Specifics of Determination of Human Biological Age by Blood Samples Using Epigenetic Markers

Abstract Our research focused on the selection of already known markers, as well as the search for other infonormative markers based on data made publicly available on the GEO NCBI platform (genome-wide DNA methylation projects using the Infinium Human Methylation 450K BeadChip (Illumina ©)). The main objective of the study was to demonstrate that the accuracy of determining the biological age of a person in the presence of chronic diseases using linear-dependent methylation markers is comparable to the accuracy of determining the biological age of a healthy person. Criminologists, as a rule, do not have information about the chronic diseases of a person who has left a biological trace at the scene (blood, for example). However, the lack of this information, as we have shown for a some of diseases, does not play a critical role in the precise determination of biological age. Additionally, an obstacle was removed when transferring the information content of markers from Infinium Human Methylation 450K BeadChip chips to SNaPshot technology. The analysis was carried out on a sample of 236 Belarusians, for whom the methylation profile for 7 Cpg markers is presented. It is shown that the information content of markers is preserved Our analysis shows the possibility of creating the universal test system for predicting biological age according to marker methylation. The system can be used in the work of the most criminalist in the world with the same task.

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Genome Wide Search to Identify Reference Genes candidates for Gene Expression Analysis in Gossypium hirsutum

10.21203/rs.2.10200/v2 ◽

2019 ◽

Author(s):

Smitha P K ◽

Vishnupriyan K ◽

Ananya S. Kar ◽

Anil Kumar M ◽

Christopher Bathula ◽

...

Keyword(s):

Gossypium Hirsutum ◽

Reference Genes ◽

Data Science ◽

Natural Fiber ◽

Quantitative Polymerase Chain Reaction ◽

Critical Role ◽

Genome Wide ◽

Cotton Species ◽

Genome Wide Search ◽

Selection Of

Abstract Background: Cotton is one of the most important commercial crops as the source of natural fiber, oil and fodder. To protect it from harmful pest populations number of newer transgenic lines have been developed. For quick expression checks in successful agriculture qPCR (quantitative polymerase chain reaction) have become extremely popular. The selection of appropriate reference genes plays a critical role in the outcome of such experiments as the method quantifies expression of the target gene in comparison with the reference. Traditionally most commonly used reference genes are the “ house-keeping genes”, involved in basic cellular processes. However, expression levels of such genes often vary in response to experimental conditions, forcing the researchers to validate the reference genes for every experimental platform. This study presents a data science driven unbiased genome-wide search for the selection of reference genes by assessing variation of >50,000 genes in a publicly available RNA- seq dataset of cotton species Gossypium hirsutum . Result: Five genes ( TMN5, TBL6, UTR5B, AT1g65240 and CYP76B6 ) identified by data-science driven analysis, along with two commonly used reference genes found in literature ( PP2A1 and UBQ14 ) were taken through qPCR in a set of 33 experimental samples consisting of different tissues (leaves, square, stem and root), different stages of leaf (young and mature) and square development (small, medium and large) in both transgenic and non-transgenic plants. Expression stability of the genes was evaluated using four algorithms - geNorm , BestKeeper , NormFinder and RefFinder. Conclusion: Based on the results we recommend the usage of TMN5 and TBL6 as the optimal candidate reference genes in qPCR experiments with normal and transgenic cotton plant tissues. AT1g65240 and PP2A1 can also be used if expression study includes squares. This study, for the first time successfully displays a data science driven genome-wide search method followed by experimental validation as a method of choice for selection of stable reference genes over the selection based on function alone.

