酿酒酵母进级进化过程中的基因丢失现象初探

酿酒酵母进级进化过程中的基因丢失问题很少被研究．利用现有的蛋白质数据库，通过设定判断标准，预期可以获得更多这方面的案例以便进行相关问题的研究．利用SMART蛋白质域家族数据库，根据在已完成测序的7种真核生物蛋白质域家族成员中存在或不存在酿酒酵母蛋白质域信号，判断是否发生了基因丢失．通过这种方法，共有6个酿酒酵母基因判断为在进级进化过程中发生了丢失，还探讨了这些基因发生丢失的可能机制．     

基因频率的计算问题例析

基因频率是指某群体中,某一等位基因在该位点上可能出现的基因总数中所占的比率。关于基因频率的计算问题是常见的一类题型,大体可以分为两类:常染色体上的基因频率计算和X染色体上的基因频率计算。由于X染色体上的基因在Y上没有等位基因,是成单存在的,因此其计算方法与常染色体基因不同,需要特别注意。     

使用线性微分方程构建初步的乳腺癌转移相关基因网络模型

随着基因芯片的技术的推广,越来越多的表达数据需要被处理和分析．利用这些表达数据提取基因调控矩阵从而构建基因网络是一个重要的问题．通过线性微分方程模型可以初步构建基因网络,了解网络结构,提取最显著的信息．然而由于分子生物学的条件限制或者数据来源的限制,导致实验数据不充分,使方程组无解．本文使用三次样条方法,对26例临床、病理资料完备的具有淋巴结转移的乳腺癌基因表达数据进行插值处理,使表达数据满秩,从而使用最小二乘法解出加权矩阵,构建初步的表达基因调控网络．通过对构建的基因网络的初步分析表明:乳腺癌转移的形成是由多基因异常引起多条传导通路异常,致使细胞恶性转化的结果,这与生物学上公认的看法是相一致的．因此,利用此线性模型方法对基因表达谱进行分析兵有一定可行性,在认识乳腺癌转移机制,乳腺癌诊断和治疗方面具有一定的理论和应用价值．     

连锁条件下基因互作形式的判定

如何根据子代的表型判断基因互作形式,是遗传学上重要也是困难的问题.文[l～2］在自由组合条件下给出了判定方法.本文得到了基因连锁时互作形式的判定法则,它是文［l～2］的推广．     

基因治疗及其临床应用研究进展

基因治疗可定义为在某一个体的细胞中引入新的遗传物质,从而使该个体的疾病得到治疗的方法．基因治疗主要研究免疫治疗、细胞素／药物传递基因、药物敏感基因、药物抗性基因和选择性抗性基因治疗等．基因治疗尚仅限于体细胞,生殖细胞的基因治疗由于技术难度更大,且涉及伦理学与社会学的问题．还不在考虑之列．目前基因治疗的对象主要以恶性肿瘤为重点,同时兼顾心血管及少数遗传病。基因治疗的基本内容包括;引起疾病的缺陷基因定位（基因诊断）;选择适当的载体及载体的加工、修饰与包装（基因载体）;外源基因导入人体靶细胞（基因转移）的临床研究．体外基因转移已广泛应用于各类基因病的临床治疗研究;而体内基因转移目前尚未走出实验室．继美国之后,世界上许多国家都已开始实施各自的基因治疗研究计划．人类的基因病有４０００多种,基因治疗前景广阔．     

真核基因PolyA信号的人工神经网络识别研究

本文采用神经网络方法对真核基因的PolyA信号进行识别．文中选择了人类、牛、猪、猫、山羊、兔、绵羊、大鼠、小鼠、小马、鸡、仓鼠共12种真核生物的270个基因组作为研究对象，训练组包括230个基因，预测组包括40个基因．结果表明，结合PolyA上游的碱基顺序特异性（紧挨PolyA的上游地GC），可以从神经网络识别的大量可能PolyA信号中得到正确PolyA信号．     

