Progress in Biological Sciences最新文献_第8页

Enhancing the effect of soybean oil refinery byproducts on erythromycin production by Saccharopolyspora erythraea 提高大豆油精制副产物对红糖多孢子菌生产红霉素的影响

Progress in Biological Sciences Pub Date : 2015-06-01 DOI: 10.22059/PBS.2015.53970

J. Hamedi, M. Rezadehbashi, M. Bahmaei

引用次数: 3

Bioactivity of endophytic bacteria and yeasts isolated from Thymus 胸腺内生细菌和酵母菌的生物活性

Progress in Biological Sciences Pub Date : 2015-06-01 DOI: 10.22059/PBS.2015.53953

S. Masumi, S. Mirzaei, D. Zafari, R. Kalvandi, A. Keshtkar

{"title":"Bioactivity of endophytic bacteria and yeasts isolated from Thymus","authors":"S. Masumi, S. Mirzaei, D. Zafari, R. Kalvandi, A. Keshtkar","doi":"10.22059/PBS.2015.53953","DOIUrl":"https://doi.org/10.22059/PBS.2015.53953","url":null,"abstract":"Endophytes are important resources of bioactive compounds and due to their potential in theproduction of secondary metabolites, they are regarded as a potential reservoir ofbiotechnological applications. In this study, the bioactivity of bacteria and yeasts endophytesresiding in Thymus sp. was evaluated. During April to October 2011, symptomless and healthytissues of Thymus sp. were collected. A total of 23 strains of endophytic bacteria and 6 yeastswere isolated. The bio-effects of the endophytes were studied on Botrytis cinerea and plantpathogenic bacteria Xanthomonas arboricola pv. juglandis and Streptomyces scabies andhuman pathogens Escherichia coli ATCC 25922 and Staphylococcus aureus ATCC. Growthinhibition mechanisms of the endophytes against B. cinerea were evaluated and it seems that theantimicrobial effects of bacterial endophytes are related to the production of protease enzyme,hydrogen cyanide and volatile compounds. Bacterial strains were identified as Bacillus,Pseudomonas and Xanthomonas of which Bacillus was the predominant isolate. For the firsttime, Bacillus is reported from Thymus eriocalyx, T. lancifolius, T. fallax, T. kotschyanus and T.vulgaris and Pseudomonas and Xanthomonas as endophytic bacteria from Thymus.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"41 1","pages":"33-42"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84754019","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

Isolation and identification of new beneficial bacterial strains from rhizosphere of Citrus sinensis orchards 柑桔根际有益菌的分离与鉴定

Progress in Biological Sciences Pub Date : 2015-06-01 DOI: 10.22059/PBS.2015.53957

M. Ramezani, A. R. Madvar, M. Khaleghi, R. Hemmati

{"title":"Isolation and identification of new beneficial bacterial strains from rhizosphere of Citrus sinensis orchards","authors":"M. Ramezani, A. R. Madvar, M. Khaleghi, R. Hemmati","doi":"10.22059/PBS.2015.53957","DOIUrl":"https://doi.org/10.22059/PBS.2015.53957","url":null,"abstract":"The rhizosphere is the area around the root of a plant occupied by a unique population of usefulbacteria known as plant growth promoting rhizobacteria (PGPR). In this study, the isolation andidentification of rhizobacteria from orange (Citrus sinensis) orchards using 16S rRNA gene, as well asbiological and biochemical assays is reported. Analysis of 16S rRNA gene was confirmed bybiological and biochemical assays and showed that the isolated bacteria belong to the genera Bacilli,Enterobacter and Pseudomonas. Accordingly, Enterobacterkobei MR-R2, Pseudomonas putida MRR5,Bacillus cereus MR-R, Bacillus thuringiensis MR-R1 and Bacillus mycoides MR-R4 wereidentified and registered in GenBank. The results of phosphate solubilization testing revealed that themaximum rate of phosphate solubilization was observed for B. thuringiensis, and E. kobei; however,B. cereus, B. mycoides, and P. putida indicated the least activity. It can be concluded that the isolatedstrains (especially B. thuringiensis) are newly identified phosphate solubilizing bacterial strains,among which B. thuringiensis can be used for growth promotion of orange trees.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"25 1","pages":"75-84"},"PeriodicalIF":0.0,"publicationDate":"2015-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81181830","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: 1

Automatic classification of highly related Malate Dehydrogenase and L-Lactate Dehydrogenase based on 3D-pattern of active sites 基于活性位点3d模式的高度相关苹果酸脱氢酶和l -乳酸脱氢酶的自动分类

Progress in Biological Sciences Pub Date : 2014-12-01 DOI: 10.22059/PBS.2014.52303

