Examinations of a common biological reference organism, (E. coli), demonstrate that NSGA-II is able to provide a series of compressions at various ratios, allows a biologist to examine the organism’s connective networks with a measure of certainty of connectiveness. This is due to a novel method of scoring the similarity of the compressed network to the origional during the graph’s creation based on the number of false links added to the graph during the compression method.
{"title":"NSGA-II for biological graph compression","authors":"A. Zakirov, J. A. Brown","doi":"10.12988/ASB.2017.61143","DOIUrl":"https://doi.org/10.12988/ASB.2017.61143","url":null,"abstract":"Examinations of a common biological reference organism, (E. coli), demonstrate that NSGA-II is able to provide a series of compressions at various ratios, allows a biologist to examine the organism’s connective networks with a measure of certainty of connectiveness. This is due to a novel method of scoring the similarity of the compressed network to the origional during the graph’s creation based on the number of false links added to the graph during the compression method.","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"50 1","pages":"1-7"},"PeriodicalIF":0.0,"publicationDate":"2017-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90625014","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}
S. Barinova, Izaz Khuram, Asadullah, N. Ahmad, Samin Jan, D. Shin
Altogether 209 species of algae and cyanobacteria has been revealed in 2014-2015 from four sites in the Kabul River that flow across the Peshawar Valley. Green algae, diatoms, and Charophyta filamentous algae were diverse and characterize regional feature in the river basin with high agricultural activity. Species richness and algal abundance were increase down the river. Index saprobity S varied between 1.55 and 1.59 (Class III of water quality) and reflects decreasing of water quality down the river as a result of pollutants impact, which brings mostly the Swat tributary. Bio-indication results show prevalence of benthic or plankto-benthic species, temperate temperature indicators, slow streaming middle oxygenated waters inhabitants, salinity-indifferents, eurysaprobes, mesotrophes, and autotrophic algae with tolerance to middle concentration of Nitrates that reflects middle polluted waters III-IV Class of Water 152 Sophia Barinova et al. Quality in the Kabul River. Our analysis shows that integral bio-indication in water quality assessment with using of algal communities can give relevant results of self-purification possibility, which can be employed in purpose of monitoring the regional water quality as economy and resultative method.
{"title":"How water quality in the Kabul River, Pakistan, can be determined with algal bio-indication","authors":"S. Barinova, Izaz Khuram, Asadullah, N. Ahmad, Samin Jan, D. Shin","doi":"10.12988/ASB.2016.6830","DOIUrl":"https://doi.org/10.12988/ASB.2016.6830","url":null,"abstract":"Altogether 209 species of algae and cyanobacteria has been revealed in 2014-2015 from four sites in the Kabul River that flow across the Peshawar Valley. Green algae, diatoms, and Charophyta filamentous algae were diverse and characterize regional feature in the river basin with high agricultural activity. Species richness and algal abundance were increase down the river. Index saprobity S varied between 1.55 and 1.59 (Class III of water quality) and reflects decreasing of water quality down the river as a result of pollutants impact, which brings mostly the Swat tributary. Bio-indication results show prevalence of benthic or plankto-benthic species, temperate temperature indicators, slow streaming middle oxygenated waters inhabitants, salinity-indifferents, eurysaprobes, mesotrophes, and autotrophic algae with tolerance to middle concentration of Nitrates that reflects middle polluted waters III-IV Class of Water 152 Sophia Barinova et al. Quality in the Kabul River. Our analysis shows that integral bio-indication in water quality assessment with using of algal communities can give relevant results of self-purification possibility, which can be employed in purpose of monitoring the regional water quality as economy and resultative method.","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"24 1","pages":"151-171"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81301571","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}
Sanaz Naderi, H. Nahrevanian, V. Khalaj, M. Farahmand
Visceral leishmaniasis (VL) is a fatal disease caused by Leishmania infantum in the Mediterranean basin and Iran. Different methods are used for diagnosis of VL. The aims of this study were expression and purification of recombinant A2 (rA2) protein of L.infantum and its application in the diagnosis of VL. The serological diagnosis of VL was applied using rA2 protein. In this study, A2 gene of L.infantum sequence was ordered for the synthesis, cloned in E.coli strain TOP10F' and proliferated in pET22-b vector. The expression and purification of rA2 proteins applied in host via BL21 and Ni-NTA respectively. The A2 gene sequences were synthesized and the construct transformed to pET22-b vector. A 102 Sanaz Naderi et al. 520bp fragment was identified in digested pEASY-A2 plasmid. The gene was successfully cloned in to pET22-b standard expression vector and transformed in E.coli BL21. Expression of rA2 was confirmed by SDS-PAGE and a 27KD protein was detected. The antigenicity of A2 protein was assessed using both pooled dog sera and C9 anti-A2 monoclonal Ab. This study recommends rA2ELISA as alternative assay to detect VL. More evaluation should be made to develop a cheap and reliable serologic test for detection of L.infantum among infected hosts.
