Adaptive Amplification

ABSTRACT

Modern techniques are revealing that repetition of segments of the genome, called amplification or gene amplification, is very common. Amplification is found in all domains of life, and occurs under conditions where enhanced expression of the amplified genes is advantageous. Amplification extends the range of gene expression beyond that which is achieved by control systems. It also is reversible because it is unstable, breaking down by homologous recombination. Amplification is believed to be the driving force in the clustering of related functions, in that it allows them to be amplified together. Amplification provides the extra copies of genes that allow evolution of functions to occur while retaining the original function. Amplification can be induced in response to cellular stressors. In many cases, it has been shown that the genomic regions that are amplified include those genes that are appropriate to upregulate for a specific stressor. There is some evidence that amplification occurs as part of a broad, general stress response, suggesting that organisms have the capacity to induce structural changes in the genome. This then allows adaptation to the stressful conditions. The mechanisms by which amplification arises are now being studied at the molecular level, but much is still unknown about the mechanisms in all organisms. Recent advances in our understanding of amplification in bacteria suggests new interpretations of events leading to human copy number variation, as well as evolution in general.     

ExCyto PCR Amplification

Background

ExCyto PCR cells provide a novel and cost effective means to amplify DNA transformed into competent bacterial cells. ExCyto PCR uses host E. coli with a chromosomally integrated gene encoding a thermostable DNA polymerase to accomplish robust, hot-start PCR amplification of cloned sequences without addition of exogenous enzyme.

Results

Because the thermostable DNA polymerase is stably integrated into the bacterial chromosome, ExCyto cells can be transformed with a single plasmid or complex library, and then the expressed thermostable DNA polymerase can be used for PCR amplification. We demonstrate that ExCyto cells can be used to amplify DNA from different templates, plasmids with different copy numbers, and master mixes left on ice for up to two hours. Further, PCR amplification with ExCyto cells is comparable to amplification using commercial DNA polymerases. The ability to transform a bacterial strain and use the endogenously expressed protein for PCR has not previously been demonstrated.

Conclusions

ExCyto PCR reduces pipetting and greatly increases throughput for screening EST, genomic, BAC, cDNA, or SNP libraries. This technique is also more economical than traditional PCR and thus broadly useful to scientists who utilize analysis of cloned DNAs in their research.     

Origin-Dependent Inverted-Repeat Amplification: Tests of a Model for Inverted DNA Amplification

DNA replication errors are a major driver of evolution—from single nucleotide polymorphisms to large-scale copy number variations (CNVs). Here we test a specific replication-based model to explain the generation of interstitial, inverted triplications. While no genetic information is lost, the novel inversion junctions and increased copy number of the included sequences create the potential for adaptive phenotypes. The model—Origin-Dependent Inverted-Repeat Amplification (ODIRA)—proposes that a replication error at pre-existing short, interrupted, inverted repeats in genomic sequences generates an extrachromosomal, inverted dimeric, autonomously replicating intermediate; subsequent genomic integration of the dimer yields this class of CNV without loss of distal chromosomal sequences. We used a combination of in vitro and in vivo approaches to test the feasibility of the proposed replication error and its downstream consequences on chromosome structure in the yeast Saccharomyces cerevisiae. We show that the proposed replication error—the ligation of leading and lagging nascent strands to create “closed” forks—can occur in vitro at short, interrupted inverted repeats. The removal of molecules with two closed forks results in a hairpin-capped linear duplex that we show replicates in vivo to create an inverted, dimeric plasmid that subsequently integrates into the genome by homologous recombination, creating an inverted triplication. While other models have been proposed to explain inverted triplications and their derivatives, our model can also explain the generation of human, de novo, inverted amplicons that have a 2:1 mixture of sequences from both homologues of a single parent—a feature readily explained by a plasmid intermediate that arises from one homologue and integrates into the other homologue prior to meiosis. Our tests of key features of ODIRA lend support to this mechanism and suggest further avenues of enquiry to unravel the origins of interstitial, inverted CNVs pivotal in human health and evolution.     