Amir Rahimi, A. Madadkar-Sobhani, Rouzbeh Touserkani, B. Goliaei

{"title":"Automatic classification of highly related Malate Dehydrogenase and L-Lactate Dehydrogenase based on 3D-pattern of active sites","authors":"Amir Rahimi, A. Madadkar-Sobhani, Rouzbeh Touserkani, B. Goliaei","doi":"10.22059/PBS.2014.52303","DOIUrl":"https://doi.org/10.22059/PBS.2014.52303","url":null,"abstract":"Accurate protein function prediction is an important subject in bioinformatics, especially wheresequentially and structurally similar proteins have different functions. Malate dehydrogenaseand L-lactate dehydrogenase are two evolutionary related enzymes, which exist in a widevariety of organisms. These enzymes are sequentially and structurally similar and sharecommon active site residues, spatial patterns and molecular mechanisms. Here, we studyvarious features of the active site cavity of 229 PDB chain entries and try to classify themautomatically by various classifiers including the support vector machine, k nearest neighbourand random forest methods. The results show that the support vector machine yields the highestpredictive performance among mentioned classifiers. Despite very close and conserved patternsamong Malate dehydrogenases and L-lactate dehydrogenases, the SVM predicts the functionefficiently and achieves 0.973 Matthew’s correlation coefficient and 0.987 F-score. The sameapproach can be used in other enzyme families for automatic discrimination betweenhomologous enzymes with common active site elements, however, acting on differentsubstrates.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"34 1","pages":"245-260"},"PeriodicalIF":0.0,"publicationDate":"2014-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78167769","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 QUANTITATIVE COMPETITOR PCR ASSAY TO DETECT GENETICALLY MODIFIED ROUNDUP-READY SOYBEANS IN COMMERCIALLY SOLD FOODS IN IRAN 在伊朗商业销售的食品中检测转基因抗草甘膦大豆的定量竞争者PCR测定

Progress in Biological Sciences Pub Date : 2014-12-01 DOI: 10.22059/PBS.2014.52302

E. Ghazizadeh, A. Mousavi, Faranak Hadi

引用次数: 1

Flavonoid Patterns and their Diversity in ten Stachys L. (Lamiaceae) Species from Iran 伊朗10种石竹属植物黄酮类化合物的分布及其多样性

Progress in Biological Sciences Pub Date : 2014-12-01 DOI: 10.22059/PBS.2014.52300

N. Kharazian, M. Mohammadi

{"title":"Flavonoid Patterns and their Diversity in ten Stachys L. (Lamiaceae) Species from Iran","authors":"N. Kharazian, M. Mohammadi","doi":"10.22059/PBS.2014.52300","DOIUrl":"https://doi.org/10.22059/PBS.2014.52300","url":null,"abstract":"Stachys genus with medicinal properties and high polymorphic features has been considered one of the largest genera of Lamiaceae. The aim of this study was to determine the flavonoid pattern variations and flavonoid groups in ten Stachys species belonging to two sections; Fragilicaulis, and Aucheriana. The studied species were collected from natural habitats in Iran and analysed for their flavonoid constituents using thin layer chromatography with silica gel. The purification of the flavonoid compounds of each species was carried out using column chromatography with sephadex LH20. The identification of flavonoid class was confirmed by spectral data. In order to study the flavonoid variations, cluster analysis was used with SPSS ver.20 software. The results of this study showed that the highest variations were found in Stachys pilifera Benth., Stachys aucheri Benth., Stachys ballotiformis Vatke and Stachys benthamiana Boiss. Based on the results, six flavonoid classes were identified. Most of the flavonoid classes were found to be flavones. The flavones and isoflavones were observed in section Fragilicaulis and flavanones, flavonols, isoflavones, dihydroflavonol, chalcones and flavones were in section Aucheriana. It can be concluded that the flavonoid compounds are appropriate markers in chemotaxonomic studies of the Stachys genus.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"1003 1","pages":"203-218"},"PeriodicalIF":0.0,"publicationDate":"2014-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"77152055","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

Alterations in antioxidant defence in the early life stages of silver carp, Hypophthalmichthys molitrix 鲢鱼生命早期抗氧化防御的变化

Progress in Biological Sciences Pub Date : 2014-12-01 DOI: 10.22059/PBS.2014.52298

Fatemeh Liravi, A. Salati, F. Asadi, Hossein Pasha-Zanoosi

引用次数: 6

Silicon alleviates salt stress in pistachio plants 硅减轻了开心果植物的盐胁迫

Progress in Biological Sciences Pub Date : 2014-12-01 DOI: 10.22059/PBS.2014.52299