{"title":"Cloning, expression and purification of recombinant A2 protein from Leishmania infantum for diagnosis of visceral leishmaniasis in Iran","authors":"Sanaz Naderi, H. Nahrevanian, V. Khalaj, M. Farahmand","doi":"10.12988/ASB.2016.6413","DOIUrl":"https://doi.org/10.12988/ASB.2016.6413","url":null,"abstract":"Visceral leishmaniasis (VL) is a fatal disease caused by Leishmania infantum in the Mediterranean basin and Iran. Different methods are used for diagnosis of VL. The aims of this study were expression and purification of recombinant A2 (rA2) protein of L.infantum and its application in the diagnosis of VL. The serological diagnosis of VL was applied using rA2 protein. In this study, A2 gene of L.infantum sequence was ordered for the synthesis, cloned in E.coli strain TOP10F' and proliferated in pET22-b vector. The expression and purification of rA2 proteins applied in host via BL21 and Ni-NTA respectively. The A2 gene sequences were synthesized and the construct transformed to pET22-b vector. A 102 Sanaz Naderi et al. 520bp fragment was identified in digested pEASY-A2 plasmid. The gene was successfully cloned in to pET22-b standard expression vector and transformed in E.coli BL21. Expression of rA2 was confirmed by SDS-PAGE and a 27KD protein was detected. The antigenicity of A2 protein was assessed using both pooled dog sera and C9 anti-A2 monoclonal Ab. This study recommends rA2ELISA as alternative assay to detect VL. More evaluation should be made to develop a cheap and reliable serologic test for detection of L.infantum among infected hosts.","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"2016 1","pages":"101-110"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87950960","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}
Phenomenon of aging came to existence simultaneously with formation of cell associations and multicellular organisms and played an adaptive role at the early stages of evolution. This phenomenon may be the result of formation of mechanisms that control cellular growth in compliance with nutrient factors limit. Multicellular organisms function as complex systems where the cell division is regulated both by intracellular processes and general systemic organization. The developmental process is determined by a kinetic curve of population growth, which is typical of every cell association. The systemic structural hypothesis considers every multicellular organism as a system that consists of various cellular associations in symbiotic interaction. One of these associations limits the developmental kinetics of the whole organism. Life duration is determined by potential of limiting cell association stem cells. It is offered to introduce a special term – regeneration submodule a unit that consists of cells and tissues which have a general regeneration complex – a group of stem cells that renovate strictly these cells and tissues. Such regeneration submodules are formed within organs and systems; one of them is a dominating unit which determines the life duration.
{"title":"Systemic structural hypothesis of aging","authors":"A. Kolomiytsev","doi":"10.12988/ASB.2016.612","DOIUrl":"https://doi.org/10.12988/ASB.2016.612","url":null,"abstract":"Phenomenon of aging came to existence simultaneously with formation of cell associations and multicellular organisms and played an adaptive role at the early stages of evolution. This phenomenon may be the result of formation of mechanisms that control cellular growth in compliance with nutrient factors limit. Multicellular organisms function as complex systems where the cell division is regulated both by intracellular processes and general systemic organization. The developmental process is determined by a kinetic curve of population growth, which is typical of every cell association. The systemic structural hypothesis considers every multicellular organism as a system that consists of various cellular associations in symbiotic interaction. One of these associations limits the developmental kinetics of the whole organism. Life duration is determined by potential of limiting cell association stem cells. It is offered to introduce a special term – regeneration submodule a unit that consists of cells and tissues which have a general regeneration complex – a group of stem cells that renovate strictly these cells and tissues. Such regeneration submodules are formed within organs and systems; one of them is a dominating unit which determines the life duration.","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"4 1","pages":"17-25"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83395027","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}
Angiogenesis, formation of new vessels from the primary vessels is involved in physiological condition such as reproduction, wound healing and pathological like Diabetes and tumor. Tumor progression associates with persistent unregulated angiogenesis. This study aimed to investigate the effect of leaves aqueous extract of Stachys lavandulifolia on the angiogenesis in chorioallantoic membrane and choroids plexus of chick embryos. In this experimental study, 30 fertilized eggs of Hy-line race were randomly divided into 5 groups: control group, sham-exposed group and four experimental groups (n=6). In the second day of incubation in sterile condition, a window was opened on eggs. On 8th day, chorioallantoic membrane (CAM) was treated at sham-exposed group with normal saline and at experimental groups with Stachys lavandulifolia aqueous extract (25, 50, 100 mg/kg). On 12th day CAMs, the length and number of vessels were examined and 66 Maryam Tehranipour and Saeide Zafar Balanezhad morphological disorders were studied. Data were calculated and analyzed statistically using t-test and ANOVA. There is no significant difference in the mean number and length of vessels in the control group with the sham-exposed groups. The mean of number and length in all experimental groups shows a meaningful increase in compare with sham group (P<0/05).Morphological abnormalities were not observed in fetuses. According to the results of this research, low doses of Stachys lavandulifolia aqueous extract increase angiogenesis in chorioallantoic membrane and choroids plexus, but it has antiangiogenesis effect in high doses. No significant effect on chick embryo's morphological characteristics observed.
