[Advances in clustered regularly interspaced short palindromic repeats--a review].
Wang, Lili; He, Jin; Wang, Jieping
2011-08-01
The recently discovered Clustered Regularly Interspaced Short Palindromic Repeat (CRISPRs) can protect bacteria and archaea with adaptive and heritable defense systems against the invasion of phage- and plasmid- associated mobile genetic elements. Here, we review the structure, diversity, mechanism of interference and self versus non-self discrimination of CRISPR systems. We also discuss the potential applications of this novel interference system.
CTD2 researchers at the University of California in San Francisco developed a modified Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) CRISPR/dCas9 system. Catalytically inactive dCas9 enables modular and programmable RNA-guided genome regulation in eukaryotes.
CTD2 researchers at the University of California in San Francisco developed a modified Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) CRISPR/dCas9 system. Catalytically inactive dCas9 enables modular and programmable RNA-guided genome regulation in eukaryotes.
CTD2 researchers at the University of California in San Francisco developed a modified Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) CRISPR/dCas9 system. Catalytically inactive dCas9 enables modular and programmable RNA-guided genome regulation in eukaryotes.
Cui, Yujun; Li, Yanjun; Yan, Yanfeng; Yang, Ruifu
2008-11-01
CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats), the basis of spoligotyping technology, can provide prokaryotes with heritable adaptive immunity against phages' invasion. Studies on CRISPR loci and their associated elements, including various CAS (CRISPR-associated) proteins and leader sequences, are still in its infant period. We introduce the brief history', structure, function, bioinformatics research and application of this amazing immunity system in prokaryotic organism for inspiring more scientists to find their interest in this developing topic.
Camporesi, Silvia; Cavaliere, Giulia
2016-01-01
This paper provides an overview of the ethical issues in the international clustered regularly interspaced short palindromic repeats (CRISPR) genome editing debate from March 2015 to September 2016. We present the regulatory framework for embryo research in the UK, and explain why CRISPR is not a significant break with the past. We discuss the ethical issues arising from CRISPR applications beyond human embryos, namely the use of gene drive-engineered mosquitoes to eradicate diseases, enginee...
CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats
Grissa, Ibtissem; Vergnaud, Gilles; Pourcel, Christine
2008-01-01
Clustered regularly interspaced short palindromic repeat (CRISPR) elements are a particular family of tandem repeats present in prokaryotic genomes, in almost all archaea and in about half of bacteria, and which participate in a mechanism of acquired resistance against phages. They consist in a succession of direct repeats (DR) of 24–47 bp separated by similar sized unique sequences (spacers). In the large majority of cases, the direct repeats are highly conserved, while the number and nature...
Peter C Fineran; Chang, James T.; Corinna Richter
2012-01-01
Phages are the most abundant biological entities on earth and pose a constant challenge to their bacterial hosts. Thus, bacteria have evolved numerous ‘innate’ mechanisms of defense against phage, such as abortive infection or restriction/modification systems. In contrast, the clustered regularly interspaced short palindromic repeats (CRISPR) systems provide acquired, yet heritable, sequence-specific ‘adaptive’ immunity against phage and other horizontally-acquired elements, such as plasmids....
Al-Attar, S.; Westra, E.R.; Oost, van der J.; Brouns, S.J.J.
2011-01-01
Many prokaryotes contain the recently discovered defense system against mobile genetic elements. This defense system contains a unique type of repetitive DNA stretches, termed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs). CRISPRs consist of identical repeated DNA sequences
Al-Attar, S.; Westra, E.R.; Oost, van der J.; Brouns, S.J.J.
2011-01-01
Many prokaryotes contain the recently discovered defense system against mobile genetic elements. This defense system contains a unique type of repetitive DNA stretches, termed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs). CRISPRs consist of identical repeated DNA sequences (re
Goren, Moran G; Yosef, Ido; Auster, Oren; Qimron, Udi
2012-10-12
We analyzed sequences of newly inserted repeats in an Escherichia coli CRISPR (clustered regularly interspaced short palindromic repeats) array in vivo and showed that a base previously thought to belong to the repeat is actually derived from a protospacer. Based on further experimental results, we propose to use the term "duplicon" for a repeated sequence in a CRISPR array that serves as a template for a new duplicon. Our findings suggest the possibility of redrawing the borders between repeats, spacers, and protospacer adjacent motifs.
Grissa, Ibtissem; Vergnaud, Gilles; Pourcel, Christine
2009-01-01
Clustered regularly interspaced short palindromic repeats (CRISPRs) are DNA sequences composed of a succession of repeats (23- to 47-bp long) separated by unique sequences called spacers. Polymorphism can be observed in different strains of a species and may be used for genotyping. We describe protocols and bioinformatics tools that allow the identification of CRISPRs from sequenced genomes, their comparison, and their component determination (the direct repeats and the spacers). A schematic representation of the spacer organization can be produced, allowing an easy comparison between strains.
He, Jiankui; Deem, Michael W.
2010-09-01
Clustered regularly interspaced short palindromic repeats (CRISPR) in bacterial and archaeal DNA have recently been shown to be a new type of antiviral immune system in these organisms. We here study the diversity of spacers in CRISPR under selective pressure. We propose a population dynamics model that explains the biological observation that the leader-proximal end of CRISPR is more diversified and the leader-distal end of CRISPR is more conserved. This result is shown to be in agreement with recent experiments. Our results show that the CRISPR spacer structure is influenced by and provides a record of the viral challenges that bacteria face.
Li, Hao; Qiu, Shaofu; Song, Hongbin
2013-10-04
In survival competition with phage, bacteria and archaea gradually evolved the acquired immune system--Clustered regularly interspaced short palindromic repeats (CRISPR), presenting the trait of transcribing the crRNA and the CRISPR-associated protein (Cas) to silence or cleaving the foreign double-stranded DNA specifically. In recent years, strong interest arises in prokaryotes primitive immune system and many in-depth researches are going on. Recently, researchers successfully repurposed CRISPR as an RNA-guided platform for sequence-specific gene expression, which provides a simple approach for selectively perturbing gene expression on a genome-wide scale. It will undoubtedly bring genome engineering into a more convenient and accurate new era.
Guo, Lijun; Xu, Kun; Liu, Zhiyuan; Zhang, Cunfang; Xin, Ying; Zhang, Zhiying
2015-06-01
In addition to the advantages of scalable, affordable, and easy to engineer, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) technology is superior for multiplex targeting, which is laborious and inconvenient when achieved by cloning multiple gRNA expressing cassettes. Here, we report a simple CRISPR array assembling method which will facilitate multiplex targeting usage. First, the Streptococcus thermophilus CRISPR3/Cas locus was cloned. Second, different CRISPR arrays were assembled with different crRNA spacers. Transformation assays using different Escherichia coli strains demonstrated efficient plasmid DNA targeting, and we achieved targeting efficiency up to 95% with an assembled CRISPR array with three crRNA spacers. Copyright © 2015 Elsevier Inc. All rights reserved.
Camporesi, Silvia; Cavaliere, Giulia
2016-11-01
This paper provides an overview of the ethical issues in the international clustered regularly interspaced short palindromic repeats (CRISPR) genome editing debate from March 2015 to September 2016. We present the regulatory framework for embryo research in the UK, and explain why CRISPR is not a significant break with the past. We discuss the ethical issues arising from CRISPR applications beyond human embryos, namely the use of gene drive-engineered mosquitoes to eradicate diseases, engineering nonhuman animals to harvest organs for human transplant and engineering crops. We discuss the experiments that have demonstrated the technical feasibility of cultivating embryos in vitro for up to 14 days, and possibly beyond this limit, and the ethical issues arising from the proposal to extend the limit beyond 14 days.
[Clustered regularly interspaced short palindromic repeats (CRISPR) site in Bacillus anthracis].
Gao, Zhiqi; Wang, Dongshu; Feng, Erling; Wang, Bingxiang; Hui, Yiming; Han, Shaobo; Jiao, Lei; Liu, Xiankai; Wang, Hengliang
2014-11-04
To investigate the polymorphism of clustered regularly interspaced short palindromic repeats (CRISPR) in Bacillu santhracis and the application to molecular typing based on the polymorphism of CRISPR in B. anthracis. We downloaded the whole genome sequence of 6 B. anthracis strains and extracted the CRISPR sites. We designed the primers of CRISPR sites and amplified the CRISPR fragments in 193 B. anthracis strains by PCR and sequenced these fragments. In order to reveal the polymorphism of CRISPR in B. anthracis, wealigned all the extracted sequences and sequenced results by local blasting. At the same time, we also analyzed the CRISPR sites in B. cereus and B. thuringiensis. We did not find any polymorphism of CRISPR in B. anthracis. The molecular typing approach based on CRISPR polymorphism is not suitable for B. anthracis, but it is possible for us to distinguish B. anthracis from B. cereus and B. thuringiensis.
CRISPRFinder: a web tool to identify clustered regularly interspaced short palindromic repeats.
Grissa, Ibtissem; Vergnaud, Gilles; Pourcel, Christine
2007-07-01
Clustered regularly interspaced short palindromic repeats (CRISPRs) constitute a particular family of tandem repeats found in a wide range of prokaryotic genomes (half of eubacteria and almost all archaea). They consist of a succession of highly conserved regions (DR) varying in size from 23 to 47 bp, separated by similarly sized unique sequences (spacer) of usually viral origin. A CRISPR cluster is flanked on one side by an AT-rich sequence called the leader and assumed to be a transcriptional promoter. Recent studies suggest that this structure represents a putative RNA-interference-based immune system. Here we describe CRISPRFinder, a web service offering tools to (i) detect CRISPRs including the shortest ones (one or two motifs); (ii) define DRs and extract spacers; (iii) get the flanking sequences to determine the leader; (iv) blast spacers against Genbank database and (v) check if the DR is found elsewhere in prokaryotic sequenced genomes. CRISPRFinder is freely accessible at http://crispr.u-psud.fr/Server/CRISPRfinder.php.
Peter C. Fineran
2012-10-01
Full Text Available Phages are the most abundant biological entities on earth and pose a constant challenge to their bacterial hosts. Thus, bacteria have evolved numerous ‘innate’ mechanisms of defense against phage, such as abortive infection or restriction/modification systems. In contrast, the clustered regularly interspaced short palindromic repeats (CRISPR systems provide acquired, yet heritable, sequence-specific ‘adaptive’ immunity against phage and other horizontally-acquired elements, such as plasmids. Resistance is acquired following viral infection or plasmid uptake when a short sequence of the foreign genome is added to the CRISPR array. CRISPRs are then transcribed and processed, generally by CRISPR associated (Cas proteins, into short interfering RNAs (crRNAs, which form part of a ribonucleoprotein complex. This complex guides the crRNA to the complementary invading nucleic acid and targets this for degradation. Recently, there have been rapid advances in our understanding of CRISPR/Cas systems. In this review, we will present the current model(s of the molecular events involved in both the acquisition of immunity and interference stages and will also address recent progress in our knowledge of the regulation of CRISPR/Cas systems.
CRISPRcompar: a website to compare clustered regularly interspaced short palindromic repeats.
Grissa, Ibtissem; Vergnaud, Gilles; Pourcel, Christine
2008-07-01
Clustered regularly interspaced short palindromic repeat (CRISPR) elements are a particular family of tandem repeats present in prokaryotic genomes, in almost all archaea and in about half of bacteria, and which participate in a mechanism of acquired resistance against phages. They consist in a succession of direct repeats (DR) of 24-47 bp separated by similar sized unique sequences (spacers). In the large majority of cases, the direct repeats are highly conserved, while the number and nature of the spacers are often quite diverse, even among strains of a same species. Furthermore, the acquisition of new units (DR + spacer) was shown to happen almost exclusively on one side of the locus. Therefore, the CRISPR presents an interesting genetic marker for comparative and evolutionary analysis of closely related bacterial strains. CRISPRcompar is a web service created to assist biologists in the CRISPR typing process. Two tools facilitates the in silico investigation: CRISPRcomparison and CRISPRtionary. This website is freely accessible at http://crispr.u-psud.fr/CRISPRcompar/.
Botelho, Ana; Canto, Ana; Leão, Célia; Cunha, Mónica V
2015-01-01
Typical CRISPR (clustered, regularly interspaced, short palindromic repeat) regions are constituted by short direct repeats (DRs), interspersed with similarly sized non-repetitive spacers, derived from transmissible genetic elements, acquired when the cell is challenged with foreign DNA. The analysis of the structure, in number and nature, of CRISPR spacers is a valuable tool for molecular typing since these loci are polymorphic among strains, originating characteristic signatures. The existence of CRISPR structures in the genome of the members of Mycobacterium tuberculosis complex (MTBC) enabled the development of a genotyping method, based on the analysis of the presence or absence of 43 oligonucleotide spacers separated by conserved DRs. This method, called spoligotyping, consists on PCR amplification of the DR chromosomal region and recognition after hybridization of the spacers that are present. The workflow beneath this methodology implies that the PCR products are brought onto a membrane containing synthetic oligonucleotides that have complementary sequences to the spacer sequences. Lack of hybridization of the PCR products to a specific oligonucleotide sequence indicates absence of the correspondent spacer sequence in the examined strain. Spoligotyping gained great notoriety as a robust identification and typing tool for members of MTBC, enabling multiple epidemiological studies on human and animal tuberculosis.
Bland, Charles; Ramsey, Teresa L.; Sabree, Fareedah; Lowe,Micheal; Brown, Kyndall; Kyrpides, Nikos C.; Hugenholtz, Philip
2007-05-01
Clustered Regularly Interspaced Palindromic Repeats (CRISPRs) are a novel type of direct repeat found in a wide range of bacteria and archaea. CRISPRs are beginning to attract attention because of their proposed mechanism; that is, defending their hosts against invading extrachromosomal elements such as viruses. Existing repeat detection tools do a poor job of identifying CRISPRs due to the presence of unique spacer sequences separating the repeats. In this study, a new tool, CRT, is introduced that rapidly and accurately identifies CRISPRs in large DNA strings, such as genomes and metagenomes. CRT was compared to CRISPR detection tools, Patscan and Pilercr. In terms of correctness, CRT was shown to be very reliable, demonstrating significant improvements over Patscan for measures precision, recall and quality. When compared to Pilercr, CRT showed improved performance for recall and quality. In terms of speed, CRT also demonstrated superior performance, especially for genomes containing large numbers of repeats. In this paper a new tool was introduced for the automatic detection of CRISPR elements. This tool, CRT, was shown to be a significant improvement over the current techniques for CRISPR identification. CRT's approach to detecting repetitive sequences is straightforward. It uses a simple sequential scan of a DNA sequence and detects repeats directly without any major conversion or preprocessing of the input. This leads to a program that is easy to describe and understand; yet it is very accurate, fast and memory efficient, being O(n) in space and O(nm/l) in time.
[Molecular characteristics of Clustered Regularly Interspaced Short Palindromic Repeat in Shigella].
Xue, Zerun; Wang, Yingfang; Duan, Guangcai; Yang, Haiyan; Xi, Yuanlin; Wang, Pengfei; Wang, Linlin; Guo, Xiangjiao
2015-08-01
To detect the molecular characteristics of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) in Shigella and to analyze the distribution of CRISPR related to the time of isolation. Of the 52 Shigella strains, 41 were isolated from Henan, 6 from Jiangxi and 5 isolated from Beijing. Both CRISPR locus of S1, S2, S3 and S4 in Shigella were detected by polymerase chain reaction (PCR). The PCR products were sequenced and compared. The positive rates of CRISPR locus in Shigella were 33.69% (S1), 50.00% (S2), 82.69% (S3) and 73.08% (S4), respectively. Two subtypes were discovered in S1 and S3 locus. Three subtypes were discovered in S2 locus. Four different subtypes were discovered in S4 locus. The isolates from Henan strains were divided into two groups by the time of isolation. Distributions of S1 were different, before or after 2004, on Shigella. S1 could not be detected after 2004. There were no statistical differences of S2, S3 and S4 in two groups. Different CRISPR subtypes or Shigella were discovered. A significant correlation was noticed between the CRISPR S1 related to the time of isolation but not between S2, S3 or S4 on the time of isolation.
Richter, Corinna; Chang, James T; Fineran, Peter C
2012-10-19
Phages are the most abundant biological entities on earth and pose a constant challenge to their bacterial hosts. Thus, bacteria have evolved numerous 'innate' mechanisms of defense against phage, such as abortive infection or restriction/modification systems. In contrast, the clustered regularly interspaced short palindromic repeats (CRISPR) systems provide acquired, yet heritable, sequence-specific 'adaptive' immunity against phage and other horizontally-acquired elements, such as plasmids. Resistance is acquired following viral infection or plasmid uptake when a short sequence of the foreign genome is added to the CRISPR array. CRISPRs are then transcribed and processed, generally by CRISPR associated (Cas) proteins, into short interfering RNAs (crRNAs), which form part of a ribonucleoprotein complex. This complex guides the crRNA to the complementary invading nucleic acid and targets this for degradation. Recently, there have been rapid advances in our understanding of CRISPR/Cas systems. In this review, we will present the current model(s) of the molecular events involved in both the acquisition of immunity and interference stages and will also address recent progress in our knowledge of the regulation of CRISPR/Cas systems.
Briner, Alexandra E; Barrangou, Rodolphe
2014-02-01
Clustered regularly interspaced short palindromic repeats (CRISPR) in combination with associated sequences (cas) constitute the CRISPR-Cas immune system, which uptakes DNA from invasive genetic elements as novel "spacers" that provide a genetic record of immunization events. We investigated the potential of CRISPR-based genotyping of Lactobacillus buchneri, a species relevant for commercial silage, bioethanol, and vegetable fermentations. Upon investigating the occurrence and diversity of CRISPR-Cas systems in Lactobacillus buchneri genomes, we observed a ubiquitous occurrence of CRISPR arrays containing a 36-nucleotide (nt) type II-A CRISPR locus adjacent to four cas genes, including the universal cas1 and cas2 genes and the type II signature gene cas9. Comparative analysis of CRISPR spacer content in 26 L. buchneri pickle fermentation isolates associated with spoilage revealed 10 unique locus genotypes that contained between 9 and 29 variable spacers. We observed a set of conserved spacers at the ancestral end, reflecting a common origin, as well as leader-end polymorphisms, reflecting recent divergence. Some of these spacers showed perfect identity with phage sequences, and many spacers showed homology to Lactobacillus plasmid sequences. Following a comparative analysis of sequences immediately flanking protospacers that matched CRISPR spacers, we identified a novel putative protospacer-adjacent motif (PAM), 5'-AAAA-3'. Overall, these findings suggest that type II-A CRISPR-Cas systems are valuable for genotyping of L. buchneri.
Price, Erin P; Smith, Helen; Huygens, Flavia; Giffard, Philip M
2007-05-01
A novel method for genotyping the clustered, regularly interspaced short-palindromic-repeat (CRISPR) locus of Campylobacter jejuni is described. Following real-time PCR, CRISPR products were subjected to high-resolution melt (HRM) analysis, a new technology that allows precise melt profile determination of amplicons. This investigation shows that the CRISPR HRM assay provides a powerful addition to existing C. jejuni genotyping methods and emphasizes the potential of HRM for genotyping short sequence repeats in other species.
Brown Kyndall
2007-06-01
Full Text Available Abstract Background Clustered Regularly Interspaced Palindromic Repeats (CRISPRs are a novel type of direct repeat found in a wide range of bacteria and archaea. CRISPRs are beginning to attract attention because of their proposed mechanism; that is, defending their hosts against invading extrachromosomal elements such as viruses. Existing repeat detection tools do a poor job of identifying CRISPRs due to the presence of unique spacer sequences separating the repeats. In this study, a new tool, CRT, is introduced that rapidly and accurately identifies CRISPRs in large DNA strings, such as genomes and metagenomes. Results CRT was compared to CRISPR detection tools, Patscan and Pilercr. In terms of correctness, CRT was shown to be very reliable, demonstrating significant improvements over Patscan for measures precision, recall and quality. When compared to Pilercr, CRT showed improved performance for recall and quality. In terms of speed, CRT proved to be a huge improvement over Patscan. Both CRT and Pilercr were comparable in speed, however CRT was faster for genomes containing large numbers of repeats. Conclusion In this paper a new tool was introduced for the automatic detection of CRISPR elements. This tool, CRT, showed some important improvements over current techniques for CRISPR identification. CRT's approach to detecting repetitive sequences is straightforward. It uses a simple sequential scan of a DNA sequence and detects repeats directly without any major conversion or preprocessing of the input. This leads to a program that is easy to describe and understand; yet it is very accurate, fast and memory efficient, being O(n in space and O(nm/l in time.