重组酶聚合酶扩增技术：一种新的核酸扩增策略

重组酶聚合酶扩增 (recombinase polymerase amplification, RPA)是近年来兴起的一种等温核酸扩增技术,它比聚合酶链式反应(polymerase chain reaction, PCR)及其它等温扩增技术更快速、便捷、高效。本文将详细介绍RPA这项新颖的技术,并对其在医疗诊断、农业、食品、生物安全等方面的研究及应用进展进行综述。期望这项技术得到更多的关注,使其发展更加完善,将来在更多的领域充分发挥作用,甚至书写核酸检测历史新篇章。     

Selective Amplification of Classical and Atypical Prions Using Modified Protein Misfolding Cyclic Amplification

With the development of protein misfolding cyclic amplification (PMCA), the topic of faithful propagation of prion strain-specific structures has been constantly debated. Here we show that by subjecting brain material of a synthetic strain consisting of a mixture of self-replicating states to PMCAb, selective amplification of PrP^Sc could be achieved, and that PMCAb mimicked the evolutionary trend observed during serial transmission in animals. On the other hand, using modified PMCAb conditions that employ partially deglycosylated PrP^C (dgPMCAb), an alternative transmissible state referred to as atypical protease-resistant form of the prion protein (atypical PrPres) was selectively amplified from a mixture. Surprisingly, when hamster-adapted strains (263K and Hyper) were subjected to dgPMCAb, their proteinase K digestion profile underwent a dramatic transformation, suggesting that a mixture of atypical PrPres and PrP^Sc might be present in brain-derived materials. However, detailed analysis revealed that the proteinase K-resistant profile of PrP^Sc changed in response to dgPMCAb. Despite these changes, the 263K strain-specific disease phenotype was preserved after passage through dgPMCAb. This study revealed that the change in PrP^Sc biochemical phenotype does not always represent an irreversible transformation of a strain, but rather demonstrated the existence of a wide range of variation for strain-specific physical features in response to a change in prion replication environment. The current work introduced a new PMCA technique for amplification of atypical PrPres and raised a number of questions about the need for a clever distinction between actual strain mutation and variation of strain-specific features in response to a change in the replication environment.     

高GC含量DNA模板的PCR扩增

目的：探索高GC含量DNA的PCR扩增条件,为扩增达托霉素生物合成基因簇及拼接奠定基础。方法：在PCR扩增体系中,使用高保真的聚合酶及添加不同浓度的DMSO、7-deaza-dGTP等增强剂,并选择合适的PCR循环程序,优化富含GC的DNA的PCR扩增条件。结果：向反应体系中额外添加1%~4%的DMSO可以显著提高富含GC的DNA的PCR扩增产物量,但会降低其特异性;7-deaza-dGTP可以提高扩增产物的特异性及保真度,但产量会有所下降。应用touch down PCR并在体系中添加7-deaza-dGTP能够提高扩增产物的特异性和产率,增加扩增的保真度。结论：应用优化的PCR扩增条件将所有达托霉素生物合成基因簇分段扩增出来,并可扩增出长达6 kb的片段,且序列完全正确,可以进行后续拼接。     

Amplification of actin polymerization forces

The actin cytoskeleton drives many essential processes in vivo, using molecular motors and actin assembly as force generators. We discuss here the propagation of forces caused by actin polymerization, highlighting simple configurations where the force developed by the network can exceed the sum of the polymerization forces from all filaments.

