Miaomiao Jiang, Qichao Yu, Jianming Xie, Shiping Liu
Single cell RNA-sequencing (scRNA-Seq) has emerged as a popular transcriptomic profiling approach to address long-standing questions on developmental biology and cancer biology. With the advent of increasing single-cell computational methods, it is not easy to determine which profiler to use. Here, we provide an integrated pipeline for both gene expression and genomic architecture analysis in single cells. Our pipeline reveals the global expression profile of the populations, and also identifies the changes in transcriptome/genome including alternative splicing (AS), single-nucleotide polymorphisms (SNPs), RNA editing and gene fusion.
{"title":"Establishment of an Integrated Computational Workflow for Single Cell RNA-Seq Dataset","authors":"Miaomiao Jiang, Qichao Yu, Jianming Xie, Shiping Liu","doi":"10.1145/3314367.3314375","DOIUrl":"https://doi.org/10.1145/3314367.3314375","url":null,"abstract":"Single cell RNA-sequencing (scRNA-Seq) has emerged as a popular transcriptomic profiling approach to address long-standing questions on developmental biology and cancer biology. With the advent of increasing single-cell computational methods, it is not easy to determine which profiler to use. Here, we provide an integrated pipeline for both gene expression and genomic architecture analysis in single cells. Our pipeline reveals the global expression profile of the populations, and also identifies the changes in transcriptome/genome including alternative splicing (AS), single-nucleotide polymorphisms (SNPs), RNA editing and gene fusion.","PeriodicalId":20485,"journal":{"name":"Proceedings of the 2019 9th International Conference on Bioscience, Biochemistry and Bioinformatics - ICBBB '19","volume":"71 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81606973","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
L. Yaping, Zhao Bo, E. Kalamiyets, Wu Peng, Chu Jie
Single factor optimization experiment and response surface optimization experiment were designed to research the influence of different culture medium components to bacteriostatic active substances produced by bacillus amyloliquefaciens GN59 strain, and a culture medium formula suitable for the GN59 strain to produce the bacteriostatic active substances was screened. In the single factor experiment, the optimal formula was: glucose 10.0g/L, K2HPO4·3H2O 1.2 g/L, KH2PO4 1.0 g/L, (NH4)2SO4 2.00 g/L, Na3C6H5O7·3H2O 0.9 g/L, and MgSO4·7H2O 0.15 g/L, and the bacteriostatic activity was improved by 14.32% in comparison with that before optimization. In the response surface optimization experiment, the optimal culture medium components were glucose 6.15 g/L, K2HPO4·3H2O 1.2 g/L, KH2PO4 1.0 g/L, (NH4)2SO4 2.50 g/L, Na3C6H5O7·3H2O 1.01 g/L, and MgSO4·7H2O 0.15 g/L, the bacteriostatic activity was improved by 31.18% in comparison with that before optimization, and meanwhile, the product cost was lowered, and batch low-cost and efficient fermentation production of the bacillus amyloliquefaciens GN59 strain was realized.
