SNP教学模式在生物模型建构教学中的运用——以《基因是有遗传效应的 DNA 片段》为例

SNP教学模式是大概念统领下的建模-论证教学 活动,师生和生生之间围绕模型建构展开讨论和论证,通过建 模和论证的多次交互和循环,克服了单一论证或建模教学动力 不足的限制。笔者以《基因是有遗传效应的DNA片段》为例, 谈谈自己在生物教学中对SNP教学模式的运用。     

一氧化氮对灵芝多糖产量的影响

采用硝普钠(Sodium nitroprusride,SNP)作为外源一氧化氮(nitric oxide,NO)供体,研究了一氧化氮对深层发酵灵芝胞外多糖和胞内多糖产量的影响。结果表明,0.5 mmol/L SNP处理对灵芝菌丝生长具有明显的促进作用,并且显著提高灵芝胞外多糖和胞内多糖的产量,同时添加SNP和NO清除剂c-PTIO时上述产量增加现象消失;当SNP处理浓度大干4.0 mmol/L时,灵芝菌丝体生物量、灵芝胞外多糖和胞内多糖的产量均呈现下降趋势。     

指向科学思维培养的SNP教学模式的应用

在阐述SNP教学模式的基础上,以苏科版“能量的释放和利用”一节为例,详细介绍了SNP模式的具体应用,旨在探索一种形式新颖、行之有效的培养科学思维能力的方法。     

基于mBagging的随机森林

随机森林是采用Bagging组合方法集成的决策树集合,在数据分类、预测领域应用广泛.Bagging组合方法在机器学习中具有代表性,但对于实际的大数据挖掘仍存在一些不足.mBagging是基于Bagging组合方法的一种改进,具有更高的统计功效、更低的假阳率以及更快的运算速度.采用全基因组SNP仿真数据集的实验表明,基于mBagging的随机森林运算速度明显快于传统的随机森林,且在保证OOB袋外错误率不劣化的前提下,判断风险SNP的准确率得到了提高.     

“SNP”教学模式在高中生物课堂教学中的应用——以《生物膜的流动镶嵌模型》一课为例论证高中生物科学史

"SNP"教学模式是一种在新式教育环境下,随着教育者与教育接受者的需求而衍生的一种教学方法。本文将针对当前高中生物课堂上应用"SNP"教学模式的具体策略展开分析,并且结合当前高中生物科学史的教学内容进行全面的探索与研究。为详细教学策略,提高学生学习效率,笔者将结合《生物膜的流动镶嵌模型》这一课题进行论证,希望能给广大教师提供一些帮助。     

纳米材料构建的电化学生物传感器及其应用研究进展

近年来,生物传感器已广泛应用于基础研究、生物组分检测、临床疾病诊断、过程控制与检测、环境监控与保护等许多领域,电化学生物传感器是其中一个重要分支.纳米材料的尺寸小、比表面积大、表面原子配位不足、活性位点多等特性为生物传感器研究提供了新的途径,其迅猛发展对新型生物传感器的研制具有重要应用价值和意义.本文着重探讨了纳米材料在构建新型电化学生物传感器中的应用研究.     

基于多位点连锁度量的标签SNP选择方法研究

针对标签SNP选择过程中存在时间复杂度高、重构准确度低以及缺乏生物含义等不足,本文提出了一种基于多位点连锁不平衡的标签SNP选择方法,该方法首先利用最小等位基因频率等指标对数据集进行预处理,排除噪声位点等,然后根据标签SNP选择过程的特点设计并改进了蚁群算法,以获取候选标签子集,最后,为了进一步提高重构准确度,本文以重构准确度为目标,利用支持向量机作为学习模型,采用后向淘汰策略对候选标签子集进行精选。实验结果表明,先过滤再精选的策略,不仅降低了时间复杂度,而且在样本重构准确度也有一定程度优势。     

变性高效液相色谱法检测单核苷酸多态性

变性高效液相色谱(denaturing high-performance liquid chromatography,DHPLC)是新发展起来的检测基因组单核苷酸多态(single nucleotide polymorphism,SNP)的技术,在部分变性的条件下,根据发生错配的异源双链DNA和完全匹配的同源双链DNA分子的特点进行SNP检测.DHPLC具有自动化程度高、准确灵敏、快速、经济等特点,已成为分子生物学和基因组学研究中的重要方法.     

