Progress in Biological Sciences最新文献_第5页

Identification of Alzheimer disease-relevant genes using a novel hybrid method 用一种新的杂交方法鉴定阿尔茨海默病相关基因

Progress in Biological Sciences Pub Date : 2016-06-01 DOI: 10.22059/PBS.2016.59006

Seyyedhassan Paylakhi, Seyedeh Zahra Paylakhi, S. Ozgoli

{"title":"Identification of Alzheimer disease-relevant genes using a novel hybrid method","authors":"Seyyedhassan Paylakhi, Seyedeh Zahra Paylakhi, S. Ozgoli","doi":"10.22059/PBS.2016.59006","DOIUrl":"https://doi.org/10.22059/PBS.2016.59006","url":null,"abstract":"Identifying genes underlying complex diseases/traits that generally involve multiple etiological mechanisms and contributing genes is difficult. Although microarray technology has enabled researchers to investigate gene expression changes, but identifying pathobiologically relevant genes remains a challenge. To address this challenge, we apply a new method for selecting the disease-relevant genes from a published microarray dataset. The approach is comprised of combination of fisher criteria, SAM (Significance Analysis for Microarrays), and GA/SVM (Genetic Algorithm/ Support Vector Machine). To get rid of noisy and redundant genes in high dimensional microarray data, the Fisher method is used. SAM technique is utilized and different subsets of highly informative genes are selected by GA/SVM which uses different training sets. The final subset, highly informative genes, is achieved by analyzing the number of times each gene occurs in the different gene subsets. The proposed method was tested on microarray data of Alzheimer’s disease (AD) and the biological significance of identified genes was evaluated, and the results were compared with those of previous studies. The results indicate that the proposed method has a good selection and classification performance, which can produce 94.55 of classification accuracy by use of only 44 genes. From biological point of view, at least 24 (55%) of these genes are Alzheimer associated genes. Analysis of these genes by GO and KEGG led to identification of AD-related terms and pathways. These genes can act as predictors of the disease as well as a mean to find new candidate genes.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"44 1","pages":"37-46"},"PeriodicalIF":0.0,"publicationDate":"2016-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76772845","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

Male and female gametophyte development in Achillea tenuifolia (Asteraceae) 菖蒲雌雄配子体发育的研究

Progress in Biological Sciences Pub Date : 2016-06-01 DOI: 10.22059/PBS.2016.59011

A. Chehregani, H. Salehi

{"title":"Male and female gametophyte development in Achillea tenuifolia (Asteraceae)","authors":"A. Chehregani, H. Salehi","doi":"10.22059/PBS.2016.59011","DOIUrl":"https://doi.org/10.22059/PBS.2016.59011","url":null,"abstract":"The anther, pollen and ovule development in Achillea tenuifolia were studied with a bright field microscopy. Results showed that the anther is of tetrasporangiate type and the anther wall is composed by four layers: an epidermis, an endothecium, one middle layer and a tapetum layer. Tapetum is of secretory type and its cells showed polyploidy. Pollen tetrads were tetrahedral, microspores were very irregular and contained large amounts of starch at the time of dispersion. Pollen grains were generally tricolporate, and in some cases were tetracolporate or even pentacolporate with spines on surface. The size of the pollen grains varied and ranging from 18-42.5 μm at the polar axis and from 16.5-35.5 μm at the equatorial axis. Ovule is anatropous, unitegmic and tenuiucellate. The archesporium may consist of one or more archeosporial cells, but only one of them undergoes meiosis, forming a linear or T-shaped tetrad. A 7-celled embryo sac is formed corresponding to the Polygonum type. Embryo sac is very tiny at the beginning of its development, its size was increased considerably at late growth stages. The relationship between Asteraceae, Calyceraceae and Goodeniaceae are discussed but based on embryological evidence, Goodeniaceae appear to be the putative sister group of Asteraceae. To understand more exact relationships within the order Asterales, embryological studies are recommended.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"80 1","pages":"85-94"},"PeriodicalIF":0.0,"publicationDate":"2016-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"74779112","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

The indumentum of vegetative and reproductive parts of annual Silene L. species (Caryophyllaceae) in Iran 标题伊朗一年生石竹属植物(石竹科)营养和生殖部分的毛被

Progress in Biological Sciences Pub Date : 2016-06-01 DOI: 10.22059/PBS.2016.59013