Introduction

Mechanical amplification is something we experience every day, in the form of gears, pulleys, and levers. While climbing a hill on a bicycle, for instance, shifting gears increases the force on the wheels while limiting the pressure required on the pedals. However, energy has to be conserved, and because mechanical work is defined as force × displacement, an increase in force can only be obtained at the expense of displacement. Thus, although shifting gears allows one to develop the additional force needed to go uphill, speed is reduced as each pedal stroke produces a smaller turn of the wheels. Cells have similarly developed microscopic force amplification strategies during evolution. Here, we discuss some amplification schemes for one of the major force generators in the cell—actin polymerization.Actin plays a ubiquitous role in cell motility and morphogenesis, spanning many scales of space and time. In fission yeast, for example, a miniature actin machinery only ∼100 nm across can induce the invagination of an endocytic vesicle in just a few seconds (Picco et al., 2015). However, to sever the entire yeast cell, a cytokinetic ring forms with an initial perimeter of ∼10 µm and requires ∼30 min to drive division (Proctor et al., 2012). These assemblies differ dramatically in both size and duration. In other species, considerably larger actin assemblies exist that reach the scale of centimeters, such as in muscle cells. Clearly, actin and its associated factors need to be specifically organized to achieve these different functions (Fig. 1). From a functional point of view, a key problem is to understand how the global architecture of an actin network allows forces that are produced at the molecular scale to be productive for the cell. In this respect, we can distinguish two sorts of components. Active components generate forces from chemical sources of energy and include molecular motors, as well as actin itself, which can push by polymerizing (Kovar and Pollard, 2004) and possibly pull while depolymerizing. Passive components, such as actin cross-linkers, are essential but can only transmit forces generated by other elements.Open in a separate windowFigure 1.Different actin networks. Networks of actin filaments are essential for many biological processes at the cellular level, and the organization of the filaments in space must be adapted to the task. Here, polymerization force (orange) of actin filaments (red) occurs near the plasma membrane (blue). Linear filopodia bundles with fascin (black) can produce high speeds, but represent a weak configuration for force generation. Lamellipodia are thin cellular extensions in which filaments are nearly parallel to the substrate on which the cell is crawling. The 2D branched network, created by Arp2/3 actin-nucleating complexes (black), can produce higher forces at the expense of displacement. During endocytosis in yeast, actin forms a 3D network at the site of the invagination that appears roughly spherical, but the organization of actin filaments in space is not known. The coat structure (yellow) enables actin to pull the membrane inward and actin polymerizes near the base of the structure, where Arp2/3 nucleators are shown in black (Picco et al., 2015). Endocytosis requires strong force amplification to pull the invagination against the turgor pressure.The forces developed by an actin meshwork are determined by the organization of its components. Ultimately, these forces must be sufficient to drive biological processes, and thus their scale depends on the physical characteristics of the cell. For example, in the case of endocytosis in yeast, the turgor pressure pushing the surface of the invagination outward reaches ∼1,000 pN, which the actin machinery must overcome (Basu et al., 2014). During cytokinesis, the actomyosin ring also works against the turgor pressure, which produces high forces on the furrow (Proctor et al., 2012). For both cases, these forces have been calculated from measured cellular parameters, particularly the turgor pressure and the dimensions over which the membrane is deformed. Hence, for these processes at least, the two ends of the problem are known: the forces produced by the molecular components make up the input and the force required for the cellular process to occur represents the output. Yet the force balance within the system must be considered to understand how the actin machinery harvests the input to produce this output.In this comment, we focus on the transmission of forces produced by the polymerization of actin, setting aside turnover and the contribution of molecular motors. We discuss specifically how the arrangement of the filaments in the system regulates the amount of productive force. In many ways, the actin machinery behaves analogously to a cyclist: though its power is limited, it can “shift gears” to favor either more displacement (high gears) or more force (low gears).