{"title":"Research on Response Surface Optimization of Culture Medium for Antibacterial Substances Produced by Bacillus Amyloliquefaciens GN59","authors":"L. Yaping, Zhao Bo, E. Kalamiyets, Wu Peng, Chu Jie","doi":"10.1145/3314367.3314368","DOIUrl":"https://doi.org/10.1145/3314367.3314368","url":null,"abstract":"Single factor optimization experiment and response surface optimization experiment were designed to research the influence of different culture medium components to bacteriostatic active substances produced by bacillus amyloliquefaciens GN59 strain, and a culture medium formula suitable for the GN59 strain to produce the bacteriostatic active substances was screened. In the single factor experiment, the optimal formula was: glucose 10.0g/L, K2HPO4·3H2O 1.2 g/L, KH2PO4 1.0 g/L, (NH4)2SO4 2.00 g/L, Na3C6H5O7·3H2O 0.9 g/L, and MgSO4·7H2O 0.15 g/L, and the bacteriostatic activity was improved by 14.32% in comparison with that before optimization. In the response surface optimization experiment, the optimal culture medium components were glucose 6.15 g/L, K2HPO4·3H2O 1.2 g/L, KH2PO4 1.0 g/L, (NH4)2SO4 2.50 g/L, Na3C6H5O7·3H2O 1.01 g/L, and MgSO4·7H2O 0.15 g/L, the bacteriostatic activity was improved by 31.18% in comparison with that before optimization, and meanwhile, the product cost was lowered, and batch low-cost and efficient fermentation production of the bacillus amyloliquefaciens GN59 strain was realized.","PeriodicalId":20485,"journal":{"name":"Proceedings of the 2019 9th International Conference on Bioscience, Biochemistry and Bioinformatics - ICBBB '19","volume":"7 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84436397","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. Malmakova, V. Yu, N. Kystaubayeva, A. Zazybin, T. E. Li
Herein we report on the synthesis the synthesis of new dimethyl [1-(benzyl-, 2-phenylethyl-) -4-hydroxypiperidin-4-yl)]phosphonates obtained by reacting 1-(benzyl- or 2-phenylethyl-)piperidone-4 with dimethylphosphite in presence of sodium methylate in hexane. NMR spectroscopy showed that the complexation of β-cyclodextrin (β-CD) (host) with the hydroxyphosphonate (guest) is accompanied by the entry of a hydrophobic aromatic fragment of the substrate molecule into the inner sphere of the host molecule. In addition, the supramolecular interaction of the hydrophilic part of the guest molecule with the outer surface of β-CD is shown. As a result, a 1:1 complex is formed. Dimethyl [1-(benzyl-, 2-phenylethyl-)-4-hydroxypiperidin-4-yl)]phosphonates showed perceptible stimulation of growth and development of stems and/or roots of spring wheat Triticum aestivum Kazakhstanskaya-10, Severyanka and Miras.
{"title":"β-Cyclodextrin Inclusion Complex with Dimethyl[4-hydroxypiperidin-4-yl]Phosphonates as Green Plant Growth Stimulators","authors":"A. Malmakova, V. Yu, N. Kystaubayeva, A. Zazybin, T. E. Li","doi":"10.1145/3314367.3314381","DOIUrl":"https://doi.org/10.1145/3314367.3314381","url":null,"abstract":"Herein we report on the synthesis the synthesis of new dimethyl [1-(benzyl-, 2-phenylethyl-) -4-hydroxypiperidin-4-yl)]phosphonates obtained by reacting 1-(benzyl- or 2-phenylethyl-)piperidone-4 with dimethylphosphite in presence of sodium methylate in hexane. NMR spectroscopy showed that the complexation of β-cyclodextrin (β-CD) (host) with the hydroxyphosphonate (guest) is accompanied by the entry of a hydrophobic aromatic fragment of the substrate molecule into the inner sphere of the host molecule. In addition, the supramolecular interaction of the hydrophilic part of the guest molecule with the outer surface of β-CD is shown. As a result, a 1:1 complex is formed. Dimethyl [1-(benzyl-, 2-phenylethyl-)-4-hydroxypiperidin-4-yl)]phosphonates showed perceptible stimulation of growth and development of stems and/or roots of spring wheat Triticum aestivum Kazakhstanskaya-10, Severyanka and Miras.","PeriodicalId":20485,"journal":{"name":"Proceedings of the 2019 9th International Conference on Bioscience, Biochemistry and Bioinformatics - ICBBB '19","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88289497","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Rungnattakan Ploenkutham, Preeyapa Sripromma, Suksan Amornraksa, P. Yasurin, M. Sriariyanun, S. Asavasanti, A. Soontrunnarudrungsri
Centella asiatica has known as medical plant that used for treating bruises and reducing swelling. From the previous research lately, it reported that C.asiatica has properties to improve memory recognition and promote healthy skin. C.asiatica is herbal plant that available in the market, it has been developed to enhance the amount of antioxidant. Therefore, this study was aimed to determine the most effective brewing process of C.asiatica tea and study the amount of antioxidant activities. The temperature was vary with 80°C, 85°C, and 90°C and time was 2, 3, 4, and 5 minutes. The formation of consuming tea was determined by 30 target panelists. The result showed that there was no significant difference among all temperature and time that were determined. The best temperature and time for brewing is 80°C at 5 minutes because it saves energy and can extract the highest amount of antioxidant from herbal tea.
