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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
Pub Date : 2016-06-01 DOI: 10.22059/PBS.2016.59006
Seyyedhassan Paylakhi, Seyedeh Zahra Paylakhi, S. Ozgoli
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.
识别复杂疾病/特征背后的基因通常涉及多种病因机制和致病基因是困难的。虽然微阵列技术使研究人员能够研究基因表达的变化,但识别病理相关基因仍然是一个挑战。为了解决这一挑战,我们采用了一种新的方法从已发表的微阵列数据集中选择疾病相关基因。该方法由fisher准则、SAM(微阵列显著性分析)和GA/SVM(遗传算法/支持向量机)的组合组成。为了去除高维微阵列数据中的噪声和冗余基因,采用Fisher方法。利用SAM技术,采用不同的训练集,通过GA/SVM选择不同的高信息量基因子集。通过分析每个基因在不同基因子集中出现的次数,获得了最后一个子集,即信息量很大的基因。在阿尔茨海默病(Alzheimer’s disease, AD)的微阵列数据上对所提出的方法进行了测试,评估了鉴定基因的生物学意义,并将结果与前人的研究结果进行了比较。结果表明,该方法具有良好的选择和分类性能,仅使用44个基因就能获得94.55%的分类准确率。从生物学角度来看,这些基因中至少有24个(55%)是阿尔茨海默病相关基因。通过GO和KEGG对这些基因进行分析,确定了ad相关的术语和途径。这些基因可以作为疾病的预测因子,也可以作为寻找新的候选基因的手段。
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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
Pub Date : 2016-06-01 DOI: 10.22059/PBS.2016.59011
A. Chehregani, H. Salehi
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.
用明光显微镜研究了细毛阿喀琉叶的花药、花粉和胚珠发育。结果表明,该花药为四聚囊型,花药壁由表皮、内膜、中间层和绒毡层四层组成。绒毡层为分泌型,细胞呈多倍体。花粉四分体呈四面体,小孢子非常不规则,分散时含有大量淀粉。花粉粒一般为三聚体,也有四聚体,甚至五聚体,表面有刺。花粉粒大小变化较大,极轴为18 ~ 42.5 μm,赤道轴为16.5 ~ 35.5 μm。胚珠倒生,单胞和具细苞。古孢子可由一个或多个古孢子细胞组成,但其中只有一个细胞进行减数分裂,形成线形或t形四分体。形成与蓼型相对应的7细胞胚囊。胚囊在发育初期很小,在发育后期增大较大。讨论了菊科、萼花科和菊科之间的关系,但根据胚胎学证据,菊科可能是菊科的姐妹类群。为了更准确地了解星形目之间的关系,建议进行胚胎学研究。
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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
Pub Date : 2016-06-01 DOI: 10.22059/PBS.2016.59013
E. Hoseini, F. Ghahremaninejad, M. Assadi
Large and diverse genera, such as Silene need more reliable morphological traits for the credible identification and delimitation of the species. Despite the fact that the type of indumentum among the species of Silene had been addressed in most available revisions, monographs and floristic studies, the trichome-based features and their adaptational importance have not been investigated explicitly. In the present study, the trichomes of annual species of Silene in Iran are studied. Beside other floral traits and vegetative features, the presence, distribution and mixture of the glandular and eglandular trichomes on stems, leaves, inflorescence axes, pedicels, anthophores, inner and outer surfaces of calyces, petals and styles are proved to be of diagnostic importance in Silene. Indumentum of the inner calyx among the studied species is investigated here for the first time. An identification key is performed mainly based on indumentum features. In addition, a putative trichome-based defense strategy is proposed in the examined species.
大而多样的属,如沉默属,需要更可靠的形态特征来进行可靠的物种鉴定和划界。尽管在现有的大多数修订、专著和区系研究中都讨论了毛被的类型,但毛状体的特征及其适应重要性尚未得到明确的研究。在本研究中,研究了伊朗一年生物种Silene的毛状体。除了其他的花性状和营养特征外,茎、叶、花序轴、花梗、花药、花萼内外表面、花瓣和花柱上腺毛和腺毛的存在、分布和混合也被证明是Silene的诊断价值。本文首次对所研究种内花萼的毛被进行了研究。识别键的执行主要基于文档特征。此外,在研究的物种中提出了一种假定的基于毛状体的防御策略。
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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
Pub Date : 2016-06-01 DOI: 10.22059/PBS.2016.59012
S. Afsharzadeh, Shabnam Abbasi
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.