胃癌差异表达基因在染色体上的定位及其功能分析

利用标准化的Affymetrix公司生产的U133A基因芯片检测胃癌（T）与切缘正常胃黏膜（C）基因表达谱差异,并利用生物信息学方法对检测结果进行差异基因在染色体定位和功能分析。结果表明：胃癌与正常胃黏膜比较差异8倍以上共有270个基因,其中表达上调[信号比的对数值（SLR）≥3]有157个,表达下调（SLR≤-3）有113个。从表达差异的基因在染色体定位分析,发现除4个基因未知其定位外,其余所有差异表达基因散在分布和各条染色体上,但以1号染色体为最多,有26个（占9．8％）,其次是11和19号染色体上分别有24个（各占9．1％）。而差异表达的基因发生在染色体短臂（q）上有173个（占65％）。从表达差异的基因功能分类看,属于酶和酶调控子基因最多（67个,24．8占％）,其次是信号传导基因（43个,占15．9％）,第3类是核酸结合基因（17个,占6．3％）,第4类是转运子基因（15个,占5．5％）,第5类是蛋白结合基因（12个,占4．4％）,还有功能未知的基因有50个,占18．5％。以上5大类共占基因总数56．9％。胃癌差异表达基因散在分布在各条染色体上,但以1、11、19号染色体差异表达基因居多。这5大类（酶和酶调控子、信号传导、核酸结合、转运子、蛋白结合）相关基因异常是今后研究胃癌的重要基因。     

世界转基因棉推广种植情况

１　转基因棉的主要手段１．１　农杆菌携带Ｂｔ基因８０年代初，棉花外源基因的转育主要是农杆菌携带法，这种方法主要受限于遗传特殊性。比如，利用这种方法的成功率主要限于美国的Ｃｏｋｅｒ棉和澳大利亚的Ｓｉｏｋｒａ品种类型。在这两个类型的品种中，Ｓｉｏｋｒａ更容易长出愈伤组织。通过回交，再转入其它品种中，一般是回交３～４次，即可获得理想的商用转基因品种。目前生产上推广的转基因品种的表现证明，回交到第三代时，基因转育的成功率在９４％。１．２　质粒加速转育８０年代应用。这种直接将分生组织转育的转育法可以避免先…     

人HTR1E基因在不同细胞系和多种组织中的表达及其功能

人的HTR1E基因是五羟色胺受体（HTR）家族中的一员．这个家族里面的基因都和精神分裂症、抑郁症以及人的自杀活动有关．但是对于其具体的作用机制目前研究不多．采用实时定量PCR方法分析了HTR1E基因在各个组织和不同细胞系中的表达情况．亚细胞定位发现HTR1E位于细胞膜上,萤光素酶实验分析确定HTR1E可以抑制原癌基因erbB2启动子的转录活性．这些研究结果为进一步研究HTR1E基因在疾病发生中的作用奠定了一定的基础．     

应用基因表达数量性状基因座定位（eQTL）研究PINK1表达调控

Pink 1基因编码定位于线粒体上的丝/苏氨酸激酶（即PARK6）,为常染色体隐性遗传性帕金森病（Parkinsons disease, PD）连锁的基因．该基因在遗传性和散发性PD的发病中起重要作用,但其发病机理尚未明确．本研究以近交系C57BL/6J (B6) 和DBA/2J (D2)小鼠制作MPTP诱导的PD鼠为模型,借助基因表达数量性状基因座(eQTL),结合分子生物学方法,分析Pink1的表达调控．结果显示,Pink 1基因在PD模型组中表达显著升高．区间连锁分析检测显示,引起Pink 1基因表达水平差异的染色体区域,定位于4号染色体上,距Pink 1基因自身5 Mb范围之类,属于顺式调节eQTL．Pearson相关分析表明,在BXD 基因重组近交系（recombinant inbred,RI）小鼠脑中,Camk2n等30个基因的表达与Pink 1基因高度相关,相互间可能存在一定的协同作用．Pink 1基因在行使特定生物学功能时,很可能协同这些基因一起发挥相应的作用,这部分基因是深入研究Pink 1基因在PD发病中分子机制的重要靶点．     

