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Dynamics and Control of DNA Sequence Amplification  [PDF]
Karthikeyan Marimuthu,Raj Chakrabarti
Quantitative Biology , 2014, DOI: 10.1063/1.4899053
Abstract: DNA amplification is the process of replication of a specified DNA sequence \emph{in vitro} through time-dependent manipulation of its external environment. A theoretical framework for determination of the optimal dynamic operating conditions of DNA amplification reactions, for any specified amplification objective, is presented based on first-principles biophysical modeling and control theory. Amplification of DNA is formulated as a problem in control theory with optimal solutions that can differ considerably from strategies typically used in practice. Using the Polymerase Chain Reaction (PCR) as an example, sequence-dependent biophysical models for DNA amplification are cast as control systems, wherein the dynamics of the reaction are controlled by a manipulated input variable. Using these control systems, we demonstrate that there exists an optimal temperature cycling strategy for geometric amplification of any DNA sequence and formulate optimal control problems that can be used to derive the optimal temperature profile. Strategies for the optimal synthesis of the DNA amplification control trajectory are proposed. Analogous methods can be used to formulate control problems for more advanced amplification objectives corresponding to the design of new types of DNA amplification reactions.
Whole-genome screening indicates a possible burst of formation of processed pseudogenes and Alu repeats by particular L1 subfamilies in ancestral primates
Kazuhiko Ohshima, Masahira Hattori, Tetsusi Yada, Takashi Gojobori, Yoshiyuki Sakaki, Norihiro Okada
Genome Biology , 2003, DOI: 10.1186/gb-2003-4-11-r74
Abstract: The human genome was queried and 3,664 candidate PPs were identified. The most abundant were copies of genes encoding keratin 18, glyceraldehyde-3-phosphate dehydrogenase and ribosomal protein L21. A simple method was developed to estimate the level of nucleotide substitutions (and therefore the age) of PPs. A Poisson-like age distribution was obtained with a mean age close to that of the Alu repeats, the predominant human short interspersed elements. These data suggest a nearly simultaneous burst of PP and Alu formation in the genomes of ancestral primates. The peak period of amplification of these two distinct retrotransposons was estimated to be 40-50 million years ago. Concordant amplification of certain L1 subfamilies with PPs and Alus was observed.We suggest that a burst of formation of PPs and Alus occurred in the genome of ancestral primates. One possible mechanism is that proteins encoded by members of particular L1 subfamilies acquired an enhanced ability to recognize cytosolic RNAs in trans.The abundance of pseudogenes is a remarkable feature of mammalian genomes. Aptly named, pseudogenes are copies of specific genes and are present in every mammalian chromosome [1-5]. In general, pseudogenes are thought to be nonfunctional [2] as they have accumulated vast numbers of mutations during evolution and have lost the ability to be transcribed. Pseudogenes fall into two distinct categories depending on the mechanism by which they are generated: processed pseudogenes (PPs) are reverse transcribed from mRNAs (and thus do not contain introns) whereas nonprocessed pseudogenes arise from duplications of genomic DNA [2,4]. Among the abundant PPs, there are a substantial number of 'processed genes' or 'retrogenes' of novel function that also derive from mRNAs of various intron-containing genes [6-8].In addition to PPs, mammalian genomes contain a large number of retrotransposons (retroposons) that represent a reverse flow of genetic information via RNA [9-13]. In huma
Dynamics of parametric matter wave amplification  [PDF]
Robert Bücker,Ulrich Hohenester,Tarik Berrada,Sandrine van Frank,Aurélien Perrin,Stephanie Manz,Thomas Betz,Julian Grond,Thorsten Schumm,J?rg Schmiedmayer
Physics , 2012, DOI: 10.1103/PhysRevA.86.013638
Abstract: We develop a model for parametric amplification, based on a density matrix approach, which naturally accounts for the peculiarities arising for matter waves: significant depletion and explicit time-dependence of the source state population, long interaction times, and spatial dynamics of the amplified modes. We apply our model to explain the details in an experimental study on twin-atom beam emission from a one-dimensional degenerate Bose gas.
LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss
Clémentine Vitte, Olivier Panaud, Hadi Quesneville
BMC Genomics , 2007, DOI: 10.1186/1471-2164-8-218
Abstract: Using a new method to estimate the insertion date of both truncated and complete copies, we estimated these two forces more accurately than previous studies based on other methods. We show that LTR retrotransposons have undergone bursts of amplification within the past 5 My. These bursts vary both in date and copy number among families, revealing that each family has a particular amplification history. The number of solo LTR varies among families and seems to correlate with LTR size, suggesting that solo LTR formation is a family-dependent process. The deletion rate estimate leads to the prediction that the half-life of LTR retrotransposon sequences evolving neutrally is about 19 My in rice, suggesting that other processes than the formation of small deletions are prevalent in rice DNA removal.Our work provides insights into the dynamics of LTR retrotransposons in the rice genome. We show that transposable element families have distinct amplification patterns, and that the turn-over of LTR retrotransposons sequences is rapid in the rice genome.Transposable elements (TEs) make up a large part of eukaryotic genomes. They represent a genomic fraction of 3% in baker's yeast [1], ~20% in fruit fly [2-5], 45% in human [6,7] and over 80% in maize [8,9]. Due to their repetitive nature and to the fact that they harbor regulatory signals, TEs are responsible for chromosomal rearrangements [10], fragmental gene movements [11,12] and for the evolution of gene regulation and function [13,14]. Hence, the activity of TEs is currently considered to be one of the major processes in genome evolution.In plants, Long Terminal Repeat (LTR) retrotransposons are the most common type of TE: they are ubiquitous in the plant kingdom [15] and are the main constituents of large plant genomes [15,16]. Moreover, these elements have been shown to be responsible for wide genome expansions [8,9,17-21] and are considered to be major players in the remarkable variation of genome size observed in flow
Alu pair exclusions in the human genome
George W Cook, Miriam K Konkel, James D Major, Jerilyn A Walker, Kyudong Han, Mark A Batzer
Mobile DNA , 2011, DOI: 10.1186/1759-8753-2-10
Abstract: We performed a comprehensive analysis of all (> 800,000) full-length Alu elements in the human genome. This large sample size permits detection of small differences in the ratio between inverted and direct Alu pairs (I:D). We have discovered a significant depression in the full-length Alu pair I:D ratio that extends to repeat pairs separated by ≤ 350,000 bp. Within this imbalance bubble (those Alu pairs separated by ≤ 350,000 bp), direct pairs outnumber inverted pairs. Using PCR, we experimentally verified several examples of inverted Alu pair exclusions that were caused by deletions.Over 50 million full-length Alu pairs reside within the I:D imbalance bubble. Their collective impact may represent one source of Alu element-related human genomic instability that has not been previously characterized.Retrotransposons are mobile DNA elements that populate genomes via their respective RNA transcripts. The retrotransposon with the highest copy number in the human genome is the Alu element [1]. Alu elements lack the necessary repertoire of enzymes to effect their independent insertion and are thus classified as non-autonomous mobile elements. For recent reviews, see [2-4].Following transcription, Alu RNA is thought to require the assistance of the LINE1 open reading frame 2 protein (ORF2p) both for nicking the genome at the insertion site and for reverse transcription of the Alu RNA transcript [5,6]. The endonuclease and reverse transcriptase functions of ORF2p are referred to as L1EN and L1RT, respectively. While L1EN has been shown to have some tolerance for target site variation, it most frequently cleaves at the T/A transition within the sequence, 5'-TTTTAA-3' [7-10]. Following cleavage, the poly-T sequence of the target site becomes accessible to the complementary poly(A) tail of Alu RNA. Hybridization of these two sequences results in a short RNA-DNA hybrid that both orients the RNA transcript and primes reverse transcription of the Alu RNA by L1RT. Identical sequen
Alu elements: know the SINEs
Prescott Deininger
Genome Biology , 2011, DOI: 10.1186/gb-2011-12-12-236
Abstract: Alu elements represent one of the most successful of all mobile elements, having a copy number well in excess of 1 million copies in the human genome [1] (contributing almost 11% of the human genome). They belong to a class of retroelements termed SINEs (short interspersed elements) and are primate specific. These elements are non-autonomous, in that they acquire trans-acting factors for their amplification from the only active family of autonomous human retroelements: LINE-1 [2].Although active at higher levels earlier in primate evolution, Alu elements continue to insert in modern humans, including somatic insertion events, creating genetic diversity and contributing to disease through insertional mutagenesis. They are also a major factor contributing to non-allelic homologous recombination events causing copy number variation