本文报道了一种有效的DNA分离方案,专门用于获得分子研究所需的纯质量DNA。以几种水生植物为研究对象,分别为马铃薯属植物、长尾角藻属植物和细刺狐尾藻属植物。该方案将有助于获得高纯度的DNA。代替使用现有的DNA提取试剂盒,该方案可用于获得纯质量的DNA,不含蛋白质和多糖化合物。通过分光光度计和NanoDrop仪检测到A260/A280的吸光度为1.92±0.069,A260/A230的吸光度为1.73,表明样品基因组DNA纯度高,不含蛋白质和多酚类/多糖化合物。260 nm处DNA浓度最高,为640±340.58 ng/μl。当我们在琼脂糖凝胶上运行时,分离的DNA呈现出清晰而锐利的条带。因此,在分离的DNA样品进行分子分析之前,DNA不需要任何额外的纯化。该方法简便、经济,在水生植物基因组学研究中具有广泛的应用前景。
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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
Pub Date : 2016-06-01 DOI: 10.22059/PBS.2016.59001
M. Bideli, J. Gittins, H. Pezeshk
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.
本文介绍了一种基于混合贝叶斯/频率的随机优化方法来解决临床试验中样本量的确定问题。假设数据来自均值和方差都未知的正态分布。与通常的贝叶斯决策理论方法(假设只有一个决策者)相反,我们的方法认识到存在三个决策者,即:进行试验的公司,决定其规模;药品销售许可必须经其批准的监管机构;以及决定最终用途的广大公众。此外,我们通过对实际行为的合理假设对后续使用进行建模。应用蒙特卡洛马尔可夫链来确定进行试验的最大期望效用。样本量确定问题是试验计划中的一个重要问题。这个问题可以用统计术语正式表述。最常用的方法是根据所需的大小和特定治疗效果的试验能力。一些作者已经认识到在样本量计算中使用先验分布而不是点估计的价值。
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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
Pub Date : 2016-06-01 DOI: 10.22059/PBS.2016.59005
G. Zarrini, Leila Taheran, M. Zakerhamidi, S. Khorram
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.
医用聚合物,如导尿管是广泛使用的生物材料。导尿管使用的主要问题之一是其表面形成生物膜,当它们在体内长时间使用时。表皮葡萄球菌作为生物膜生长时,其毒力和致病性往往增强。目前已经提出了许多通过表面修饰来减少生物膜形成的技术。允许这种表面修饰的最具革命性的技术之一是等离子体表面修饰。本文研究了血浆对尿导管表面表皮葡萄球菌生物膜形成的影响。等离子体在含有氮气的耐热玻璃管中产生,压力为1.6×10-1 Torr,用于导管表面的等离子体处理。放电电压约1.2 kV,电流为150 mA。每组经血浆处理的导管样品均接种表皮葡萄球菌于50 ml Tryptic大豆肉汁培养基上,在37℃、100 rpm的摇培养箱中培养48 h。然后用结晶紫结合法和超声法测定聚合物表面生物膜的形成量。实验结果表明,与未改性表面相比,改性表面的生物膜形成减少了约50-60%。该研究表明,等离子体表面改性可用于减少医用聚合物(如导尿管)上的生物膜形成。
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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
Pub Date : 2016-06-01 DOI: 10.22059/PBS.2016.59004
Abbas Salihi, Mudhir Shekha, Omar A. M. Al-Habib
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.
研究了一氧化氮(NO)、硫化氢(H2S)和二氧化硫(SO2)的血管扩张反应,以确定这些气体递质在控制大鼠主动脉张力中的作用及其相互作用的意义。记录了五组独立实验的等长张力。硝普钠(SNP;NO供体),二硫化钠(Na2S;在峰值时加入H2S供体、SO2衍生物和它们的配对组合,以引起苯肾上腺素(PE)的收缩。然后每隔5分钟计算4次最大松弛率。采用四乙基铵(TEA)和格列本脲(GLIB)研究了这些气体的分子机理。而在另一组实验中,我们在使用气体递质之前使用了l -精氨酸(L-Arg)、l -半胱氨酸(l -囊肿)或l -硝基精氨酸甲酯(L-NAME)。SNP与SO2联合时,松弛率最高,松弛时间延长。TEA和GLIB预处理可阻断Na2S和so2联合诱导的血管松弛。l -囊肿与SNP相比松弛减少,与SO2诱导的血管松弛相反。l -精氨酸显著减弱了Na2S和SO2衍生物的弛豫响应。与Na2S和SO2相比,L-NAME也延迟了弛豫。这些结果表明,H2S、NO和SO2的外源性配对组合可以增强和延长主动脉舒张速率。同时,带前体的主动脉环预孵育可减弱外源性研究气体的扩张效应。
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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
Pub Date : 2016-06-01 DOI: 10.22059/PBS.2016.59010
A. Riahi-Madvar, M. Aminizadeh, Mehdi Mohammadi
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.