{"title":"Effected Brewing Time and Temperature of Centella Asiatica Tea on Antioxidant Activity and Consumer Acceptance","authors":"Rungnattakan Ploenkutham, Preeyapa Sripromma, Suksan Amornraksa, P. Yasurin, M. Sriariyanun, S. Asavasanti, A. Soontrunnarudrungsri","doi":"10.1145/3314367.3314371","DOIUrl":"https://doi.org/10.1145/3314367.3314371","url":null,"abstract":"Centella asiatica has known as medical plant that used for treating bruises and reducing swelling. From the previous research lately, it reported that C.asiatica has properties to improve memory recognition and promote healthy skin. C.asiatica is herbal plant that available in the market, it has been developed to enhance the amount of antioxidant. Therefore, this study was aimed to determine the most effective brewing process of C.asiatica tea and study the amount of antioxidant activities. The temperature was vary with 80°C, 85°C, and 90°C and time was 2, 3, 4, and 5 minutes. The formation of consuming tea was determined by 30 target panelists. The result showed that there was no significant difference among all temperature and time that were determined. The best temperature and time for brewing is 80°C at 5 minutes because it saves energy and can extract the highest amount of antioxidant from herbal tea.","PeriodicalId":20485,"journal":{"name":"Proceedings of the 2019 9th International Conference on Bioscience, Biochemistry and Bioinformatics - ICBBB '19","volume":"53 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87441842","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Fidelity of cell division depends on the ability of an internal cell structure called the mitotic spindle, to maintain the structural integrity of the cellular architecture despite being subject to high compressive loading. We propose a generic software tool called Spindle FEA that employs continuum mechanics and finite elements analysis (FEA) code Abaqus CAE to study the stability of mitotic spindles in various phases of mitosis. The proposed application has a modular structure which allows easy modification of any part of the analysis which is of particular importance considering that new knowledge of spindles is constantly emerging. Thanks to the highly optimised finite element solver used in Abaqus CAE, Spindle FEA is highly suitable for large multi-parametric studies which in turn may significantly benefit the planning of new experiments or identifying new key properties of the spindle. We also discuss the main physiological properties of spindles and show how they are modelled with the proposed technique as well as discuss all the essential analysis steps. We use Spindle FEA to study the buckling of a mitotic spindle in anaphase B to show how the additional stiffness of the lateral support of the spindle affects the left-right symmetry of cell division as well as to demonstrate the capacities of the proposed technique.
{"title":"Stability of Mitotic Spindle Using Computational Mechanics","authors":"A. Iakovliev, S. Dasmahapatra, A. Bhaskar","doi":"10.1145/3314367.3314373","DOIUrl":"https://doi.org/10.1145/3314367.3314373","url":null,"abstract":"Fidelity of cell division depends on the ability of an internal cell structure called the mitotic spindle, to maintain the structural integrity of the cellular architecture despite being subject to high compressive loading. We propose a generic software tool called Spindle FEA that employs continuum mechanics and finite elements analysis (FEA) code Abaqus CAE to study the stability of mitotic spindles in various phases of mitosis. The proposed application has a modular structure which allows easy modification of any part of the analysis which is of particular importance considering that new knowledge of spindles is constantly emerging. Thanks to the highly optimised finite element solver used in Abaqus CAE, Spindle FEA is highly suitable for large multi-parametric studies which in turn may significantly benefit the planning of new experiments or identifying new key properties of the spindle. We also discuss the main physiological properties of spindles and show how they are modelled with the proposed technique as well as discuss all the essential analysis steps. We use Spindle FEA to study the buckling of a mitotic spindle in anaphase B to show how the additional stiffness of the lateral support of the spindle affects the left-right symmetry of cell division as well as to demonstrate the capacities of the proposed technique.","PeriodicalId":20485,"journal":{"name":"Proceedings of the 2019 9th International Conference on Bioscience, Biochemistry and Bioinformatics - ICBBB '19","volume":"36 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85357797","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
CRISPR from Prevotella and Francisella 1 (Cpf1), a RNA-guided DNA endonuclease that belongs to a novel class II CRISPR system, has recently become a popular tool for genome editing. How to improve the on-target efficiency and specificity of this system is an important and challenging problem. This paper presents a method for CRISPR-Cpf1 guide RNA activity prediction. Convolutional Neural Network (CNN) and support vector regression (SVR) are combined for this purpose. In the proposed framework, single-base substitution mutation data augmentation technique is applied to generate guide RNAs with indel frequencies, thus increasing the labeled data. In the hybrid CNN-SVR model, CNN works as a trainable feature extractor and SVR performs as the regression operator. Specifically, a merged CNN-based regression model is used to pre-train the model for predicting Cpf1 activity based on target sequence composition. Considering the chromatin accessibility information, the SVR is used to generate the predictions. Experiments on the commonly datasets show that our algorithm outperforms the available state-of-the-art tools.
