Noise propagation in gene networks

Accurately predicting noise propagation in gene networks is crucial for understanding signal fidelity in natural networks and designing noise-tolerant gene circuits. To quantify how noise propagates through gene networks, we measured expression correlations between genes in single cells. We found that noise in a gene was determined by its intrinsic fluctuations, transmitted noise from upstream genes, and global noise affecting all genes. A model was developed that explains the complex behavior exhibited by the correlations and reveals the dominant noise sources. The model successfully predicts the correlations as the network is systematically perturbed. This approach provides a step toward understanding and manipulating noise propagation in more complex gene networks.     

Tunability and noise dependence in differentiation dynamics

The dynamic process of differentiation depends on the architecture, quantitative parameters, and noise of underlying genetic circuits. However, it remains unclear how these elements combine to control cellular behavior. We analyzed the probabilistic and transient differentiation of Bacillus subtilis cells into the state of competence. A few key parameters independently tuned the frequency of initiation and the duration of competence episodes and allowed the circuit to access different dynamic regimes, including oscillation. Altering circuit architecture showed that the duration of competence events can be made more precise. We used an experimental method to reduce global cellular noise and showed that noise levels are correlated with frequency of differentiation events. Together, the data reveal a noise-dependent circuit that is remarkably resilient and tunable in terms of its dynamic behavior.     

Oligonucleotide-modified gold nanoparticles for intracellular gene regulation

We describe the use of gold nanoparticle-oligonucleotide complexes as intracellular gene regulation agents for the control of protein expression in cells. These oligonucleotide-modified nanoparticles have affinity constants for complementary nucleic acids that are higher than their unmodified oligonucleotide counterparts, are less susceptible to degradation by nuclease activity, exhibit greater than 99% cellular uptake, can introduce oligonucleotides at a higher effective concentration than conventional transfection agents, and are nontoxic to the cells under the conditions studied. By chemically tailoring the density of DNA bound to the surface of gold nanoparticles, we demonstrated a tunable gene knockdown.     

cDNA Cloning of Goat DNA Methyltransferase 1,Screening of shRNA Vectors and Influences to Development of Nuclear Transfer Embryos

This study was designed to clone cDNA of goat DNA methyltransferase 1（DNMT1） gene,to screen an effective shRNAproducing vector targeting goat DNA methyltransferase 1 and to improve the developmental competence of goat nuclear transfer embryos by decreasing the DNMT1 expression in donor cells.In this study,PCR primers were designed against regions of high homology between bovine and sheep sequences and then used to amplify the larger portions of the coding regions.Next,3 RNAi oligonucleotides were designed based on the cloned sequences and inserted into pRNAT-U6.1/Neo vector,acquiring 3 new vectors,respectively termed pRNAD1,pRNAD2 and pRNAD3.Then the positive cells were sorted by flow cytometry after transfection and detected by real-time PCR analysis and sodium bisulfite genomic sequencing.Finally,the developmental rates of nuclear transfer（NT） embryos generated using donor cells with and without the effective shRNA vector respectively,as well as in vitro fertilization（IVF） embryos were observed and recorded.The results showed that the coding regions of goat DNA methyltransferase 1 gene was successfully cloned（GenBank no.FJ617538）.Furthermore,an effective interfering shRNA（pRNAD2） was obtained,with its interference effect being 47.88%.Finally,NT embryos with shRNA vector harbored better developmental competence during morula and blastocyst stage compared to controls（P 〈 0.05）,reaching the similar rates to IVF embryos（P 〉 0.05）.In conclusion,goat DNA methyltransferase 1 gene cDNA was cloned and sequenced,an effective shRNA vector responsible for inhibiting DNA methyltransferase 1 expression was developed and the developmental competence of goat nuclear transfer morulae and blastcysts was significantly improved,which provided a feasible pathway for improving goat nuclear transfer embryo development competence by decreasing the methylation level in donor cells through RNAi-mediated manner.     

金黄色葡萄球菌wood46株eno基因的克隆及原核表达

为获得Eno的重组蛋白,采用PCR法从金黄色葡萄球菌wood46株基因组扩增eno基因,并连接到pMD18-T载体上,转化至BL21感受态细胞中;重组质粒经PCR及酶切鉴定后,送上海生工测序。将鉴定正确的质粒酶切回收产物与原核表达载体pET-32a连接,然后转化至BL21感受态细胞,对平板筛选的阳性质粒进行PCR和酶切鉴定。对鉴定正确的重组菌进行诱导表达并纯化。实验结果表明成功构建了pET32a-eno表达载体,并获得了该纯化蛋白。该实验结果为S.aureus亚单位疫苗研究奠定了一定的基础。     

