{"title":"Optimizing Genetic Algorithm Parameters for Multiple Sequence Alignment Based on Structural Information","authors":"M. R. K. Sueno, J. Addawe","doi":"10.12988/ASB.2016.51250","DOIUrl":"https://doi.org/10.12988/ASB.2016.51250","url":null,"abstract":"Multiple sequence alignments (MSAs) are commonly used approaches in the analysis of sequence structure relationships. MSA is generally the alignment of three or more protein or nucleic acid sequences that maximises the similarities between sequences. In this paper, we use genetic algorithm to compute multiple sequence alignment using the structural information as the scoring scheme implemented in the program Multiobjective Optimizer for Sequence Alignments based on Structural Evaluations (MOSAStrE). We performed numerical experiments on datasets obtained from benchmark alignment database (BAliBASE) to solve multiple sequence alignment. To test the performance of the proposed algorithm, numerical simulations were carried out in deciding the appropriate set of parameter values for the","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"5 1","pages":"9-16"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90402382","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}
P. F. Tehrani, A. Majd, H. Mahmoodzadeh, T. N. Satari
{"title":"Effect of red and blue light-emitting diodes on germination, morphological and anatomical features of Brassica napus","authors":"P. F. Tehrani, A. Majd, H. Mahmoodzadeh, T. N. Satari","doi":"10.12988/ASB.2016.6832","DOIUrl":"https://doi.org/10.12988/ASB.2016.6832","url":null,"abstract":"Effect of red and blue light on seed germination, anatomical and ultrastructural features of chloroplasts were studied in oilseed rape (Brassica napus ‘Modena’). Oilseed rape seeds were germinated in 2, 4 and 8 h light under various light emitting-diodes (LED) treatments: white light (control), red light (638 nm) and blue light (450 nm) in the laboratory. In greenhouse experiment, potted plants were grown under 4, 8 and 12 days of blue and red lights and white light at the background. The photoperiod of 16 h and 28/18 °C day/night temperature and 30 % relative humidity were maintained in the greenhouse. Seed germination percentage under red light increased significantly when compared with the control; however, blue light decreased significantly germination percentage of oilseed rape seeds. Red and blue lights had negative effect on shoot and seminal root growth of oilseed rape in all the treatments. In greenhouse experiment, shoot length, plant biomass, stem diameter, were significantly increased by blue light treatment. It seems blue light treatment induces higher photosynthesis in leaves and produced higher biomass of the whole plant in this treatment than the control or red light treatment. 174 P. Farrokh Tehrani et al.","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"76 1","pages":"173-180"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83874572","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}
{"title":"Calcium Oxalate Crystal (CaOx) Composition at Different Growth Stages of Petiole in Vitis Vinifera (Vitaceae)","authors":"Şenay Süngü Şeker, M. Akbulut, G. Şenel","doi":"10.12988/ASB.2016.51146","DOIUrl":"https://doi.org/10.12988/ASB.2016.51146","url":null,"abstract":"Most plants accumulate inorganic inclusions called calcium oxalate crystals (CaOx) in both vegetative and reproductive organs. In these studies, the similarities and differences for the type and distribution of calcium oxalate (CaOx) crystals were examined in both young and mature petiole Vitis vinifera L. (Vitaceae). Transverse, radial, and tangential sections were obtained from epidermis, cortex, xylem and phloem tissue of different specimens. Crystal measurements of young and mature petiole were statically analyzed. Significant differences were determined between young and mature petiole in terms of distribution in the tissues and varieties of crystal.","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"4 1","pages":"1-8"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90594871","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}
B. Esfandiari, H. Nahrevanian, M. Pourshafie, M. Gouya, P. Khaki, E. Mostafavi, J. Darvish, S. M. Bidhendi, H. Hanifi, M. Gharakhani
{"title":"Association of prevalent Leptospira species with different rodents of three northern provinces in Iran using microscopic agglutination test","authors":"B. Esfandiari, H. Nahrevanian, M. Pourshafie, M. Gouya, P. Khaki, E. Mostafavi, J. Darvish, S. M. Bidhendi, H. Hanifi, M. Gharakhani","doi":"10.12988/ASB.2016.625","DOIUrl":"https://doi.org/10.12988/ASB.2016.625","url":null,"abstract":"Purpose: Leptospirosis as a zoonotic disease is caused by Leptospira bacteria. Transmission occurs by contact with contaminated biological fluids of the infected animals. Rodents are major sources of infection for humans or other animals. The disease is distributed mainly in tropical regions with rainfall like northern part of Iran. The aim of this study was to find association of prevalent Leptospira