Yujun Cui
Full Text Available BACKGROUND: Yersinia pestis, the pathogen of plague, has greatly influenced human history on a global scale. Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR, an element participating in immunity against phages' invasion, is composed of short repeated sequences separated by unique spacers and provides the basis of the spoligotyping technology. In the present research, three CRISPR loci were analyzed in 125 strains of Y. pestis from 26 natural plague foci of China, the former Soviet Union and Mongolia were analyzed, for validating CRISPR-based genotyping method and better understanding adaptive microevolution of Y. pestis. METHODOLOGY/PRINCIPAL FINDINGS: Using PCR amplification, sequencing and online data processing, a high degree of genetic diversity was revealed in all three CRISPR elements. The distribution of spacers and their arrays in Y. pestis strains is strongly region and focus-specific, allowing the construction of a hypothetic evolutionary model of Y. pestis. This model suggests transmission route of microtus strains that encircled Takla Makan Desert and ZhunGer Basin. Starting from Tadjikistan, one branch passed through the Kunlun Mountains, and moved to the Qinghai-Tibet Plateau. Another branch went north via the Pamirs Plateau, the Tianshan Mountains, the Altai Mountains and the Inner Mongolian Plateau. Other Y. pestis lineages might be originated from certain areas along those routes. CONCLUSIONS/SIGNIFICANCE: CRISPR can provide important information for genotyping and evolutionary research of bacteria, which will help to trace the source of outbreaks. The resulting data will make possible the development of very low cost and high-resolution assays for the systematic typing of any new isolate.
Fu, Qiang; Su, Zhixin; Cheng, Yuqiang; Wang, Zhaofei; Li, Shiyu; Wang, Heng'an; Sun, Jianhe; Yan, Yaxian
In order to investigate the diverse characteristics of clustered, regularly interspaced short palindromic repeat (CRISPR) arrays and the distribution of virulence factor genes in avian Escherichia coli, 80 E. coli isolates obtained from chickens with avian pathogenic E. coli (APEC) or avian fecal commensal E. coli (AFEC) were identified. Using the multiplex polymerase chain reaction (PCR), five genes were subjected to phylogenetic typing and examined for CRISPR arrays to study genetic relatedness among the strains. The strains were further analyzed for CRISPR loci and virulence factor genes to determine a possible association between their CRISPR elements and their potential virulence. The strains were divided into five phylogenetic groups: A, B1, B2, D and E. It was confirmed that two types of CRISPR arrays, CRISPR1 and CRISPR2, which contain up to 246 distinct spacers, were amplified in most of the strains. Further classification of the isolates was achieved by sorting them into nine CRISPR clusters based on their spacer profiles, which indicates a candidate typing method for E. coli. Several significant differences in invasion-associated gene distribution were found between the APEC isolates and the AFEC isolates. Our results identified the distribution of 11 virulence genes and CRISPR diversity in 80 strains. It was demonstrated that, with the exception of iucD and aslA, there was no sharp demarcation in the gene distribution between the pathogenic (APEC) and commensal (AFEC) strains, while the total number of indicated CRISPR spacers may have a positive correlation with the potential pathogenicity of the E. coli isolates. Copyright © 2016. Published by Elsevier Masson SAS.
Al-Attar, Sinan; Westra, Edze R; van der Oost, John; Brouns, Stan J J
2011-04-01
Many prokaryotes contain the recently discovered defense system against mobile genetic elements. This defense system contains a unique type of repetitive DNA stretches, termed Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs). CRISPRs consist of identical repeated DNA sequences (repeats), interspaced by highly variable sequences referred to as spacers. The spacers originate from either phages or plasmids and comprise the prokaryotes' 'immunological memory'. CRISPR-associated (cas) genes encode conserved proteins that together with CRISPRs make-up the CRISPR/Cas system, responsible for defending the prokaryotic cell against invaders. CRISPR-mediated resistance has been proposed to involve three stages: (i) CRISPR-Adaptation, the invader DNA is encountered by the CRISPR/Cas machinery and an invader-derived short DNA fragment is incorporated in the CRISPR array. (ii) CRISPR-Expression, the CRISPR array is transcribed and the transcript is processed by Cas proteins. (iii) CRISPR-Interference, the invaders' nucleic acid is recognized by complementarity to the crRNA and neutralized. An application of the CRISPR/Cas system is the immunization of industry-relevant prokaryotes (or eukaryotes) against mobile-genetic invasion. In addition, the high variability of the CRISPR spacer content can be exploited for phylogenetic and evolutionary studies. Despite impressive progress during the last couple of years, the elucidation of several fundamental details will be a major challenge in future research.
Pride, David T; Salzman, Julia; Relman, David A
2012-09-01
Explorations of human microbiota have provided substantial insight into microbial community composition; however, little is known about interactions between various microbial components in human ecosystems. In response to the powerful impact of viral predation, bacteria have acquired potent defences, including an adaptive immune response based on the clustered regularly interspaced short palindromic repeats (CRISPRs)/Cas system. To improve our understanding of the interactions between bacteria and their viruses in humans, we analysed 13 977 streptococcal CRISPR sequences and compared them with 2 588 172 virome reads in the saliva of four human subjects over 17 months. We found a diverse array of viruses and CRISPR spacers, many of which were specific to each subject and time point. There were numerous viral sequences matching CRISPR spacers; these matches were highly specific for salivary viruses. We determined that spacers and viruses coexist at the same time, which suggests that streptococcal CRISPR/Cas systems are under constant pressure from salivary viruses. CRISPRs in some subjects were just as likely to match viral sequences from other subjects as they were to match viruses from the same subject. Because interactions between bacteria and viruses help to determine the structure of bacterial communities, CRISPR-virus analyses are likely to provide insight into the forces shaping the human microbiome.
Zheng, Po-Xing; Chan, Yuen-Chi; Chiou, Chien-Shun; Chiang-Ni, Chuan; Wang, Shu-Ying; Tsai, Pei-Jane; Chuang, Woei-Jer; Lin, Yee-Shin; Liu, Ching-Chuan; Wu, Jiunn-Jong
2015-01-01
Clustered regularly interspaced short palindromic repeats (CRISPR) are the bacterial adaptive immune system against foreign nucleic acids. Given the variable nature of CRISPR, it could be a good marker for molecular epidemiology. Group A streptococcus is one of the major human pathogens. It has two CRISPR loci, including CRISPR01 and CRISPR02. The aim of this study was to analyze the distribution of CRISPR-associated gene cassettes (cas) and CRISPR arrays in highly prevalent emm types. The cas cassette and CRISPR array in two CRISPR loci were analyzed in a total of 332 strains, including emm1, emm3, emm4, emm12, and emm28 strains. The CRISPR type was defined by the spacer content of each CRISPR array. All strains had at least one cas cassette or CRISPR array. More than 90% of the spacers were found in one emm type, specifically. Comparing the consistency between emm and CRISPR types by Simpson's index of diversity and the adjusted Wallace coefficient, CRISPR01 type was concordant to emm type, and CRISPR02 showed unidirectional congruence to emm type, suggesting that at least for the majority of isolates causing infection in high income countries, the emm type can be inferred from CRISPR analysis, which can further discriminate isolates sharing the same emm type.
Po-Xing Zheng
Full Text Available Clustered regularly interspaced short palindromic repeats (CRISPR are the bacterial adaptive immune system against foreign nucleic acids. Given the variable nature of CRISPR, it could be a good marker for molecular epidemiology. Group A streptococcus is one of the major human pathogens. It has two CRISPR loci, including CRISPR01 and CRISPR02. The aim of this study was to analyze the distribution of CRISPR-associated gene cassettes (cas and CRISPR arrays in highly prevalent emm types. The cas cassette and CRISPR array in two CRISPR loci were analyzed in a total of 332 strains, including emm1, emm3, emm4, emm12, and emm28 strains. The CRISPR type was defined by the spacer content of each CRISPR array. All strains had at least one cas cassette or CRISPR array. More than 90% of the spacers were found in one emm type, specifically. Comparing the consistency between emm and CRISPR types by Simpson's index of diversity and the adjusted Wallace coefficient, CRISPR01 type was concordant to emm type, and CRISPR02 showed unidirectional congruence to emm type, suggesting that at least for the majority of isolates causing infection in high income countries, the emm type can be inferred from CRISPR analysis, which can further discriminate isolates sharing the same emm type.
Stachler, Aris-Edda; Marchfelder, Anita
2016-01-01
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system is used by bacteria and archaea to fend off foreign genetic elements. Since its discovery it has been developed into numerous applications like genome editing and regulation of transcription in eukaryotes and bacteria. For archaea currently no tools for transcriptional repression exist. Because molecular biology analyses in archaea become more and more widespread such a tool is vital for investigating the biological function of essential genes in archaea. Here we use the model archaeon Haloferax volcanii to demonstrate that its endogenous CRISPR-Cas system I-B can be harnessed to repress gene expression in archaea. Deletion of cas3 and cas6b genes results in efficient repression of transcription. crRNAs targeting the promoter region reduced transcript levels down to 8%. crRNAs targeting the reading frame have only slight impact on transcription. crRNAs that target the coding strand repress expression only down to 88%, whereas crRNAs targeting the template strand repress expression down to 8%. Repression of an essential gene results in reduction of transcription levels down to 22%. Targeting efficiencies can be enhanced by expressing a catalytically inactive Cas3 mutant. Genes can be targeted on plasmids or on the chromosome, they can be monocistronic or part of a polycistronic operon. PMID:27226589
Stachler, Aris-Edda; Marchfelder, Anita
2016-07-15
The clustered regularly interspaced short palindromic repeats (CRISPR)-Cas system is used by bacteria and archaea to fend off foreign genetic elements. Since its discovery it has been developed into numerous applications like genome editing and regulation of transcription in eukaryotes and bacteria. For archaea currently no tools for transcriptional repression exist. Because molecular biology analyses in archaea become more and more widespread such a tool is vital for investigating the biological function of essential genes in archaea. Here we use the model archaeon Haloferax volcanii to demonstrate that its endogenous CRISPR-Cas system I-B can be harnessed to repress gene expression in archaea. Deletion of cas3 and cas6b genes results in efficient repression of transcription. crRNAs targeting the promoter region reduced transcript levels down to 8%. crRNAs targeting the reading frame have only slight impact on transcription. crRNAs that target the coding strand repress expression only down to 88%, whereas crRNAs targeting the template strand repress expression down to 8%. Repression of an essential gene results in reduction of transcription levels down to 22%. Targeting efficiencies can be enhanced by expressing a catalytically inactive Cas3 mutant. Genes can be targeted on plasmids or on the chromosome, they can be monocistronic or part of a polycistronic operon. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.
Rezzonico, Fabio; Smits, Theo H M; Duffy, Brion
2011-06-01
The clustered regularly interspaced short palindromic repeat (CRISPR)/Cas system confers acquired heritable immunity against mobile nucleic acid elements in prokaryotes, limiting phage infection and horizontal gene transfer of plasmids. In CRISPR arrays, characteristic repeats are interspersed with similarly sized nonrepetitive spacers derived from transmissible genetic elements and acquired when the cell is challenged with foreign DNA. New spacers are added sequentially and the number and type of CRISPR units can differ among strains, providing a record of phage/plasmid exposure within a species and giving a valuable typing tool. The aim of this work was to investigate CRISPR diversity in the highly homogeneous species Erwinia amylovora, the causal agent of fire blight. A total of 18 CRISPR genotypes were defined within a collection of 37 cosmopolitan strains. Strains from Spiraeoideae plants clustered in three major groups: groups II and III were composed exclusively of bacteria originating from the United States, whereas group I generally contained strains of more recent dissemination obtained in Europe, New Zealand, and the Middle East. Strains from Rosoideae and Indian hawthorn (Rhaphiolepis indica) clustered separately and displayed a higher intrinsic diversity than that of isolates from Spiraeoideae plants. Reciprocal exclusion was generally observed between plasmid content and cognate spacer sequences, supporting the role of the CRISPR/Cas system in protecting against foreign DNA elements. However, in several group III strains, retention of plasmid pEU30 is inconsistent with a functional CRISPR/Cas system.
Hara, Yasushi; Hayashi, Kyohei; Nakajima, Takuya; Kagawa, Shizuko; Tazumi, Akihiro; Moore, John E; Matsuda, Motoo
2013-09-01
Clustered regularly interspaced short palindromic repeats (CRISPRs), of approximately 10,000 base pairs (bp) in length, were shown to occur in the Japanese Taylorella equigenitalis strain, EQ59. The locus was composed of the putative CRISPRs-associated with 5 (cas5), RAMP csd1, csd2, recB, cas1, a leader region, 13 CRISPR consensus sequence repeats (each 32 bp; 5'-TCAGCCACGTTCGCGTGGCTGTGTGTTTAAAG-3'). These were in turn separated by 12 non repetitive unique spacer regions of similar length. In addition, a leader region, a transposase/IS protein, a leader region, and cas3 were also seen. All seven putative open reading frames carry their ribosome binding sites. Promoter consensus sequences at the -35 and -10 regions and putative intrinsic ρ-independent transcription terminator regions also occurred. A possible long overlap of 170 bp in length occurred between the recB and cas1 loci. Positive reverse transcription PCR signals of cas5, RAMP csd1, csd2-recB/cas1, and cas3 were generated. A putative secondary structure of the CRISPR consensus repeats was constructed. Following this, CRISPR results of the T. equigenitalis EQ59 isolate were subsequently compared with those from the Taylorella asinigenitalis MCE3 isolate.
Nam, Ki Hyun; Ding, Fran; Haitjema, Charles; Huang, Qingqiu; DeLisa, Matthew P; Ke, Ailong
2012-10-19
The CRISPR (clustered regularly interspaced short palindromic repeats) system is a prokaryotic RNA-based adaptive immune system against extrachromosomal genetic elements. Cas2 is a universally conserved core CRISPR-associated protein required for the acquisition of new spacers for CRISPR adaptation. It was previously characterized as an endoribonuclease with preference for single-stranded (ss)RNA. Here, we show using crystallography, mutagenesis, and isothermal titration calorimetry that the Bacillus halodurans Cas2 (Bha_Cas2) from the subtype I-C/Dvulg CRISPR instead possesses metal-dependent endonuclease activity against double-stranded (ds)DNA. This activity is consistent with its putative function in producing new spacers for insertion into the 5'-end of the CRISPR locus. Mutagenesis and isothermal titration calorimetry studies revealed that a single divalent metal ion (Mg(2+) or Mn(2+)), coordinated by a symmetric Asp pair in the Bha_Cas2 dimer, is involved in the catalysis. We envision that a pH-dependent conformational change switches Cas2 into a metal-binding competent conformation for catalysis. We further propose that the distinct substrate preferences among Cas2 proteins may be determined by the sequence and structure in the β1-α1 loop.
Mashimo, Tomoji
2013-01-01
The laboratory rat has been widely used as an animal model in biomedical science for more than 150 years. Applying zinc-finger nucleases or transcription activator-like effector nucleases to rat embryos via microinjection is an efficient genome editing tool for generating targeted knockout rats. Recently, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated endonucleases have been used as an effective tool for precise and multiplex genome editing in mice and ra...
Price, Erin P; Smith, Helen; Huygens, Flavia; Giffard, Philip M.
2007-01-01
A novel method for genotyping the clustered, regularly interspaced short-palindromic-repeat (CRISPR) locus of Campylobacter jejuni is described. Following real-time PCR, CRISPR products were subjected to high-resolution melt (HRM) analysis, a new technology that allows precise melt profile determination of amplicons. This investigation shows that the CRISPR HRM assay provides a powerful addition to existing C. jejuni genotyping methods and emphasizes the potential of HRM for genotyping short ...
Wehnes, C A; Rehberger, T G; Barrangou, R; Smith, A H
2014-10-01
Salmonella enterica ssp. enterica is a foodborne pathogen able to cause disease in both humans and animals. Diverse serovars of this pathogen exist, some of which are host specific, causing a range of clinical symptoms from asymptomatic infection through morbidity and mortality. According to a 2007 survey by the USDA National Animal Health Monitoring System, fecal shedding of Salmonella from healthy cows occurs on 39.7% of dairy farms in the United States. Certain serovars are frequently isolated from dairy farms and the majority of isolates from the National Animal Health Monitoring System study were represented by 5 serovars; however, genotypic diversity was not examined. The objective of this study was to determine the diversity of clustered regularly interspaced short palindromic repeats (CRISPR) loci in Salmonella collected from 8 dairy farms with a previous history of salmonellosis. None of the cows or calves sampled on 2 of the 8 dairy farms were shedding Salmonella, although Salmonella was detected in a cow bedding sample on 1 of these farms. Salmonella populations were discrete on each farm, according to CRISPR typing, with the exception of an Anatum var. 15+ type on farms 5 and 6 and the Montevideo type on farms 1 and 2. One to 4 distinct CRISPR genotypes were identified per farm. The CRISPR typing differed within serovars, as Montevideo, Anatum var. 15+, and Muenster serovars had no overlap of spacer content, even on the same farm, reflecting between- and within-serovar genetic diversity. The dynamic nature of Salmonella populations was shown in a farm that was sampled longitudinally over 13.5 mo. Changes in serovar from 3,19:-:z27 to Montevideo was observed between the first sampling time and 8 mo later, with concomitant change in CRISPR alleles. The results indicate that Salmonella strains present in smaller dairy herds (<500 head) are specific to that farm and new Salmonella strains may emerge over time. Copyright © 2014 American Dairy Science
Chen, Jing; Li, Tiancheng; Zhou, Xuedong; Cheng, Lei; Huo, Yuanyuan; Zou, Jing; Li, Yuqing
2017-07-29
The aim of this study was to analyze the characteristics of the clustered regularly interspaced short palindromic repeats (CRISPR) sites in 45 clinical Streptococcus mutans strains and their relationship to the clinical manifestations of early childhood caries (ECC). Forty-five S. mutans strains were isolated from the plaque samples taken from sixty-three children. CRISPR sites were sequenced and BLAST was used to compare these sites to those in the CRISPRTarget database. The association between the distribution of CRISPR sites and the manifestation of caries was analyzed by Chi-Square test. Further, biofilm formation (by crystal violet staining) and the synthesis of polysaccharide (by anthrone-sulfuric method) of all clinical isolated S. mutans strains with both CRISPR sites and no CRISPR site were comapared. Finally, acidogenicity and acidurity of two typical strains were determined using pH drop and acid tolerance assays. Biofilm formation and EPS synthesis by two typical strains were compared by 3D CLSM (Confocal Laser Scanning Microscope) assays and the expression of gtf genes were evaluated using qPCR. We found that most of the spacers in the clinical S. mutans strains were derived from Streptococcus phages APCM01 and M102. The number of CRISPR sites in these strains was associated with the clinical manifestations of ECC. Moreover, we found that the biofilm formation and EPS synthesis ability of the S. mutans strains with both CRISPR sites was significant improved. An association was found between the distribution of CRISPR sites and the clinical manifestations of caries. The CRISPR sites might contribute to the cariogenic potential of S. mutans. Copyright © 2017 Elsevier Ltd. All rights reserved.
Mashimo, Tomoji
2014-01-01
The laboratory rat has been widely used as an animal model in biomedical science for more than 150 years. Applying zinc-finger nucleases or transcription activator-like effector nucleases to rat embryos via microinjection is an efficient genome editing tool for generating targeted knockout rats. Recently, clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated endonucleases have been used as an effective tool for precise and multiplex genome editing in mice and rats. In this review, the advantages and disadvantages of these site-specific nuclease technologies for genetic analysis and manipulation in rats are discussed.
