for the maximum linear range of the detector and can work with out-of range peaks.
Factor analysis is widely used [1] for separation of incompletely separated chromatographic peaks... more Factor analysis is widely used [1] for separation of incompletely separated chromatographic peaks. We combined this technique with an analysis of the angle derivative of the multi-channel chromatogram to get a better choice of basic spectra. Improvement in the algorithm is demonstrated through examples.
Internal Standard (ISTD) is a well-known chromatographic technique, aimed to compensate sample si... more Internal Standard (ISTD) is a well-known chromatographic technique, aimed to compensate sample size variations, where known amount of a component, called internal standard is added to both standard and unknown samples. The classic Internal Standard quantification method plots the response ratio (analyte to internal standard) versus amount ratio (again analyte to internal standard). Internal standard component itself does not have any calibration curve. Quantification procedure uses this plot to get concentration ratio from response ratio.
The Exponentially Modified Gaussian (EMG) peak shape [1] is widely used for peak approximation in... more The Exponentially Modified Gaussian (EMG) peak shape [1] is widely used for peak approximation in chromatography. We constructed the EMG peak deconvolution routine for chromatography, using a combination of two EMG formulas [1,2] and linear optimization methods. This routine accounts for the maximum linear range of the detector and can work with out-of range peaks.
[Transcription of the SV40 genome in Saccharomyces cerevisiae yeasts]
Doklady Akademii nauk SSSR, 1985
Journal of Chemometrics, 2011
A method of noise filtering based on confidence interval evaluation is described. In the case of ... more A method of noise filtering based on confidence interval evaluation is described. In the case of the approximation of a function, measured with error by a polynomial or other functions that allow estimation of the confidence interval, a minimal confidence interval is used as a criterion for the selection of the proper parameters of the approximating function. In the case of the polynomial approximation optimized parameters include the degree of the polynomial, the number of points (window) used for the approximation, and the position of the window center with respect to the approximated point. The Method is demonstrated using generated and measured chromatograms. The special considerations on confidence interval evaluation and quality of polynomial fit using noise properties of the 2 data array are discussed. The Method provides the lowest possible confidence interval for every data point.
FEBS Letters, 1986
We used electron microscopy and computer analysis to study the ~aciil~ ~b~~~~ ~bofla~n opcron tra... more We used electron microscopy and computer analysis to study the ~aciil~ ~b~~~~ ~bofla~n opcron transcription. The size of the ~~~avin opcron has been shown to be 2.4Ort 0.15 MDa. Tran~~ption maps of the riboflavin operon in vitro and in viva have been obtained. In the riboflavin operon region four tran-.%xipts are sythesizcd in vivo having the following approximate boundary positions in the map of pLPIO2: 46-52,46-72, 62-72 and 55-58 map units. The riboflavin operon is transcribed from three promoters, at 46,58 and 72 map positions. A scheme of the riboflavin operon transcription in B. subtih is suggested.
Electron microscopy of the melting of sequenced DNA
Biopolymers, 1985
ABSTRACT
A study of the reversibility of helix-coil transition in DNA
Nucleic Acids Research, 1981
The reversibility of DNA melting has been thoroughly investigated at different ionic strengths. W... more The reversibility of DNA melting has been thoroughly investigated at different ionic strengths. We concentrated on those stages of the process that do not involve a complete separation of the strands of the double helix. The differential melting curves of pBR 322 DNA and a fragment of T7 phage DNA in a buffer containing 0.02M Na+ have been shown to differ substantially from the differential curves of renaturation. Electron-microscopic mapping of pBR 322 DNA at different degrees of unwinding (by a previously elaborated technique) has shown that the irreversibility of melting under real experimental conditions is connected with the stage of forming new helical regions during renaturation. In a buffer containing 0.2M Na+ the melting curves of the DNAs used (pBR322, a fragment of T7 phage DNA, a fragment of phage Lambda DNA, a fragment of phiX174 phage DNA) coincide with the renaturation curves, i.e. the process is equilibrium. We have carried out a semi-quantitative analysis of the emergence of irreversibility in the melting of a double helix. The problem of comparing theoretical and experimental melting curves is discussed.