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DISTANCE MEASUREMENTS USING FREQUENCY STABILIZED Nd:YAG LASERS

Journal of Nonlinear Optical Physics & Materials ◽

10.1142/s0218863596000362 ◽

1996 ◽

Vol 05 (03) ◽

pp. 543-550

Author(s):

VERED MAHAL ◽

ADY ARIE

Keyword(s):

Frequency Stability ◽

Precise Determination ◽

Phase Shifting ◽

Distance Measurements ◽

Fringe Contrast ◽

Nd:Yag Lasers ◽

Wide Range ◽

Diode Pumped ◽

Selection Of

Two diode-pumped tunable Nd:YAG lasers locked to sub-Doppler transitions of 127I2 and 133 Cs 2 are used as a source for two-wavelength interferometry. The synthetic wavelength, Λ=c/∆ν, is highly stable and accurate, owing to the frequency stability of the locked lasers and the precise determination of the frequency difference Δν between Cs 2 and I 2 transitions. The dense spectra of these molecules allows selection of Λ over a wide range, between 8.5 mm and several meters, thus enabling distance measurements with a large non-ambiguity range. Fringe contrast and phase-shifting methods are used to measure the phase difference. An accuracy of 70 μm is achieved for Λ~19 mm, i.e. Λ/260.

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Genome wide search to identify reference genes candidates for gene expression analysis in Gossypium hirsutum

BMC Plant Biology ◽

10.1186/s12870-019-1988-3 ◽

2019 ◽

Vol 19 (1) ◽

Cited By ~ 3

Author(s):

P. K. Smitha ◽

K. Vishnupriyan ◽

Ananya S. Kar ◽

M. Anil Kumar ◽

Christopher Bathula ◽

...

Keyword(s):

Gossypium Hirsutum ◽

Reference Genes ◽

Data Science ◽

Natural Fiber ◽

Quantitative Polymerase Chain Reaction ◽

Critical Role ◽

Genome Wide ◽

Cotton Species ◽

Genome Wide Search ◽

Selection Of

Abstract Background Cotton is one of the most important commercial crops as the source of natural fiber, oil and fodder. To protect it from harmful pest populations number of newer transgenic lines have been developed. For quick expression checks in successful agriculture qPCR (quantitative polymerase chain reaction) have become extremely popular. The selection of appropriate reference genes plays a critical role in the outcome of such experiments as the method quantifies expression of the target gene in comparison with the reference. Traditionally most commonly used reference genes are the “house-keeping genes”, involved in basic cellular processes. However, expression levels of such genes often vary in response to experimental conditions, forcing the researchers to validate the reference genes for every experimental platform. This study presents a data science driven unbiased genome-wide search for the selection of reference genes by assessing variation of > 50,000 genes in a publicly available RNA-seq dataset of cotton species Gossypium hirsutum. Result Five genes (TMN5, TBL6, UTR5B, AT1g65240 and CYP76B6) identified by data-science driven analysis, along with two commonly used reference genes found in literature (PP2A1 and UBQ14) were taken through qPCR in a set of 33 experimental samples consisting of different tissues (leaves, square, stem and root), different stages of leaf (young and mature) and square development (small, medium and large) in both transgenic and non-transgenic plants. Expression stability of the genes was evaluated using four algorithms - geNorm, BestKeeper, NormFinder and RefFinder. Conclusion Based on the results we recommend the usage of TMN5 and TBL6 as the optimal candidate reference genes in qPCR experiments with normal and transgenic cotton plant tissues. AT1g65240 and PP2A1 can also be used if expression study includes squares. This study, for the first time successfully displays a data science driven genome-wide search method followed by experimental validation as a method of choice for selection of stable reference genes over the selection based on function alone.

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HingeInflex: a MATLAB-based method for precise selection of the hinge and the inflection points in folds

Geological Magazine ◽

10.1017/s0016756809990641 ◽

2009 ◽

Vol 147 (2) ◽

pp. 233-241 ◽

Cited By ~ 2

Author(s):

DEEPAK C. SRIVASTAVA ◽

VIPUL RASTOGI

Keyword(s):

Precise Determination ◽

Visual Selection ◽

Interpolation Algorithm ◽

Polynomial Curve ◽

Inflection Points ◽

User Friendly ◽

Selection Of

AbstractSubjectivity in visual selection of hinge and inflection points leads to significant errors in analyses of fold shapes in profile sections. This article gives a method for precise determination of these points. The method: (1) imports a fold image into Matlab, (2) digitizes points on the image, (3) increases the number of available points by using an interpolation algorithm, (4) fits a polynomial curve to the points, and (5) searches for the hinge and the inflection points mathematically. Tests on several folds confirm that the ‘HingeInflex’ is a rapid, robust and user-friendly method for precise selection of the hinge and inflection points.