Lintner, Nathanael G; Kerou, Melina; Brumfield, Susan K
2011-01-01
In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA....... The Escherichia coli "CRISPR-associated complex for antiviral defense" (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5......a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2...
Duijn, E. van; Barbu, I.M.; Barendregt, A.; Jore, M.M.; Wiedenheft, B.; Lundgren, M.; Westra, E.R.; Brouns, S.J.J.; Doudna, J.A.; van der Oost, J.; Heck, A.J.R.
2012-01-01
The CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) immune system of bacteria and archaea provides acquired resistance against viruses and plasmids, by a strategy analogous to RNA-interference. Key components of the defense system are ribonucleoprotein
Lintner, Nathanael G.; Kerou, Melina; Brumfield, Susan K.; Graham, Shirley; Liu, Huanting; Naismith, James H.; Sdano, Matthew; Peng, Nan; She, Qunxin; Copié, Valérie; Young, Mark J.; White, Malcolm F.; Lawrence, C. Martin
2011-01-01
In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA. The Escherichia coli “CRISPR-associated complex for antiviral defense” (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2-Cas5a complex is sufficient to bind crRNA and complementary ssDNA. The structure of Csa2 reveals a crescent-shaped structure unexpectedly composed of a modified RNA-recognition motif and two additional domains present as insertions in the RNA-recognition motif. Conserved residues indicate potential crRNA- and target DNA-binding sites, and the H160A variant shows significantly reduced affinity for crRNA. We propose a general subunit architecture for CASCADE in other bacteria and Archaea. PMID:21507944
Nam, Ki Hyun; Kurinov, Igor; Ke, Ailong (Cornell); (NWU)
2012-05-22
Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 {angstrom} tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is {approx}26 {angstrom} wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an {alpha}/{beta} domain and an {alpha}-helical domain; significant hinge motion was observed between these two domains. Ca{sup 2+} was located at strategic positions in the oligomerization interface. We further showed that removal of Ca{sup 2+} ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca{sup 2+} ions.
Tasaki, E; Hirayama, J; Tazumi, A; Hayashi, K; Hara, Y; Ueno, H; Moore, J E; Millar, B C; Matsuda, M
2012-02-01
Novel clustered regularly-interspaced short palindromic repeats (CRISPRs) locus [7,500 base pairs (bp) in length] occurred in the urease-positive thermophilic Campylobacter (UPTC) Japanese isolate, CF89-12. The 7,500 bp gene loci consisted of the 5'-methylaminomethyl-2-thiouridylate methyltransferase gene, putative (P) CRISPR associated (p-Cas), putative open reading frames, Cas1 and Cas2, leader sequence region (146 bp), 12 CRISPRs consensus sequence repeats (each 36 bp) separated by a non-repetitive unique spacer region of similar length (26-31 bp) and the phosphatidyl glycerophosphatase A gene. When the CRISPRs loci in the UPTC CF89-12 and five C. jejuni isolates were compared with one another, these six isolates contained p-Cas, Cas1 and Cas2 within the loci. Four to 12 CRISPRs consensus sequence repeats separated by a non-repetitive unique spacer region occurred in six isolates and the nucleotide sequences of those repeats gave approximately 92-100% similarity with each other. However, no sequence similarity occurred in the unique spacer regions among these isolates. The putative σ(70) transcriptional promoter and the hypothetical ρ-independent terminator structures for the CRISPRs and Cas were detected. No in vivo transcription of p-Cas, Cas1 and Cas2 was confirmed in the UPTC cells.
Zheng, P-X; Chiang-Ni, C; Wang, S-Y; Tsai, P-J; Kuo, C-F; Chuang, W-J; Lin, Y-S; Liu, C-C; Wu, J-J
2014-06-01
Clustered regularly interspaced short palindromic repeats (CRISPR) are composed of numerous repeat-spacer units and are considered a prokaryotic defence system against foreign nucleic acids. Since antibiotic-resistant genes are frequently encoded in foreign nucleic acids, the aim of this study was to test whether erythromycin susceptibility in group A streptococcus (Streptococcus pyogenes) is associated with characteristics of CRISPR elements. Erythromycin susceptibility of 330 isolates collected between 1997 and 2003 was analysed. Among 29 emm types, emm12, emm75 and emm92 showed significant changes in erythromycin-resistance rates. By sequencing the spacers from two CRISPR loci, spacer contents in emm12, emm75 and emm92 strains were associated with erythromycin susceptibility. Strains with fewer spacers were more resistant to erythromycin. Moreover, in emm4 strains, which showed no significant change in their annual erythromycin-resistance rate, CRISPR type and number of spacers were not correlated with erythromycin susceptibility. These results highlight a novel association between CRISPR spacer content and erythromycin susceptibility in group A streptococcus.
Hatoum-Aslan, Asma; Maniv, Inbal; Marraffini, Luciano A
2011-12-27
Precise RNA processing is fundamental to all small RNA-mediated interference pathways. In prokaryotes, clustered, regularly interspaced, short palindromic repeats (CRISPR) loci encode small CRISPR RNAs (crRNAs) that protect against invasive genetic elements by antisense targeting. CRISPR loci are transcribed as a long precursor that is cleaved within repeat sequences by CRISPR-associated (Cas) proteins. In many organisms, this primary processing generates crRNA intermediates that are subject to additional nucleolytic trimming to render mature crRNAs of specific lengths. The molecular mechanisms underlying this maturation event remain poorly understood. Here, we defined the genetic requirements for crRNA primary processing and maturation in Staphylococcus epidermidis. We show that changes in the position of the primary processing site result in extended or diminished maturation to generate mature crRNAs of constant length. These results indicate that crRNA maturation occurs by a ruler mechanism anchored at the primary processing site. We also show that maturation is mediated by specific cas genes distinct from those genes involved in primary processing, showing that this event is directed by CRISPR/Cas loci.
Liu, Fenyun; Kariyawasam, Subhashinie; Jayarao, Bhushan M; Barrangou, Rodolphe; Gerner-Smidt, Peter; Ribot, Efrain M; Knabel, Stephen J; Dudley, Edward G
2011-07-01
Salmonella enterica subsp. enterica serovar Enteritidis is a major cause of food-borne salmonellosis in the United States. Two major food vehicles for S. Enteritidis are contaminated eggs and chicken meat. Improved subtyping methods are needed to accurately track specific strains of S. Enteritidis related to human salmonellosis throughout the chicken and egg food system. A sequence typing scheme based on virulence genes (fimH and sseL) and clustered regularly interspaced short palindromic repeats (CRISPRs)-CRISPR-including multi-virulence-locus sequence typing (designated CRISPR-MVLST)-was used to characterize 35 human clinical isolates, 46 chicken isolates, 24 egg isolates, and 63 hen house environment isolates of S. Enteritidis. A total of 27 sequence types (STs) were identified among the 167 isolates. CRISPR-MVLST identified three persistent and predominate STs circulating among U.S. human clinical isolates and chicken, egg, and hen house environmental isolates in Pennsylvania, and an ST that was found only in eggs and humans. It also identified a potential environment-specific sequence type. Moreover, cluster analysis based on fimH and sseL identified a number of clusters, of which several were found in more than one outbreak, as well as 11 singletons. Further research is needed to determine if CRISPR-MVLST might help identify the ecological origins of S. Enteritidis strains that contaminate chickens and eggs.
Yosef, Ido; Goren, Moran G; Kiro, Ruth; Edgar, Rotem; Qimron, Udi
2011-12-13
Prokaryotic DNA arrays arranged as clustered regularly interspaced short palindromic repeats (CRISPR), along with their associated proteins, provide prokaryotes with adaptive immunity by RNA-mediated targeting of alien DNA or RNA matching the sequences between the repeats. Here, we present a thorough screening system for the identification of bacterial proteins participating in immunity conferred by the Escherichia coli CRISPR system. We describe the identification of one such protein, high-temperature protein G (HtpG), a homolog of the eukaryotic chaperone heat-shock protein 90. We demonstrate that in the absence of htpG, the E. coli CRISPR system loses its suicidal activity against λ prophage and its ability to provide immunity from lysogenization. Transcomplementation of htpG restores CRISPR activity. We further show that inactivity of the CRISPR system attributable to htpG deficiency can be suppressed by expression of Cas3, a protein that is essential for its activity. Accordingly, we also find that the steady-state level of overexpressed Cas3 is significantly enhanced following HtpG expression. We conclude that HtpG is a newly identified positive modulator of the CRISPR system that is essential for maintaining functional levels of Cas3.
Nam, Ki Hyun; Kurinov, Igor; Ke, Ailong
2011-09-02
Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated protein genes (cas genes) are widespread in bacteria and archaea. They form a line of RNA-based immunity to eradicate invading bacteriophages and malicious plasmids. A key molecular event during this process is the acquisition of new spacers into the CRISPR loci to guide the selective degradation of the matching foreign genetic elements. Csn2 is a Nmeni subtype-specific cas gene required for new spacer acquisition. Here we characterize the Enterococcus faecalis Csn2 protein as a double-stranded (ds-) DNA-binding protein and report its 2.7 Å tetrameric ring structure. The inner circle of the Csn2 tetrameric ring is ∼26 Å wide and populated with conserved lysine residues poised for nonspecific interactions with ds-DNA. Each Csn2 protomer contains an α/β domain and an α-helical domain; significant hinge motion was observed between these two domains. Ca(2+) was located at strategic positions in the oligomerization interface. We further showed that removal of Ca(2+) ions altered the oligomerization state of Csn2, which in turn severely decreased its affinity for ds-DNA. In summary, our results provided the first insight into the function of the Csn2 protein in CRISPR adaptation by revealing that it is a ds-DNA-binding protein functioning at the quaternary structure level and regulated by Ca(2+) ions.
Lintner, Nathanael G; Kerou, Melina; Brumfield, Susan K; Graham, Shirley; Liu, Huanting; Naismith, James H; Sdano, Matthew; Peng, Nan; She, Qunxin; Copié, Valérie; Young, Mark J; White, Malcolm F; Lawrence, C Martin
2011-06-17
In response to viral infection, many prokaryotes incorporate fragments of virus-derived DNA into loci called clustered regularly interspaced short palindromic repeats (CRISPRs). The loci are then transcribed, and the processed CRISPR transcripts are used to target invading viral DNA and RNA. The Escherichia coli "CRISPR-associated complex for antiviral defense" (CASCADE) is central in targeting invading DNA. Here we report the structural and functional characterization of an archaeal CASCADE (aCASCADE) from Sulfolobus solfataricus. Tagged Csa2 (Cas7) expressed in S. solfataricus co-purifies with Cas5a-, Cas6-, Csa5-, and Cas6-processed CRISPR-RNA (crRNA). Csa2, the dominant protein in aCASCADE, forms a stable complex with Cas5a. Transmission electron microscopy reveals a helical complex of variable length, perhaps due to substoichiometric amounts of other CASCADE components. A recombinant Csa2-Cas5a complex is sufficient to bind crRNA and complementary ssDNA. The structure of Csa2 reveals a crescent-shaped structure unexpectedly composed of a modified RNA-recognition motif and two additional domains present as insertions in the RNA-recognition motif. Conserved residues indicate potential crRNA- and target DNA-binding sites, and the H160A variant shows significantly reduced affinity for crRNA. We propose a general subunit architecture for CASCADE in other bacteria and Archaea.
Li, Xu; Gao, Min; Choi, Jong Min; Kim, Beom-Jun; Zhou, Mao-Tian; Chen, Zhen; Jain, Antrix N; Jung, Sung Yun; Yuan, Jingsong; Wang, Wenqi; Wang, Yi; Chen, Junjie
2017-04-01
Neurofibromin (NF1) is a well known tumor suppressor that is commonly mutated in cancer patients. It physically interacts with RAS and negatively regulates RAS GTPase activity. Despite the importance of NF1 in cancer, a high quality endogenous NF1 interactome has yet to be established. In this study, we combined clustered, regularly interspaced short palindromic repeats (CRISPR)/Cas9-mediated gene knock-out technology with affinity purification using antibodies against endogenous proteins, followed by mass spectrometry analysis, to sensitively and accurately detect NF1 protein-protein interactions in unaltered in vivo settings. Using this system, we analyzed endogenous NF1-associated protein complexes and identified 49 high-confidence candidate interaction proteins, including RAS and other functionally relevant proteins. Through functional validation, we found that NF1 negatively regulates mechanistic target of rapamycin signaling (mTOR) in a LAMTOR1-dependent manner. In addition, the cell growth and survival of NF1-deficient cells have become dependent on hyperactivation of the mTOR pathway, and the tumorigenic properties of these cells have become dependent on LAMTOR1. Taken together, our findings may provide novel insights into therapeutic approaches targeting NF1-deficient tumors. © 2017 by The American Society for Biochemistry and Molecular Biology, Inc.
Maier, Lisa-Katharina; Stachler, Aris-Edda; Saunders, Sita J.; Backofen, Rolf; Marchfelder, Anita
2015-01-01
The prokaryotic immune system CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) is a defense system that protects prokaryotes against foreign DNA. The short CRISPR RNAs (crRNAs) are central components of this immune system. In CRISPR-Cas systems type I and III, crRNAs are generated by the endonuclease Cas6. We developed a Cas6b-independent crRNA maturation pathway for the Haloferax type I-B system in vivo that expresses a functional crRNA, which we termed independently generated crRNA (icrRNA). The icrRNA is effective in triggering degradation of an invader plasmid carrying the matching protospacer sequence. The Cas6b-independent maturation of the icrRNA allowed mutation of the repeat sequence without interfering with signals important for Cas6b processing. We generated 23 variants of the icrRNA and analyzed them for activity in the interference reaction. icrRNAs with deletions or mutations of the 3′ handle are still active in triggering an interference reaction. The complete 3′ handle could be removed without loss of activity. However, manipulations of the 5′ handle mostly led to loss of interference activity. Furthermore, we could show that in the presence of an icrRNA a strain without Cas6b (Δcas6b) is still active in interference. PMID:25512373
Kuno, Sotaro; Yoshida, Takashi; Kaneko, Takakazu; Sako, Yoshihiko
2012-08-01
Clustered regularly interspaced short palindromic repeats (CRISPR) confer sequence-dependent, adaptive resistance in prokaryotes against viruses and plasmids via incorporation of short sequences, called spacers, derived from foreign genetic elements. CRISPR loci are thus considered to provide records of past infections. To describe the host-parasite (i.e., cyanophages and plasmids) interactions involving the bloom-forming freshwater cyanobacterium Microcystis aeruginosa, we investigated CRISPR in four M. aeruginosa strains and in two previously sequenced genomes. The number of spacers in each locus was larger than the average among prokaryotes. All spacers were strain specific, except for a string of 11 spacers shared in two closely related strains, suggesting diversification of the loci. Using CRISPR repeat-based PCR, 24 CRISPR genotypes were identified in a natural cyanobacterial community. Among 995 unique spacers obtained, only 10 sequences showed similarity to M. aeruginosa phage Ma-LMM01. Of these, six spacers showed only silent or conservative nucleotide mutations compared to Ma-LMM01 sequences, suggesting a strategy by the cyanophage to avert CRISPR immunity dependent on nucleotide identity. These results imply that host-phage interactions can be divided into M. aeruginosa-cyanophage combinations rather than pandemics of population-wide infectious cyanophages. Spacer similarity also showed frequent exposure of M. aeruginosa to small cryptic plasmids that were observed only in a few strains. Thus, the diversification of CRISPR implies that M. aeruginosa has been challenged by diverse communities (almost entirely uncharacterized) of cyanophages and plasmids.
Toro, Magaly; Cao, Guojie; Ju, Wenting; Allard, Marc; Barrangou, Rodolphe; Zhao, Shaohua; Brown, Eric; Meng, Jianghong
2014-02-01
Shiga toxin-producing Escherichia coli (STEC) strains (n = 194) representing 43 serotypes and E. coli K-12 were examined for clustered regularly interspaced short palindromic repeat (CRISPR) arrays to study genetic relatedness among STEC serotypes. A subset of the strains (n = 81) was further analyzed for subtype I-E cas and virulence genes to determine a possible association of CRISPR elements with potential virulence. Four types of CRISPR arrays were identified. CRISPR1 and CRISPR2 were present in all strains tested; 1 strain also had both CRISPR3 and CRISPR4, whereas 193 strains displayed a short, combined array, CRISPR3-4. A total of 3,353 spacers were identified, representing 528 distinct spacers. The average length of a spacer was 32 bp. Approximately one-half of the spacers (54%) were unique and found mostly in strains of less common serotypes. Overall, CRISPR spacer contents correlated well with STEC serotypes, and identical arrays were shared between strains with the same H type (O26:H11, O103:H11, and O111:H11). There was no association identified between the presence of subtype I-E cas and virulence genes, but the total number of spacers had a negative correlation with potential pathogenicity (P CRISPR-cas system and potential virulence needs to be determined on a broader scale, and the biological link will need to be established.
Chen, Shuqing; Hou, Chengxiang; Bi, Honglun; Wang, Yueqiang; Xu, Jun; Li, Muwang; James, Anthony A; Huang, Yongping; Tan, Anjiang
2017-04-15
We developed a novel antiviral strategy by combining transposon-based transgenesis and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system for the direct cleavage of Bombyx mori nucleopolyhedrovirus (BmNPV) genome DNA to promote virus clearance in silkworms. We demonstrate that transgenic silkworms constitutively expressing Cas9 and guide RNAs targeting the BmNPV immediate early-1 (ie-1) and me53 genes effectively induce target-specific cleavage and subsequent mutagenesis, especially large (∼7-kbp) segment deletions in BmNPV genomes, and thus exhibit robust suppression of BmNPV proliferation. Transgenic animals exhibited higher and inheritable resistance to BmNPV infection than wild-type animals. Our approach will not only contribute to modern sericulture but also shed light on future antiviral therapy.IMPORTANCE Pathogen genome targeting has shown its potential in antiviral research. However, transgenic CRISPR/Cas9 system-mediated viral genome targeting has not been reported as an antiviral strategy in a natural animal host of a virus. Our data provide an effective approach against BmNPV infection in a real-world biological system and demonstrate the potential of transgenic CRISPR/Cas9 systems in antiviral research in other species. Copyright © 2017 Chen et al.
Maier, Lisa-Katharina; Stachler, Aris-Edda; Saunders, Sita J; Backofen, Rolf; Marchfelder, Anita
2015-02-13
The prokaryotic immune system CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) is a defense system that protects prokaryotes against foreign DNA. The short CRISPR RNAs (crRNAs) are central components of this immune system. In CRISPR-Cas systems type I and III, crRNAs are generated by the endonuclease Cas6. We developed a Cas6b-independent crRNA maturation pathway for the Haloferax type I-B system in vivo that expresses a functional crRNA, which we termed independently generated crRNA (icrRNA). The icrRNA is effective in triggering degradation of an invader plasmid carrying the matching protospacer sequence. The Cas6b-independent maturation of the icrRNA allowed mutation of the repeat sequence without interfering with signals important for Cas6b processing. We generated 23 variants of the icrRNA and analyzed them for activity in the interference reaction. icrRNAs with deletions or mutations of the 3' handle are still active in triggering an interference reaction. The complete 3' handle could be removed without loss of activity. However, manipulations of the 5' handle mostly led to loss of interference activity. Furthermore, we could show that in the presence of an icrRNA a strain without Cas6b (Δcas6b) is still active in interference. © 2015 by The American Society for Biochemistry and Molecular Biology, Inc.