Noise filtering: the ultimate solution?
ABSTRACT
Computer Analysis of Genetic Texts
ABSTRACT
[Transcription of the riboflavin operon in Bacillus subtilis]
Doklady Akademii nauk SSSR
Factor analysis is widely used [1] for separation of incompletely separated chromatographic peaks... more Factor analysis is widely used [1] for separation of incompletely separated chromatographic peaks. We combined this technique with an analysis of the angle derivative of the multi-channel chromatogram to get a better choice of basic spectra. Improvement in the algorithm is demonstrated through examples. The technique used facilitates doubling the peak capacity of the column, as baseline separation requirement is replaced with requirement to separate peaks so, that for every component there is a time point, where it elutes pure.
The Exponentially Modified Gaussian (EMG) peak shape [1] is widely used for peak approximation in... more The Exponentially Modified Gaussian (EMG) peak shape [1] is widely used for peak approximation in chromatography. We constructed the EMG peak deconvolution routine for chromatography, using a combination of two EMG formulas [1,2] and linear optimization methods. This routine accounts for the maximum linear range of the detector and can work with out-of range peaks.
Factor analysis is widely used [1] for separation of incompletely separated chromatographic peaks... more Factor analysis is widely used [1] for separation of incompletely separated chromatographic peaks. We combined this technique with an analysis of the angle derivative of the multi-channel chromatogram to get a better choice of basic spectra. Improvement in the algorithm is demonstrated through examples.
Internal Standard (ISTD) is a well-known chromatographic technique, aimed to compensate sample si... more Internal Standard (ISTD) is a well-known chromatographic technique, aimed to compensate sample size variations, where known amount of a component, called internal standard is added to both standard and unknown samples. The classic Internal Standard quantification method plots the response ratio (analyte to internal standard) versus amount ratio (again analyte to internal standard). Internal standard component itself does not have any calibration curve. Quantification procedure uses this plot to get concentration ratio from response ratio.
The Exponentially Modified Gaussian (EMG) peak shape [1] is widely used for peak approximation in... more The Exponentially Modified Gaussian (EMG) peak shape [1] is widely used for peak approximation in chromatography. We constructed the EMG peak deconvolution routine for chromatography, using a combination of two EMG formulas [1,2] and linear optimization methods. This routine accounts for the maximum linear range of the detector and can work with out-of range peaks.
[Transcription of the SV40 genome in Saccharomyces cerevisiae yeasts]
Doklady Akademii nauk SSSR, 1985
Journal of Chemometrics, 2011
A method of noise filtering based on confidence interval evaluation is described. In the case of ... more A method of noise filtering based on confidence interval evaluation is described. In the case of the approximation of a function, measured with error by a polynomial or other functions that allow estimation of the confidence interval, a minimal confidence interval is used as a criterion for the selection of the proper parameters of the approximating function. In the case of the polynomial approximation optimized parameters include the degree of the polynomial, the number of points (window) used for the approximation, and the position of the window center with respect to the approximated point. The Method is demonstrated using generated and measured chromatograms. The special considerations on confidence interval evaluation and quality of polynomial fit using noise properties of the 2 data array are discussed. The Method provides the lowest possible confidence interval for every data point.
FEBS Letters, 1986
We used electron microscopy and computer analysis to study the ~aciil~ ~b~~~~ ~bofla~n opcron tra... more We used electron microscopy and computer analysis to study the ~aciil~ ~b~~~~ ~bofla~n opcron transcription. The size of the ~~~avin opcron has been shown to be 2.4Ort 0.15 MDa. Tran~~ption maps of the riboflavin operon in vitro and in viva have been obtained. In the riboflavin operon region four tran-.%xipts are sythesizcd in vivo having the following approximate boundary positions in the map of pLPIO2: 46-52,46-72, 62-72 and 55-58 map units. The riboflavin operon is transcribed from three promoters, at 46,58 and 72 map positions. A scheme of the riboflavin operon transcription in B. subtih is suggested.
Electron microscopy of the melting of sequenced DNA
Biopolymers, 1985
ABSTRACT