载体浓度和感受态对大分子载体转化效率的影响

[目的]研究载体量和感受态对阳性克隆率的影响。[方法]利用引物拼接PCR技术,自行设计26条引物合成一个835 bp的目的基因,将该基因与约20 kb的大分子载体连接构成重组质粒。在1 500 ng目的基因底物量的基础上,设置50、100、150、200、250、300 ng 6个梯度载体量,得到的重组反应产物再转化入Top10F'、DH5α、Stbl3、Epi400、JM108、SCSI 6种不同的感受态中,组成36个试验组合。[结果]不同载体量阳性克隆率由大到小依次为200、250、300、150、100、50 ng,200 ng的阳性克隆率最高可达75%,平均达28.5%。不同感受态细胞阳性克隆率由大到小依次为Stbl3、Top10F'、DH5α、JM108、Epi400、SCSI,Stbl3在任何载体浓度下均高于其他感受态,平均阳性克隆率为42.4%。[结论]载体量和感受态均明显影响阳性克隆率,最佳组合为200 ng的载体分子量配合Stbl3感受态,阳性克隆率可达75%。     

Genetic properties influencing the evolvability of gene expression

Identifying the properties of gene networks that influence their evolution is a fundamental research goal. However, modes of evolution cannot be inferred solely from the distribution of natural variation, because selection interacts with demography and mutation rates to shape polymorphism and divergence. We estimated the effects of naturally occurring mutations on gene expression while minimizing the effect of natural selection. We demonstrate that sensitivity of gene expression to mutations increases with both increasing trans-mutational target size and the presence of a TATA box. Genes with greater sensitivity to mutations are also more sensitive to systematic environmental perturbations and stochastic noise. These results provide a mechanistic basis for gene expression evolvability that can serve as a foundation for realistic models of regulatory evolution.     

微卫星的起源、作用以及在基因组中的分布与进化动力学(英文)

微卫星 ,即简单重复序列 (SSR ,1～ 6个碱基单元 ) ,广泛存在于基因组中 ,具有丰富的多态性。本文对SSR的起源与可移动因子 (如逆转录转座子 )之间的联系进行了探讨和分析 ,表明许多SSR的起源与逆转录转座子有关。同时分析了SSR在基因表达、染色质的结构、重组、DNA的复制和细胞周期等方面的重要作用 ,结果表明SSR是使有机组织的正常生长和保持种族特异性的重要DNA片段。就SSR的进化机制而言 ,跳跃复制和重组是产生SSR变异的内因 ;相反 ,通过不同形式的自然选择使得SSR广布于整个基因组 ,并且限定重复片段大小的上、下限临界值以及位点专一性变异和群体差异     

Effects of molecular memory and bursting on fluctuations in gene expression

Many cellular components are present in such low numbers per cell that random births and deaths of individual molecules can cause substantial "noise" in concentrations. But biochemical events do not necessarily occur in single steps of individual molecules. Some processes are greatly randomized when synthesis or degradation occurs in large bursts of many molecules during a short time interval. Conversely, each birth or death of a macromolecule could involve several small steps, creating a memory between individual events. We present a generalized theory for stochastic gene expression, formulating the variance in protein abundance in terms of the randomness of the individual gene expression events. We show that common types of molecular mechanisms can produce gestation and senescence periods that reduce noise without requiring higher abundances, shorter lifetimes, or any concentration-dependent control loops. We also show that most single-cell experimental methods cannot distinguish between qualitatively different stochastic principles, although this in turn makes such methods better suited for identifying which components introduce fluctuations. Characterizing the random events that give rise to noise in concentrations instead requires dynamic measurements with single-molecule resolution.     

拟南芥bZIP23基因过量表达载体的构建及过表达植株的筛选

[目的]以拟南芥为材料克隆bZIP23基因,构建bZIP23基因的过量表达载体和筛选过表达植株,为验证其功能奠定基础.[方法]提取拟南芥总RNA和RT-PCR克隆bZIP23基因,用限制性内切酶切割和T4 DNA连接酶连接,使bZIP23基因连接到35S强启动子的pART27载体上;将连接产物转化到Trans1-T1感受态细胞中,筛选阳性单克隆进行菌落PCR鉴定并测序验证,获得重组质粒.将该重组质粒电激转化至根瘤农杆菌GV3101菌株,浸花法转化拟南芥野生型植株.[结果]通过单菌落PCR鉴定和DNA测序结果显示,bZIP23基因与35S过量表达载体已连接,获得了重组载体;抗性筛选与遗传鉴定获得相应的转基因过量表达阳性植株.[结论]构建的过量表达载体及筛选得到的过量表达植株为验证bZIP23基因功能奠定了基础.     