{"title":"The effects of Stachys lavandulifolia leaves aqueous extract on angiogenesis in chick embryos chorioalantoic membrane and choroids plexus","authors":"M. Tehranipour, S. Balanezhad","doi":"10.12988/ASB.2016.638","DOIUrl":"https://doi.org/10.12988/ASB.2016.638","url":null,"abstract":"Angiogenesis, formation of new vessels from the primary vessels is involved in physiological condition such as reproduction, wound healing and pathological like Diabetes and tumor. Tumor progression associates with persistent unregulated angiogenesis. This study aimed to investigate the effect of leaves aqueous extract of Stachys lavandulifolia on the angiogenesis in chorioallantoic membrane and choroids plexus of chick embryos. In this experimental study, 30 fertilized eggs of Hy-line race were randomly divided into 5 groups: control group, sham-exposed group and four experimental groups (n=6). In the second day of incubation in sterile condition, a window was opened on eggs. On 8th day, chorioallantoic membrane (CAM) was treated at sham-exposed group with normal saline and at experimental groups with Stachys lavandulifolia aqueous extract (25, 50, 100 mg/kg). On 12th day CAMs, the length and number of vessels were examined and 66 Maryam Tehranipour and Saeide Zafar Balanezhad morphological disorders were studied. Data were calculated and analyzed statistically using t-test and ANOVA. There is no significant difference in the mean number and length of vessels in the control group with the sham-exposed groups. The mean of number and length in all experimental groups shows a meaningful increase in compare with sham group (P<0/05).Morphological abnormalities were not observed in fetuses. According to the results of this research, low doses of Stachys lavandulifolia aqueous extract increase angiogenesis in chorioallantoic membrane and choroids plexus, but it has antiangiogenesis effect in high doses. No significant effect on chick embryo's morphological characteristics observed.","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"117 1","pages":"65-75"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86800301","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}
R. Á. Pozos, Andrey M. Montoya, Gladys Elena Salcedo Echeverry
Here we propose a statistical approach to characterize interspike signals of the electrical activity of peptidergic neurons from their timescale similarity. The approach provides a novel way to compare and classify a set of non-stationary time series based on the comparison of their wavelet transforms.
{"title":"A wavelet analysis to classify the interspike activity of peptidergic neurons","authors":"R. Á. Pozos, Andrey M. Montoya, Gladys Elena Salcedo Echeverry","doi":"10.12988/ASB.2016.6829","DOIUrl":"https://doi.org/10.12988/ASB.2016.6829","url":null,"abstract":"Here we propose a statistical approach to characterize interspike signals of the electrical activity of peptidergic neurons from their timescale similarity. The approach provides a novel way to compare and classify a set of non-stationary time series based on the comparison of their wavelet transforms.","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"9 1","pages":"141-149"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84250802","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. Balkrishna, H. K. Manikyam, V. Sharma, Niti Sharma
Picrorhiza kurroa is a recognized herb in the Ayurvedic and Chinese system of traditional medicine. It is effective in treating a variety of diseases ranging from digestion problems to paralysis. Thus it is essential to rule out any kind of toxicity, mutagenicity or carcinogenicity in the plant to be used as a medicine. The study was conducted to evaluate ability of Picrorhiza kurroa to induce reverse mutations at the histidine locus in several strains of Salmonella typhimurium in the absence or presence of exogenous metabolic activation system (S9) containing microsomal enzymes. The bacterial reverse mutation assay has been shown to be a sensitive, rapid and accurate indicator of mutagenic activity of a wide range of chemical classes. All bacterial strains showed negative responses over the entire dose range. No significant dose related increase was observed in the number of revertants in the two independent experiments. Based on the results 128 Acharya Balkrishna et al. of this study it is concluded that Picrorhiza kurroa rhizome extract is not mutagenic in the Salmonella typhimurium reverse mutation assay.