and disease. Alu elements code for low levels of RNA polymerase III transcribed RNAs that contribute to retrotransposition. However, the ubiquitous presence of Alu elements throughout the human genome has led to their presence in a large number of genes and their transcripts. Many individual Alu elements have wide-ranging influences on gene expression, including influences on polyadenylation [3,4], splicing [5-7] and ADAR (adenosine deaminase that acts on RNA) editing [8-10].This review focuses heavily on studies generated as a result of the advent of high-throughput genomics providing huge datasets of genome sequences, and data on gene expression and epigenetics. These data provide tremendous insight into the role of Alu elements in genetic instability and genome evolution, as well as their many impacts on expression of the genes in their vicinity. These roles then influence normal cellular health and function, as well as having a broad array of impacts on human health.The general structure of an Alu element is presented in Figure 1a. The body of the Alu element is about 280 bases in length, formed from two diverged dimers, ancestrally deri
Analysis of the human Alu Ye lineage
Abdel-Halim Salem, David A Ray, Dale J Hedges, Jerzy Jurka, Mark A Batzer
BMC Evolutionary Biology , 2005, DOI: 10.1186/1471-2148-5-18
Abstract: A total of 153 Alu elements from the Ye subfamily were extracted from the draft sequence of the human genome. Analysis of these elements resulted in the discovery of two new Alu subfamilies, Ye4 and Ye6, complementing the previously described Ye5 subfamily. DNA sequence analysis of each of the Alu Ye subfamilies yielded average age estimates of ~14, ~13 and ~9.5 million years old for the Alu Ye4, Ye5 and Ye6 subfamilies, respectively. In addition, 120 Alu Ye4, Ye5 and Ye6 loci were screened using polymerase chain reaction (PCR) assays to determine their phylogenetic origin and levels of human genomic diversity.The Alu Ye lineage appears to have started amplifying relatively early in primate evolution and continued propagating at a low level as many of its members are found in a variety of hominoid (humans, greater and lesser ape) genomes. Detailed sequence analysis of several Alu pre-integration sites indicated that multiple types of events had occurred, including gene conversions, near-parallel independent insertions of different Alu elements and Alu-mediated genomic deletions. A potential hotspot for Alu insertion in the Fer1L3 gene on chromosome 10 was also identified.The proliferation of Alu elements has had a significant impact on the architecture of primate genomes [1]. They comprise over 10% of the human genome by mass and are the most abundant short interspersed element (SINE) in primate genomes [2]. Alu elements have achieved this copy number by duplicating via an RNA intermediate in a process termed retroposition [3]. During retroposition the RNA copy is reverse transcribed by target primed reverse transcription (TPRT) and subsequently integrated into the genome [4-6]. While unable to retropose autonomously, Alu elements are thought to borrow the factors that are required for their amplification from the LINE (long interspersed element) elements [6-9], which encode a protein with endonuclease and reverse transcriptase activity [10,11]. Because of their hig
Proliferation of Ty3/gypsy-like retrotransposons in hybrid sunflower taxa inferred from phylogenetic data
Mark C Ungerer, Suzanne C Strakosh, Kaitlin M Stimpson
BMC Biology , 2009, DOI: 10.1186/1741-7007-7-40
Abstract: We demonstrate that Ty3/gypsy-like retrotransposons exist as multiple well supported sublineages in both the parental and hybrid derivative species and that the same element sublineage served as the source lineage of proliferation in each hybrid species' genome. This inference is based on patterns of species-specific element numerical abundance within different phylogenetic sublineages as well as through signals of proliferation events present in the distributions of element divergence values. Employing methods to date paralogous sequences within a genome, proliferation events in the hybrid species' genomes are estimated to have occurred approximately 0.5 to 1 million years ago.Proliferation of the same retrotransposon major sublineage in each hybrid species indicates that similar dynamics of element derepression and amplification likely occurred in each hybrid taxon during their formation. Temporal estimates of these proliferation events suggest an earlier origin for these hybrid species than previously supposed.The genomes of flowering plants are remarkably variable in nuclear DNA content, with >1,000-fold differences among some taxa [1,2]. While differences in ploidy and large-scale segmental duplication account for some of this variability, differential accumulation (and loss) of mobile genetic elements, especially the class I transposable elements known as long terminal repeat (LTR) retrotransposons, represents an additional and important process through which genome size can vary between individual plant species [3,4]. Plant LTR retrotransposons represent ancient lineages that are ubiquitous in plant genomes [5,6] and can account for >70% of the nuclear DNA of some plant species [4]. Transposition of these elements is via an RNA intermediate, which enables new copies to be synthesized, reverse transcribed and subsequently integrated into host chromosomal DNA. This mode of transposition can result in large-scale genome expansion because each intact and function
