Progress in Biological Sciences最新文献_第3页

Simple procedure for production of short DNA size markers of 100 to 2000 bp 简单的程序生产短DNA大小标记100至2000 bp

Progress in Biological Sciences Pub Date : 2017-09-19 DOI: 10.22059/PBS.2016.590021

Hamed Hekmatnezhad, F. Moradian, S. H. Hashemi-Petroudi

{"title":"Simple procedure for production of short DNA size markers of 100 to 2000 bp","authors":"Hamed Hekmatnezhad, F. Moradian, S. H. Hashemi-Petroudi","doi":"10.22059/PBS.2016.590021","DOIUrl":"https://doi.org/10.22059/PBS.2016.590021","url":null,"abstract":"DNA size markers (ladder) are essential tools in molecular biology, genetics and biotechnology. In this study, a simple and cost-effective method for laboratory production of DNA ladders is introduced. For this purpose, different sizes of 100 to 2000 bp DNA segments were designed using PCR technique. For producing 14 different gene fragments as DNA molecular weight markers, recombinant plasmid pET28a containing α-amylase gene as a DNA source and one forward and 14 reverse primers were used. The gene fragments containing 100 to 400bp segments with a distance of 50 bp and 400 to 1600 bp segments with a distance of 200 bp as well as 1600 to 2000 bp segments with the distance of 400 bp were generated in a single run of PCR. The present technique could prove to be simple, time saving, inexpensive and good quality approach as compared to the usual DNA ladder preparation procedures. Also, according to the same conditions for designed primers there is a possibility of producing other marker sizes by choosing different types of forward and reverse primers. The PCR product mixture could be directly loaded onto the agarose gel and used as a molecular weight marker without further purification because that was as reliable and uniform as markers from commercial sources. Finally, this marker can be useful for most of molecular biology laboratory techniques.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"1 1","pages":"199-204"},"PeriodicalIF":0.0,"publicationDate":"2017-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"91118903","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}

引用次数: 0

Degradation of naphthalene by bacterial isolates from the Gol Gohar Mine, Iran 伊朗Gol Gohar矿分离细菌对萘的降解

Progress in Biological Sciences Pub Date : 2017-09-19 DOI: 10.22059/PBS.2016.590018

M. Hassanshahian, Moslem Abarian, Arastoo Badoei-dalfard

{"title":"Degradation of naphthalene by bacterial isolates from the Gol Gohar Mine, Iran","authors":"M. Hassanshahian, Moslem Abarian, Arastoo Badoei-dalfard","doi":"10.22059/PBS.2016.590018","DOIUrl":"https://doi.org/10.22059/PBS.2016.590018","url":null,"abstract":"Naphthalene is an ubiquitous pollutant of the environment and the biodegradation of this pollutant has been receiving constant scientific consideration. The aim of this study was to isolate and identify bacteria that could degrade naphthalene from three regions of the Gol Gohar Mine at Sirjan, Iran. In this study, the total naphthalene degrading bacteria were quantified with the most probable number (MPN) and the colony forming unit (CFU) methods. The results showed that most of the bacteria communities capable of degrading naphthalene aggregated in the (WG) site. Among 22 isolated bacteria, seven strains were selected for their ability to grow at higher concentrations of naphthalene (300 and 400 mg/l) and biochemical characteristics. Finally, two strains named isolates 72N and 79N were selected for analysis of the 16S rRNA sequences. Strain 72N was identified as Pseudomonas fluorescens AHB72N and strain 79N was shown to be related to Pseudomonas gessardii AHB79N. The results of biodegradation tests showed that these two strains could degrade 600 mg/l naphthalene in 7 days. The results indicated that strain 79N showed higher potential for removing naphthalene than strain 72N. Practical application of bacterial strains for the degradation of naphthalene from the industrial zones opens interesting prospects. The results of this study provide useful information in evaluating naphthalene degraders isolated from wastewater and industrial sites.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"112 1","pages":"171-180"},"PeriodicalIF":0.0,"publicationDate":"2017-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86791186","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}

引用次数: 4

Evaluation of growth inhibition activity of myxobacterial extracts against multi-drug resistant Acinetobacter baumannii 黏菌提取物对多重耐药鲍曼不动杆菌生长抑制活性的评价

Progress in Biological Sciences Pub Date : 2017-09-19 DOI: 10.22059/PBS.2016.590019