{"title":"CNN-SVR for CRISPR-Cpf1 Guide RNA Activity Prediction with Data Augmentation","authors":"Guishan Zhang, X. Dai","doi":"10.1145/3314367.3314383","DOIUrl":"https://doi.org/10.1145/3314367.3314383","url":null,"abstract":"CRISPR from Prevotella and Francisella 1 (Cpf1), a RNA-guided DNA endonuclease that belongs to a novel class II CRISPR system, has recently become a popular tool for genome editing. How to improve the on-target efficiency and specificity of this system is an important and challenging problem. This paper presents a method for CRISPR-Cpf1 guide RNA activity prediction. Convolutional Neural Network (CNN) and support vector regression (SVR) are combined for this purpose. In the proposed framework, single-base substitution mutation data augmentation technique is applied to generate guide RNAs with indel frequencies, thus increasing the labeled data. In the hybrid CNN-SVR model, CNN works as a trainable feature extractor and SVR performs as the regression operator. Specifically, a merged CNN-based regression model is used to pre-train the model for predicting Cpf1 activity based on target sequence composition. Considering the chromatin accessibility information, the SVR is used to generate the predictions. Experiments on the commonly datasets show that our algorithm outperforms the available state-of-the-art tools.","PeriodicalId":20485,"journal":{"name":"Proceedings of the 2019 9th International Conference on Bioscience, Biochemistry and Bioinformatics - ICBBB '19","volume":"20 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76968303","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
In this paper, we describe the calcium signaling phenomena using finite element method in a typical neuron cell. Neuron being the fundamental cell of the brain has many important roles to perform. The approximated geometry of the neuron is considered to approximate the calcium flow in it. Calcium is considered to be the important second messenger which helps in maintaining plethora of functions like synaptogenesis, proliferation, cell differentiation, etc. The level of the cell calcium is maintained by several important physiological parameters of the calcium toolkit like buffers, endoplasmic reticulum, mitochondria, voltage gated calcium channel, etc. Here, we have considered the cytoplasmic calcium binding buffers in knowing its effect on cytosolic calcium concentration. Exogenous buffers EGTA and BAPTA are considered here. Mathematical model involving two-dimensional partial differential equation is used to delineate the calcium diffusion in presence of calcium binding buffers. Appropriate boundary conditions matching with the physiology of the brain are incorporated. To obtain the desired results finite element technique is used. Discretization and further refinement of the mesh is done to obtain more better approximation of the calcium flow. The results obtained here clearly show the significant impact of buffers on calcium diffusion.