Alu Mobile Elements: From Junk DNA to Genomic Gems  [PDF]
Sami Dridi
Scientifica , 2012, DOI: 10.6064/2012/545328
Abstract: Alus, the short interspersed repeated sequences (SINEs), are retrotransposons that litter the human genomes and have long been considered junk DNA. However, recent findings that these mobile elements are transcribed, both as distinct RNA polymerase III transcripts and as a part of RNA polymerase II transcripts, suggest biological functions and refute the notion that Alus are biologically unimportant. Indeed, Alu RNAs have been shown to control mRNA processing at several levels, to have complex regulatory functions such as transcriptional repression and modulating alternative splicing and to cause a host of human genetic diseases. Alu RNAs embedded in Pol II transcripts can promote evolution and proteome diversity, which further indicates that these mobile retroelements are in fact genomic gems rather than genomic junks. 1. Introduction Alu repeat elements are the most abundant interspersed repeats in the human genome. They are a family of short interspersed nuclear elements (SINEs) that use the reverse transcriptase and nuclease encoded by long interspersed nuclear elements (LINEs) to integrate into the host genome [1–3] and are found in the human genome in a number of ~1.100,000 copies, covering ~10% of its total length [4]. Functioning as transacting regulators of gene expression, pol III transcribed Alu and B1/2 (Alu-like elements in mouse) RNAs can interact with pol II and repress mRNA transcription [5–7]. Inverted Alu repeats are target for A-to-I editing by adenosine deaminases (ADARs) and can cause alternative splicing and drive proteome diversity [8]. Beside its role in human genomic evolution and diversity, Alu insertions and Alu-mediated unequal recombination contribute to a significant proportion of human genetic diseases [9]. Alu RNAs can also induce age-related macular degeneration following direct cytotoxicity to retinal pigment epithelium (RPE) cells [10]. In this brief paper, the author will describe the structure of human (Alu) and murine (B1, B2, ID, and B4) retroelements, a broad overview of the contribution of Alu retrotransposition to human diseases, and finally describe in depth a novel role of double-stranded Alu RNAs affecting the progression of age-related macular degeneration (AMD) and Alu editing by ADARs. 2. Structure of Alu and Murine Mobile Elements Alu typical sequences are ~300 nucleotides long and are classified into subfamilies according to their relative ages (for review see [11]). They have a dimeric structure and are composed of two similar but distinct monomers: left and right arms of 100 and 200 nucleotides long,
Methylation status of individual CpG sites within Alu elements in the human genome and Alu hypomethylation in gastric carcinomas
Shengyan Xiang, Zhaojun Liu, Baozhen Zhang, Jing Zhou, Bu-Dong Zhu, Jiafu Ji, Dajun Deng
BMC Cancer , 2010, DOI: 10.1186/1471-2407-10-44
Abstract: Bisulfite clone sequencing was carried out in 14 human gastric samples initially. A Cac8I COBRA-DHPLC assay was developed to detect methylated-Alu proportion in cell lines and 48 paired gastric carcinomas and 55 gastritis samples. DHPLC data were statistically interpreted using SPSS version 16.0.From the results of 427 Alu bisulfite clone sequences, we found that only 27.2% of CpG sites within Alu elements were preserved (4.6 of 17 analyzed CpGs, A ~ Q) and that 86.6% of remaining-CpGs were methylated. Deamination was the main reason for low preservation of methylation targets. A high correlation coefficient of methylation was observed between Alu clones and CpG site J (0.963), A (0.950), H (0.946), D (0.945). Comethylation of the sites H and J were used as an indicator of the proportion of methylated-Alu in a Cac8I COBRA-DHPLC assay. Validation studies showed that hypermethylation or hypomethylation of Alu elements in human cell lines could be detected sensitively by the assay after treatment with 5-aza-dC and M.SssI, respectively. The proportion of methylated-Alu copies in gastric carcinomas (3.01%) was significantly lower than that in the corresponding normal samples (3.19%) and gastritis biopsies (3.23%).Most Alu CpG sites are deaminated in the genome. 27% of Alu CpG sites represented in our amplification products. 87% of the remaining CpG sites are methylated. Alu hypomethylation in primary gastric carcinomas could be detected with the Cac8I COBRA-DHPLC assay quantitatively.The Alu element is a member of the SINE family of repetitive elements. It is an example of a non-automatic retrotransposon. It is the most abundant gene in the human genome (more than one million copies per haploid genome), representing 10% of the genome mass [1]. Alu elements are mainly distributed in gene-rich regions. About 75% of gene promoters in the genome contain Alu elements [2].A consensus Alu element usually contains 24 CpG sites (Figure 1) [3]. In fact, the CpGs within Alu element
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