M. Dehhaghi, F. Mohammadipanah

{"title":"Evaluation of growth inhibition activity of myxobacterial extracts against multi-drug resistant Acinetobacter baumannii","authors":"M. Dehhaghi, F. Mohammadipanah","doi":"10.22059/PBS.2016.590019","DOIUrl":"https://doi.org/10.22059/PBS.2016.590019","url":null,"abstract":"The worldwide dissemination of multi drug resistant Acinetobacter baumannii strains has caused serious concern and high rate of mortality in recent decades that originate from limited effective antibiotics in the treatment of A. baumannii infections. Myxobacteria are Gram-negative bacteria that are important for their complex lifestyle and production of novel structurally secondary metabolites with diverse bioactivities. In this study, a total of 60 myxobacterial strains were purified by culturing and investigation of 130 soil samples. Secondary metabolite extracts of the selected strains were screened for antibacterial activity against multi-drug resistant (MDR) Acinetobacter baumannii. The most potent extracts derived from Stigmatella sp. UTMC 4081, Stigmatella sp. UTMC 4072, and Archangium sp. UTMC 4070 which were investigated by recording percentage of growth inhibition, MIC, MBC, and IC50 values. The results showed that the MIC value of extract No. 4072 was 2.5 μg/ml and its MBC value against A. baumannii recorded as 5 μg/ml. Extract No. 4081 was known to be active with MIC of 2.5 μg/ml and MBC of 10 μg/ml. In addition, MIC and MBC values of extract No. 4070 were found to be 10 and 25 μg/ml, respectively. Myxobacterial extracts showed no toxicity against Artemia salina. This study demonstrated the importance of myxobacterial metabolites as promising antimicrobial agents against multi drug resistant A. baumannii Keywords: Myxobacteria; Stigmatella; Antimicrobial activity; Multi-drug resistant bacteria","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"83 1","pages":"181-187"},"PeriodicalIF":0.0,"publicationDate":"2017-09-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"73919242","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}

引用次数: 8

Neighborhood matrix: A new idea in matching of two dimensional gel images 邻域矩阵:二维凝胶图像匹配的新思路

Progress in Biological Sciences Pub Date : 2017-09-18 DOI: 10.22059/PBS.2016.590015

B. A. Savareh, Azadeh Bashiri, M. Mostafavi

{"title":"Neighborhood matrix: A new idea in matching of two dimensional gel images","authors":"B. A. Savareh, Azadeh Bashiri, M. Mostafavi","doi":"10.22059/PBS.2016.590015","DOIUrl":"https://doi.org/10.22059/PBS.2016.590015","url":null,"abstract":"Automated data analysis and pattern recognition techniques are the requirements of biological and proteomicsresearch studies. The analysis of proteins consists of some stages among which the analysis of two dimensionalelectrophoresis (2-DE) images is crucial. The aim of image capturing is to generate a Photostat that can be used infuture works such as image comparison. The researchers introduced a new method for matching two 2-DE gelimages. In this method, a neighborhood circular region is defined to obtain information about spots’ neighbors. Inthe present paper, the information obtained by this region is reordered into a matrix as a descriptor of the neighborsof each spot. The matrix is then used in matching the spots between two images. All conducted tests to evaluate themethod’s performance showed the power of the method in spot matching, even when the number of candidatematching spots in the second images increased. The proposed method provides a robust automatic comparison ideain gel images matching. Despite its low speed, its accuracy is excellent. The Novelty of the present study is the useof matrices as neighborhood descriptor. This idea is applicable in any other similar domain.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"170 1","pages":"129-137"},"PeriodicalIF":0.0,"publicationDate":"2017-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74804879","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}

引用次数: 2

Radical scavengering of pigments from novel strains of Dietzia schimae and Microbacterium esteraromaticum 木兰花和酯芳微杆菌新菌株对色素自由基的清除作用

Progress in Biological Sciences Pub Date : 2017-09-18 DOI: 10.22059/PBS.2016.590017

Sayyede Narjes Zamanian, Z. Etemadifar

{"title":"Radical scavengering of pigments from novel strains of Dietzia schimae and Microbacterium esteraromaticum","authors":"Sayyede Narjes Zamanian, Z. Etemadifar","doi":"10.22059/PBS.2016.590017","DOIUrl":"https://doi.org/10.22059/PBS.2016.590017","url":null,"abstract":"Radiation resistant bacteria have adopted a variety of ingenious strategies for survival under the high dose of radiation, for example through their pigments. In the present study, two ultraviolet-C (UVC) radiation tolerant bacteria, named NM1 and NM3 strains, were isolated from the industrial waste and soil that identified by the molecular analysis. Survival assay of irradiated bacteria was performed by plate counting and flow cytometry (by a fluorescent dye, Rhodamin 123). Also, hydrogen peroxide tolerance of the isolated strains was analyzed by turbidimetric microplate technique. The 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging assay and EC50 values in reducing power were measured to evaluate antioxidant activity and reductive power of their methanol extracted pigments. Phylogenetic analysis based on 16S rRNA gene sequencing indicated that the NM1 and NM3 strains belonged to Microbacterium esteraromaticum and Dietzia schimae with 99% identity, respectively. Both of them showed much high resistance to 15 and 20 J/cm2 UVC irradiation (254nm). Visible spectra of their methanolic extracted pigments were considered identical with λmax at 413, 439 and 468nm for Microbacterium NM1 and λmax at 451nm for Dietzia NM3. EC50 values in reducing power were 35.26 and 36.13 µg/ml for pigments of NM1 and NM3 strains, respectively. Whereas scavenging abilities of DPPH radicals were 3.42 and 1.58 mg/ml for pigments of NM1 and NM3 strains, respectively. Based on the results, the pigments of isolated UVC tolerant bacteria displayed strong antioxidant activity. These bacteria may be a good source for antioxidative-related functional foods and the pharmaceutical industry.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"1 1","pages":"159-170"},"PeriodicalIF":0.0,"publicationDate":"2017-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83114915","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}