The force generated by actin polymerization

Actin polymerization can produce force. Indeed if an actin monomer in solution binds the barbed end of a filament, there is a change of free energy (ΔG_p) and polymerization will occur if ΔG_p < 0 (Fig. 2 A). This reaction depends on the concentration (C) of monomeric actin and will take place only above a critical concentration (C* of ∼0.14 µM; Pollard, 1986). It is associated with ΔG_p = −k_BT ln(C/C*), where k_B is the Boltzmann constant and T is the absolute temperature. If actin is polymerizing against a load and producing work (W), the change in free energy is ΔG_p + W. In this case, polymerization will occur spontaneously if the change is negative, i.e., ΔG_p + W < 0. Consider an actin filament pushing against a force (f) applied parallel to the filament axis (Fig. 2 B). Because the addition of one actin monomer produces a displacement (δ = 2.75 nm; Holmes et al., 1990), the mechanical work is W = f × δ. Forces that are antagonistic to elongation can impede actin assembly (Peskin et al., 1993). The critical force under which the filament would cease to elongate is called the polymerization force (f_a). Using a physiological concentration (C of ∼40 µM; Wu and Pollard, 2005), the polymerization force is thermodynamically limited to k_BT ln(C/C*)/δ = ∼9 pN (Hill, 1981). Within such limits, the force developed by polymerization will depend on the conditions of assembly. Direct measurements of the polymerization force using single-molecule techniques are scarce. A first study used optical traps on bare filaments, giving a force of ∼1 pN (Footer et al., 2007). By monitoring the buckling of filaments capped with formins, a second study found the force to be ∼1.3 pN (Kovar and Pollard, 2004). In both cases, the concentration of actin was an order of magnitude lower than in vivo, and the measured forces were in fact close to the theoretical maximum under the experimental conditions. Here, we will thus consider that f_a is within 1 and 9 pN. We further assume that an actin filament is able to elongate as long as the parallel component of the antagonistic force at its barbed end remains lower than f_a, irrespective of the perpendicular components (Fig. 2 C). We discuss various examples of force amplification in which the network develops forces that exceed f_a per filament, without breaking the thermodynamic requirement for actin polymerization (ΔG_p + W < 0).Open in a separate windowFigure 2.Polymerization mechanics. (A) During polymerization, the addition of one actin monomer (orange) corresponds to an elongation (δ) at the barbed end of an actin filament (red) and is associated with a change of free energy (ΔG_p = −k_b T ln(C/C*)). (B) The work required to push a load over a distance (h) with a force (f) is f × h, and thus assembly remains favorable as long as ΔG_p + f × h < 0. In the case where polymerization occurs straight against a load (h = δ), the maximal force (f_a) is f_a = k_b T ln(C/C*)/δ (Hill, 1981). (C) If the filament encounters the load with an angle (θ), then h = δ sinθ and the maximal force is consequently increased: f_θ = f_a/sinθ. (D) In the branched network of a lamellipod, actin grows against the leading membrane at an angle (θ = ∼54°). In the absence of friction, the force between the polymerizing tip (orange) of the actin and the membrane (blue) is perpendicular to the membrane. It can then reach a maximum magnitude of f_a/sinθ. The sum of the forces produced by the two filaments is then ∼2.5 f_a. (E) Higher forces arise by polymerizing with shallow angles. The device illustrated here is composed of a growing actin filament with a “leg” on its side. By elongating, the filament will induce rotation around the pivot point, where the leg is contacting the membrane. High forces can be exerted on a load supported at the branch point, as a result of the amplification achieved by the lever arm and contact angle. (F) The highest forces are generated if a filament polymerizes parallel to the surface. In the illustrated configuration, elongation of the filament will cause a load (green dome) to separate from the membrane. The maximal force is calculated as in E, except that anchoring has to be assumed at the pivot point to balance forces horizontally. The device can sustain high forces applied on the top of the dome because the upward movement is small compared with the elongation of the filament.

Table 1.

Physical characteristics of actin

Theoretical Consideration of Amplification Strategies

Experimentalists would like to perform large-scale expression analysis on samples drawn from small cell populations and even single cells. Amplification of the source material is required to assay such small samples under all existing array technologies. In this report we consider the very different theoretical properties of linear and PCR-based amplification. A suggestion is made concerning a hybrid amplification strategy incorporating the advantages offered by both approaches.     

甜菜碱增强长片段PCR的扩增

聚合酶链式反应(PCR)作为一项非常成熟的技术可以用于基因组序列的扩增。普通的PCR技术只适合于短片段DNA的扩增,一般在6kb以下。对于6kb至十几kb甚至几十kb以上的DNA片段的扩增就非常困难。通过添加不同化学物质,发现甜菜碱对长片段PCR的扩增有非常有效的增强作用。通过对玉米总DNA以及质粒DNA的扩增,发现1mol／L到2．5mol／L甜菜碱对改进PCR扩增效果明显。通过添加甜菜碱,可以从玉米基因组中扩增出9kb以上的单拷贝片段,从质粒中扩增出16kb以上片段。经过试验,发现不同GC含量的引物需要使用不同浓度的甜菜碱。甜菜碱可以减少甚至消除长片段PCR中的非特异性扩增。同时,我们发现其它的添加物,如DMSO,甘油,甲酰胺对长片段PCR的作用不明显。     

Amplification by enzymatic cycling

Summary Enzymatic cycling provides a methodology for virtually unlimited amplification of analytical sensitivity. The most widely applicable cycling systems are those for NAD and NADP, since these can be used to increase the sensitivity of methods for a host of other substances. However, cycling systems for ATP plus ADP, GTP+ GDP, glutathione and coenzyme A have also proven tb be very useful.A total of 19 cycling procedures are described in greater or lesser detail. Some of these are capable of amplification rates in excess of 20,000 per hour in a single cycling step (20,000 × 20,000 with two one hour cycling steps). Advantages, disadvantages, limitations and other practical considerations are stressed, as well as the means for coupling the cycling systems to assays for other substances.     