Mulepati, Sabin; Bailey, Scott
2011-09-09
RNA transcribed from clustered regularly interspaced short palindromic repeats (CRISPRs) protects many prokaryotes from invasion by foreign DNA such as viruses, conjugative plasmids, and transposable elements. Cas3 (CRISPR-associated protein 3) is essential for this CRISPR protection and is thought to mediate cleavage of the foreign DNA through its N-terminal histidine-aspartate (HD) domain. We report here the 1.8 Å crystal structure of the HD domain of Cas3 from Thermus thermophilus HB8. Structural and biochemical studies predict that this enzyme binds two metal ions at its active site. We also demonstrate that the single-stranded DNA endonuclease activity of this T. thermophilus domain is activated not by magnesium but by transition metal ions such as manganese and nickel. Structure-guided mutagenesis confirms the importance of the metal-binding residues for the nuclease activity and identifies other active site residues. Overall, these results provide a framework for understanding the role of Cas3 in the CRISPR system.
Cheng, Man; Jin, Xubin; Mu, Lili; Wang, Fangyu; Li, Wei; Zhong, Xiaoling; Liu, Xuan; Shen, Wenchen; Liu, Ying; Zhou, Yan
2016-09-01
In utero electroporation (IUE) is commonly used to study cortical development of cerebrum by downregulating or overexpressing genes of interest in neural progenitor cells (NPCs) of small mammals. However, exogenous plasmids are lost or diluted over time. Furthermore, gene knockdown based on short-hairpin RNAs may exert nonspecific effects that lead to aberrant neuronal migration. Genomic engineering by the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system has great research and therapeutic potentials. Here we integrate the CRISPR/Cas9 components into the piggyBac (PB) transposon system (the CRISPR/Cas9-PB toolkit) for cortical IUEs. The mouse Sry-related HMG box-2 (Sox2) gene was selected as the target for its application. Most transduced cortical NPCs were depleted of SOX2 protein as early as 3 days post-IUE, whereas expressions of SOX1 and PAX6 remained intact. Furthermore, both the WT Cas9 and the D10A nickase mutant Cas9n showed comparable knockout efficiency. Transduced cortical cells were purified with fluorescence-activated cell sorting, and effective gene editing at the Sox2 loci was confirmed. Thus, application of the CRISPR/Cas9-PB toolkit in IUE is a promising strategy to study gene functions in cortical NPCs and their progeny. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.
Yu L
2014-12-01
Full Text Available Lan Yu, Xiaoli Wang, Da Zhu, Wencheng Ding, Liming Wang, Changlin Zhang, Xiaohui Jiang, Hui Shen, Shujie Liao, Ding Ma, Zheng Hu, Hui Wang Cancer Biology Research Center, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, People's Republic of China Abstract: High-risk human papillomavirus (HPV, especially HPV16, is considered a main causative agent of cervical cancer. Upon HPV infection, the viral oncoprotein E6 disrupts the host tumor-suppressor protein p53, thus promoting malignant transformation of normal cervical cells. Here, we used the newly developed programmable ribonucleic acid-guided clustered regularly interspaced short palindromic repeat (CRISPR/Cas system to disrupt the HPV16 E6 gene. We showed that HPV16 E6 deoxyribonucleic acid was cleaved at specific sites, leading to apoptosis and growth inhibition of HPV16-positive SiHa and CaSki cells, but not HPV-negative C33A or human embryonic kidney 293 cells. We also observed downregulation of the E6 protein and restoration of the p53 protein. These data proved that the HPV16 E6 ribonucleic acid-guided CRISPR/Cas system might be an effective therapeutic agent in treating HPV infection-related cervical malignancy. Keywords: CRISPR/Cas system, E6, p53, SiHa, CaSki, cervical cancer
Li, Hao; Li, Peng; Xie, Jing; Yi, Shengjie; Yang, Chaojie; Wang, Jian; Sun, Jichao; Liu, Nan; Wang, Xu; Wu, Zhihao; Wang, Ligui; Hao, Rongzhang; Wang, Yong; Jia, Leili; Li, Kaiqin; Qiu, Shaofu; Song, Hongbin
2014-08-01
A clustered regularly interspaced short palindromic repeat (CRISPR) typing method has recently been developed and used for typing and subtyping of Salmonella spp., but it is complicated and labor intensive because it has to analyze all spacers in two CRISPR loci. Here, we developed a more convenient and efficient method, namely, CRISPR locus spacer pair typing (CLSPT), which only needs to analyze the two newly incorporated spacers adjoining the leader array in the two CRISPR loci. We analyzed a CRISPR array of 82 strains belonging to 21 Salmonella serovars isolated from humans in different areas of China by using this new method. We also retrieved the newly incorporated spacers in each CRISPR locus of 537 Salmonella isolates which have definite serotypes in the Pasteur Institute's CRISPR Database to evaluate this method. Our findings showed that this new CLSPT method presents a high level of consistency (kappa = 0.9872, Matthew's correlation coefficient = 0.9712) with the results of traditional serotyping, and thus, it can also be used to predict serotypes of Salmonella spp. Moreover, this new method has a considerable discriminatory power (discriminatory index [DI] = 0.8145), comparable to those of multilocus sequence typing (DI = 0.8088) and conventional CRISPR typing (DI = 0.8684). Because CLSPT only costs about $5 to $10 per isolate, it is a much cheaper and more attractive method for subtyping of Salmonella isolates. In conclusion, this new method will provide considerable advantages over other molecular subtyping methods, and it may become a valuable epidemiologic tool for the surveillance of Salmonella infections. Copyright © 2014, American Society for Microbiology. All Rights Reserved.
Ren, Lu; Deng, Lin-Hua; Zhang, Ri-Peng; Wang, Cheng-Dong; Li, De-Sheng; Xi, Li-Xin; Chen, Zhen-rong; Yang, Rui; Huang, Jie; Zeng, Yang-ru; Wu, Hong-Lin; Cao, San-Jie; Wu, Rui; Huang, Yong; Yan, Qi-Gui
2017-01-01
Abstract Background: To detect drug resistance in Shigella obtained from the dung of the giant panda, explore the factors leading to drug resistance in Shigella, understand the characteristics of clustered, regularly interspaced, short, palindromic repeats (CRISPR), and assess the relationship between CRISPR and drug resistance. Methods: We collected fresh feces from 27 healthy giant pandas in the Giant Panda Conservation base (Wolong, China). We identified the strains of Shigella in the samples by using nucleotide sequence analysis. Further, the Kirby-Bauer paper method was used to determine drug sensitivity of the Shigella strains. CRISPR-associated protein genes cas1 and cas2 in Shigella were detected by polymerase chain reaction (PCR), and the PCR products were sequenced and compared. Results: We isolated and identified 17 strains of Shigella from 27 samples, including 14 strains of Shigella flexneri, 2 strains of Shigella sonnei, and 1 strain of Shigella dysenteriae. Further, drug resistance to cefazolin, imipenem, and amoxicillin–clavulanic acid was identified as a serious problem, as multidrug-resistant strains were detected. Further, cas1 and cas2 showed different degrees of point mutations. Conclusion: The CRISPR system widely exists in Shigella and shares homology with that in Escherichia coli. The cas1 and cas 2 mutations contribute to the different levels of resistance. Point mutations at sites 3176455, 3176590, and 3176465 in cas1 (a); sites 3176989, 3176992, and 3176995 in cas1 (b); sites 3176156 and 3176236 in cas2 may affect the resistance of bacteria, cause emergence of multidrug resistance, and increase the types of drug resistance. PMID:28207509
高志奇; 王东澍; 冯尔玲; 王秉翔; 惠一鸣; 韩少波; 焦磊; 刘先凯; 王恒樑
2014-01-01
[目的]考察炭疽芽胞杆菌中规律成簇的间隔短回文序列(Clustered regularly interspaced short palindromic repeats,CRISPR)位点多态性情况及基于CRISPR位点多态性的分子分型方法是否在炭疽芽胞杆菌分型中适用.[方法]下载NCBI数据库中6株炭疽芽胞杆菌基因组并截取其中CRISPR位点片段序列.根据炭疽芽胞杆菌内CRISPR位点信息,设计相关引物,以193株炭疽芽胞杆菌基因组为模板PCR扩增CRISPR位点片段,测序.本地Blast比对截取序列及测序结果,查看CRISPR位点在炭疽芽胞杆菌中的多态性情况,并比较炭疽芽胞杆菌与蜡样芽胞杆菌和苏云金芽胞杆菌内CRISPR位点情况.[结果]炭疽芽胞杆菌内CRISPR位点不存在多态性.[结论]基于CRISPR位点多态性的分子分型方法不适用于炭疽芽胞杆菌分型,但可以用于区分炭疽芽胞杆菌与蜡样芽胞杆菌和苏云金芽胞杆菌.
Ren, Lu; Deng, Lin-Hua; Zhang, Ri-Peng; Wang, Cheng-Dong; Li, De-Sheng; Xi, Li-Xin; Chen, Zhen-Rong; Yang, Rui; Huang, Jie; Zeng, Yang-Ru; Wu, Hong-Lin; Cao, San-Jie; Wu, Rui; Huang, Yong; Yan, Qi-Gui
2017-02-01
To detect drug resistance in Shigella obtained from the dung of the giant panda, explore the factors leading to drug resistance in Shigella, understand the characteristics of clustered, regularly interspaced, short, palindromic repeats (CRISPR), and assess the relationship between CRISPR and drug resistance. We collected fresh feces from 27 healthy giant pandas in the Giant Panda Conservation base (Wolong, China). We identified the strains of Shigella in the samples by using nucleotide sequence analysis. Further, the Kirby-Bauer paper method was used to determine drug sensitivity of the Shigella strains. CRISPR-associated protein genes cas1 and cas2 in Shigella were detected by polymerase chain reaction (PCR), and the PCR products were sequenced and compared. We isolated and identified 17 strains of Shigella from 27 samples, including 14 strains of Shigella flexneri, 2 strains of Shigella sonnei, and 1 strain of Shigella dysenteriae. Further, drug resistance to cefazolin, imipenem, and amoxicillin-clavulanic acid was identified as a serious problem, as multidrug-resistant strains were detected. Further, cas1 and cas2 showed different degrees of point mutations. The CRISPR system widely exists in Shigella and shares homology with that in Escherichia coli. The cas1 and cas 2 mutations contribute to the different levels of resistance. Point mutations at sites 3176455, 3176590, and 3176465 in cas1 (a); sites 3176989, 3176992, and 3176995 in cas1 (b); sites 3176156 and 3176236 in cas2 may affect the resistance of bacteria, cause emergence of multidrug resistance, and increase the types of drug resistance.
Yin, Shuang; Jensen, Mark A; Bai, Jiawei; Debroy, Chitrita; Barrangou, Rodolphe; Dudley, Edward G
2013-09-01
The Shiga toxin-producing Escherichia coli (STEC) strains, including those of O157:H7 and the "big six" serogroups (i.e., serogroups O26, O45, O103, O111, O121, and O145), are a group of pathogens designated food adulterants in the United States. The relatively conserved nature of clustered regularly interspaced short palindromic repeats (CRISPRs) in phylogenetically related E. coli strains makes them potential subtyping markers for STEC detection, and a quantitative PCR (qPCR)-based assay was previously developed for O26:H11, O45:H2, O103:H2, O111:H8, O121:H19, O145:H28, and O157:H7 isolates. To better evaluate the sensitivity and specificity of this qPCR method, the CRISPR loci of 252 O157 and big-six STEC isolates were sequenced and analyzed along with 563 CRISPR1 and 624 CRISPR2 sequences available in GenBank. General conservation of spacer content and order was observed within each O157 and big-six serogroup, validating the qPCR method. Meanwhile, it was found that spacer deletion, the presence of an insertion sequence, and distinct alleles within a serogroup are sources of false-negative reactions. Conservation of CRISPR arrays among isolates expressing the same flagellar antigen, specifically, H7, H2, and H11, suggested that these isolates share an ancestor and provided an explanation for the false positives previously observed in the qPCR results. An analysis of spacer distribution across E. coli strains provided limited evidence for temporal spacer acquisition. Conversely, comparison of CRISPR sequences between strains along the stepwise evolution of O157:H7 from its O55:H7 ancestor revealed that, over this ∼7,000-year span, spacer deletion was the primary force generating CRISPR diversity.
Mandai, Shintaro; Mori, Takayasu; Sohara, Eisei; Rai, Tatemitsu; Uchida, Shinichi
2015-12-01
Previous genome-wide association studies identified serine threonine kinase 39 (STK39), encoding STE20/SPS1-related proline/alanine-rich kinase, as one of a limited number of hypertension susceptibility genes. A recent meta-analysis confirmed the association of STK39 intronic polymorphism rs3754777 with essential hypertension, among previously reported hypertension-associated STK39 polymorphisms. However, the biochemical function of this polymorphism in the mechanism responsible for hypertension is yet to be clarified. We generated rs3754777G>A knockin human cell lines with clustered regularly interspaced short palindromic repeats-mediated genome engineering. Homozygous (A/A) and heterozygous (G/A) knockin human embryonic kidney cell lines were generated using a double nickase, single-guide RNAs targeting STK39 intron 5 around single-nucleotide polymorphism, and a 100-bp donor single-stranded DNA oligonucleotide. Reverse transcription polymerase chain reaction with sequencing analyses revealed the identical STK39 transcripts among the wild-type and both knockin cell lines. Quantitative reverse transcription polymerase chain reaction showed increased STK39 mRNA expression, and immunoblot analysis revealed increases in total and phosphorylated STE20/SPS1-related proline/alanine-rich kinase with increased phosphorylated Na-K-Cl cotransporter isoform 1 in both knockin cell lines. The largest increases in these molecules were observed in the homozygous cell line. These findings indicated that this intronic polymorphism increases STK39 transcription, leading to activation of the STE20/SPS1-related proline/alanine-rich kinase-solute carrier family 12A signaling cascade. Increased interactions between STE20/SPS1-related proline/alanine-rich kinase and the target cation-chloride cotransporters may be responsible for hypertension susceptibility in individuals with this polymorphism.
Ostria-Hernández, Martha Lorena; Sánchez-Vallejo, Carlos Javier; Ibarra, J Antonio; Castro-Escarpulli, Graciela
2015-08-04
In recent years the emergence of multidrug resistant Klebsiella pneumoniae strains has been an increasingly common event. This opportunistic species is one of the five main bacterial pathogens that cause hospital infections worldwide and multidrug resistance has been associated with the presence of high molecular weight plasmids. Plasmids are generally acquired through horizontal transfer and therefore is possible that systems that prevent the entry of foreign genetic material are inactive or absent. One of these systems is CRISPR/Cas. However, little is known regarding the clustered regularly interspaced short palindromic repeats and their associated Cas proteins (CRISPR/Cas) system in K. pneumoniae. The adaptive immune system CRISPR/Cas has been shown to limit the entry of foreign genetic elements into bacterial organisms and in some bacteria it has been shown to be involved in regulation of virulence genes. Thus in this work we used bioinformatics tools to determine the presence or absence of CRISPR/Cas systems in available K. pneumoniae genomes. The complete CRISPR/Cas system was identified in two out of the eight complete K. pneumoniae genomes sequences and in four out of the 44 available draft genomes sequences. The cas genes in these strains comprises eight cas genes similar to those found in Escherichia coli, suggesting they belong to the type I-E group, although their arrangement is slightly different. As for the CRISPR sequences, the average lengths of the direct repeats and spacers were 29 and 33 bp, respectively. BLAST searches demonstrated that 38 of the 116 spacer sequences (33%) are significantly similar to either plasmid, phage or genome sequences, while the remaining 78 sequences (67%) showed no significant similarity to other sequences. The region where the CRISPR/Cas systems were located is the same in all the Klebsiella genomes containing it, it has a syntenic architecture, and is located among genes encoding for proteins likely involved in
王丽丽; 何进; 王阶平
2011-01-01
最近发现,在细菌和古菌中广泛存在的成簇的规律间隔的短回文重复序列(clustered regularly interspaced short palindromic repeats,CRISPR)及其相关蛋白是针对噬菌体、质粒等外源DNA的获得性和可遗传的免疫系统.本文综述了CRISPR系统的基本结构、多样性、作用机理及其区分自我与非我的机制,并对CRISPR研究和应用前景进行了展望.%The recently discovered Clustered Regularly Interspaced Short Palindromic Repeat ( CRISPRs) can protect bacteria and archaea with adaptive and heritable defense systems against the invasion of phage- and plasmid- associated mobile genetic elements. Here, we review the structure, diversity, mechanism of interference and self versus non-self discrimination of CRISPR systems. We also discuss the potential applications of this novel interference system.
陈瑾; 王素英; 董世瑞
2016-01-01
成簇的规律间隔短回文重复( CRISPR)是一类广泛分布于细菌和古细菌基因组中的DNA重复结构。重复结构与前导序列、一系列相关蛋白一起，为原核生物提供抵御噬菌体和质粒等外源基因的获得性免疫能力。综述了CRISPR系统的结构、作用机制及应用，介绍了最新的研究成果，并对其发展前景进行了展望。%Clustered regularly interspaced short palindromic repeats ( CRISPR) is a kind of repetitive DNA structure, which is widely distributed in bacterial and archaeal genomes. The structure with leader sequence and a series of associated proteins together provide acquired immunity against phage and plasmid genes for prokaryotes. In this paper, the structure, mechanism and application of CRISPR system are summarized, the latest research progress is introduced, and the prospect of its development is prospected.
崔玉军; 李艳君; 颜焱锋; 杨瑞馥
2008-01-01
规律成簇的间隔短回文重复(Clustered regularly interspaced short palindromic repeats,CRISPRs)是一类广泛分布于细菌和古菌基因组中的重复结构.最近研究表明,CRISPR与一系列相关蛋白、前导序列一起,为原核生物提供对噬菌体等外源基因的获得性免疫能力,其作用机制可能与真核生物的RNA干扰过程类似.作为基因组中高度可变的区域,CRISPR非常适合成为研究细菌种内分型和微进化的分子靶标.本文综述了CRISPR系统的结构、功能及其应用概况,并对CRISPR研究的前景进行了展望.
Duan, Yajian; Ma, Gaoen; Huang, Xionggao; D'Amore, Patricia A.; Zhang, Feng; Lei, Hetian
2016-01-01
The G309 allele of SNPs in the mouse double minute (MDM2) promoter locus is associated with a higher risk of cancer and proliferative vitreoretinopathy (PVR), but whether SNP G309 contributes to the pathogenesis of PVR is to date unknown. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonuclease (Cas) 9 from Streptococcus pyogenes (SpCas9) can be harnessed to manipulate a single or multiple nucleotides in mammalian cells. Here we delivered SpCas9 and guide RNAs using dual adeno-associated virus-derived vectors to target the MDM2 genomic locus together with a homologous repair template for creating the mutation of MDM2 T309G in human primary retinal pigment epithelial (hPRPE) cells whose genotype is MDM2 T309T. The next-generation sequencing results indicated that there was 42.51% MDM2 G309 in the edited hPRPE cells using adeno-associated viral CRISPR/Cas9. Our data showed that vitreous induced an increase in MDM2 and subsequent attenuation of p53 expression in MDM2 T309G hPRPE cells. Furthermore, our experimental results demonstrated that MDM2 T309G in hPRPE cells enhanced vitreous-induced cell proliferation and survival, suggesting that this SNP contributes to the pathogenesis of PVR. PMID:27246850
van Duijn, Esther; Barbu, Ioana M; Barendregt, Arjan; Jore, Matthijs M; Wiedenheft, Blake; Lundgren, Magnus; Westra, Edze R; Brouns, Stan J J; Doudna, Jennifer A; van der Oost, John; Heck, Albert J R
2012-11-01
The CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated genes) immune system of bacteria and archaea provides acquired resistance against viruses and plasmids, by a strategy analogous to RNA-interference. Key components of the defense system are ribonucleoprotein complexes, the composition of which appears highly variable in different CRISPR/Cas subtypes. Previous studies combined mass spectrometry, electron microscopy, and small angle x-ray scattering to demonstrate that the E. coli Cascade complex (405 kDa) and the P. aeruginosa Csy-complex (350 kDa) are similar in that they share a central spiral-shaped hexameric structure, flanked by associating proteins and one CRISPR RNA. Recently, a cryo-electron microscopy structure of Cascade revealed that the CRISPR RNA molecule resides in a groove of the hexameric backbone. For both complexes we here describe the use of native mass spectrometry in combination with ion mobility mass spectrometry to assign a stable core surrounded by more loosely associated modules. Via computational modeling subcomplex structures were proposed that relate to the experimental IMMS data. Despite the absence of obvious sequence homology between several subunits, detailed analysis of sub-complexes strongly suggests analogy between subunits of the two complexes. Probing the specific association of E. coli Cascade/crRNA to its complementary DNA target reveals a conformational change. All together these findings provide relevant new information about the potential assembly process of the two CRISPR-associated complexes.