虚拟实验软件在生物实验教学中的作用

通过对虚拟实验软件在生物实验教学中的应用研究,探索利用虚拟实验软件进行生物实验教学的模式,形成具有可借鉴、可操作的方法和案例体系,提高实验教学的质量和效率。     

单体型装配问题的研究现状

单核苷酸多态性（SNP）是指不同个体DNA序列上的单个碱基的差异,是人类基因组中最丰富的遗传变异。单体型是指位于一条染色体上或某一区域的一组相关联的SNP等位基因。研究表明在复杂性疾病研究方面,由多个变异位点组合构成的单体型所携带的信息比单个的SNP数据的信息更有价值,由此衍生了单体型装配问题。文章论述了SNP,单体型,基因型的定义,综述了求解单一个体单体型装配问题的主要模型及算法,同时阐述了求解群体单体型装配问题的5种方法及算法。     

基因芯片技术及其应用

基因芯片是通过微加工和微电子技术在固相物质表面建构的一种生物化学分析系统,由于它能够实现对核酸的准确、快速、高通量的微型自动化检测,自20世纪80年代问世以来被广泛地应用于DNA测序、基因的表达分析、寻找新基因、单核苷酸多态性研究(SNPs)等基础研究中,并向许多领域延伸,本文从基因芯片技术原理出发,综述了其特点、功能和分类。     

利用改进的罚函数集合覆盖蚁群算法识别tagSNPs

序列中的标签SNPs—tagSNPs携带了SNPs数据集的绝大部分遗传信息,因此寻找tagSNPs意义重大。但从SNPs数据集中找出tagSNPs需要耗费巨大的计算量,传统的方法效率低且费用昂贵,对于复杂的集合覆盖问题,现有算法难以得到优化解。鉴于蚁群算法有较强的近优解搜索能力,因此,将改进的罚函数集合覆盖蚁群算法(RCACO)用于tagSNPs搜索。模拟数据集上进行的算法实验结果表明,与近两年的PSO、GA两类算法相比,所提出的算法运行时间较短,且搜索结果精确度更高。     

CYP1A1多态性在上海人群中的分布

由于单核苷酸多态性(SNPs)在寻找致病基因，了解遗传多样性、环境与基因的相互作用方面有重大价值，SNPs研究已越来越多地引起了学术界和产业界的兴趣．CYP1A1编码的酶在烟草的主要几类前致癌物(如PAHs和芳香胺类物质)的代谢活化中有重要作用，其多态性与个体对环境相关的癌症的易感性密切相关．本研究采用PCR-RFLP技术在上海人群中，对CYP1Al的两个SNPs：CYP1A1 m1和m2进行了基因分型．结合其它已发表的数据，我们的研究表明，在中国人群的不同群体中，m1等位基因的频率分布比较一致，而m2等位基因的频率分布则存在着显著的不同．     

DNA标记及其在鱼类中的应用

DNA分子标记是继形态标记、细胞标记和生化标记之后发展起来的一种比较理想的遗传标记技术。本文简要介绍RFLP、RAPD、AFLP、SSR、SNP、EST、mtDNA等DNA分子标记的类型,基本原理和特点,以及分子标记技术在鱼类遗传图谱构建、基因定位和分子标记辅助育种等方面的应用前景予以展望。     

Reading and Generalist Genes

ABSTRACT— Twin-study research suggests that many (but not all) of the same genes contribute to genetic influence on diverse learning abilities and disabilities, a hypothesis called generalist genes . This generalist genes hypothesis was tested using a set of 10 DNA markers (single nucleotide polymorphisms [SNPs]) found to be associated with early reading ability in a study of 4,258 7-year-old children that screened 100,000 SNPs. Using the same sample, we show that this early reading SNP set also correlates with other aspects of literacy, components of mathematics, and more general cognitive abilities. These results provide support for the generalist genes hypothesis. Although the effect size of the current SNP set is small, such SNP sets could eventually be used to predict genetic risk for learning disabilities as well as to prescribe genetically tailored intervention and prevention programs.     