{"title":"Calcium Signaling and Finite Element Technique","authors":"Devanshi D. Dave, B. Jha","doi":"10.1145/3314367.3314377","DOIUrl":"https://doi.org/10.1145/3314367.3314377","url":null,"abstract":"In this paper, we describe the calcium signaling phenomena using finite element method in a typical neuron cell. Neuron being the fundamental cell of the brain has many important roles to perform. The approximated geometry of the neuron is considered to approximate the calcium flow in it. Calcium is considered to be the important second messenger which helps in maintaining plethora of functions like synaptogenesis, proliferation, cell differentiation, etc. The level of the cell calcium is maintained by several important physiological parameters of the calcium toolkit like buffers, endoplasmic reticulum, mitochondria, voltage gated calcium channel, etc. Here, we have considered the cytoplasmic calcium binding buffers in knowing its effect on cytosolic calcium concentration. Exogenous buffers EGTA and BAPTA are considered here. Mathematical model involving two-dimensional partial differential equation is used to delineate the calcium diffusion in presence of calcium binding buffers. Appropriate boundary conditions matching with the physiology of the brain are incorporated. To obtain the desired results finite element technique is used. Discretization and further refinement of the mesh is done to obtain more better approximation of the calcium flow. The results obtained here clearly show the significant impact of buffers on calcium diffusion.","PeriodicalId":20485,"journal":{"name":"Proceedings of the 2019 9th International Conference on Bioscience, Biochemistry and Bioinformatics - ICBBB '19","volume":"1 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78910054","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
A. E. Susanti, S. Ratnakomala, W. Mangunwardoyo, P. Lisdiyanti
Actinomycetes known as the largest antibiotic producer that has a broad range habitat. Research has been done to find a new antibiotic from the various habitats of actinomycetes. Lichens was the symbiotic structure of alga and fungi known as the ecological niche of various kinds of microbes including actinomycetes. The aim of this study in deep of isolate strain LC-23 for production of antimicrobial, characterize the metabolite profile of the ethyl acetate extract and identification based on 16S rRNA gene sequence analysis. The result revealed actinomycetes from lichen, strain LC-23 showed potency against Gram positive bacteria. Ethyl acetate extract of the strain showed positive inhibition against Staphylococcus aureus BTCC B-611 and Micrococcus luteus BTCC B-552. Minimum Inhibitory Concentration (MIC) of extract LC-23 was less than 2.106 ppm. The ethyl acetate extract was subjected to fractionation and tested against the pathogenic microbes and showed inhibition activity in column 9 and 10, and specifically in column 7E to 7G for Staphylcoccus aureus BTCC B-611 and 7E-7H for Micrococcus luteus BTCC B-552. The identification based on 16S rRNA gene sequence showed strain LC-23 was 98.51% similarity to Streptomyces palmae type strain. Neighbor-joining phylogenetic tree confirmed the relationships of this strain to other members of Streptomyces genera.
{"title":"Antimicrobial Activity of Lichens-Associated Actinomycetes Strain LC-23","authors":"A. E. Susanti, S. Ratnakomala, W. Mangunwardoyo, P. Lisdiyanti","doi":"10.1145/3314367.3314386","DOIUrl":"https://doi.org/10.1145/3314367.3314386","url":null,"abstract":"Actinomycetes known as the largest antibiotic producer that has a broad range habitat. Research has been done to find a new antibiotic from the various habitats of actinomycetes. Lichens was the symbiotic structure of alga and fungi known as the ecological niche of various kinds of microbes including actinomycetes. The aim of this study in deep of isolate strain LC-23 for production of antimicrobial, characterize the metabolite profile of the ethyl acetate extract and identification based on 16S rRNA gene sequence analysis. The result revealed actinomycetes from lichen, strain LC-23 showed potency against Gram positive bacteria. Ethyl acetate extract of the strain showed positive inhibition against Staphylococcus aureus BTCC B-611 and Micrococcus luteus BTCC B-552. Minimum Inhibitory Concentration (MIC) of extract LC-23 was less than 2.106 ppm. The ethyl acetate extract was subjected to fractionation and tested against the pathogenic microbes and showed inhibition activity in column 9 and 10, and specifically in column 7E to 7G for Staphylcoccus aureus BTCC B-611 and 7E-7H for Micrococcus luteus BTCC B-552. The identification based on 16S rRNA gene sequence showed strain LC-23 was 98.51% similarity to Streptomyces palmae type strain. Neighbor-joining phylogenetic tree confirmed the relationships of this strain to other members of Streptomyces genera.","PeriodicalId":20485,"journal":{"name":"Proceedings of the 2019 9th International Conference on Bioscience, Biochemistry and Bioinformatics - ICBBB '19","volume":"51 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76518302","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Building ancestral recombination graphs (ARG) with minimum number of recombination events for large datasets is a challenging problem. We have proposed ARG4WG and REARG heuristic algorithm for constructing ARGs with thousands of whole genome sequences. However, these algorithms do not result in ARGs with minimal number of recombination events. In this work, we propose GAMARG algorithm, an improvement of ARG4WG, to optimize the number of recombination events in ARG building process. Experiment with different datasets showed that GAMARG algorithm outperforms other heuristic algorithms in building ARGs for large datasets. It also is much better than other heuristic algorithms and comparable to exhaustive search methods for small datasets.