TOUCH-UP Gradient Amplification Method

We report a unique amplification technique that works efficiently and specifically over a temperature range, rather than at one specific temperature, throughout the amplification process. As bisulfite-modified DNA is one of the difficult to amplify templates, we used this technique to amplify regions of promoter-associated CpG island for 11 genes using this template. This technique amplified specific products for every gene without requiring any optimization.     

蛋白质错误折叠循环扩增技术

目前发现有多种人类及动物疾病是由体内蛋白质的错误折叠引起的,其中朊毒粒病因具有传染性而备受关注.朊毒粒病研究的核心问题之一是正常细胞朊蛋白（PrPc）向异常致病朊毒粒（PrPsc）转变的机制.蛋白质错误折叠循环扩增技术（protein misfolding cyclic amplification,PMCA）就是最新发明的在体外诱导朊蛋白（PrPc）产生错误折叠生成朊毒粒（prpsc）的技术.该文将概要介绍此项技术的原理、技术要点及在诊断与基础研究方面的应用前景.     

中心体扩增与肿瘤

中心体是动物细胞中非常重要的非膜结构细胞器,它除了作为微管组织中心在有丝分裂过程中具有指导两极纺锤体组装的功能外,还参与了细胞内的许多生命活动过程。中心体扩增通常导致异倍体的形成、以及染色体和细胞骨架的不稳定性。因而与肿瘤的发生、发展有着直接的关系。中心体扩增在肿瘤的诊、治中具有广阔的研究与应用前景。中心体扩增的参数可以作为肿瘤诊断以及预后的指标;中心体可望成为肿瘤治疗的靶位点。     

Amplification of Chirality at Solid Surfaces

Symmetry-breaking phenomena in two-dimensional crystallization at surfaces are reviewed and the potential impact to chiral amplification in three-dimensional systems in connection with the origin of homochirality in the biomolecular world is discussed. Adsorption of prochiral molecules leads to two-dimensional conglomerates, i.e., on a local scale spontaneously to homochiral crystal structures. Small enantiomeric excess or chiral impurities in this environment install homochirality on a global scale, that is, on the entire surface.     

乳腺珠蛋白研究及应用进展

乳腺珠蛋白是近年发现的一个具有乳腺组织特异性的分泌型蛋白,因其在乳腺癌中高度表达的特异性,而被公认为一种新型肿瘤标志物,在乳腺癌诊断、预后及治疗方面具有广阔的应用前景。     

Carcinogen-Mediated Amplification of Specific DNA Sequences

A model experimental system based on SV40-transformed Chinese hamster embryo cells and a highly sensitive in situ hybridization procedure was designed. Exposure of the cells to different categories of chemical and physical carcinogens resulted in the induction of SV40 DNA synthesis in the treated cells. Although the carcinogen-mediated amplification of SV40 DNA sequences is regulated by the viral “A” gene, neither infectious virus nor complete viral DNA molecules were rescued from the treated cells. A heterogenous collection of DNA molecules containing SV40 sequences was generated following treatment with DMBA. Restriction enzyme analysis of the amplified DNA molecules in the Hirt supernatant revealed that not all sequences in the integrated SV40 inserts are present. The possibility that the amplification of SV40 sequences is a reflection of a general gene amplification phenomenon mediated by carcinogens is discussed.     

Sequence-Dependent Biophysical Modeling of DNA Amplification

A theoretical framework for prediction of the dynamic evolution of chemical species in DNA amplification reactions, for any specified sequence and operating conditions, is reported. Using the polymerase chain reaction (PCR) as an example, we developed a sequence- and temperature-dependent kinetic model for DNA amplification using first-principles biophysical modeling of DNA hybridization and polymerization. We compare this kinetic model with prior PCR models and discuss the features of our model that are essential for quantitative prediction of DNA amplification efficiency for arbitrary sequences and operating conditions. Using this model, the kinetics of PCR is analyzed. The ability of the model to distinguish between the dynamic evolution of distinct DNA sequences in DNA amplification reactions is demonstrated. The kinetic model is solved for a typical PCR temperature protocol to motivate the need for optimization of the dynamic operating conditions of DNA amplification reactions. It is shown that amplification efficiency is affected by dynamic processes that are not accurately represented in the simplified models of DNA amplification that form the basis of conventional temperature cycling protocols. Based on this analysis, a modified temperature protocol that improves PCR efficiency is suggested. Use of this sequence-dependent kinetic model in a control theoretic framework to determine the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is discussed.