Duan, Yajian; Ma, Gaoen; Huang, Xionggao; D'Amore, Patricia A; Zhang, Feng; Lei, Hetian
2016-07-29
The G309 allele of SNPs in the mouse double minute (MDM2) promoter locus is associated with a higher risk of cancer and proliferative vitreoretinopathy (PVR), but whether SNP G309 contributes to the pathogenesis of PVR is to date unknown. The clustered regularly interspaced short palindromic repeats (CRISPR)-associated endonuclease (Cas) 9 from Streptococcus pyogenes (SpCas9) can be harnessed to manipulate a single or multiple nucleotides in mammalian cells. Here we delivered SpCas9 and guide RNAs using dual adeno-associated virus-derived vectors to target the MDM2 genomic locus together with a homologous repair template for creating the mutation of MDM2 T309G in human primary retinal pigment epithelial (hPRPE) cells whose genotype is MDM2 T309T. The next-generation sequencing results indicated that there was 42.51% MDM2 G309 in the edited hPRPE cells using adeno-associated viral CRISPR/Cas9. Our data showed that vitreous induced an increase in MDM2 and subsequent attenuation of p53 expression in MDM2 T309G hPRPE cells. Furthermore, our experimental results demonstrated that MDM2 T309G in hPRPE cells enhanced vitreous-induced cell proliferation and survival, suggesting that this SNP contributes to the pathogenesis of PVR. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.
Brendel, Jutta; Stoll, Britta; Lange, Sita J; Sharma, Kundan; Lenz, Christof; Stachler, Aris-Edda; Maier, Lisa-Katharina; Richter, Hagen; Nickel, Lisa; Schmitz, Ruth A; Randau, Lennart; Allers, Thorsten; Urlaub, Henning; Backofen, Rolf; Marchfelder, Anita
2014-03-07
The clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR-Cas) system is a prokaryotic defense mechanism against foreign genetic elements. A plethora of CRISPR-Cas versions exist, with more than 40 different Cas protein families and several different molecular approaches to fight the invading DNA. One of the key players in the system is the CRISPR-derived RNA (crRNA), which directs the invader-degrading Cas protein complex to the invader. The CRISPR-Cas types I and III use the Cas6 protein to generate mature crRNAs. Here, we show that the Cas6 protein is necessary for crRNA production but that additional Cas proteins that form a CRISPR-associated complex for antiviral defense (Cascade)-like complex are needed for crRNA stability in the CRISPR-Cas type I-B system in Haloferax volcanii in vivo. Deletion of the cas6 gene results in the loss of mature crRNAs and interference. However, cells that have the complete cas gene cluster (cas1-8b) removed and are transformed with the cas6 gene are not able to produce and stably maintain mature crRNAs. crRNA production and stability is rescued only if cas5, -6, and -7 are present. Mutational analysis of the cas6 gene reveals three amino acids (His-41, Gly-256, and Gly-258) that are essential for pre-crRNA cleavage, whereas the mutation of two amino acids (Ser-115 and Ser-224) leads to an increase of crRNA amounts. This is the first systematic in vivo analysis of Cas6 protein variants. In addition, we show that the H. volcanii I-B system contains a Cascade-like complex with a Cas7, Cas5, and Cas6 core that protects the crRNA.
Brendel, Jutta; Stoll, Britta; Lange, Sita J.; Sharma, Kundan; Lenz, Christof; Stachler, Aris-Edda; Maier, Lisa-Katharina; Richter, Hagen; Nickel, Lisa; Schmitz, Ruth A.; Randau, Lennart; Allers, Thorsten; Urlaub, Henning; Backofen, Rolf; Marchfelder, Anita
2014-01-01
The clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR-Cas) system is a prokaryotic defense mechanism against foreign genetic elements. A plethora of CRISPR-Cas versions exist, with more than 40 different Cas protein families and several different molecular approaches to fight the invading DNA. One of the key players in the system is the CRISPR-derived RNA (crRNA), which directs the invader-degrading Cas protein complex to the invader. The CRISPR-Cas types I and III use the Cas6 protein to generate mature crRNAs. Here, we show that the Cas6 protein is necessary for crRNA production but that additional Cas proteins that form a CRISPR-associated complex for antiviral defense (Cascade)-like complex are needed for crRNA stability in the CRISPR-Cas type I-B system in Haloferax volcanii in vivo. Deletion of the cas6 gene results in the loss of mature crRNAs and interference. However, cells that have the complete cas gene cluster (cas1–8b) removed and are transformed with the cas6 gene are not able to produce and stably maintain mature crRNAs. crRNA production and stability is rescued only if cas5, -6, and -7 are present. Mutational analysis of the cas6 gene reveals three amino acids (His-41, Gly-256, and Gly-258) that are essential for pre-crRNA cleavage, whereas the mutation of two amino acids (Ser-115 and Ser-224) leads to an increase of crRNA amounts. This is the first systematic in vivo analysis of Cas6 protein variants. In addition, we show that the H. volcanii I-B system contains a Cascade-like complex with a Cas7, Cas5, and Cas6 core that protects the crRNA. PMID:24459147
Lai, Frank Pui-Ling; Lau, Sin-Ting; Wong, John Kwong-Leong; Gui, Hongsheng; Wang, Reeson Xu; Zhou, Tingwen; Lai, Wing Hon; Tse, Hung-Fat; Tam, Paul Kwong-Hang; Garcia-Barcelo, Maria-Mercedes; Ngan, Elly Sau-Wai
2017-07-01
Hirschsprung disease is caused by failure of enteric neural crest cells (ENCCs) to fully colonize the bowel, leading to bowel obstruction and megacolon. Heterozygous mutations in the coding region of the RET gene cause a severe form of Hirschsprung disease (total colonic aganglionosis). However, 80% of HSCR patients have short-segment Hirschsprung disease (S-HSCR), which has not been associated with genetic factors. We sought to identify mutations associated with S-HSCR, and used the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 gene editing system to determine how mutations affect ENCC function. We created induced pluripotent stem cell (iPSC) lines from 1 patient with total colonic aganglionosis (with the G731del mutation in RET) and from 2 patients with S-HSCR (without a RET mutation), as well as RET(+/-) and RET(-/-) iPSCs. IMR90-iPSC cells were used as the control cell line. Migration and differentiation capacities of iPSC-derived ENCCs were analyzed in differentiation and migration assays. We searched for mutation(s) associated with S-HSCR by combining genetic and transcriptome data from patient blood- and iPSC-derived ENCCs, respectively. Mutations in the iPSCs were corrected using the CRISPR/Cas9 system. ENCCs derived from all iPSC lines, but not control iPSCs, had defects in migration and neuronal lineage differentiation. RET mutations were associated with differentiation and migration defects of ENCCs in vitro. Genetic and transcriptome analyses associated a mutation in the vinculin gene (VCL M209L) with S-HSCR. CRISPR/Cas9 correction of the RET G731del and VCL M209L mutations in iPSCs restored the differentiation and migration capacities of ENCCs. We identified mutations in VCL associated with S-HSCR. Correction of this mutation in iPSC using CRISPR/Cas9 editing, as well as the RET G731del mutation that causes Hirschsprung disease with total colonic aganglionosis, restored ENCC function. Our study demonstrates how human i
薛泽润; 王颖芳; 段广才; 杨海燕; 郗园林; 王鹏飞; 王琳琳; 郭向娇
2015-01-01
目的 探索志贺菌中成簇规律间隔短回文重复序列(CRISPR)的分布.方法 共选择志贺菌分离株52株,其中河南41株,江西6株,北京5株.利用PCR扩增志贺菌的4个CRISPR位点(S1、S2、S3、S4),产物送测序,分析CRISPR的重复序列和间隔序列.结果 志贺菌的4个CRISPR位点阳性率分别为33.69％(S1)、50.00％(S2)、82.69％(S3)和73.08％(S4);S1和S3包括2种亚型,S2有3种亚型,S4包括4种亚型.2004年前分离的河南分离株中检出S1位点,2004年后分离的菌株中均未检出该位点;S2、S3和S4在两组的分布没有差异.结论 志贺菌各CRISPR位点含有不同亚型,河南分离株S1的分布与细菌分离时间有关,而S2、S3及S4和分离时间无关.%Objective To detect the molecular characteristics of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) in Shigella and to analyze the distribution of CRISPR related to the time of isolation.Methods Of the 52 Shigella strains,41 were isolated from Henan,6 from Jiangxi and 5 isolated from Beijing.Both CRISPR locus of S1,S2,S3 and S4 in Shigella were detected by polymerase chain reaction (PCR).The PCR products were sequenced and compared.Results The positive rates of CRISPR locus in Shigella were 33.69％ (S 1),50.00％ (S2),82.69％(S3) and 73.08％(S4),respectively.Two subtypes were discovered in S1 and S3 locus.Three subtypes were discovered in S2 locus.Four different subtypes were discovered in S4 locus.The isolates from Henan strains were divided into two groups by the time of isolation.Distributions of S1 were different,before or after 2004,on Shigella.S 1 could not be detected after 2004.There were no statistical differences of S2,S3 and S4 in two groups.Conclusion Different CRISPR subtypes or Shigella were discovered.A significant correlation was noticed between the CRISPR S 1 related to the time of isolation but not between S2,S3 or S4 on the time of isolation.
张帆; 张兵; 向华; 胡松年
2009-01-01
[Objective] Clustered Regularly Interspaeed Short Palindromic Repeats (CRISPR) is a widespread system that provides acquired resistance against phages in bacteria and archaea. Here we aim to genome-widely analyze the CRISPR in extreme halophilic arehaea, of which the whole genome sequences are available at present time.[Methods] We used bioinformatics methods including alignment, conservation analysis, GC content and RNA structure prediction to analyze the CRISPR structures of 7 haloarehaeal genomes. [Results] We identified the CRISPR structures in 5 halophilic archaea and revealed a conserved palindromic motif in the flanking regions of these CRISPR structures. In addition, we found that the repeat sequences of large CRISPR structures in halophilie arehaea were greatly conserved, and two types of predicted RNA secondary structures derived from the repeat sequences were likely determined by the fourth base of the repeat sequence. [Conclusion] Our results support the proposal that the leader sequence may function as recognition site by having palindromic structures in flanking regions, and the stem-loop secondary structure formed by repeat sequences may function in mediating the interaction between foreign genetic elements and CAS-encoded proteins.%[目的]利用生物信息学方法了解目前拥有全基因组序列的极端嗜盐古菌中CRISPR结构的特征.[方法]通过比对,保守性分析,GC含量分析,RNA结构预测等方法对已有全基因组序列的嗜盐古菌基因组进行研究.[结果]在5株嗜盐古菌基因组中发现CRISPR结构,在leader序列内得到具有回文性质的保守motif.发现在大CRISPR结构内repeat序列具有很强的保守性.同时根据第四位碱基的不同,repeat序列可形成两类不同的RNA二级结构.[结论]leader序列中回文结构的发现对其可能为蛋白结合位点的假设提供了进一步的理论依据.Repeat序列RNA二级结构的形成提示其可能介导外源DNA或RNA与CAS编码蛋白的相互作用.
Sorokin, Valery A; Gelfand, Mikhail S; Artamonova, Irena I
2010-04-01
Clustered regularly interspaced short palindromic repeats (CRISPRs) form a recently characterized type of prokaryotic antiphage defense system. The phage-host interactions involving CRISPRs have been studied in experiments with selected bacterial or archaeal species and, computationally, in completely sequenced genomes. However, these studies do not allow one to take prokaryotic population diversity and phage-host interaction dynamics into account. This gap can be filled by using metagenomic data: in particular, the largest existing data set, generated from the Sorcerer II Global Ocean Sampling expedition. The application of three publicly available CRISPR recognition programs to the Global Ocean metagenome produced a large proportion of false-positive results. To address this problem, a filtering procedure was designed. It resulted in about 200 reliable CRISPR cassettes, which were then studied in detail. The repeat consensuses were clustered into several stable classes that differed from the existing classification. Short fragments of DNA similar to the cassette spacers were more frequently present in the same geographical location than in other locations (P, CRISPR-forming events and reconstructed the likely evolutionary history of cassettes that had common spacers. Metagenomic collections allow for relatively unbiased analysis of phage-host interactions and CRISPR evolution. The results of this study demonstrate that CRISPR cassettes retain the memory of the local virus population at a particular ocean location. CRISPR evolution may be described using a limited vocabulary of elementary events that have a natural biological interpretation.
李浩; 邱少富; 宋宏彬
2013-01-01
细菌和古细菌在与噬菌体的生存斗争中,进化出了获得性免疫系统——成簇的规律间隔的短回文重复序列(Clustered regularly interspaced short palindromic repeats,CRISPR),该结构能够通过其转录出的mRNA又称crRNA(CRISPR RNA)及CRISPR相关蛋白(CRISPR-associated,Cas)对外来某一特定单链或双链DNA实施高特异性地沉默或降解.近年来,这个存在于原核生物中的免疫系统成为了研究热点,并有着极为广泛的应用前景.特别是最近,研究人员又根据crRNA的特性和功能,利用人为改造后的sgRNA(small guide RNA)及Cas9蛋白,实现了对细菌乃至真核生物某一特定基因的精确敲除或沉默,这无疑会使基因组编辑技术进入一个更加方便而精确的新时代.
葛彩云; 陆海霞; 曲道峰; 朱军莉; 袁冬霞; 冯立芳
2015-01-01
规律成簇间隔短回文重复序列(clustered regularly interspaced short palindromic repeats,CRISPR)是大多数细菌和古细菌在生存压力下进化出的一套抵抗噬菌体干扰的防御系统.本研究主要采用生物信息学的方法,对24株分离自人体且已完成全基因组测序的副溶血性弧菌内CRISPR结构进行了分析,结果发现:只有16株细菌包含1个及以上的CRISPR结构,共计29个CRISPR;仅11个具有真座位特征的CRISPR结构含有前导序列;CRISPR结构中的重复序列所形成的RNA二级结构具有一大一小共两环或一大二小共三环的特征;目前未找到与区间序列高度同源的外源遗传物质;仅含前导序列的CRISPR结构侧翼区才存在cas基因.副溶血性弧菌的CRISPR结构可能以水平基因转移的方式整合到细菌的染色体中,CRISPR结构不适合作为细菌分类的一项指标.
杨月; 王海丞; 许舒宇; 彭靖; 江久汇; 李翠英
2015-01-01
目的 利用成簇的规律间隔的短回文重复序列(clustered regularly interspaced short palindromic repeats,CRISPR)/常间回文重复序列丛集关联蛋白系统(associated proteins,Cas)编辑纤连蛋白(fibronectin)基因抑制其可变剪接片段基因外显子A(extra domain A,EDA),并观察对腺样囊性癌(adenoid cystic carcinoma,ACC)的促肿瘤作用.方法 根据纤连蛋白序列设计两段互补于EDA上游和一段与下游互补的引导RNA (single guide RNA,sgRNA,20 bp),分别连接至PX330质粒的U6启动子下游.质粒转染至ACC细胞系SACC-83,PCR扩增基因组并测序验证其定点敲除EDA结果及效率.质粒转染后的细胞进行稳定株的筛选及鉴定,将筛选后的稳定株作为EDA敲除实验组,SACC-83细胞为对照组,进行CCK-8细胞增殖和Transwell侵袭能力检测,每组实验重复3次.结果 sgRNA连接至PX330质粒U6启动子下游,成功构建了质粒敲除模型;SACC-83的基因组EDA外显子被敲除,敲除效率达70％以上,但纤连蛋白总量未发生明显变化.筛选出3株EDA敲除稳定株(A+C-2、A+C-6、B+C-10),并通过PCR鉴定证实其可靠性.划痕实验中实验组细胞运动速率[A+C-2 (21.67±1.87) μm/h;A+C-6(12.22±2.13) μm/h;B+C-10(20.00±2.56) μm/h]相对对照组[(27.78±3.20) μm/h]降低;增殖实验显示EDA敲除组细胞倍增时间增加[对照组SACC-83 (38.52±4.26)h,实验组A+C-2(62.05±5.80)h,A+C-6(46.32±6.35)h,B+C-10(40.7±3.88)h].结论 在sgRNA的引导下,CRISPR/Cas系统能简洁、高效地敲除细胞基因组中的EDA可变剪接外显子,EDA敲除对肿瘤细胞运动和侵袭有明显抑制作用.%Objective To investigate the effect of the fibronectin extra domain A on the aggressiveness of salivary adenoid cystic carcinoma (SACC) cells,via the clustered regularly interspaced short palindromic repeats (CRISPR)/associated proteins (Cas) system.Methods One sgRNA was designed to target the upstream of the genome sequences of extra domain A
王琰; 喻婵; 王阶平; 邱宁; 何进; 孙明; 张青叶
2011-01-01
CRISPR is a novel type of microbial defense system, which is unique in that it is invaderspecific, adaptive and heritable. It is a recent breakthrough in understanding host-virus interactions.Bioinformatics methods including BLAST, multiple sequence alignment, and RNA structure prediction was used to analyze the CRISPR structures of 24 Bacillus cereus group genomes. CRISPR existed in 42％ strains. Two types of RNA secondary structures derived from the repeat sequences were predicted, and demonstrated that stemloop secondary structure might function in mediating the interaction between foreign genetic elements and CASencoded proteins. The sequence homologous among 31％ spacer, phage, plasmid and the genomes of Bacillus cereus group further verified that spacer was likely to come from the exogenous mobile genetic factor. As most of the Bacillus cereus group strains contain multiple plasmids and prophages, the CRISPR research in Bacillus cereus group by this study would be help to reveal relationship between host strains with plasmid or host strains with phage.%规律成簇间隔短回文重复序列(clustered regularly interspaced short palindromic repeats,CRISPR)是最近发现针对噬菌体等外源遗传物质的获得性和可遗传性的新型原核生物防御系统.通过BLAST、多序列比对、RNA二级结构预测等生物信息学方法对已经完成全基因组测序的蜡状芽孢杆菌群24个菌株进行CRISPR的系统分析,结果表明:42%的菌株含有该结构;8个CRISPR座位的正向重复序列可以形成RNA二级结构,提示正向重复序列可能介导外源DNA或RNA与CAS编码蛋白的相互作用;31%的间区序列与噬菌体、质粒、蜡状芽孢杆菌群基因组序列具有同源性,进一步验证间区序列很可能来源于外源可移动遗传因子.由于大部分蜡状芽孢杆菌群菌株含有多个前噬菌体和质粒,通过对蜡状芽孢杆菌群CRISPR的分析,为揭示其对宿主菌与噬菌体,以及宿主
薛泽润; 王颖芳; 段广才; 王鹏飞; 王琳琳; 郭向娇; 郗园林
2014-01-01
Objective To detect the distribution of clustered regularly interspaced short palindromic repeat(CRISPR)associated protein genes cas1 and cas2 in Shigella and to understand the characteristics of CRISPR with relationship between CRISPR and related characteristics on drug resistance. Methods CRISPR associated protein genes cas1 and cas2 in Shigella were detected by PCR,with its products sequenced and compared.Results The CRISPR-associated protein genes cas1 and cas2 were found in all the 196 Shigella isolates which were isolated at different times and locations in China. Consistencies showed through related sequencing appepared as follows:cas2,cas1 (a) and cas1(b)were 96.44%,97.61%and 96.97%,respectively. There were two mutations including 3177129 site(C→G)and 3177126 site(G→C)of cas1(b)gene in 2003135 strain which were not found in the corresponding sites of Z23 and 2008113. Results showed that in terms of both susceptibility and antibiotic-resistance,strain 2003135 was stronger than Z23 and 2008113. Conclusion CRISPR system widely existed in Shigella,with the level of drug resistance in cas1(b) gene mutant strains higher than in wild strains. Cas1(b)gene mutation might be one of the reasons causing the different levels of resistance.%目的：研究成簇规律间隔短回文重复序列（CRISPR）相关蛋白基因cas1和cas2在志贺菌中的分布，并分析cas1和cas2基因突变与细菌耐药的关系。方法采用PCR扩增196株志贺菌cas1和cas2基因。对3株志贺菌（Z23、2003135、2008113）的cas2、cas1（a）和cas1（b）基因进行测序，分析其突变与耐药之间的关系。结果196株志贺菌均检出CRISPR相关蛋白基因cas1和cas2。测序结果显示，cas2的一致性为96.44%，cas1（a）的一致性为97.61%，cas1（b）的一致性为96.97%。菌株2003135的cas1（b）基因有2个突变位点：3177129位点（C→G）及3177126位点（G→C），Z23、2008113对应位置没有突变
Detecting palindromes, patterns, and borders in regular languages
Anderson, Terry; Loftus, John; Rampersad, Narad; Santean, Nicolae; Shallit, Jeffrey
2007-01-01
Given a language L and a nondeterministic finite automaton M, we consider whether we can determine efficiently (in the size of M) if M accepts at least one word in L, or infinitely many words. Given that M accepts at least one word in L, we consider how long a shortest word can be. The languages L that we examine include the palindromes, the non-palindromes, the k-powers, the non-k-powers, the powers, the non-powers (also called primitive words), the words matching a general pattern, the bord...