species with different rodents of three Northern Provinces in Iran using microscopic agglutination test (MAT). Methods: In this study, 404 rodents were captured alive at 10 different parts of each Mazandaran, Gilan and Golestan Provinces. Identification of the infecting serovars and the antibody titers were done by MAT in the sera samples using a panel of 20 strains of live Leptospira spp. as the source of antigens. RESULTS: Antibodies against one or more serovars were detected in 94 (23.27%) sera at dilution ≥1:200 and 76.73% were detected to be negative. The prevalent Leptospira serovars were detected as L. autumnalis (25.53%), L. serjoehardjo (24.47%) and L. cynopteri (6.38%). The majority of rodents were identified during this study in three provinces included Rattus norvegicus (67.33%), Apodemus sylvaticus (13.86%) and Rattus rattus (13.61%). The common prevalent rodent in three provinces was Rattus norvegicus, which was associated with L. serjoehardjo in Mazandaran (81.8%), L. autumnalis in Gilan (67.2%) and L. canicula in Golestan (50.0%). Conclusion: The dominant srovars of leptospira were L. autumnalis, L. serjoehardjo and L. cynopteri and the most prevalent rodents as reservoir were Rattus norvegicus, Apodemus sylvaticus and Rattus rattus in three Northern provinces of Iran. The results indicated a moderate prevalence of leptospirosis in rodents during this study in north of Iran. This study provided the first epidemiological data about the association between leptospirosis with rodents in Iran.","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"5 1","pages":"53-63"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74738492","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. Ambardini, Darwis, L. Safuan, A. Zaeni, A. Sani
{"title":"The effect of manure and the bioaccumulation of heavy metals Hg, Cu and Zn at ex-gold mining land on the growth of silk tree (Paraserinthes falcataria (L.) Nielsen) in Bombana, Southeast Sulawesi","authors":"S. Ambardini, Darwis, L. Safuan, A. Zaeni, A. Sani","doi":"10.12988/ASB.2016.6411","DOIUrl":"https://doi.org/10.12988/ASB.2016.6411","url":null,"abstract":"One of the negative effects of gold mining activity is soil contamination by heavy metal. The aims of this study were two folds; to assess the effect of manures (cow, goat, chicken) (i) on the growth of silk tree (Paraserianthes falcataria (L.) Nielsen) and (ii) on the bioaccumulation of heavy metals (Hg, Cu, Zn) in the plant organs of the silk tree planted in the ex-gold mining land in Bombana. This is an experimental research design with a completely randomized 78 Sri Ambardini et al. design consisting of one control (without manure) and 4 treatments (cow, goat and chicken manures) with 5 repplicates. The plant growth parameters observed are plant height, stem diameter, number of leaves, leaf area, and metal content of Hg, Zn, and Cu in plant organs. ANOVA with Duncan Multiple Range Test (DMRT) were used for the analysis. The results showed that the treatment with manure has an impact on the parameter of plant growth and bioaccumulation of Hg, Cu and Zn in the plant organs. DMRT showed that the treatment with manures has a significant influence on the growth and bioaccumulation of Hg, Cu, and Zn in the plants. The manure with cows was better in supporting growth of silk tree compared to those with chicken, goat as well as control. Treatment with manure reduced bioaccumulation of Hg but increased bioaccumulation of Cu and Zn in the plant organs. The bioaccumulation of Hg, Cu and Zn was found the highest in the root than in the stem and leaves. The total bioaccumulation of Zn in plant organs was the highest compared with that of Cu and Hg. Keyword: Manure, Growth, Heavy Metals, Silk Tree, Ex-Gold Mining Land","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"28 1","pages":"77-89"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"80305418","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}
M. Modaresinejad, H. Nahrevanian, S. Khatami, E. Bagheri
{"title":"Biochemical association between essential trace elements and susceptibility to malaria in outbred mice after inhibition with dexamethasone or induction with lipopolysaccharide","authors":"M. Modaresinejad, H. Nahrevanian, S. Khatami, E. Bagheri","doi":"10.12988/ASB.2016.6516","DOIUrl":"https://doi.org/10.12988/ASB.2016.6516","url":null,"abstract":"","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"33 1","pages":"91-99"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87163532","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}
Elahe Tabassi, Mahmoud Zokaei, A. Jafari, J. Vaezi