牛乳素Lfcin B基因的合成及其在酵母菌中的表达研究

[目的]为临床研究和治疗某些病原微生物引起的感染提供依据。[方法]参照LfcinB的氨基酸序列,利用化学合成法合成LfcinB基因并克隆到pPIC9K载体中,转化到酵母菌GS115感受态细胞中,用抗性选择标记G418筛选出高拷贝酵母菌转化子。利用甲醇诱导表达重组LfcinB,经Tricine-SDS-PAGE电泳检测目的蛋白牛乳铁蛋白素的表达情况,同时通过体外抑菌试验检测表达产物的抑菌活性。[结果]提取的酵母菌DNA扩增出1条预期的560bp左右的特异性条带。目的基因已经成功克隆到pPIC9K载体中,并转到酵母菌GS115中而且获得了表达。重组酵母表达上清中牛乳铁蛋白素抗菌肽对沙门氏肠炎杆菌的抗菌活性为42.857IU/ml,表明LfcinB基因的酵母表达载体构建成功。[结论]该研究证明利用化学合成法直接合成编码LfcinB的DNA构建真核表达载体、通过生物发酵工程来制备LfcinB是可行的。     

耐盐基因HAL1的克隆及在原核细胞中的表达

以酵母基因组DNA为模板,采用PCR方法得到耐盐基因HAL1,插入原核表达载体pGEX-4T-1的XhoI和EcoRI酶切位点之间,构建原核表达载体pGEX-HAL1;将该载体转化到大肠杆菌中,重组菌株用IPTG诱导表达,其耐盐性比空白菌株提高50%;SDS-PAGE凝胶电泳结果显示有明显表达的蛋白质条带。     

Chitin induces natural competence in Vibrio cholerae

The mosaic-structured Vibrio cholerae genome points to the importance of horizontal gene transfer (HGT) in the evolution of this human pathogen. We showed that V. cholerae can acquire new genetic material by natural transformation during growth on chitin, a biopolymer that is abundant in aquatic habitats (e.g., from crustacean exoskeletons), where it lives as an autochthonous microbe. Transformation competence was found to require a type IV pilus assembly complex, a putative DNA binding protein, and three convergent regulatory cascades, which are activated by chitin, increasing cell density, and nutrient limitation, a decline in growth rate, or stress.     

麦长管蚜自然群体的遗传变异研究

以8个不同地区的麦长管蚜(Macrosiphumavenae)种群为虫源,每种群10个个体用6种随机引物进行RAPD分析。结果表明,引物在8个种群间共产生272个RAPD标记,种群内的相似度比种群间的高得多。利用Nei氏相似系数,对8个种群的RAPD-PCR结果进行分析可知,北京与山东试虫采集地种群遗传距离为0.0239,在8个地区中最小,山西试虫采集地种群与其他7个地区差异最大,这说明不同地区的麦长管蚜(M.ave-nae)种群的确存在着遗传变异。用UPGMA法构建的聚类图发现,麦长管蚜聚成3个群体:山东和北京群体,安徽、四川和陕西群体,新疆群体,呈梯度分布,单纯以地理隔离不能解释麦长管蚜自然群体间的遗传变异。     

仙客来热激蛋白基因HSP21.4植物表达载体构建及鉴定

试验以仙客来热激蛋白基因HSP21.4为材料,经PCR扩增的方法在目的片断两端添加SacⅠ位点,然后与植物表达载体pBI121连接,转化感受态大肠杆菌,经PCR和SacⅠ及XbaⅠ酶切验证,确定已将该热激蛋白基因连接到植物表达载体上,将重组质粒命名为pBI-CpHSP21.4,并采用冻融法完成了对pBI-CpHSP21.4质粒的农杆菌转化,为验证该热激蛋白基因的功能及转基因植物表达奠定基础。     

表观遗传变异与作物遗传改良

植物天然群体中存在大量遗传变异,这些变异是随机突变和自然选择的结果,也是物种赖以生存和进化的原料.此外,不同植物种间乃至属间的天然远缘杂交是经常发生的事件,也是新种形成的重要方式,而远缘杂交为高度分歧的物种之间的基因交流提供了机会,因此也是产生新的遗传变异的重要途径.近年来的大量研究表明,植物天然群体中还存在一类不基于DNA序列差异的变异,被称为表观遗传变异(epigeneticvariation).植物发生远缘杂交以及此后的多倍体化过程可以产生大量的表观遗传变异,其遗传行为不能用经典遗传规律解释.表观遗传变异的另外一个重要来源是环境中的各种生物和非生物胁迫.研究较深入的表观遗传变异主要是编码基因和转座子DNA甲基化水平和模式的改变,但可以推测与之相关的组蛋白修饰和染色质结构也可能发生变化.目前对此类表观遗传变异的分子机理尚缺乏深入研究,但不难想像可能与各类non-coding RNA有关.这些表观遗传变异的后果是基因表达的大规模改变并由此产生新表型.作物远缘杂交育种实践表明,这些不能用经典遗传学理论解释的变异中蕴含许多在育种上有重要价值的变异并可能与杂种优势密切相关,对它们的产生机理和遗传规律的深入解析将有助于其在作物改良中的有效利用.     