陈晓芳; 练桂丽; 黄邦邦; 谢良地
2016-01-01
Objective To knock out aquaporin 2 (Aqp2) gene in mouse renal inner medullary collecting duct 3 (m-IMCD3) epithelial cells by clustered regularly interspaced short palindromic repeats(CRISPR)/CRISPR-associated protein 9(Cas9) system.Methods Four small guide RNAs (sgRNA) targeting exon 1 and 4 (sgRNA1-1,sgRNA1-2,sgRNA4-1,sgRNA4-2) of Aqp2 gene were designed respectively and successfully ligated to LentiCRISPR V2 vector.The plasmid containing a corresponding sgRNA was transfected into m-IMCD3 cells.The genomic DNA of new monoclonal cell lines was extracted and the target DNA fragment was amplified by polymerase chain reaction (PCR).Then the product of PCR was sequenced.The expression of Aqp2 was determined by reverse transcription polymerase chain reaction (RT-PCR) and immunofluorescence.Results The lentiviral CRISPR vector 2 containing a corresponding sgRNA were successfully constructed.The four sgRNAs could cut the Aqp2 gene.The combination of sgRNA1-1 and sgRNA4-2 could successfully knock out the DNA fragment of 5500 bp between them.The expressions of Aqp2 mRNA and protein in the Aqp2 knockout monoclonal cell line were not detected by RT-PCR and immunofluorescence.Conclusion Aqp2 knockout m-IMCD3 epithelial cell line was established via CRISPR/Cas9 system.%目的 利用常间回文重复序列丛集(CRISPR)/CRISPR相关蛋白9(Cas9)系统敲除小鼠肾内髓集合管3(m-I MCD3)上皮细胞的水通道蛋白2(Aqp2)基因.方法 在小鼠Aqp2基因的第1、4个外显子上各设计两个小向导RNA(sgRNA),分别为sgRNA1-1、sgRNA1-2、sgRNA4-1、sgRNA4-2,并将其成功克隆进常间回文重复序列丛集慢病毒载体2上.将测序正确的质粒转染到m-IMCD3细胞中,提取各单克隆细胞系的基因组DNA,通过聚合酶链反应扩增出sgRNA作用靶点的DNA片段并测序.利用逆转录聚合酶链反应(RT-PCR)及免疫荧光检测Aqp2的表达.结果 成功构建出含有相应sgRNA的载体;4个sgRNA对Aqp2基因的
Clustered regularly interspaced short palindromic repeats cas systems: a comprehensive review
Shahin Mahmud
2015-08-01
Full Text Available The CRISPR system was recently identified as a bacterial defense mechanism against phages and plasmids. The CRISPR system is composed of DNA arrays containing short sequences identical to those present in phages and plasmids. These short DNAs are transcribed and processed by CRISPR associated proteins that also guide other CRISPR proteins to target the invading DNA. Only a few of the CRISPR components have been characterized to date and their mechanism of action is still largely unknown. Phage defense mechanisms probably have co-evolved against the CRISPR system, but none have yet been found. We propose to identify phage genes that counteract the CRISPR system. [Int J Basic Clin Pharmacol 2015; 4(4.000: 613-622
Tanaka, R; Murakami, H; Ote, M; Yamamoto, D
2016-08-01
How behavioural diversity emerged in evolution is an unexplored subject in biology. To tackle this problem, genes and circuits for a behaviour need to be determined in different species for phylogenetic comparisons. The recently developed clustered regulatory interspaced short palindromic repeats/CRISPR associated protein9 (CRISPR/Cas9) system made such a challenge possible by providing the means to induce mutations in a gene of interest in any organism. Aiming at elucidating diversification in genetic and neural networks for courtship behaviour, we attempted to generate a genetic tool kit in Drosophila subobscura, a nonmodel species distantly related to the genetic model Drosophila melanogaster. Here we report the generation of yellow (y) and white mutations with the aid of the CRISPR/Cas9 system, and the rescue of the y mutant phenotype by germline transformation of the newly established y mutant fly line with a y(+) -marked piggyBac vector. This successful mutagenesis and transformation in D. subobscura open up an avenue for comprehensive genetic analyses of higher functions in this and other nonmodel Drosophila species, representing a key step toward systematic comparisons of genes and circuitries underlying behaviour amongst species. © 2016 The Royal Entomological Society.
Han, Pu; Deem, Michael W
2017-02-01
CRISPR is a newly discovered prokaryotic immune system. Bacteria and archaea with this system incorporate genetic material from invading viruses into their genomes, providing protection against future infection by similar viruses. The condition for coexistence of prokaryots and viruses is an interesting problem in evolutionary biology. In this work, we show an intriguing phase diagram of the virus extinction probability, which is more complex than that of the classical predator-prey model. As the CRISPR incorporates genetic material, viruses are under pressure to evolve to escape recognition by CRISPR. When bacteria have a small rate of deleting spacers, a new parameter region in which bacteria and viruses can coexist arises, and it leads to a more complex coexistence patten for bacteria and viruses. For example, when the virus mutation rate is low, the virus extinction probability changes non-montonically with the bacterial exposure rate. The virus and bacteria coevolution not only alters the virus extinction probability, but also changes the bacterial population structure. Additionally, we show that recombination is a successful strategy for viruses to escape from CRISPR recognition when viruses have multiple proto-spacers, providing support for a recombination-mediated escape mechanism suggested experimentally. Finally, we suggest that the re-entrant phase diagram, in which phages can progress through three phases of extinction and two phases of abundance at low spacer deletion rates as a function of exposure rate to bacteria, is an experimentally testable phenomenon. © 2017 The Author(s).
2017-06-30
advantage of RNA-guided gene drives. • Development time: The CRISPR-Cas9 technology has made it much easier and faster to make transgenic organisms ...environmental risk, public perception, and regulatory issues surrounding the development and field release of CRISPR-Cas9- engineered organisms . 4.7.1... ORGANIZATION NAME(S) AND ADDRESS(ES) U.S. Army Engineer Research and Development Center (ERDC) Environmental Laboratory Waterways Experiment Station, 3909
Yu L
2015-02-01
Full Text Available Yu L, Wang XL, Zhu D, et al. Onco Targets Ther. 2015;8:37–44. On page 1 Ding Ma is listed as a correspondence contact in error. The correct contact is Zheng Hu, email huzheng1998@163.com. All other contact details remain the same.Read the original article
Schmid-Burgk, Jonathan L; Chauhan, Dhruv; Schmidt, Tobias; Ebert, Thomas S; Reinhardt, Julia; Endl, Elmar; Hornung, Veit
2016-01-01
Inflammasomes are high molecular weight protein complexes that assemble in the cytosol upon pathogen encounter. This results in caspase-1-dependent pro-inflammatory cytokine maturation, as well as a special type of cell death, known as pyroptosis. The Nlrp3 inflammasome plays a pivotal role in pathogen defense, but at the same time, its activity has also been implicated in many common sterile inflammatory conditions. To this effect, several studies have identified Nlrp3 inflammasome engagement in a number of common human diseases such as atherosclerosis, type 2 diabetes, Alzheimer disease, or gout. Although it has been shown that known Nlrp3 stimuli converge on potassium ion efflux upstream of Nlrp3 activation, the exact molecular mechanism of Nlrp3 activation remains elusive. Here, we describe a genome-wide CRISPR/Cas9 screen in immortalized mouse macrophages aiming at the unbiased identification of gene products involved in Nlrp3 inflammasome activation. We employed a FACS-based screen for Nlrp3-dependent cell death, using the ionophoric compound nigericin as a potassium efflux-inducing stimulus. Using a genome-wide guide RNA (gRNA) library, we found that targeting Nek7 rescued macrophages from nigericin-induced lethality. Subsequent studies revealed that murine macrophages deficient in Nek7 displayed a largely blunted Nlrp3 inflammasome response, whereas Aim2-mediated inflammasome activation proved to be fully intact. Although the mechanism of Nek7 functioning upstream of Nlrp3 yet remains elusive, these studies provide a first genetic handle of a component that specifically functions upstream of Nlrp3. © 2016 by The American Society for Biochemistry and Molecular Biology, Inc.
Li, Wan; Bian, Xin; Evivie, Smith Etareri; Huo, Gui-Cheng
2016-09-01
The CRISPR-Cas (CRISPR together with CRISPR-associated proteins) modules are the adaptive immune system, acting as an adaptive and heritable immune system in bacteria and archaea. CRISPR-based immunity acts by integrating short virus sequences in the cell's CRISPR locus, allowing the cell to remember, recognize, and clear infections. In this study, the homology of CRISPRs sequence in BIMs (bacteriophage-insensitive mutants) of Streptococcus thermophilus St-I were analyzed. Secondary structures of the repeats and the PAMs (protospacer-associated motif) of each CRISPR locus were also predicted. Results showed that CRISPR1 has 27 repeat-spacer units, 5 of them had duplicates; CRISPR2 has one repeat-spacer unit; CRISPR3 has 28 repeat-spacer units. Only BIM1 had a new spacer acquisition in CRISPR3, while BIM2 and BIM3 had no new spacers' insertion, thus indicating that while most CRISPR1 were more active than CRISPR3, new spacer acquisition occurred just in CRSPR3 in some situations. These findings will help establish the foundation for the study of CRSPR-Cas systems in lactic acid bacteria.
Gawryszewska, Iwona; Malinowska, Katarzyna; Kuch, Alicja; Chrobak-Chmiel, Dorota; Trokenheim, Lucja Laniewska-; Hryniewicz, Waleria; Sadowy, Ewa
2017-03-01
Enterococcus faecalis represents an important factor of hospital-associated infections (HAIs). The knowledge on its evolution from a commensal to an opportunistic pathogen is still limited; thus, we performed a study to characterise distribution of factors that may contribute to this adaptation. Using a collection obtained from various settings (hospitalised patients, community carriers, animals, fresh food, sewage, water), we investigated differences in antimicrobial susceptibility, distribution of antimicrobial resistance genes, virulence-associated determinants and phenotypes, and CRISPR loci in the context of the clonal relatedness of isolates. Bayesian Analysis of Population Structure revealed the presence of three major groups; two subgroups comprised almost exclusively HAI isolates, belonging to previously proposed enterococcal high-risk clonal complexes (HiRECCs) 6 and 28. Isolates of these two subgroups were significantly enriched in antimicrobial resistance genes, presumably produced a polysaccharide capsule and often carried the aggregation substance asa1; distribution of other virulence-associated genes, such as esp and cyl, formation of a biofilm and gelatinase production were more variable. Moreover, both subgroups showed a low prevalence of CRISPR-Cas 1 and 3 and presence of small CRISPR2 variants. Our study confirms the importance of HiRECCs in the population of E. faecalis and their confinement to the hospital settings. © FEMS 2017. All rights reserved. For permissions, please e-mail: journals.permissions@oup.com.
Esther Betrán
2012-01-01
Full Text Available We look at sex-limited chromosome (Y or W evolution with particular emphasis on the importance of palindromes. Y chromosome palindromes consist of inverted duplicates that allow for local recombination in an otherwise nonrecombining chromosome. Since palindromes enable intrachromosomal gene conversion that can help eliminate deleterious mutations, they are often highlighted as mechanisms to protect against Y degeneration. However, the adaptive significance of recombination resides in its ability to decouple the evolutionary fates of linked mutations, leading to both a decrease in degeneration rate and an increase in adaptation rate. Our paper emphasizes the latter, that palindromes may exist to accelerate adaptation by increasing the potential targets and fixation rates of incoming beneficial mutations. This hypothesis helps reconcile two enigmatic features of the “palindromes as protectors” view: (1 genes that are not located in palindromes have been retained under purifying selection for tens of millions of years, and (2 under models that only consider deleterious mutations, gene conversion benefits duplicate gene maintenance but not initial fixation. We conclude by looking at ways to test the hypothesis that palindromes enhance the rate of adaptive evolution of Y-linked genes and whether this effect can be extended to palindromes on other chromosomes.
Recursive Palindromic Smarandache Values
Earls, Jason
2005-01-01
In [1] Recursive Prime Numbers were studied and shown to be finite. This article deals with the same "recursive" topic, but applies the method to numbers whose Smarandache value, S(n), gives a palindromic number. Here, S(n) denotes the Smarandache function of least m such that n divides m!, and a palindrome is an integer that reads the same forwards and backwards (23432, for example). This sequence of recursive palindromic Smarandache values is shown to be finite...
The development of clustered regularly intespaced short palindromic repeats%规律成簇的短回文重复序列/Cas9的研究进展∗
虞飞; 王亚楠; 张学明
2016-01-01
规律成簇的短回文重复序列( clustered regularly intespaced short palindromic repeats,CRISPR)/Cas系统是最近兴起的一项基因编辑技术,在基因编辑中有着不可或缺的作用。 CRISPR是继锌指人工核酸酶( zinc finger nuclease, ZFN)和类转录激活因子样效应物核酸酶( transcription activator-like effectors nuclease,TALEN)之后的第三代人工合成的核酸酶,有着ZFN、TALEN不具备的众多优点,所以CRISPR正在慢慢取代ZFN和TALEN,成为最主要的人工核酸酶并广泛应用在基因编辑中。而CRISPR/Cas9是CRISPR/Cas系统中最为简单的,也是现在基因编辑技术中应用最为广泛的一种。下面从CRISPR/Cas9的工作原理、构建和研究进展等几个方面对其做一个简要综述,为在这一个领域的研究工作者提供一个参考。%Clustered regularly intespaced short palindromic repeats ( CRISPR) /Cas system is a newly developed gene editing technology, which plays an indispensable role in genetic editing. CRISPR is the third generation of artificial nuclease after zinc finger nuclease ( ZFN) and tran-scription activator-like effectors nuclease ( TALEN) , with more advantages than ZFN and TALEN. Therefore, CRISPR is gradually replacing ZFN and TALEN, becoming the main artificial nuclease and is widely used in genetic modification. CRISPR/Cas9 is the simplest in the CRISPR/Cas system and is widely used in genetic modification. This review describes the mechanism, the design and the application of CRISPR/Cas9 system, providing reference for the researches in the field.
Pezeshk Hamid
2008-06-01
Full Text Available Abstract Background It has been previously shown that palindromic sequences are frequently observed in proteins. However, our knowledge about their evolutionary origin and their possible importance is incomplete. Results In this work, we tried to revisit this relatively neglected phenomenon. Several questions are addressed in this work. (1 It is known that there is a large chance of finding a palindrome in low complexity sequences (i.e. sequences with extreme amino acid usage bias. What is the role of sequence complexity in the evolution of palindromic sequences in proteins? (2 Do palindromes coincide with conserved protein sequences? If yes, what are the functions of these conserved segments? (3 In case of conserved palindromes, is it always the case that the whole conserved pattern is also symmetrical? (4 Do palindromic protein sequences form regular secondary structures? (5 Does sequence similarity of the two "sides" of a palindrome imply structural similarity? For the first question, we showed that the complexity of palindromic peptides is significantly lower than randomly generated palindromes. Therefore, one can say that palindromes occur frequently in low complexity protein segments, without necessarily having a defined function or forming a special structure. Nevertheless, this does not rule out the possibility of finding palindromes which play some roles in protein structure and function. In fact, we found several palindromes that overlap with conserved protein Blocks of different functions. However, in many cases we failed to find any symmetry in the conserved regions of corresponding Blocks. Furthermore, to answer the last two questions, the structural characteristics of palindromes were studied. It is shown that palindromes may have a great propensity to form α-helical structures. Finally, we demonstrated that the two sides of a palindrome generally do not show significant structural similarities. Conclusion We suggest that the
ITER Port Interspace Pressure Calculations
Carbajo, Juan J [ORNL; Van Hove, Walter A [ORNL
2016-01-01
The ITER Vacuum Vessel (VV) is equipped with 54 access ports. Each of these ports has an opening in the bioshield that communicates with a dedicated port cell. During Tokamak operation, the bioshield opening must be closed with a concrete plug to shield the radiation coming from the plasma. This port plug separates the port cell into a Port Interspace (between VV closure lid and Port Plug) on the inner side and the Port Cell on the outer side. This paper presents calculations of pressures and temperatures in the ITER (Ref. 1) Port Interspace after a double-ended guillotine break (DEGB) of a pipe of the Tokamak Cooling Water System (TCWS) with high temperature water. It is assumed that this DEGB occurs during the worst possible conditions, which are during water baking operation, with water at a temperature of 523 K (250 C) and at a pressure of 4.4 MPa. These conditions are more severe than during normal Tokamak operation, with the water at 398 K (125 C) and 2 MPa. Two computer codes are employed in these calculations: RELAP5-3D Version 4.2.1 (Ref. 2) to calculate the blowdown releases from the pipe break, and MELCOR, Version 1.8.6 (Ref. 3) to calculate the pressures and temperatures in the Port Interspace. A sensitivity study has been performed to optimize some flow areas.
Settu Sridhar
Full Text Available The analyses of 3967 representative proteins selected from the Protein Data Bank revealed the presence of 2803 pentapeptide and large palindrome sequences with known secondary structure conformation. These represent 2014 unique palindrome sequences. 60% palindromes are not associated with any regular secondary structure and 28% are in helix conformation, 11% in strand conformation and 1% in the coil conformation. The average solvent accessibility values are in the range between 0-155.28 Å2 suggesting that the palindromes in proteins can be either buried, exposed to the solvent or share an intermittent property. The number of residue neighborhood contacts defined by interactions ≤ 3.2 Ǻ is in the range between 0-29 residues. Palindromes of the same length in helix, strand and coil conformation are associated with different amino acid residue preferences at the individual positions. Nearly, 20% palindromes interact with catalytic/active site residues, ligand or metal ions in proteins and may therefore be important for function in the corresponding protein. The average hydrophobicity values for the pentapeptide and large palindromes range between -4.3 to +4.32 and the number of palindromes is almost equally distributed between the negative and positive hydrophobicity values. The palindromes represent 107 different protein families and the hydrolases, transferases, oxidoreductases and lyases contain relatively large number of palindromes.