E. Hoseini, F. Ghahremaninejad, M. Assadi

引用次数: 2

An efficient and simple CTAB based method for total genomic DNA isolation from low amounts of aquatic plants leaves with a high level of secondary metabolites 一种高效、简单的基于CTAB的方法，用于从少量具有高水平次生代谢产物的水生植物叶片中分离总基因组DNA

Progress in Biological Sciences Pub Date : 2016-06-01 DOI: 10.22059/PBS.2016.59012

S. Afsharzadeh, Shabnam Abbasi

{"title":"An efficient and simple CTAB based method for total genomic DNA isolation from low amounts of aquatic plants leaves with a high level of secondary metabolites","authors":"S. Afsharzadeh, Shabnam Abbasi","doi":"10.22059/PBS.2016.59012","DOIUrl":"https://doi.org/10.22059/PBS.2016.59012","url":null,"abstract":"An efficient DNA isolation protocol specifically modified to get pure quality DNA required for molecular studieshas been reported in this paper. Some aquatic plants (Potamogeton spp., Ceratophyllum demersum and Myriophyllum spicatum) were used for the study. The protocol developed will be useful in getting high and pure DNA. Instead of using the available DNA extraction kits, this protocol can be used to get pure quality DNA, freefrom proteins and polysaccharide compounds. The absorbance rate A260/A280 was 1.92 ± 0.069 and A260/A230 was 1.73 by spectrophotometer and NanoDrop machines which showed the sample genomic DNA is pure, free from contaminant proteins and polyphenolics/polysaccharides compound. The highest concentration of DNA was 640 ± 340.58 ng/μl when measured at 260 nm. When we run on agarose gel also, the isolated DNA gave a clear and sharp band. Thus, the DNA does not need any additional purification before proceeding for molecular analysis of the isolated DNA samples. This protocol is very simple and economical which will find wide applications in genomic studies of aquatic plants.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"38 1","pages":"95-106"},"PeriodicalIF":0.0,"publicationDate":"2016-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"76823984","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: 6

A mixed Bayesian/Frequentist approach in sample size determination problem for clinical trials 临床试验样本量确定问题的贝叶斯/频率混合方法

Progress in Biological Sciences Pub Date : 2016-06-01 DOI: 10.22059/PBS.2016.59001

M. Bideli, J. Gittins, H. Pezeshk

{"title":"A mixed Bayesian/Frequentist approach in sample size determination problem for clinical trials","authors":"M. Bideli, J. Gittins, H. Pezeshk","doi":"10.22059/PBS.2016.59001","DOIUrl":"https://doi.org/10.22059/PBS.2016.59001","url":null,"abstract":"In this paper we introduce a stochastic optimization method based ona mixed Bayesian/frequentist approach to a sample size determinationproblem in a clinical trial. The data are assumed to come from a nor-mal distribution for which both the mean and the variance are unknown.In contrast to the usual Bayesian decision theoretic methodology, whichassumes a single decision maker, our method recognizes the existence ofthree decision makers, namely: the company conducting the trial, whichdecides on its size; the regulator, whose approval is necessary for the drugto be licensed for sale; and the public at large, who determine ultimateusage. Moreover, we model the subsequent usage by plausible assumptionsfor actual behaviour. A Monte Carlo Markov Chain is applied to nd themaximum expected utility of conducting the trial.Sample size determination problem is an important task in the planning oftrials. The problem may be formulated formally in statistical terms. Themost frequently used methods are based on the required size, and power of thetrial for a specifed treatment efect Several authors haverecognized the value of using prior distributions rather than point estimatesin sample size calculations.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"93 1","pages":"1-10"},"PeriodicalIF":0.0,"publicationDate":"2016-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79784456","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

Plasma can reduce Staphylococcus epidermidis biofilm formation on medical polymers 血浆可减少医用聚合物上表皮葡萄球菌生物膜的形成

Progress in Biological Sciences Pub Date : 2016-06-01 DOI: 10.22059/PBS.2016.59005