Polymorphisms of the <Emphasis Type="Italic">IGF1</Emphasis> gene and their association with growth traits,serum concentration and expression rate of <Emphasis Type="Italic">IGF1</Emphasis> and <Emphasis Type="Italic">IGF1R</Emphasis> in buffalo

The insulin-like growth factor 1 (IGF1) gene is a member of the group of somatotropin axis genes that play a significant role in cell proliferation and growth of muscles. Here, we searched for polymorphisms in buffalo IGF1 and found two novel single nucleotide polymorphisms (SNPs), G64A and G280A, in the noncoding sequences of exon 1 and exon 4, respectively. Statistical analysis of different genotypes showed that the individuals with GG genotypes had significantly (P<0.05) higher body weight (BW) and average daily gain (ADG) than those with other genotypes at ages of 3–6 months in G64A SNP and 6–9 months in G280A SNP. The combined genotypes of these two SNPs produced three haplotypes, GG/GG, AG/AG, and AA/AA, which were significantly associated (P<0.0001) with BW and ADG at an age from 3 to 12 months. Buffaloes with the homozygous GG/GG haplotype showed higher growth performance than other buffaloes. The two SNPs were correlated with mRNA levels of IGF1 and IGF1 receptor (IGF1R) in semitendinosus muscle as well as with the serum concentration level of IGF1. Also, buffaloes with GG/GG haplotype showed higher mRNA and serum concentration levels. The data revealed that these two SNPs could be valuable genetic markers for selection of Egyptian buffaloes for better performance in the population.     

Association of CASP9, CASP10 gene polymorphisms and tea drinking with colorectal cancer risk in the Han Chinese population

The initiators caspase-9(CASP9) and caspase-10(CASP10) are two key controllers of apoptosis and play important roles in carcinogenesis.This study aims to explore the association between CASPs gene polymorphisms and colorectal cancer(CRC) susceptibility in a population-based study.A two-stage designed population-based case-control study was carried out,including a testing set with 300 cases and 296 controls and a validation set with 206 cases and 845 controls.A total of eight tag selected single nucleotide polymorphisms(SNPs) in CASP9 and CASP10 were chosen based on HapMap and the National Center of Biotechnology Information(NCBI) datasets and genotyped by restriction fragment length polymorphism(RFLP) assay.Multivariate logistic regression models were applied to evaluate the association of SNPs with CRC risk.In the first stage,from eight tag SNPs,three polymorphisms rs4646077(odds ratio(OR) AA+AG:0.654,95% confidence interval(CI):0.406-1.055;P=0.082),rs4233532(OR CC:1.667,95% CI:0.967-2.876;OR CT:1.435,95% CI:0.998-2.063;P=0.077),and rs2881930(OR CC:0.263,95% CI:0.095-0.728,P=0.036) showed possible association with CRC risk.However,none of the three SNPs,rs4646077(OR AA+AG:1.233,95% CI:0.903-1.683),rs4233532(OR CC:0.892,95% CI:0.640-1.243;OR CT:1.134,95% CI:0.897-1.433),and rs2881930(OR CC:1.096,95% CI:0.620-1.938;OR CT:1.009,95% CI:0.801-1.271),remained significant with CRC risk in the validation set,even after stratification for different tumor locations(colon or rectum).In addition,never tea drinking was associated with a significantly increased risk of CRC in testing set together with validation set(OR:1.755,95% CI:1.319-2.334).Our results found that polymorphisms of CASP9 and CASP10 genes may not contribute to CRC risk in Chinese population and thereby the large-scale case-control studies might be in consideration.In addition,tea drinking was a protective factor for CRC.     