{"title":"Safety evaluation of Picrorhiza kurroa rhizome extract by bacterial reverse mutation test","authors":"A. Balkrishna, H. K. Manikyam, V. Sharma, Niti Sharma","doi":"10.12988/asb.2016.6620","DOIUrl":"https://doi.org/10.12988/asb.2016.6620","url":null,"abstract":"Picrorhiza kurroa is a recognized herb in the Ayurvedic and Chinese system of traditional medicine. It is effective in treating a variety of diseases ranging from digestion problems to paralysis. Thus it is essential to rule out any kind of toxicity, mutagenicity or carcinogenicity in the plant to be used as a medicine. The study was conducted to evaluate ability of Picrorhiza kurroa to induce reverse mutations at the histidine locus in several strains of Salmonella typhimurium in the absence or presence of exogenous metabolic activation system (S9) containing microsomal enzymes. The bacterial reverse mutation assay has been shown to be a sensitive, rapid and accurate indicator of mutagenic activity of a wide range of chemical classes. All bacterial strains showed negative responses over the entire dose range. No significant dose related increase was observed in the number of revertants in the two independent experiments. Based on the results 128 Acharya Balkrishna et al. of this study it is concluded that Picrorhiza kurroa rhizome extract is not mutagenic in the Salmonella typhimurium reverse mutation assay.","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"16 1","pages":"127-140"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84211142","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}
The present research has examined petiole anatomical characteristics of 10 Nepeta species (Lamiaceae family) growing in the Razavi, Northern and southern Khorassan provinces (NE) Iran. For this, cross sections of their petioles were prepared and stained by differential staining. In petiole internal structure, some differences such as the outline shape of petioles cross section, the shape of epidermis cells and vessels were noticed. Finally, based on above characteristics an identification key of studied Nepeta species was prepared.
{"title":"Comparative anatomical studies on petioles of Nepeta L. species (Lamiaceae) in NE Iran","authors":"S. M. M. Shahri, A. Jafari, H. Mahmoodzadeh","doi":"10.12988/ASB.2016.6728","DOIUrl":"https://doi.org/10.12988/ASB.2016.6728","url":null,"abstract":"The present research has examined petiole anatomical characteristics of 10 Nepeta species (Lamiaceae family) growing in the Razavi, Northern and southern Khorassan provinces (NE) Iran. For this, cross sections of their petioles were prepared and stained by differential staining. In petiole internal structure, some differences such as the outline shape of petioles cross section, the shape of epidermis cells and vessels were noticed. Finally, based on above characteristics an identification key of studied Nepeta species was prepared.","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"50 1","pages":"119-126"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81771085","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}
Today, generation of waste is increasing and despite the advancement of science and technology, its management has changed into a complex problem. The aim of this study was to reduce solid waste from the source by designing and building home composter and also detect of extended spectrum β-lactamase (ESBL)producing Pseudomonas aeruginosa and Enterobacteriaceae isolates in composting processes by phenotypic and molecular methods. AUTOCAD, Photoshop and 3ds MAX were used to model and design the components of device. Composter was built using galvanized iron sheet with the dimensions 35 × 36 × 32 cm and its defects were resolved step by step. The effect of produced compost was determined on the growth of selected plants. Gram negative bacteria were isolated from the materials undergoing composting, the leachate, and mature compost in two repetitions. Composting process took long 38 days. 40 Ehsan Yousefi and Mahboobeh Nakhaei Moghaddam Produced compost significantly increased the growth of cranesbill and wheat in comparison with the growth hormone and chemical fertilizer (p<0.05). The frequency of bacteria isolated in the initial waste was larger than in the maturity stage. Antibiotic resistance was low among isolates and none of them were ESBLproducer. Colony PCR revealed that all isolates harbored the oprL and exoA genes. The results showed that the built composter had a good efficiency and the produced compost could be used as a suitable alternative to chemical fertilizers.