G. Habibi, Fahimeh Norouzi, R. Hajiboland

{"title":"Silicon alleviates salt stress in pistachio plants","authors":"G. Habibi, Fahimeh Norouzi, R. Hajiboland","doi":"10.22059/PBS.2014.52299","DOIUrl":"https://doi.org/10.22059/PBS.2014.52299","url":null,"abstract":"In this work, the effects of silicon (Si) supplementation were studied in pistachio (Pistacia veraL. cv Ahmadaghaii) plants exposed to high salinity stress. Plants were grown in pots undercontrol and salt (EC=15 dS m-1) conditions without or with Si treatment (0.35 g Na2SiO3 Kg-1soil) under field conditions. Salt stress reduced the plants’ growth significantly in both –Si and+Si plants; however, Si-supplied plants had a higher root and shoot dry weight as compared tothose without Si supply under salinity conditions. Salt stress caused a significant reduction ofleaf photochemical activities; however, Si application ameliorated these effects. The reductionof the net CO2 assimilation rate under salinity stress was alleviated by Si application,accompanied by an increase in water-use-efficiency. The concentration of Na in the leaves androots was significantly reduced by Si, while root K and leaf Ca concentrations were higher inSi-treated plants under salt stress compared with –Si ones. The activity of antioxidativeenzymes increased under salt stress and Si application caused a further increase, beingsignificant for superoxide dismutase (SOD). Salt stress induced membrane damage, as wasindicated by a higher malondialdehyde (MDA) concentration. In Si-supplemented plants,however, the MDA amount did not increase under salt stress. The results indicated that the Simediatedalleviation of salt stress in pistachio plants is related to higher photosynthesis andwater-use efficiency, a reduction of Na uptake and transport, and the stimulation of the plant’santioxidative defence capacity.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"8 1","pages":"189-202"},"PeriodicalIF":0.0,"publicationDate":"2014-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84604152","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: 16

Demystifying EPR: A Rookie Guide to the Application of Electron Paramagnetic Resonance Spectroscopy on Biomolecules 揭秘EPR:电子顺磁共振波谱在生物分子上应用的新手指南

Progress in Biological Sciences Pub Date : 2014-12-01 DOI: 10.22059/PBS.2014.52305

Yaser NejatyJahromy, E. Schubert

{"title":"Demystifying EPR: A Rookie Guide to the Application of Electron Paramagnetic Resonance Spectroscopy on Biomolecules","authors":"Yaser NejatyJahromy, E. Schubert","doi":"10.22059/PBS.2014.52305","DOIUrl":"https://doi.org/10.22059/PBS.2014.52305","url":null,"abstract":"Electron Paramagnetic Resonance (EPR) spectroscopy, also known as Electron Spin Resonance(ESR) especially among physicists, is a strong and versatile spectroscopic method forinvestigation of paramagnetic systems, i.e. systems like free radicals and most transition metalions, which have unpaired electrons. The sensitivity and selectivity of EPR are notable andintriguing as compared to other spectroscopic methods and approaches. As a qualitative method,EPR can detect species down to the nanomolar range. On the other hand, the specificity of themethod stems from spectral features which directly depend on the types, distances, and relativeorientations of the atoms in the neighborhood of the electron spin centers. In addition tostructural information, EPR can be used to elucidate time dependent behavior of the studiedsystem and it is applicable to systems of different size, ranging from small molecules tomacromolecules. The following short review of general EPR methods is intended for anaudience with little prior knowledge about EPR. It includes examples of suitable representativesystems, techniques for the study of short lived paramagnetic species and even diamagneticmolecules, and introduces the reader to tools necessary for making sense of the spectra. Thispaper focuses only on continuous wave (cw) EPR and does not elaborate on the more advancedpulsed EPR methods.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"33 1","pages":"133-152"},"PeriodicalIF":0.0,"publicationDate":"2014-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86233389","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

Apoptotic protease-activating factor 1 (Apaf-1) as a liable gene for spontaneous mutations in vitro 凋亡蛋白酶激活因子1 (Apaf-1)作为体外自发突变的易感基因

Progress in Biological Sciences Pub Date : 2014-12-01 DOI: 10.22059/PBS.2014.52304

T. Azad, Amin Tashakor, M. Ghahremani, R. Hemmati, F. Ataei, S. Hosseinkhani

{"title":"Apoptotic protease-activating factor 1 (Apaf-1) as a liable gene for spontaneous mutations in vitro","authors":"T. Azad, Amin Tashakor, M. Ghahremani, R. Hemmati, F. Ataei, S. Hosseinkhani","doi":"10.22059/PBS.2014.52304","DOIUrl":"https://doi.org/10.22059/PBS.2014.52304","url":null,"abstract":"The apoptotic protease-activating factor 1 (Apaf-1) receives the death signal in the intrinsic ormitochondrial pathway of apoptosis. Upon the releasing of cytochrome c from theintermembrane space of mitochondria and binding to Apaf-1 molecules, a heptamericapoptosome complex is formed and triggers the downstream cascade of caspases. Here, for thefirst time we present spontaneous mutations and recombinations of the Apaf-1 gene and itsneighbouring sequences. We sequence 48 colonies containing pcDNA3.1 vector withNluc/Apaf1 and Cluc/Apaf1 obtained through the quick-change site-directed mutagenesismethod, transforming to DH5-α and XL10-Gold at two temperatures, 18 and 37oC. In 21 ofthese cases, we found 38 different mutations. Our data suggest that there is a direct relationshipbetween bacterial incubation temperatures and the number of unwanted spontaneous mutations.During our experiment we found that the Apaf-1 gene is much less susceptible to spontaneousmutations when it is transformed into XL10-Gold at 18 oC . In contrast, a large number ofspontaneous mutations were found when the gene of interest transformed into DH5α at 37oC .","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"93 1","pages":"261-273"},"PeriodicalIF":0.0,"publicationDate":"2014-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"81683280","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: 1