G. Zarrini, Leila Taheran, M. Zakerhamidi, S. Khorram

{"title":"Plasma can reduce Staphylococcus epidermidis biofilm formation on medical polymers","authors":"G. Zarrini, Leila Taheran, M. Zakerhamidi, S. Khorram","doi":"10.22059/PBS.2016.59005","DOIUrl":"https://doi.org/10.22059/PBS.2016.59005","url":null,"abstract":"Medical polymers, such as urinary catheters are widely used biomaterials. One of the main problem for using the urinary catheters is biofilm formation on their surface, when they are used in a long time in the body. Virulence and pathogenicity of Staphylococcus epidermidis is often enhanced when growing as a biofilm. Many techniques have been presented to reduce the biofilm formation by surface modification. One of the most revolutionary techniques allowing such surface modifications is the plasma surface modification. In this work, plasma effects on S. epidermidis biofilm formation on urinary catheter surface have been investigated. Plasma was produced in a Pyrex glass tube containing nitrogen with pressure 1.6×10-1 Torr for plasma treatment of a catheter surface. Discharge voltage was about 1.2 kV and current was 150 mA. Each set of plasma treated catheter samples was inoculated by cultivation of S. epidermidis on 50 ml of Tryptic soy broth medium in the shaking incubator for 48 h at 37°C and 100 rpm. Then, amount of biofilm formation on the surface of polymer were assessed by crystal violet binding assay and sonication method. The results of these experiments indicated reduced biofilm formation on the modified surface around 50-60% compared to non-modified surface. This study shows that plasma surface modification can be used to reduce biofilm formation on medical polymers such as urinary catheter.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"45 1","pages":"31-36"},"PeriodicalIF":0.0,"publicationDate":"2016-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85684509","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

Vasodilatory effects of nitric oxide, hydrogen sulfide and sulfur dioxide in rats: Time-dependent interaction study 一氧化氮、硫化氢和二氧化硫对大鼠血管的舒张作用:时间依赖性相互作用研究

Progress in Biological Sciences Pub Date : 2016-06-01 DOI: 10.22059/PBS.2016.59004

Abbas Salihi, Mudhir Shekha, Omar A. M. Al-Habib

{"title":"Vasodilatory effects of nitric oxide, hydrogen sulfide and sulfur dioxide in rats: Time-dependent interaction study","authors":"Abbas Salihi, Mudhir Shekha, Omar A. M. Al-Habib","doi":"10.22059/PBS.2016.59004","DOIUrl":"https://doi.org/10.22059/PBS.2016.59004","url":null,"abstract":"The vasodilator response of nitric oxide (NO), hydrogen sulfide (H2S) and sulfur dioxide (SO2) were studied todetermine the significance of the actions and interactions of these gasotransmitters for controlling aortic tone in rats. The isometric tension of five separate sets of experiments was recorded. Sodium nitroprusside (SNP; NO donor), sodium disulphide (Na2S; H2S donor), SO2 derivatives and their paired combinations were added to phenylephrine (PE)-induced contraction during the peak value. Then maximal relaxation rate was calculated four times at 5 min intervals. Tetraethylammonium (TEA) and Glibenclamide (GLIB) were applied for investigating the molecular mechanism of the gasses. While, in a separate set of experiments, we used either L-Arginine (L-Arg), L-Cysteine (L-Cyst) or L-nitroarginine methyl ester (L-NAME) before applying gasotransmitters. Highest and prolonged relaxation rate were recorded when SNP was combined with SO2. The combination of Na2S and SO2-induced vasorelaxation was blocked by TEA and GLIB pretreatments. L-Cyst decreased relaxation compared to SNP and vice versa to SO2 induced vasorelaxation. L-Arg markedly attenuated relaxation responses of Na2S and SO2 derivatives. Also, L-NAME delayed relaxation compared to Na2S and SO2. These results suggest that exogenous paired combinations of H2S, NO and SO2 will enhance and elongate the rate of aortic relaxation. Meanwhile, preincubation of aortic rings with precursors attenuate the dilatory effects of exogenous studied gases.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"40 1","pages":"19-30"},"PeriodicalIF":0.0,"publicationDate":"2016-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"84112247","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

Nano-Metal oxides induced sulforaphane production and peroxidase activity in seedlings of Lepidium draba (Brassicaceae) 纳米金属氧化物对大白菜幼苗萝卜硫素产量和过氧化物酶活性的影响

Progress in Biological Sciences Pub Date : 2016-06-01 DOI: 10.22059/PBS.2016.59010