CBS在医学微生物学教学中的应用

CBS(CaseBasedStudy)是一种新的教学方法。CBS就是给出一个案例,要求学生围绕案例回答一系列问题。在整个教学过程中主要由分成小组的学生自己去寻找解决方案。他们必须将案例所提供的信息综合起来,找出其中的关键问题及其相关联系,通过回顾、复习和学习课本或理论课讲授的相关知识,应用获取的知识去分析问题、解决问题。CBS的应用使得科学知识更具相关性、系统性,使学生对知识的学习更具积极性、主动性。     

《遗传学》教学中若干问题的数学解析Ⅱ

遗传学教学过程中会发现一系列启发性的问题,涉及孟德尔遗传、数量遗传、群体遗传和人类遗传等领域,这些问题对许多学生来讲有趣且有一定难度。收集了若干启发性问题,包括自交后代各种表型可能出现的频率、多次回交的目的、显性性状是否在群体中占有更大的比例、为什么母亲的年龄与子女的正常与否有很大的关系、遗传力的估算方法等,并用数学方法一一进行剖析,以供相关同学和同行借鉴和思考。     

Participation and Contribution in Crowdsourced Surveys

This paper identifies trends within and relationships between the amount of participation and the quality of contributions in three crowdsourced surveys. Participants were asked to perform a collective problem solving task that lacked any explicit incentive: they were instructed not only to respond to survey questions but also to pose new questions that they thought might-if responded to by others-predict an outcome variable of interest to them. While the three surveys had very different outcome variables, target audiences, methods of advertisement, and lengths of deployment, we found very similar patterns of collective behavior. In particular, we found that: the rate at which participants submitted new survey questions followed a heavy-tailed distribution; the distribution in the types of questions posed was similar; and many users posed non-obvious yet predictive questions. By analyzing responses to questions that contained a built-in range of valid response we found that less than 0.2% of responses lay outside of those ranges, indicating that most participants tend to respond honestly to surveys of this form, even without explicit incentives for honesty. While we did not find a significant relationship between the quantity of participation and the quality of contribution for both response submissions and question submissions, we did find several other more nuanced participant behavior patterns, which did correlate with contribution in one of the three surveys. We conclude that there exists an optimal time for users to pose questions early on in their participation, but only after they have submitted a few responses to other questions. This suggests that future crowdsourced surveys may attract more predictive questions by prompting users to pose new questions at specific times during their participation and limiting question submission at non-optimal times.     

Increasing student involvement in lectures: (very) low tech innovations in a biochemistry lecture class

The inherent passivity of the traditional lecture format makes this a poor mode for learning. In this paper I outline a simple but effective approach for eliciting student participation in the intermediate size lecture course (50–100 students). Two types of question are employed to increase student involvement. Each lecture ends with a set of questions directly related to concepts that will be covered in the next session. At the following lecture, specific students, chosen at random from the class list, are called on to answer these questions. Classroom participation is also elicited by calling on students to answer questions which focus on the major points during each lecture. Finally, students are invited to submit questions for inclusion on each exam. These devices make the lecture a more active and participatory experience.     

Models of coalition or alliance formation

More than half a century has now elapsed since coalition or alliance formation theory (CAFT) was first developed. During that time, researchers have amassed a vast amount of detailed and high-quality data on coalitions or alliances among primates and other animals. But models have not kept pace, and more relevant theory is needed. In particular, even though CAFT is primarily an exercise in polyadic game theory, game theorists have devoted relatively little attention to questions that motivate field research, and much remains largely unexplored. The state of the art is both a challenge and an opportunity. In this review we describe a variety of game-theoretic and related modelling approaches that have much untapped potential to address the questions that field biologists ask.     