Epigenetic reprogramming in mammalian development

DNA methylation is a major epigenetic modification of the genome that regulates crucial aspects of its function. Genomic methylation patterns in somatic differentiated cells are generally stable and heritable. However, in mammals there are at least two developmental periods-in germ cells and in preimplantation embryos-in which methylation patterns are reprogrammed genome wide, generating cells with a broad developmental potential. Epigenetic reprogramming in germ cells is critical for imprinting; reprogramming in early embryos also affects imprinting. Reprogramming is likely to have a crucial role in establishing nuclear totipotency in normal development and in cloned animals, and in the erasure of acquired epigenetic information. A role of reprogramming in stem cell differentiation is also envisaged. DNA methylation is one of the best-studied epigenetic modifications of DNA in all unicellular and multicellular organisms. In mammals and other vertebrates, methylation occurs predominantly at the symmetrical dinucleotide CpG (1-4). Symmetrical methylation and the discovery of a DNA methyltransferase that prefers a hemimethylated substrate, Dnmt1 (4), suggested a mechanism by which specific patterns of methylation in the genome could be maintained. Patterns imposed on the genome at defined developmental time points in precursor cells could be maintained by Dnmt1, and would lead to predetermined programs of gene expression during development in descendants of the precursor cells (5, 6). This provided a means to explain how patterns of differentiation could be maintained by populations of cells. In addition, specific demethylation events in differentiated tissues could then lead to further changes in gene expression as needed. Neat and convincing as this model is, it is still largely unsubstantiated. While effects of methylation on expression of specific genes, particularly imprinted ones (7) and some retrotransposons (8), have been demonstrated in vivo, it is still unclear whether or not methylation is involved in the control of gene expression during normal development (9-13). Although enzymes have been identified that can methylate DNA de novo (Dnmt3a and Dnmt3b) (14), it is unknown how specific patterns of methylation are established in the genome. Mechanisms for active demethylation have been suggested, but no enzymes have been identified that carry out this function in vivo (15-17). Genomewide alterations in methylation-brought about, for example, by knockouts of the methylase genes-result in embryo lethality or developmental defects, but the basis for abnormal development still remains to be discovered (7, 14). What is clear, however, is that in mammals there are developmental periods of genomewide reprogramming of methylation patterns in vivo. Typically, a substantial part of the genome is demethylated, and after some time remethylated, in a cell- or tissue-specific pattern. The developmental dynamics of these reprogramming events, as well as some of the enzymatic mechanisms involved and the biological purposes, are beginning to be understood. Here we look at what is known about reprogramming in mammals and discuss how it might relate to developmental potency and imprinting.     

野猪肌细胞生成素基因的克隆与序列分析

参考家猪(X89007)MyoG基因序列设计2对特异引物,用PCR方法首次从野猪基因组中扩增出2个大小分别约为1.6 kb和1.0 kb的DNA片段,其PCR产物经pMD-18T载体转化感受态DH5α株大肠杆菌,获得重组克隆子。DNA测序和序列拼接表明:野猪肌细胞生成素基因DNA序列长2 466bp,含完整的3个外显子和2个内含子,与家猪、牛、马、狗、小鼠和人的MyoG基因的cDNA序列同源性分别为99.8%、92.4%、92.7%、89.7%、90.8%和94%,其cDNA编码氨基酸序列与家猪、牛、马、狗、小鼠和人的同源性分别为100%、96.4%、95.9%、94.1%、96.4%、96.8%;对野猪MyoG基因组序列与9个家猪品种的相应同源序列进行比较,检出16个核苷酸变异位点,且其中有5个为家猪中不具有的新变异位点,其变异位点主要发生在内含子部分,尤其是内含子1中的变异位点比例最大(11个)。这些结果表明,野猪肌细胞生成素基因的编码序列在进化过程中是高度保守的,而内含子部分尤其是第1内含子具有丰富的序列多态性。对117个限制性酶切位点扫描分析发现,野猪MyoG基因核苷酸序列中含有78个酶切位点,其中有5个酶切位点包含变异位点,尤其是1 153位点的T突变成G所产生的SmaI(CCC/GGG)或XmaI(C/CCGGG)酶切位点为野猪所特有。所测DNA序列已提交到GenBank中,获得的序列号为:FJ356697。