引用次数: 8

Optimization for high level expression of cold and pH tolerant amylase in a newly isolated Pedobacter sp. through Response Surface Methodology 响应面法优化新分离的耐冷耐pH淀粉酶的高表达

Progress in Biological Sciences Pub Date : 2017-09-18 DOI: 10.22059/PBS.2016.590016

Razie Ghazi-Birjandi, Bahar Shahnavaz, Maryam Mahjoubin-Tehran

{"title":"Optimization for high level expression of cold and pH tolerant amylase in a newly isolated Pedobacter sp. through Response Surface Methodology","authors":"Razie Ghazi-Birjandi, Bahar Shahnavaz, Maryam Mahjoubin-Tehran","doi":"10.22059/PBS.2016.590016","DOIUrl":"https://doi.org/10.22059/PBS.2016.590016","url":null,"abstract":"Amylase is one of the most widely used enzymes in the industry. Cold environments are the most ubiquitous environments in the world that have been occupied by cold tolerant microorganisms. The enzymes of these microorganisms have a wide range of applications in various areas of biotechnology. The aim of this study was to isolate cold-active amylase producing bacteria. A total of 64 cold-tolerant bacteria producing amylase were isolated from Binaloud Mountain soil, Iran. An isolate (Pedobacter sp. BTR84) registered under accession number KM459538 with the highest enzyme productivity was selected for production optimization. The production of amylase was evaluated via One-factor-at-a-timemethod and RSM (Response Surface Methodology). The enzyme production was optimized at 20°C, pH 9, starch 2% (w/v), and inoculation level 3% (v/v) by One-factor-at-a-timemethod. Then, in order to investigate the interaction between these variables and determine the final optimal conditions, optimization was carried out through the response surface methodology (RSM). Four variables were evaluated at three levels using the Box-Behnken design. Starch concentration and inoculation level variables had a significant effect on amylase production (p<0.05). The final optimum conditions for amylase production in the isolates were temperature 25°C, pH 7, starch concentration 2.5% (w/v), and inoculation level 3% (v/v). The current study suggests that Psychrotrophic local bacteria are capable of producing extracellular hydrolytic enzymes that have a good potential to be applied in biotechnological industries.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"55 1","pages":"139-150"},"PeriodicalIF":0.0,"publicationDate":"2017-09-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83676931","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}

引用次数: 0

A generalization of Profile Hidden Markov Model (PHMM) using one-by-one dependency between sequences 利用序列间一一依赖关系的轮廓隐马尔可夫模型(PHMM)的推广

Progress in Biological Sciences Pub Date : 2017-09-18 DOI: 10.22059/PBS.2016.590014

Vahid Rezaei Tabar, H. Pezeshk

引用次数: 0

Effect of salinity on some physiological and biochemical responses in the cyanobacterium Synechococcus elongatus 盐度对长聚藻蓝细菌某些生理生化反应的影响

Progress in Biological Sciences Pub Date : 2017-06-01 DOI: 10.22059/PBS.2018.230997.1260

M. Rezayian, V. Niknam, M. Faramarzi

{"title":"Effect of salinity on some physiological and biochemical responses in the cyanobacterium Synechococcus elongatus","authors":"M. Rezayian, V. Niknam, M. Faramarzi","doi":"10.22059/PBS.2018.230997.1260","DOIUrl":"https://doi.org/10.22059/PBS.2018.230997.1260","url":null,"abstract":"In this study, some physiological and biochemical responses of Synechococcus elongatus to salt stress were investigated. The cyanobactrium was grown in BG-11 medium under different concentrations of NaCl (0, 0.5, 1 M). The results indicated that the growth of S. elongatus was significantly inhibited under salt stress on days 5, 9 and 12. Protein content increased in S. elongatus on day 12 in presence of salt. Salinity induced proline accumulation at 1 M NaCl on day 12 and caused a significant enhance in hydrogen peroxide content on day 5. Catalase (CAT) activity continuously increased on day 5. An increasing trend in polyphenol oxidase (PPO) activity was indicated on days 5 and 9. Superoxide dismutase (SOD) activity gradually induced with increasing NaCl concentrations on day 5. Salt stress decreased chlorophyll content compared to that of control in three stages of growth, and carotenoid content declined on days 9 and 12. The contents of phycobiliprotein (PBP), phycoerythrin (PE) and phycocyanin (PC) enhanced significantly under different NaCl concentrations on days 5 and 9. These results show that S. elongatus has limited adaptative potential to salinity, and the optimum medium for its culture should not bear NaCl even at a moderate level, if production of carotenoids is aimed.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"111 1","pages":"67-77"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84160164","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}