Divided genomes: negotiating the cell cycle in prokaryotes with multiple chromosomes

Historically, the prokaryotic genome was assumed to consist of a single circular replicon. However, as more microbial genome sequencing projects are completed, it is becoming clear that multipartite genomes comprised of more than one chromosome are not unusual among prokaryotes. Chromosomes are distinguished from plasmids by the presence of essential genes as well as characteristic cell cycle-linked replication kinetics; unlike plasmids, chromosomes initiate replication once per cell cycle. The existence of multipartite prokaryotic genomes raises several questions regarding how multiple chromosomes are replicated and segregated during the cell cycle. These divided genomes also introduce questions regarding chromosome evolution and genome stability. In this review, we discuss these and other issues, with particular emphasis on the cholera pathogen Vibrio cholerae.     

Discussing Truth and Lies in Interviews With Children: Whether,Why, and How?

Two studies examined discussions of truth and lying during interviews with children. In Study 1, truth-lie discussions (TLDs) during 132 actual sexual abuse interviews were analyzed, focusing on the types of questions asked and their developmental appropriateness. TLDs, which were fairly common for all ages of children interviewed, typically involved asking children closed-ended questions and did not differ in quality or form by age of child interviewed. Study 2 compared the typical TLDs (found in Study 1) to either no discussion or a more elaborate discussion in their effects on preschoolers' (n = 67) reports of an interactive event. Children given the extended TLD were significantly more accurate than those questioned following a typical or no TLD. The results suggest that discussing truth and lying with young children is effective only if the discussion is more elaborate than those typically conducted in forensic interviews.     

How informed is patients' consent to release of medical information to insurance companies?

A study was conducted to assess how informed the consent of patients is to the release of confidential information to insurance companies. Questionnaires were sent to 226 consecutive patients from four practices whose general practitioners had received requests to complete a personal medical attendant''s report for an insurance company. In total 195 patients returned the questionnaire, whose six questions required only a yes or no answer. More than half of the patients (102 (52%] could not recall having given their consent and 79 (40%) had one or more objections to the questions commonly asked by insurance companies. Questions about sexually transmitted diseases and AIDS led to the greatest proportion of objections (85% (67/79) and 80% (63/79) respectively). Over half (111 (57%) of the 195 respondents expected their doctor to withhold sensitive information. Of the 93 patients who gave their informed consent, 63 (68%) did not expect that their doctor would be asked to answer one or more of the common questions. In most cases the consent of patients to the release of confidential information to insurance companies is neither knowingly given nor informed.     

The more the merrier: Multi-species experiments in ecology

A major objective in ecology is to find general patterns, and to establish the rules and underlying mechanisms that generate those patterns. Nevertheless, most of our current insights in ecology are based on case studies of a single or few species, whereas multi-species experimental studies remain rare. We underline the power of the multi-species experimental approach for addressing general ecological questions, e.g. on species environmental responses or on patterns of among- and within-species variation. We present simulations that show that the accuracy of estimates of between-group differences is increased by maximizing the number of species rather than the number of populations or individuals per species. Thus, the more species a multi-species experiment includes, the more powerful it is. In addition, we discuss some inevitable methodological challenges of multi-species experiments. While we acknowledge the value of single- or few-species experiments, we strongly advocate the use of multi-species experiments for addressing ecological questions at a more general level.     

A guide to the genomics of ecological speciation in natural animal populations

Interest in ecological speciation is growing, as evidence accumulates showing that natural selection can lead to rapid divergence between subpopulations. However, whether and how ecological divergence can lead to the buildup of reproductive isolation remains under debate. What is the relative importance of natural selection vs. neutral processes? How does adaptation generate reproductive isolation? Can ecological speciation occur despite homogenizing gene flow? These questions can be addressed using genomic approaches, and with the rapid development of genomic technology, will become more answerable in studies of wild populations than ever before. In this article, we identify open questions in ecological speciation theory and suggest useful genomic methods for addressing these questions in natural animal populations. We aim to provide a practical guide for ecologists interested in incorporating genomic methods into their research programs. An increased integration between ecological research and genomics has the potential to shed novel light on the origin of species.