Deletions in the genomes of fifteen inbred mouse lines and their possible implications for fat accumulation

Copy number variants (CNVs) are pieces of genomic DNA of 1000 base pairs or longer which occur in a given genome at a different frequency than in a reference genome. Their importance as a source for phenotypic variability has been recognized only in the last couple of years. Chromosomal deletions can be seen as a special case of CNVs where stretches of DNA are missing in certain lines when compared to the reference genome of the mouse line C57BL/6, for example. Based upon more than 8 million single nucleotide polymorphisms (SNPs) in the fifteen inbred mouse lines which were determined in a whole genome chip based resequencing project by Perlegen Sciences, we detected 20166 such long chromosomal deletions. They cover altogether between 4.4 million and 8.8 million base pairs, depending on the mouse line. Thus, their extent is comparable to that of SNPs. The chromosomal deletions were found by searching for clusters of missing values in the genotyping data by applying bioinformatics and biostatistical methods. In contrast to isolated missing values, clusters are likely the consequence of missing DNA probe rather than of a failed hybridization or deficient oligos. We analyzed these deletion sites in various ways. Twenty-two percent of these deletion sites overlap with exons; they could therefore affect a gene's functioning. The corresponding genes seem to exist in alternative forms, a phenomenon that reminds of the alternative forms of mRNA generated during gene splicing. We furthermore detected statistically significant association between hundreds of deletion sites and fat weight at the age of eight weeks.     

Investigation of the association between all-trans-retinol dehydrogenase (RDH8) polymorphisms and high myopia in Chinese

Retinoic acid level in the retina/choroid is altered in induced myopia models. All-trans-retinol dehydrogenase (RDH8) is an important enzyme of retinoic acid metabolism. This study aimed to investigate the association of the RDH8 gene with high myopia. Three single nucleotide polymorphisms (SNPs) [RDH851 (rs2233789), RDH8E5a (rs1644731), and RDH855b (rs3760753)] were selected, based on the linkage disequilibrium pattern of RDH8 from a previous study, and genotyped for 160 Han Chinese nuclear families with highly myopic (−10 diopters or worse) offspring as well as in an independent group with 166 highly myopic cases (−10 diopters or worse) and 211 controls. Family-based association analysis was performed using the family-based association test (FBAT) package, and genotype relative risk (GRR) was calculated using the GenAssoc program. Population-based association analysis was performed using Chi-square test. These SNPs were in linkage equilibrium with each other. SNPs RDH851 (rs2233789) and RDH8E5a (rs1644731) both did not show association with high myopia. SNP RDH855b (rs3760753) demonstrated significant association (P=0.0269) with a GRR of 0.543 (95% confidence interval=0.304–0.968, P=0.038). The association became statistically insignificant, however, after multiple comparison correction. Haplotype analysis did not show a significant association either. Population-based association analysis also showed no significant association (P>0.05). Our family- and population-based data both suggest that the RDH8 gene is unlikely to be associated with high myopia in Chinese.     

Population structure and linkage disequilibrium in elite barley breeding germplasm from the United States

Cultivated barley is known to have a complex population structure and extensive linkage disequilibrium (LD). To conduct robust association mapping (AM) studies of economically important traits in US barley breeding germplasm, population structure and LD decay were examined in a complete panel of US barley breeding germplasm (3 840 lines) genotyped with 3 072 single nucleotide polymorphisms (SNPs). Nine subpopulations (sp1‒sp9) were identified by the program STRUCTURE and subsequently confirmed by principle component analysis (PCA). Out of the nine subpopulations, seven were very similar to the respective subpopulations identified by Hamblin et al. (2010) which were based on half of the germplasm and half of the SNP markers, but two subpopulations were found to be new. One subpopulation was dominated by six-rowed spring lines from Utah State University (UT) and the other was composed of six-rowed spring lines from multiple breeding programs (USDA-ARS Aberdeen (AB), Busch Agricultural Resources Inc. (BA), UT, and Washington State University (WA)). LD was found to decay across a range from 4.0 to 19.8 cM. This result indicates that the germplasm genotyped with 3 072 SNPs would be robust for mapping and possibly identifying the causal polymorphisms contributing to disease resistance and perhaps other traits.