引用次数: 2

Characterization of native ethanol producing Zymomonas spp. isolated from natural environments in Iran 从伊朗自然环境中分离的产乙醇酵母菌的特性

Progress in Biological Sciences Pub Date : 2017-06-01 DOI: 10.22059/PBS.2018.239475.1276

M. Mohseni, Hoda Ebrahimi

{"title":"Characterization of native ethanol producing Zymomonas spp. isolated from natural environments in Iran","authors":"M. Mohseni, Hoda Ebrahimi","doi":"10.22059/PBS.2018.239475.1276","DOIUrl":"https://doi.org/10.22059/PBS.2018.239475.1276","url":null,"abstract":"Ethanol is renewable and safe fuel and it is mainly produced based on microbial fermentation. The present study aims to isolate and identify ethanol producing Zymomonas spp. from natural environments with characterization, optimization and evaluation of their ethanol productivity. Samples were screened for ethanol producing bacteria on RM medium. Ethanol producing isolates were selected for characterization. In addition, bacterial growth and ethanol production conditions were optimized based on pH, temperature, agitation, time and initial glucose concentration. The morphological, physiological and molecular characterization was investigated for identification of the isolates. Of all the 10 ethanol producing isolates, two highest producers were selected for further studies. Both of them were motile and catalase positive but failed to hydrolyze gelatin and produce H2S. Among them, ZYM6 was exhibited highest ethanol yield 6.28 gL-1 with optimum pH 6 and growth temperature 30˚C. In addition, ZYM6 and ZYM10 were exhibited highest ethanol yield 15.00 gL-1 and 12.00 gL-1 with xylose and tryptophan, respectively. Thus the optimum condition for ethanol production was a medium composed of pH 6, growth temperature 30-35 ˚C for 24-48 hours and xylose and tryptophan as carbon and nitrogen sources. The results of morphological and physiological characteristics showed that ZYM6 and ZYM10 were belonging to Zymomonas. Moreover, 16S rRNA sequencing and phylogenetic analyses exhibited that ZYM6 and ZYM10 were similar to Zymomonas mobilis with 99% homology. These native Zymomonas spp. can produce ethanol with high yield. In addition, xylose is a feasible feedstock for ethanol fermentation with high efficiency using these isolates.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"56 2 1","pages":"21-30"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90097863","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}

引用次数: 0

Magnetic nanoparticles: a promising component in RNA extraction process 磁性纳米颗粒:RNA提取过程中有前景的组分

Progress in Biological Sciences Pub Date : 2017-06-01 DOI: 10.22059/PBS.2018.244649.1285

F. Khatami, F. Najafi, F. Yari, R. Khavari-Nejad

{"title":"Magnetic nanoparticles: a promising component in RNA extraction process","authors":"F. Khatami, F. Najafi, F. Yari, R. Khavari-Nejad","doi":"10.22059/PBS.2018.244649.1285","DOIUrl":"https://doi.org/10.22059/PBS.2018.244649.1285","url":null,"abstract":"Magnetic nanoparticles separation technology is a method for quick and easy extraction biomolecules such as proteins, DNA and RNA. The present work describes total RNA isolation procedure from transformed rose petals in our laboratory using magnetic nanoparticles as a solid phase absorbant. Petals are the main sources of secondary metabolites, i.e. carotenoids, anthocyanins, flavonoids and phenolic compounds, which interfere with nucleic acids isolation. The physical basis of this technique relies on the interaction with external magnetic fields, and therefore the magnetic moment of the particles and nucleic acid plays the main role. The present work showed that, quantity and quality of extracted RNA by magnetic procedure were higher than that of the conventional method in all tested samples. Additionally, preparing RNA samples, take less than 50 minutes as against several hours taken by common protocols. Furthermore, successful RNA isolation was found to follow-up reactions such as PCR amplification and restriction endonuclease digestion especially in colorful petals. The solid-phase extraction method for the isolation of RNA in this research offers several advantages over the conventional methods using phenol-chloroform extraction: it is convenient to use, rapid, time-saving and reducing the consumption of toxic organic solvents; therefore, making it more amenable to automation.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"57 1","pages":"47-52"},"PeriodicalIF":0.0,"publicationDate":"2017-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83638442","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}

引用次数: 2