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Evaluation of the Quality of Conical Picks and the Possibility of Predicting the Costs of Their Use

Multidisciplinary Aspects of Production Engineering ◽

10.2478/mape-2020-0041 ◽

2020 ◽

Vol 3 (1) ◽

pp. 491-504

Author(s):

Krzysztof Krauze ◽

Kamil Mucha ◽

Tomasz Wydro

Keyword(s):

Wear Rate ◽

Precise Determination ◽

Unit Price ◽

Conical Pick ◽

Pick Body ◽

Rate Intensity ◽

Conical Picks ◽

Selection Of

AbstractCurrently, the user’s choice of a conical pick involves specifying its geometric and material parameters, taking into account the place and conditions of its work. The selection is then made, usually on the basis of solely one criterion, which is the price. Thus, at the stage of both purchase and operation, the quality of picks and their suitability for a specific machine and the processed mineral are not assessed. Therefore, a method was developed to enable conducting tests that determine the geometric parameters of a pick, the types of materials of the pick body and WC insert as well as the pick wear rate (intensity) in a laboratory workstation. The wear rate (intensity) is described by the C2 index – the smaller is its value, the slower is the pick’s wear. The C2 index has been used to forecast the wear of picks and to determine their unit price and operating costs. This allows for precise determination of investment requirements and a proper selection of the pick.

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Genome Wide Search to Identify Reference Genes candidates for Gene Expression Analysis in Gossypium hirsutum

10.21203/rs.2.10200/v1 ◽

2019 ◽

Author(s):

Smitha P K ◽

Vishnupriyan K ◽

Ananya S. Kar ◽

Anil Kumar M ◽

Christopher Bathula ◽

...

Keyword(s):

Gossypium Hirsutum ◽

Reference Genes ◽

Data Science ◽

Experimental Validation ◽

Quantitative Polymerase Chain Reaction ◽

Critical Role ◽

Genome Wide ◽

Cotton Species ◽

Genome Wide Search ◽

Selection Of

Abstract Background: With the advent of newer breeds and transgenic varieties of commercial crops, qPCR (quantitative polymerase chain reaction) experiments have become extremely popular for quick expression checks. Selection of appropriate reference genes plays a critical role in quantifying the expression of target gene. Most commonly used reference genes in expression studies are the “house-keeping genes”, involved in basic cellular processes. However, expression levels of such genes often vary in response to experimental conditions, forcing the researchers to validate the reference genes in every experiment. This study presents a data science driven unbiased genome-wide search results for selection of reference genes by assessing variation of >50,000 genes in a publicly available RNA-seq dataset of cotton species Gossypium hirsutum. Selected candidate genes were validated experimentally across 33 samples from normal and transgenic G. hirsutum plants, harvested from different areas of the plant at different time points under various developmental conditions. Experimental validation also includes commonly used genes from literature to suggest the most stable set of 5 genes to be used for assessment of quantitative expression in cotton plants (Fig.1). Result: Five genes (TMN5, TBL6, UTR5B, AT1g65240, CYP76B6) identified by data-driven analysis, along with two commonly used reference genes for cotton found in literature (GhPP2A1 and GhuBQ14) were validated using qPCR in a set of 33 experimental samples consisting of different tissues (leaves, square, stem and root), different stages of leaf (young and mature) and square development (small, medium and large) in both transgenic and non-transgenic plants. Expression stability of the genes was evaulated using four different algorithms - DeltaCT, Genorm, BestKeeper and Normfinder. GhPP2A1 and TMN5 were identified as the most stable genes, followed by GhuBQ14 across all the samples tested. Conclusion: This study, for the first time successfully displays a data science driven genome-wide search method followed by experimental validation as a method of choice for selection of stable reference genes for experiment with cotton species. Based on the results we recommend use of GhPP2A1, TMN5 and GhuBQ14 as the optimal candidate reference genes in qPCR experiments with normal or transgenic cotton plant tissues.

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