{"title":"Design and construction of household composter and detection of extended spectrum β-lactamase producing Pseudomonas aeruginosa and Enterobacteriaceae in compost","authors":"E. Yousefi, M. N. Moghaddam","doi":"10.12988/ASB.2016.626","DOIUrl":"https://doi.org/10.12988/ASB.2016.626","url":null,"abstract":"Today, generation of waste is increasing and despite the advancement of science and technology, its management has changed into a complex problem. The aim of this study was to reduce solid waste from the source by designing and building home composter and also detect of extended spectrum β-lactamase (ESBL)producing Pseudomonas aeruginosa and Enterobacteriaceae isolates in composting processes by phenotypic and molecular methods. AUTOCAD, Photoshop and 3ds MAX were used to model and design the components of device. Composter was built using galvanized iron sheet with the dimensions 35 × 36 × 32 cm and its defects were resolved step by step. The effect of produced compost was determined on the growth of selected plants. Gram negative bacteria were isolated from the materials undergoing composting, the leachate, and mature compost in two repetitions. Composting process took long 38 days. 40 Ehsan Yousefi and Mahboobeh Nakhaei Moghaddam Produced compost significantly increased the growth of cranesbill and wheat in comparison with the growth hormone and chemical fertilizer (p<0.05). The frequency of bacteria isolated in the initial waste was larger than in the maturity stage. Antibiotic resistance was low among isolates and none of them were ESBLproducer. Colony PCR revealed that all isolates harbored the oprL and exoA genes. The results showed that the built composter had a good efficiency and the produced compost could be used as a suitable alternative to chemical fertilizers.","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"73 1","pages":"39-52"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72990147","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}
The formation of multiple helical-linear segments of a polymer in a solvent is investigated analytically. Winding probability functions for diffusive polypeptides is obtained for a drift coefficient f(s) involving Fourier cosine function of the variable s along the chain. Applications to protein chains are explored where the formation of α-helices between linear segments is compared to the conformation of myoglobin (4mbn) found in the Protein Data Bank (PDB). The results generated are also comparable to the results of the well-known APSSP2 secondary structure prediction server of Raghava which employed a sophisticated Example Based Learning (EBL) approach with a combination of neural network and nearest neighbour algorithm. Considering the large amount of data from Protein Data Bank (PDB), we can conveniently predict or mimic the structure of 28 Wilson I. Barredo and Henry P. Aringa other α-helical proteins in solvents with much less computing times which can be used to explore the protein folding problem.
用解析的方法研究了聚合物在溶剂中螺旋-线性多链段的形成。得到了扩散多肽的缠绕概率函数，其漂移系数f(s)涉及沿链的变量s的傅立叶余弦函数。将线性片段之间α-螺旋的形成与蛋白质数据库(PDB)中发现的肌红蛋白(4mbn)的构象进行比较，探索了蛋白质链的应用。所生成的结果也可与Raghava著名的APSSP2二级结构预测服务器的结果相媲美，该服务器采用了一种复杂的基于示例的学习(EBL)方法，结合了神经网络和最近邻算法。考虑到蛋白质数据库(Protein data Bank, PDB)的大量数据，我们可以方便地预测或模拟28种Wilson I. Barredo和Henry P. Aringa等α-螺旋蛋白在溶剂中的结构，大大减少了计算时间，可用于研究蛋白质折叠问题。
{"title":"Drift coefficient and simulation of amino acid-solvent interactions for proteins whose main chain have alpha-helical secondary structures","authors":"W. Barredo, Henry P. Aringa","doi":"10.12988/asb.2016.611","DOIUrl":"https://doi.org/10.12988/asb.2016.611","url":null,"abstract":"The formation of multiple helical-linear segments of a polymer in a solvent is investigated analytically. Winding probability functions for diffusive polypeptides is obtained for a drift coefficient f(s) involving Fourier cosine function of the variable s along the chain. Applications to protein chains are explored where the formation of α-helices between linear segments is compared to the conformation of myoglobin (4mbn) found in the Protein Data Bank (PDB). The results generated are also comparable to the results of the well-known APSSP2 secondary structure prediction server of Raghava which employed a sophisticated Example Based Learning (EBL) approach with a combination of neural network and nearest neighbour algorithm. Considering the large amount of data from Protein Data Bank (PDB), we can conveniently predict or mimic the structure of 28 Wilson I. Barredo and Henry P. Aringa other α-helical proteins in solvents with much less computing times which can be used to explore the protein folding problem.","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"100 1","pages":"27-38"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90342133","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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