Palindromic widths of nilpotent and wreath products
Valeriy G Bardakov; Oleg V Bryukhanov; Krishnendu Gongopadhyay
2017-02-01
We prove that the nilpotent product of a set of groups $A_1, \\ldots , A_s$ has finite palindromic width if and only if the palindromic widths of $A_i$, $i = 1, \\ldots , s$, are finite. We give a new proof that the commutator width of $F_n \\wr K$ is infinite, where $F_n$ is a free group of rank $n\\geq 2$ and $K$ is a finite group. This result, combining with a result of Fink [9] gives examples of groups with infinite commutator width but finite palindromic width with respect to some generating set.
丁瑜芝; 胡仔仲; 袁松涛; 刘庆淮
2016-01-01
基因改造动物模型可用于基因的功能学研究,传统基因改造费时费力.规律成簇的间隔短回文重复序列/Cas内切酶基因编辑技术是一种新型的基因打靶技术,构建简单、方便且成本较低,能在单个受精卵时期快速实现多个精确的靶基因突变,用于检测基因组中的基因表达和相互作用,明确基因功能.目前该项技术虽处于研究的初步阶段,稳定性方面尚无定论;但因高效的基因改造效率,使得该项技术具有较强的应用前景.通过建立合适的眼部疾病动物模型可以推动遗传性视网膜疾病的基因功能学研究,为基因治疗在眼科领域的开展打下基础.%Clustered regularly interspersed short palindromic repeats/Cas system is a powerful genome-editing tool for efficient and precise genome engineering both in vitro and in vivo,with the advantages of easy,convenient and low cost.This technology makes it possible to simultaneously mutate multiple genes in a single fertilized egg,thus to study the gene expression,genetic interaction and gene function.Even though this method is still in its immature stage and its stability is inconclusive,making precision models of ocular diseases through genome editing may provide a positive effect to explore gene targeted therapy in genetic eye disease.
Musical Palindromes for Liberal Arts Students
von Renesse, Christine
2012-01-01
This paper shows how to teach a mathematics for liberal arts class in an inquiry-based way using ideas from music to launch the mathematical activities. No musical knowledge is required to understand and teach the material. The main activity is analyzing the differences between two kinds of rhythmic palindromes. The content is mathematically…
An algorithm to find all palindromic sequences in proteins
N Prasanth; M Kirti Vaishnavi; K Sekar
2013-03-01
A palindrome is a set of characters that reads the same forwards and backwards. Since the discovery of palindromic peptide sequences two decades ago, little effort has been made to understand its structural, functional and evolutionary significance. Therefore, in view of this, an algorithm has been developed to identify all perfect palindromes (excluding the palindromic subset and tandem repeats) in a single protein sequence. The proposed algorithm does not impose any restriction on the number of residues to be given in the input sequence. This avant-garde algorithm will aid in the identification of palindromic peptide sequences of varying lengths in a single protein sequence.
Polynomials with Palindromic and Unimodal Coeﬃ cients
Hua SUN; Yi WANG; Hai Xia ZHANG
2015-01-01
Let f(q) = arqr +· · ·+asqs, with ar = 0 and as = 0, be a real polynomial. It is a palindromic polynomial of darga n if r+s = n and ar+i = as−i for all i. Polynomials of darga n form a linear subspace Pn(q) of R(q)n+1 of dimension ? n2 ?+1. We give transition matrices between two bases ?qj(1+q+· · ·+qn−2j)? , ?qj(1+q)n−2j? and the standard basis ?qj(1+qn−2j)? of Pn(q). We present some characterizations and sufficcient conditions for palindromic polynomials that can be expressed in terms of these two bases with nonnegative coefficients. We also point out the link between such polynomials and rank-generating functions of posets.
Palindromes drive the re-assortment in Influenza A.
Zubaer, Abdullah; Thapa, Simrika
2011-01-01
Different subtypes of Influenza A virus are associated with species specific, zoonotic or pandemic Influenza. The cause of its severity underlies in complicated evolution of its segmented RNA genome. Although genetic shift and genetic drift are well known in the evolution of this virus, we reported the significant role of unique RNA palindromes in its evolution. Our computational approach identified the existence of unique palindromes in each subtype of Influenza A virus with its absence in Influenza B relating the fact of virulence and vigorous genetic hitchhiking in Influenza A. The current study focused on the re-assortment event responsible for the emergence of pandemic-2009 H1N1 virus, which is associated with outgrow of new palindrome and in turn, changing its RNA structure. We hypothesize that the change in RNA structure due to the presence of palindrome facilitates the event of re-assortment in Influenza A. Thus the evolutionary process of Influenza A is much more complicated as previously known, and that has been demonstrated in this study.
Areej M. Abduldaim
2013-01-01
Full Text Available We introduced and studied -regular modules as a generalization of -regular rings to modules as well as regular modules (in the sense of Fieldhouse. An -module is called -regular if for each and , there exist and a positive integer such that . The notion of -pure submodules was introduced to generalize pure submodules and proved that an -module is -regular if and only if every submodule of is -pure iff is a -regular -module for each maximal ideal of . Many characterizations and properties of -regular modules were given. An -module is -regular iff is a -regular ring for each iff is a -regular ring for finitely generated module . If is a -regular module, then .
Repeat Sequences and Base Correlations in Human Y Chromosome Palindromes
Neng-zhi Jin; Zi-xian Liu; Yan-jiao Qi; Wen-yuan Qiu
2009-01-01
On the basis of information theory and statistical methods, we use mutual information, n-tuple entropy and conditional entropy, combined with biological characteristics, to analyze the long range correlation and short range correlation in human Y chromosome palindromes. The magnitude distribution of the long range correlation which can be reflected by the mutual information is P5>P5a>P5b (P5a and P5b are the sequences that replace solely Alu repeats and all interspersed repeats with random uncorrelated sequences in human Y chromosome palindrome 5, respectively); and the magnitude distribution of the short range correlation which can be reflected by the n-tuple entropy and the conditional entropy is P5>P5a>P5b>random uncorrelated sequence. In other words, when the Alu repeats and all interspersed repeats replace with random uncorrelated sequence, the long range and short range correlation decrease gradually. However, the random uncorrelated sequence has no correlation. This research indicates that more repeat sequences result in stronger correlation between bases in human Y chromosome. The analyses may be helpful to understand the special structures of human Y chromosome palindromes profoundly.
Taneja, Inder Jeet
2011-01-01
In this short paper we have produced different kinds of upside down magic squares based on a palindromic day 11.02.2011. In this day appear only the algorisms 0, 1 and 2. Some of the magic squares are bimagic and some are palindromic. Magic sums of the magic squares of order 3x3, 4x4 and 5x5 satisfies the Pythagoras theorem. Bimagic squares of order 9x9 are produced with 4, 6 and 8 digits. The bimagic square of order 9x9 with 8 digits is with palindromic numbers. We have given bimagic squares of order 16x16 and 25x25, where the magic sum S1 in both the cases is same. In order to make these magic squares upside down, i.e., 180 degrees rotation, we have used the numbers in the digital form. All these magic square are only with three digits, 0, 1 and 2 appearing in the day 11.02.2011.
[Lumbar herniated disks treated with a dynamic interspacer].
Cueva-del Castillo Mendoza, J F; Franco-López, E A; Hinojosa-Sandoval, F; de León-Martínez, U A; Cueva-del Castillo Mendoza, F J
2013-01-01
Lumbar herniated disks result in lumbar pain with neurologic involvement. Medical treatment and rehabilitation provide improvement for this type of lumbar pain at the early stages. When conservative treatment fails, the surgical option offers the possibility of improving patients' health status. Moojen considers that the application of interspinous spacers provides good results. The purpose of this research is to assess the clinical and imaging results in patients with contained lumbar herniated disk treated with the DYNAMIC INTERSPACER interspinous spacer, a Mexican product. The efficacy of the interspinous device was assessed by means of a near-investigational and longitudinal study conducted at "General Ignacio Zaragoza" ISSSTE Regional Hospital in patients with a diagnosis of lumbar pain. The mean age of the sample is 46.1 years, with an age range of 26-55 years. The treated levels were 6 L5-S1 and 5 L4-L5; two levels were treated in two patients. The mean preoperative VAS score was 8.1. The mean VAS score at postoperative year three was 1.6. Multiple types and brands of foreign interspinous devices are applied in Mexico which results in patients' clinical improvement. We proved that the use of the Mexican interspinous device can clinically improve patients with lumbar pain due to herniated disk. A decrease in the compression of the sac or the nerve roots by the hernia was observed in the comparative preoperative and postoperative MRI images.
Tóth, L Fejes; Ulam, S; Stark, M
1964-01-01
Regular Figures concerns the systematology and genetics of regular figures. The first part of the book deals with the classical theory of the regular figures. This topic includes description of plane ornaments, spherical arrangements, hyperbolic tessellations, polyhedral, and regular polytopes. The problem of geometry of the sphere and the two-dimensional hyperbolic space are considered. Classical theory is explained as describing all possible symmetrical groupings in different spaces of constant curvature. The second part deals with the genetics of the regular figures and the inequalities fo
Hidehito Inagaki
2016-07-01
Full Text Available Palindromic DNA sequences, which can form secondary structures, are widely distributed in the human genome. Although the nature of the secondary structure—single-stranded hairpin or double-stranded cruciform—has been extensively investigated in vitro, the existence of such unusual non-B DNA in vivo remains controversial. Here, we review palindrome-mediated gross chromosomal rearrangements possibly induced by non-B DNA in humans. Recent advances in next-generation sequencing have not yet overcome the difficulty of palindromic sequence analysis. However, a dozen palindromic AT-rich repeat (PATRR sequences have been identified at the breakpoints of recurrent or non-recurrent chromosomal translocations in humans. The breakages always occur at the center of the palindrome. Analyses of polymorphisms within the palindromes indicate that the symmetry and length of the palindrome affect the frequency of the de novo occurrence of these palindrome-mediated translocations, suggesting the involvement of non-B DNA. Indeed, experiments using a plasmid-based model system showed that the formation of non-B DNA is likely the key to palindrome-mediated genomic rearrangements. Some evidence implies a new mechanism that cruciform DNAs may come close together first in nucleus and illegitimately joined. Analysis of PATRR-mediated translocations in humans will provide further understanding of gross chromosomal rearrangements in many organisms.
Unusually long palindromes are abundant in mitochondrial control regions of insects and nematodes.
K P Arunkumar
Full Text Available BACKGROUND: Palindromes are known to be involved in a variety of biological processes. In the present investigation we carried out a comprehensive analysis of palindromes in the mitochondrial control regions (CRs of several animal groups to study their frequency, distribution and architecture to gain insights into the origin of replication of mtDNA. METHODOLOGY/PRINCIPAL FINDINGS: Many species of Arthropoda, Nematoda, Mollusca and Annelida harbor palindromes and inverted repeats (IRs in their CRs. Lower animals like cnidarians and higher animal groups like chordates are almost devoid of palindromes and IRs. The study revealed that palindrome occurrence is positively correlated with the AT content of CRs, and that IRs are likely to give rise to longer palindromes. CONCLUSIONS/SIGNIFICANCE: The present study attempts to explain possible reasons and gives in silico evidence for absence of palindromes and IRs from CR of vertebrate mtDNA and acquisition and retention of the same in insects. Study of CRs of different animal phyla uncovered unique architecture of this locus, be it high abundance of long palindromes and IRs in CRs of Insecta and Nematoda, or short IRs of 10-20 nucleotides with a spacer region of 12-14 bases in subphylum Chelicerata, or nearly complete of absence of any long palindromes and IRs in Vertebrata, Cnidaria and Echinodermata.
Unusually long palindromes are abundant in mitochondrial control regions of insects and nematodes.
Arunkumar, K P; Nagaraju, Javaregowda
2006-12-20
Palindromes are known to be involved in a variety of biological processes. In the present investigation we carried out a comprehensive analysis of palindromes in the mitochondrial control regions (CRs) of several animal groups to study their frequency, distribution and architecture to gain insights into the origin of replication of mtDNA. Many species of Arthropoda, Nematoda, Mollusca and Annelida harbor palindromes and inverted repeats (IRs) in their CRs. Lower animals like cnidarians and higher animal groups like chordates are almost devoid of palindromes and IRs. The study revealed that palindrome occurrence is positively correlated with the AT content of CRs, and that IRs are likely to give rise to longer palindromes. The present study attempts to explain possible reasons and gives in silico evidence for absence of palindromes and IRs from CR of vertebrate mtDNA and acquisition and retention of the same in insects. Study of CRs of different animal phyla uncovered unique architecture of this locus, be it high abundance of long palindromes and IRs in CRs of Insecta and Nematoda, or short IRs of 10-20 nucleotides with a spacer region of 12-14 bases in subphylum Chelicerata, or nearly complete of absence of any long palindromes and IRs in Vertebrata, Cnidaria and Echinodermata.
Fei Qi
2007-10-01
Full Text Available Abstract Background In idiopathic scoliosis patients, after anterior spinal fusion and instrumentation, the discs (interspace angle between the lowest instrumented vertebra (LIV and the next caudal vertebra became more wedged. We reviewed these patients and analyzed the changes of the angle. Methods By reviewing the medical records and roentgenograms of adolescent idiopathic scoliosis patients underwent anterior spinal fusion and instrumentation, Cobb angle of the curve, correction rate, coronal balance, LIV rotation, interspace angle were measured and analyzed. Results There were total 30 patients included. The mean coronal Cobb angle of the main curve (thoracolumbar/lumbar curve before and after surgery were 48.9° and 11.7°, respectively, with an average correction rate of 76.1%. The average rotation of LIV before surgery was 2.1 degree, and was improved to 1.2 degree after surgery. The interspace angle before surgery, on convex side-bending films, after surgery, at final follow up were 3.2°, -2.3°, 1.8° and 4.9°, respectively. The difference between the interspace angle after surgery and that preoperatively was not significant (P = 0.261, while the interspace angle at final follow-up became larger than that after surgery, and the difference was significant(P = 0.012. The interspace angle after surgery was correlated with that on convex side-bending films (r = 0.418, P = 0.022, and the interspace angle at final follow-up was correlated with that after surgery (r = 0.625, P = 0.000. There was significant correlation between the loss of the interspace angle and the loss of coronal Cobb angle of the main curve during follow-up(r = 0.483, P = 0.007. Conclusion The interspace angle could be improved after anterior correction and instrumentation surgery, but it became larger during follow-up. The loss of the interspace angle was correlated with the loss of coronal Cobb angle of the main curve during follow-up.
Unravelling the structural and mechanistic basis of CRISPR-Cas systems
Oost, van der J.; Westra, E.R.; Jackson, R.N.; Wiedenheft, B.
2014-01-01
Bacteria and archaea have evolved sophisticated adaptive immune systems, known as CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) systems, which target and inactivate invading viruses and plasmids. Immunity is acquired by integrating short fragments
CRISPR-Cas : revolutionising genome engineering : in practice - clinical update
Pepper, M.S; Nicholson, S.A
2016-01-01
... technologies, genome engineering looks set to become a clinical reality in the near future. This article discusses recent advancements in the technology called 'clustered regularly interspaced palindromic repeat (CRISPR)-associated genes' (CRISPR-Cas...
Pearson, Bruce M.; Louwen, Rogier; Baarlen, Van Peter; Vliet, Van Arnoud H.M.
2015-01-01
CRISPR (clustered regularly interspaced palindromic repeats)-Cas (CRISPR-associated) systems are sequence-specific adaptive defenses against phages and plasmidswhich are widespread in prokaryotes. Herewehave studiedwhether phylogenetic relatedness or sharing of environmental niches affects the
B.M. Pearson (Bruce M.); R.P.L. Louwen (Rogier); P. van Baarlen (Peter); A.H.M. van Vliet (Arnoud)
2015-01-01
textabstractCRISPR (clustered regularly interspaced palindromic repeats)-Cas (CRISPR-associated) systems are sequence-specific adaptive defenses against phages and plasmidswhich are widespread in prokaryotes. Herewehave studiedwhether phylogenetic relatedness or sharing of environmental niches
Unravelling the structural and mechanistic basis of CRISPR-Cas systems
Oost, van der J.; Westra, E.R.; Jackson, R.N.; Wiedenheft, B.
2014-01-01
Bacteria and archaea have evolved sophisticated adaptive immune systems, known as CRISPR–Cas (clustered regularly interspaced short palindromic repeats–CRISPR-associated proteins) systems, which target and inactivate invading viruses and plasmids. Immunity is acquired by integrating short fragments
Pearson, Bruce M.; Louwen, Rogier; Baarlen, Van Peter; Vliet, Van Arnoud H.M.
2015-01-01
CRISPR (clustered regularly interspaced palindromic repeats)-Cas (CRISPR-associated) systems are sequence-specific adaptive defenses against phages and plasmidswhich are widespread in prokaryotes. Herewehave studiedwhether phylogenetic relatedness or sharing of environmental niches affects the di
B.M. Pearson (Bruce M.); R.P.L. Louwen (Rogier); P. van Baarlen (Peter); A.H.M. van Vliet (Arnoud)
2015-01-01
textabstractCRISPR (clustered regularly interspaced palindromic repeats)-Cas (CRISPR-associated) systems are sequence-specific adaptive defenses against phages and plasmidswhich are widespread in prokaryotes. Herewehave studiedwhether phylogenetic relatedness or sharing of environmental niches affec
T.R. Sampson (Timothy); B.A. Napier (Brooke); M.R. Schroeder (Max); R.P.L. Louwen (Rogier); J. Zhao (Jinkou); C.-Y. Chin (Chui-Yoke); H.K. Ratner (Hannah); A.C. Llewellyn (Anna); C.L. Jones (Crystal); H. Laroui (Hamed); D. Merlin (Didier); P. Zhou (Pei); H.P. Endtz (Hubert); D.S. Weiss (David)
2014-01-01
textabstractClustered, regularly interspaced, short palindromic repeats-CRISPR associated (CRISPR-Cas) systems defend bacteria against foreign nucleic acids, such as during bacteriophage infection and transformation, processes which cause envelope stress. It is unclear if these machineries enhance
Shah, Shiraz Ali; Hansen, Niels R; Garrett, Roger A
2009-01-01
Transcripts from spacer sequences within chromosomal repeat clusters [CRISPRs (clusters of regularly interspaced palindromic repeats)] from archaea have been implicated in inhibiting or regulating the propagation of archaeal viruses and plasmids. For the crenarchaeal thermoacidophiles, the chromo......Transcripts from spacer sequences within chromosomal repeat clusters [CRISPRs (clusters of regularly interspaced palindromic repeats)] from archaea have been implicated in inhibiting or regulating the propagation of archaeal viruses and plasmids. For the crenarchaeal thermoacidophiles...
Interspace modification of titania-nanorod arrays for efficient mesoscopic perovskite solar cells
Chen, Peng; Jin, Zhixin; Wang, Yinglin; Wang, Meiqi; Chen, Shixin; Zhang, Yang; Wang, Lingling; Zhang, Xintong; Liu, Yichun
2017-04-01
Morphology of electron transport layers (ETLs) has an important influence on the device architecture and electronic processes of mesostructured solar cells. In this work, we thoroughly investigated the effect of the interspace of TiO2 nanorod (NR) arrays on the photovoltaic performance of the perovskite solar cells (PSCs). Along with the interspace in TiO2-NR arrays increasing, the thickness as well as the crystal size of perovskite capping layer are reduced accordingly, and the filling of perovskite in the channel becomes incomplete. Electrochemical impedance spectroscopy measurements reveal that this variation of perovskite absorber layer, induced by interspace of TiO2 NR arrays, causes the change of charge recombination process at the TiO2/perovskite interface, suggesting that a balance between capping layer and the perovskite filling is critical to obtain high charge collection efficiency of PSCs. A power conversion efficiency of 10.3% could be achieved through careful optimization of interspace in TiO2-NR arrays. Our research will shed light on the morphology control of ETLs with 1D structure for heterojunction solar cells fabricated by solution-deposited method.
Timothy R. Larsen
2012-01-01
Full Text Available Palindromic rheumatism is a rare disease associated with systemic inflammation. Negative or constrictive coronary artery remodeling is typically not seen until the 7th or 8th decade of life. We report a case of a young female with palindromic rheumatism who suffered a non-ST segment elevation myocardial infarction secondary to a flow-limiting lesion that demonstrated negative remodeling by intravascular ultrasound (IVUS.