{"title":"Nutlet micromorphology study of some species of Thymus L. (Lamiaceae) in NE Iran","authors":"Elahe Tabassi, Mahmoud Zokaei, A. Jafari, J. Vaezi","doi":"10.12988/ASB.2016.663","DOIUrl":"https://doi.org/10.12988/ASB.2016.663","url":null,"abstract":"In the present study, nutlet micromorphological features of five Thymus species growing in NE Iran were examined. For this purpose, nutlet shape and ornamentation were assessed using SEM. The results indicated that theP/E of nutlet, abscission scar position, cell shape, anticlinal wall and periclinal surface varied among the studied species. Finally an identification key was prepared basis on the mentioned characteristics for species under study.","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"7 1","pages":"111-117"},"PeriodicalIF":0.0,"publicationDate":"2016-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85092389","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}
{"title":"Control of the Applicability of the Dipole Approximation for Gold Nanoparticles","authors":"D. Barchiesi, T. Grosges","doi":"10.12988/ASB.2015.5532","DOIUrl":"https://doi.org/10.12988/ASB.2015.5532","url":null,"abstract":"Gold nanoparticles are widely used for biomedical applications such as cancer therapy, drug delivery and high resolution imaging of biological tissues (spectroscopy, Surface Enhanced Raman spectroscopy, uo","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"78 1","pages":"403-412"},"PeriodicalIF":0.0,"publicationDate":"2015-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83744062","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}
{"title":"A population-based case-control study to evaluate the role of codon 164 of beta 2-adrenergic receptor gene polymorphism in Iranian PCOS patients","authors":"Shahla Lotfi, T. Naji, A. Shakoori, D. N. Inanlou","doi":"10.12988/ASB.2015.41271","DOIUrl":"https://doi.org/10.12988/ASB.2015.41271","url":null,"abstract":"Polycystic ovary syndrome (PCOS) is a common endocrine disorder. This syndrome is a genetic disorder that involves about 5 to 10 percent of women in reproductive age. The purpose of this study was to investigate the effect of codon 164 of beta-2 adrenergic receptor (NM- _000024.5:c.491C>T) polymorphism in patients with PCOS. The normal form of this codon isACC and when polymorphism occurs, it changes to the ADRB2rs1800888 (Thr164Ile) with codon ATC. This case-control study consisted of 14 Iranian patients (mean age 26.86±1.03), along with 13 healthy controls, from Infertility Center of Valie Asre, Imam Khomaini Hospital Complex in May 2013 until Feb 2014. Data analysis was done by statistical software SPSS, version 19.0. The result shows that, two persons of control group and one individual of patient group had polymorphism codon 164. The P-value greater than 0.05 (P>0.05) demonstrated that there is no correlation between Thr164Ile polymorphism and PCOS.","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"114 1","pages":"111-119"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77717165","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}
{"title":"Physical and academic performance of vegetarian and non-vegetarian school girls (13–15 yrs)","authors":"Priyanka Pareek, S. Ayesha","doi":"10.12988/ASB.2015.41165","DOIUrl":"https://doi.org/10.12988/ASB.2015.41165","url":null,"abstract":"The study was undertaken to assess the physical and academic performance of vegetarian and non-vegetarian school girls. One hundred school going girls vegetarian (n=50) and non-vegetarian (n=50) in the age group of 13-15 years were selected purposively for the study. The data were collected through personal interview technique using the especially structured questionnaire. The general profile, status and educational details of the family, dietary habits and menarcheal profile of the subjects were collected. The height and weight of the subjects were measured by standardized methods. The BMI of the subjects were calculated and categorized accordingly. The academic performance of the girls was measured using the percentage marks obtained by the end of the academic year. Physical activity tests were conducted to assess the physical work capacity by noting the time taken and change in pulse rate after performing the activities as running (100m), jumping (25times) and touching toes (25times). In the study 32% nonvegetarian got higher scores followed by 26% of vegetarian. More than 10% vegetarian and non-vegetarian girls got lower score in academics. The mean difference in the time taken to complete the running and jumping activities came out to be non significant and the time taken to touch toes for vegetarian subjects was 80 Priyanka Pareek and Syeda Ayesha significantly lower as compared to non-vegetarian subjects. The difference was significant for the change in pulse rate after completing the running and jumping activities in both the groups, but difference was non-significant between the groups. In case of toe touching difference was non-significant for the change in pulse rate within both the groups, but difference was significant between the groups, It can be concluded as the non-vegetarian girls were found to be better physical performers. Academically, however they were better than their vegetarian correlates.","PeriodicalId":7194,"journal":{"name":"Advanced Studies in Biology","volume":"31 1","pages":"79-88"},"PeriodicalIF":0.0,"publicationDate":"2015-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83379184","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}