A. Riahi-Madvar, M. Aminizadeh, Mehdi Mohammadi

{"title":"Nano-Metal oxides induced sulforaphane production and peroxidase activity in seedlings of Lepidium draba (Brassicaceae)","authors":"A. Riahi-Madvar, M. Aminizadeh, Mehdi Mohammadi","doi":"10.22059/PBS.2016.59010","DOIUrl":"https://doi.org/10.22059/PBS.2016.59010","url":null,"abstract":"Effects of different concentrations [0, 1, 5, 10, 20 and 40 mgL-1] of Fe3O4 and CuO nano-particles (nFe3O4 and nCuO) were investigated on sulforaphane (SFN) production level in 7-day-old seedlings of Lepidium draba at different time intervals (8 and 16 hrs). According to the results, the influence of the particles on SFN contentdepends on nano-particle (NP) concentrations, time of treatment as well as chemical nature of NPs. The SFN content was significantly increased in treated seedlings with 5 mgL-1nCuO and all nFe3O4 concentrations as well as nFe3O4-treated callus after 8 hrs. However, by the increasing treatment time to 16 hrs, no significant changes on the SFN content were seen compared to the control. Furthermore, activity of peroxidase was also significantly promoted in treatment with both NPs (especially at higher concentrations) after 8 hrs and drastically decreased after 16 hrs. On the other hand, seed germination as well as the root and shoot length (except root length in treatment with nFe3O4) decreased compared to the control when seed germinated and plant growth in presence of both NPs for 7 days. Totally, these observations can be attributed to induce oxidative stress by NPs as a subsequence of their uptake by the plant. The increment in production of the phytochemicals through nano-metals treatment (nano-elicitation), opens an opportunity for induction of beneficial phytochemical content.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"24 3 1","pages":"75-83"},"PeriodicalIF":0.0,"publicationDate":"2016-06-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83159705","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: 6

Characteristics of Saccharomyces cerevisiae isolated from fruits and humus: Their suitability for bread making 从水果和腐殖质中分离的酿酒酵母的特性及其在面包制作中的适用性

Progress in Biological Sciences Pub Date : 2016-06-01 DOI: 10.22059/PBS.2016.59008

N. Komatsuzaki

引用次数: 4

Effects of soil conductivity on properties of saffron corms and in vitro production of its style explants 土壤电导率对藏红花球茎性状及花柱外植体离体生产的影响

Progress in Biological Sciences Pub Date : 2015-07-01 DOI: 10.22059/PBS.2015.56044

S. Mashayekhi, M. H. Namin

{"title":"Effects of soil conductivity on properties of saffron corms and in vitro production of its style explants","authors":"S. Mashayekhi, M. H. Namin","doi":"10.22059/PBS.2015.56044","DOIUrl":"https://doi.org/10.22059/PBS.2015.56044","url":null,"abstract":"Saffron is the dried stigmas of Crocus sativus L., a member of the Iridaceae family which ispropagated by means of corms. Corms are faced with many stresses in soil. Therefore, it isimportant to reduce these stresses and improve the quantity of saffron production. Biotic andabiotic stresses disrupt the metabolic balance of cells; thereby, resulting in accumulation ofreactive oxygen species (ROS) which cause oxidative damage. In this study, the effect of soilelectrical conductivity (EC) on biochemical indicators of corms, the percentages of callusformation and stigma-like structures (SLSs) on calli were investigated. In order to obtain calliand SLSs, immature style explants from floral buds of corms were collected from three regions(Shahroud, Mardabad and Torbat Heydarieh) and used for tissue culture. Style explants wereseparated first from the immature floral buds, then sterilized and used for tissue culture.Biochemical analysis of calli with SLSs including malondialdehyde (MDA) and prolinecontents, antioxidant enzymes activities and polysaccharides and reducing sugars contents wereinvestigated and compared. Moreover, sodium and potassium ions content and EC of soils ofthe three regions were investigated. The results indicated that corms from Shahroud with thehighest level of EC soil showed more imposed stress than that from Torbat Heidariye andMardabad but the calli percentage and number of SLSs of Mardabad’s were higher than those ofthe other two respectively. In this study, a close relationship between soil EC and in vitroproduction of saffron with a short glance on epigenetic modification was postulated.","PeriodicalId":20726,"journal":{"name":"Progress in Biological Sciences","volume":"61 1","pages":"273-286"},"PeriodicalIF":0.0,"publicationDate":"2015-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75976837","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