研究了不同浓度[0、1、5、10、20和40 mg / l]的Fe3O4和CuO纳米颗粒(nFe3O4和nCuO)在不同时间间隔(8和16 h)下对7日龄枸杞幼苗萝卜硫素(SFN)产量的影响。结果表明,纳米颗粒对SFN含量的影响取决于纳米颗粒(NP)浓度、处理时间以及纳米颗粒的化学性质。5 mg - 1ncuo和所有浓度的nFe3O4处理幼苗和nFe3O4处理的愈伤组织在8 h后SFN含量显著增加。然而,随着处理时间增加到16小时,与对照组相比,SFN含量没有明显变化。此外,两种NPs处理8小时后过氧化物酶活性也显著提高(特别是在较高浓度下),16小时后活性急剧下降。另一方面,在nFe3O4和nFe3O4处理下,种子萌发和植株生长7 d后,种子萌发和根冠长(除nFe3O4处理的根长外)均低于对照。总的来说,这些观察结果可归因于植物吸收NPs后引起的氧化应激。通过纳米金属处理(纳米激发)增加植物化学物质的产量,为诱导有益的植物化学物质含量提供了机会。
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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
Pub Date : 2016-06-01 DOI: 10.22059/PBS.2016.59008
N. Komatsuzaki
The objectives of this study were to clarify whether the wild yeast isolated from fruits and humus is suitable forbread making. Using colony PCR, assimilation of carbohydrate and 18S rRNA sequencing, seven strains fromamong 70 samples were identified as Saccharomyces cerevisiae. The ethanol and CO2 production by the 10-2 wild yeast strain were highest among the strains. The pH and utilized glucose of all strains were pH 3.00-3.60 and 99.99%, respectively. The total acid content of the 9-3 culture was the highest (82.7 mg/100 ml) among the seven strains. The acetic acid contents of 9-3 and 10-2 cultures were 56.8 mg/100 ml and 56.3 mg/100 ml, respectively. Our finding showed that the 9-3 and 10-2 strain isolated from fruits have abilities of fermentation suitable for bread making.
本研究的目的是阐明从水果和腐殖质中分离的野生酵母是否适合制作面包。通过菌落PCR、碳水化合物同化和18S rRNA测序,从70份样品中鉴定出7株为酿酒酵母菌。10-2野生酵母菌的乙醇和CO2产量最高。所有菌株的pH值为3.00 ~ 3.60,利用葡萄糖值为99.99%。9-3菌株的总酸含量最高,为82.7 mg/100 ml。9-3和10-2培养物乙酸含量分别为56.8 mg/100 ml和56.3 mg/100 ml。结果表明,从水果中分离的9-3和10-2菌株具有适合制作面包的发酵能力。
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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
Pub Date : 2015-07-01 DOI: 10.22059/PBS.2015.56044
S. Mashayekhi, M. H. Namin
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.
藏红花是鸢尾科植物Crocus sativus L.的干柱头,通过球茎繁殖。球茎在土壤中面临许多应力。因此,减少这些压力和提高藏红花产量是很重要的。生物和非生物应激破坏细胞的代谢平衡;从而导致活性氧(ROS)的积累,从而导致氧化损伤。研究了土壤电导率(EC)对愈伤组织生化指标、愈伤组织形成率和柱头样结构(SLSs)的影响。为了获得愈伤组织sls,从shahoud、Mardabad和Torbat Heydarieh三个地区的球茎花蕾中收集未成熟花柱外植体进行组织培养。花柱外植体首先从未成熟的花蕾中分离出来,然后进行灭菌和组织培养。用SLSs对愈伤组织进行生化分析,包括丙二醛(MDA)和脯氨酸含量、抗氧化酶活性、多糖和还原糖含量等。此外,还研究了3个地区土壤的钠、钾离子含量和电导率。结果表明,土壤EC含量最高的沙赫鲁德的球茎受胁迫的程度高于托尔巴特和马尔达巴德,但马尔达巴德的愈伤组织百分比和sls数量分别高于其他两种。本文从表观遗传修饰的角度探讨了土壤EC与藏红花离体生产的密切关系。
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引用次数: 2
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