{"title":"A Hybrid Approach to Optimize the Number of Recombinations in Ancestral Recombination Graphs","authors":"N. Thao, L. Vinh","doi":"10.1145/3314367.3314385","DOIUrl":"https://doi.org/10.1145/3314367.3314385","url":null,"abstract":"Building ancestral recombination graphs (ARG) with minimum number of recombination events for large datasets is a challenging problem. We have proposed ARG4WG and REARG heuristic algorithm for constructing ARGs with thousands of whole genome sequences. However, these algorithms do not result in ARGs with minimal number of recombination events. In this work, we propose GAMARG algorithm, an improvement of ARG4WG, to optimize the number of recombination events in ARG building process. Experiment with different datasets showed that GAMARG algorithm outperforms other heuristic algorithms in building ARGs for large datasets. It also is much better than other heuristic algorithms and comparable to exhaustive search methods for small datasets.","PeriodicalId":20485,"journal":{"name":"Proceedings of the 2019 9th International Conference on Bioscience, Biochemistry and Bioinformatics - ICBBB '19","volume":"59 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85175454","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Calcium (Ca2+) is a vital and very important cation for proper functioning of the nerve cells. There is abundant amount of Ca2+ in human nerve cells among them very few amount lies in the cytosol in the form of free Ca2+. These free amounts of Ca2+ react with calbindin-D28k which works as buffer species and significantly lower down the intracellular Ca2+ concentration. Parkinson's disease is a brain disorder of the human nerve cells associated with alteration in Ca2+ signalling process. In present study an attempt has been made by considering fractional advection diffusion equation to study the effect of buffer on Ca2+ diffusion in Parkinsonic nerve cells. An appropriate initial and boundary condition is taken according to the physiology of the problem. Analytical solution is obtained corresponding to time fractional advection diffusion equation and space fractional advection diffusion equation. The obtained results are simulated in MATLAB and interpreted with the Ca2+ distribution in nerve cells.
{"title":"A Fractional Mathematical Model to Study the Effect of Buffer on Calcium Distribution in Parkinson's Disease","authors":"Hardik Joshi, B. Jha","doi":"10.1145/3314367.3314378","DOIUrl":"https://doi.org/10.1145/3314367.3314378","url":null,"abstract":"Calcium (Ca2+) is a vital and very important cation for proper functioning of the nerve cells. There is abundant amount of Ca2+ in human nerve cells among them very few amount lies in the cytosol in the form of free Ca2+. These free amounts of Ca2+ react with calbindin-D28k which works as buffer species and significantly lower down the intracellular Ca2+ concentration. Parkinson's disease is a brain disorder of the human nerve cells associated with alteration in Ca2+ signalling process. In present study an attempt has been made by considering fractional advection diffusion equation to study the effect of buffer on Ca2+ diffusion in Parkinsonic nerve cells. An appropriate initial and boundary condition is taken according to the physiology of the problem. Analytical solution is obtained corresponding to time fractional advection diffusion equation and space fractional advection diffusion equation. The obtained results are simulated in MATLAB and interpreted with the Ca2+ distribution in nerve cells.","PeriodicalId":20485,"journal":{"name":"Proceedings of the 2019 9th International Conference on Bioscience, Biochemistry and Bioinformatics - ICBBB '19","volume":"33 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2019-01-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81772214","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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