Hansen, Lars Kai; Rasmussen, Carl Edward; Svarer, C.
1994-01-01
Regularization, e.g., in the form of weight decay, is important for training and optimization of neural network architectures. In this work the authors provide a tool based on asymptotic sampling theory, for iterative estimation of weight decay parameters. The basic idea is to do a gradient descent...... in the estimated generalization error with respect to the regularization parameters. The scheme is implemented in the authors' Designer Net framework for network training and pruning, i.e., is based on the diagonal Hessian approximation. The scheme does not require essential computational overhead in addition...... to what is needed for training and pruning. The viability of the approach is demonstrated in an experiment concerning prediction of the chaotic Mackey-Glass series. The authors find that the optimized weight decays are relatively large for densely connected networks in the initial pruning phase, while...
Coxeter, H S M
1973-01-01
Polytopes are geometrical figures bounded by portions of lines, planes, or hyperplanes. In plane (two dimensional) geometry, they are known as polygons and comprise such figures as triangles, squares, pentagons, etc. In solid (three dimensional) geometry they are known as polyhedra and include such figures as tetrahedra (a type of pyramid), cubes, icosahedra, and many more; the possibilities, in fact, are infinite! H. S. M. Coxeter's book is the foremost book available on regular polyhedra, incorporating not only the ancient Greek work on the subject, but also the vast amount of information
Olivier Delelis
Full Text Available BACKGROUND: HIV-1 integrase (IN catalyses the retroviral integration process, removing two nucleotides from each long terminal repeat and inserting the processed viral DNA into the target DNA. It is widely assumed that the strand transfer step has no sequence specificity. However, recently, it has been reported by several groups that integration sites display a preference for palindromic sequences, suggesting that a symmetry in the target DNA may stabilise the tetrameric organisation of IN in the synaptic complex. METHODOLOGY/PRINCIPAL FINDINGS: We assessed the ability of several palindrome-containing sequences to organise tetrameric IN and investigated the ability of IN to catalyse DNA cleavage at internal positions. Only one palindromic sequence was successfully cleaved by IN. Interestingly, this symmetrical sequence corresponded to the 2-LTR junction of retroviral DNA circles-a palindrome similar but not identical to the consensus sequence found at integration sites. This reaction depended strictly on the cognate retroviral sequence of IN and required a full-length wild-type IN. Furthermore, the oligomeric state of IN responsible for this cleavage differed from that involved in the 3'-processing reaction. Palindromic cleavage strictly required the tetrameric form, whereas 3'-processing was efficiently catalysed by a dimer. CONCLUSIONS/SIGNIFICANCE: Our findings suggest that the restriction-like cleavage of palindromic sequences may be a general physiological activity of retroviral INs and that IN tetramerisation is strongly favoured by DNA symmetry, either at the target site for the concerted integration or when the DNA contains the 2-LTR junction in the case of the palindromic internal cleavage.
Saintamand, Alexis; Vincent-Fabert, Christelle; Garot, Armand; Rouaud, Pauline; Oruc, Zeliha; Magnone, Virginie; Cogné, Michel; Denizot, Yves
2016-02-17
The IgH 3' regulatory region (3'RR) controls class switch recombination (CSR) and somatic hypermutation (SHM) in B cells. The mouse 3'RR contains four enhancer elements with hs1,2 flanked by inverted repeated sequences and the centre of a 25-kb palindrome bounded by two hs3 enhancer inverted copies (hs3a and hs3b). hs4 lies downstream of the palindrome. In mammals, evolution maintained this unique palindromic arrangement, suggesting that it is functionally significant. Here we report that deconstructing the palindromic IgH 3'RR strongly affects its function even when enhancers are preserved. CSR and IgH transcription appear to be poorly dependent on the 3'RR architecture and it is more or less preserved, provided 3'RR enhancers are present. By contrast, a 'palindromic effect' significantly lowers VH germline transcription, AID recruitment and SHM. In conclusion, this work indicates that the IgH 3'RR does not simply pile up enhancer units but also optimally exposes them into a functional architecture of crucial importance.
Schrödinger operators with Rudin-Shapiro potentials are not palindromic
Allouche, J.-P.
1997-04-01
We prove a conjecture of A. Hof, O. Knill and B. Simon [Commun. Math. Phys. 174, 149-159 (1995)] by showing that the Rudin-Shapiro sequence is not palindromic, i.e., does not contain arbitrarily long palindromes. We prove actually this property for all paperfolding sequences and all Rudin-Shapiro sequences deduced from paperfolding sequences. As a consequence and as guessed by the above authors, their method cannot be used for establishing that discrete Schrödinger operators with Rudin-Shapiro potentials have a purely singular continuous spectrum.
Bastiaan Star
Full Text Available Degradation-specific processes and variation in laboratory protocols can bias the DNA sequence composition from samples of ancient or historic origin. Here, we identify a novel artifact in sequences from historic samples of Atlantic cod (Gadus morhua, which forms interrupted palindromes consisting of reverse complementary sequence at the 5' and 3'-ends of sequencing reads. The palindromic sequences themselves have specific properties - the bases at the 5'-end align well to the reference genome, whereas extensive misalignments exists among the bases at the terminal 3'-end. The terminal 3' bases are artificial extensions likely caused by the occurrence of hairpin loops in single stranded DNA (ssDNA, which can be ligated and amplified in particular library creation protocols. We propose that such hairpin loops allow the inclusion of erroneous nucleotides, specifically at the 3'-end of DNA strands, with the 5'-end of the same strand providing the template. We also find these palindromes in previously published ancient DNA (aDNA datasets, albeit at varying and substantially lower frequencies. This artifact can negatively affect the yield of endogenous DNA in these types of samples and introduces sequence bias.
Mizuno, Ken'Ichi; Lambert, Sarah; Baldacci, Giuseppe; Murray, Johanne M; Carr, Antony M
2009-12-15
Gene amplification plays important roles in the progression of cancer and contributes to acquired drug resistance during treatment. Amplification can initiate via dicentric palindromic chromosome production and subsequent breakage-fusion-bridge cycles. Here we show that, in fission yeast, acentric and dicentric palindromic chromosomes form by homologous recombination protein-dependent fusion of nearby inverted repeats, and that these fusions occur frequently when replication forks arrest within the inverted repeats. Genetic and molecular analyses suggest that these acentric and dicentric palindromic chromosomes arise not by previously described mechanisms, but by a replication template exchange mechanism that does not involve a DNA double-strand break. We thus propose an alternative mechanism for the generation of palindromic chromosomes dependent on replication fork arrest at closely spaced inverted repeats.
Yong Hua LI; Hai Bin KAN; Bing Jun YU
2004-01-01
In this paper, a special kind of partial algebras called projective partial groupoids is defined.It is proved that the inverse image of all projections of a fundamental weak regular *-semigroup under the homomorphism induced by the maximum idempotent-separating congruence of a weak regular *-semigroup has a projective partial groupoid structure. Moreover, a weak regular *-product which connects a fundamental weak regular *-semigroup with corresponding projective partial groupoid is defined and characterized. It is finally proved that every weak regular *-product is in fact a weak regular *-semigroup and any weak regular *-semigroup is constructed in this way.
NOETHERIAN GR-REGULAR RINGS ARE REGULAR
LIHUISHI
1994-01-01
It is proved that for a left Noetherian z-graded ring A,if every finitely generated graded A-module has finite projective dimension(i.e-,A is gr-regular)then every finitely generated A-module has finite projective dimension(i.e.,A is regular).Some applications of this result to filtered rings and some classical cases are also given.
The Ehrlich-Aberth method for palindromic matrix polynomials represented in the Dickson basis
Gemignani, Luca
2011-01-01
An algorithm based on the Ehrlich-Aberth root-finding method is presented for the computation of the eigenvalues of a T-palindromic matrix polynomial. A structured linearization of the polynomial represented in the Dickson basis is introduced in order to exploit the symmetry of the roots by halving the total number of the required approximations. The rank structure properties of the linearization allow the design of a fast and numerically robust implementation of the root-finding iteration. Numerical experiments that confirm the effectiveness and the robustness of the approach are provided.
Novel Method Developed to Further the Understanding of DNA Palindromes | Poster
Editor's note: Platinum Highlight articles are noteworthy publications selected periodically by Dr. Craig Reynolds, associate director, National Cancer Institute, from among the most recently published Platinum Publications. When Alison Rattray and colleagues in the Gene Regulation and Chromosome Biology Laboratory (GRCBL) examined a mutant yeast cell they had isolated in a screen, they noticed something strange. The DNA exhibited a “very specific, but weird, rearrangement,” she explained. The arrangement turned out to be a DNA palindrome, “opening the door to studying these elusive DNA motifs,” she said.
Building the interspace: Digital library infrastructure for a University Engineering Community
Schatz, B.
1995-12-31
A large-scale digital library is being constructed and evaluated at the University of Illinois, with the goal of bringing professional search and display to Internet information services. A testbed planned to grow to 10K documents and 100K users is being constructed in the Grainger Engineering Library Information Center, as a joint effort of the University Library and the National Center for Supercomputing Applications (NCSA), with evaluation and research by the Graduate School of Library and Information Science and the Department of Computer Science. The electronic collection will be articles from engineering and science journals and magazines, obtained directly from publishers in SGML format and displayed containing all text, figures, tables, and equations. The publisher partners include IEEE Computer Society, AIAA (Aerospace Engineering), American Physical Society, and Wiley & Sons. The software will be based upon NCSA Mosaic as a network engine connected to commercial SGML displayers and full-text searchers. The users will include faculty/students across the midwestern universities in the Big Ten, with evaluations via interviews, surveys, and transaction logs. Concurrently, research into scaling the testbed is being conducted. This includes efforts in computer science, information science, library science, and information systems. These efforts will evaluate different semantic retrieval technologies, including automatic thesaurus and subject classification graphs. New architectures will be designed and implemented for a next generation digital library infrastructure, the Interspace, which supports interaction with information spread across information spaces within the Net.
Regular Expression Pocket Reference
Stubblebine, Tony
2007-01-01
This handy little book offers programmers a complete overview of the syntax and semantics of regular expressions that are at the heart of every text-processing application. Ideal as a quick reference, Regular Expression Pocket Reference covers the regular expression APIs for Perl 5.8, Ruby (including some upcoming 1.9 features), Java, PHP, .NET and C#, Python, vi, JavaScript, and the PCRE regular expression libraries. This concise and easy-to-use reference puts a very powerful tool for manipulating text and data right at your fingertips. Composed of a mixture of symbols and text, regular exp
Highly Iterated Palindromic Sequences (HIPs and Their Relationship to DNA Methyltransferases
Jeff Elhai
2015-03-01
Full Text Available The sequence GCGATCGC (Highly Iterated Palindrome, HIP1 is commonly found in high frequency in cyanobacterial genomes. An important clue to its function may be the presence of two orphan DNA methyltransferases that recognize internal sequences GATC and CGATCG. An examination of genomes from 97 cyanobacteria, both free-living and obligate symbionts, showed that there are exceptional cases in which HIP1 is at a low frequency or nearly absent. In some of these cases, it appears to have been replaced by a different GC-rich palindromic sequence, alternate HIPs. When HIP1 is at a high frequency, GATC- and CGATCG-specific methyltransferases are generally present in the genome. When an alternate HIP is at high frequency, a methyltransferase specific for that sequence is present. The pattern of 1-nt deviations from HIP1 sequences is biased towards the first and last nucleotides, i.e., those distinguish CGATCG from HIP1. Taken together, the results point to a role of DNA methylation in the creation or functioning of HIP sites. A model is presented that postulates the existence of a GmeC-dependent mismatch repair system whose activity creates and maintains HIP sequences.
Dimensional regularization is generic
Fujikawa, Kazuo
2016-01-01
The absence of the quadratic divergence in the Higgs sector of the Standard Model in the dimensional regularization is usually regarded to be an exceptional property of a specific regularization. To understand what is going on in the dimensional regularization, we illustrate how to reproduce the results of the dimensional regularization for the $\\lambda\\phi^{4}$ theory in the more conventional regularization such as the higher derivative regularization; the basic postulate involved is that the quadratically divergent induced mass, which is independent of the scale change of the physical mass, is kinematical and unphysical. This is consistent with the derivation of the Callan-Symanzik equation, which is a comparison of two theories with slightly different masses, for the $\\lambda\\phi^{4}$ theory without encountering the quadratic divergence. We thus suggest that the dimensional regularization is generic in a bottom-up approach starting with a successful low-energy theory. We also define a modified version of t...
Robust Sparse Analysis Regularization
Vaiter, Samuel; Dossal, Charles; Fadili, Jalal
2011-01-01
This paper studies the properties of L1-analysis regularization for the resolution of linear inverse problems. Most previous works consider sparse synthesis priors where the sparsity is measured as the L1 norm of the coefficients that synthesize the signal in a given dictionary. In contrast, the more general analysis regularization minimizes the L1 norm of the correlations between the signal and the atoms in the dictionary. The corresponding variational problem includes several well-known regularizations such as the discrete total variation and the fused lasso. We first prove that a solution of analysis regularization is a piecewise affine function of the observations. Similarly, it is a piecewise affine function of the regularization parameter. This allows us to compute the degrees of freedom associated to sparse analysis estimators. Another contribution gives a sufficient condition to ensure that a signal is the unique solution of the analysis regularization when there is no noise in the observations. The s...
Goyvaerts, Jan
2009-01-01
This cookbook provides more than 100 recipes to help you crunch data and manipulate text with regular expressions. Every programmer can find uses for regular expressions, but their power doesn't come worry-free. Even seasoned users often suffer from poor performance, false positives, false negatives, or perplexing bugs. Regular Expressions Cookbook offers step-by-step instructions for some of the most common tasks involving this tool, with recipes for C#, Java, JavaScript, Perl, PHP, Python, Ruby, and VB.NET. With this book, you will: Understand the basics of regular expressions through a
Pareja Eduardo
2006-03-01
Full Text Available Abstract Background Mobile elements are involved in genomic rearrangements and virulence acquisition, and hence, are important elements in bacterial genome evolution. The insertion of some specific Insertion Sequences had been associated with repetitive extragenic palindromic (REP elements. Considering that there are a sufficient number of available genomes with described REPs, and exploiting the advantage of the traceability of transposition events in genomes, we decided to exhaustively analyze the relationship between REP sequences and mobile elements. Results This global multigenome study highlights the importance of repetitive extragenic palindromic elements as target sequences for transposases. The study is based on the analysis of the DNA regions surrounding the 981 instances of Insertion Sequence elements with respect to the positioning of REP sequences in the 19 available annotated microbial genomes corresponding to species of bacteria with reported REP sequences. This analysis has allowed the detection of the specific insertion into REP sequences for ISPsy8 in Pseudomonas syringae DC3000, ISPa11 in P. aeruginosa PA01, ISPpu9 and ISPpu10 in P. putida KT2440, and ISRm22 and ISRm19 in Sinorhizobium meliloti 1021 genome. Preference for insertion in extragenic spaces with REP sequences has also been detected for ISPsy7 in P. syringae DC3000, ISRm5 in S. meliloti and ISNm1106 in Neisseria meningitidis MC58 and Z2491 genomes. Probably, the association with REP elements that we have detected analyzing genomes is only the tip of the iceberg, and this association could be even more frequent in natural isolates. Conclusion Our findings characterize REP elements as hot spots for transposition and reinforce the relationship between REP sequences and genomic plasticity mediated by mobile elements. In addition, this study defines a subset of REP-recognizer transposases with high target selectivity that can be useful in the development of new tools for
Regularization in kernel learning
Mendelson, Shahar; 10.1214/09-AOS728
2010-01-01
Under mild assumptions on the kernel, we obtain the best known error rates in a regularized learning scenario taking place in the corresponding reproducing kernel Hilbert space (RKHS). The main novelty in the analysis is a proof that one can use a regularization term that grows significantly slower than the standard quadratic growth in the RKHS norm.
Regular database update logics
Spruit, Paul; Wieringa, Roel; Meyer, John-Jules
2001-01-01
We study regular first-order update logic (FUL), which is a variant of regular dynamic logic in which updates to function symbols as well as to predicate symbols are possible. We fi1rst study FUL without making assumptions about atomic updates. Second, we look at relational algebra update logic (RAU
Regularization by External Variables
Bossolini, Elena; Edwards, R.; Glendinning, P. A.
2016-01-01
Regularization was a big topic at the 2016 CRM Intensive Research Program on Advances in Nonsmooth Dynamics. There are many open questions concerning well known kinds of regularization (e.g., by smoothing or hysteresis). Here, we propose a framework for an alternative and important kind of regula...... of regularization, by external variables that shadow either the state or the switch of the original system. The shadow systems are derived from and inspired by various applications in electronic control, predator-prey preference, time delay, and genetic regulation....
Regularized maximum correntropy machine
Wang, Jim Jing-Yan
2015-02-12
In this paper we investigate the usage of regularized correntropy framework for learning of classifiers from noisy labels. The class label predictors learned by minimizing transitional loss functions are sensitive to the noisy and outlying labels of training samples, because the transitional loss functions are equally applied to all the samples. To solve this problem, we propose to learn the class label predictors by maximizing the correntropy between the predicted labels and the true labels of the training samples, under the regularized Maximum Correntropy Criteria (MCC) framework. Moreover, we regularize the predictor parameter to control the complexity of the predictor. The learning problem is formulated by an objective function considering the parameter regularization and MCC simultaneously. By optimizing the objective function alternately, we develop a novel predictor learning algorithm. The experiments on two challenging pattern classification tasks show that it significantly outperforms the machines with transitional loss functions.
Regular Expression Containment
Henglein, Fritz; Nielsen, Lasse
2011-01-01
We present a new sound and complete axiomatization of regular expression containment. It consists of the conventional axiomatiza- tion of concatenation, alternation, empty set and (the singleton set containing) the empty string as an idempotent semiring, the fixed- point rule E* = 1 + E × E......* for Kleene-star, and a general coin- duction rule as the only additional rule. Our axiomatization gives rise to a natural computational inter- pretation of regular expressions as simple types that represent parse trees, and of containment proofs as coercions. This gives the axiom- atization a Curry......-Howard-style constructive interpretation: Con- tainment proofs do not only certify a language-theoretic contain- ment, but, under our computational interpretation, constructively transform a membership proof of a string in one regular expres- sion into a membership proof of the same string in another regular expression. We...
Regularities of Multifractal Measures
Hun Ki Baek
2008-05-01
First, we prove the decomposition theorem for the regularities of multifractal Hausdorff measure and packing measure in $\\mathbb{R}^d$. This decomposition theorem enables us to split a set into regular and irregular parts, so that we can analyze each separately, and recombine them without affecting density properties. Next, we give some properties related to multifractal Hausdorff and packing densities. Finally, we extend the density theorem in [6] to any measurable set.
T. (A)LVAREZ
2012-01-01
For a closed linear relation in a Banach space the concept of regularity is introduced and studied.It is shown that many of the results of Mbekhta and other authors for operators remain valid in the context of multivalued linear operators.We also extend the punctured neighbourhood theorem for operators to linear relations and as an application we obtain a characterization of semiFredholm linear relations which are regular.
Correlations in a Mozart's music score (K-73x) with palindromic and upside-down structure
Dagdug, Leonardo; Alvarez-Ramirez, Jose; Lopez, Carlos; Moreno, Rodolfo; Hernandez-Lemus, Enrique
2007-09-01
In this work, we study long-range correlations in a “Scherzo-Duetto di Mozart” score (K-73x) for two violins. This is a fascinating piece, as the second violin part is upside down on the same sheet below the first violin, and some parts are like a palindrome. Given such ingenious structure, it is expected the existence of long-range correlations in the score structure. In order to quantify long-range correlations, we considered the music score as a sequence of integer numbers, each of them corresponding to last common denominator units of note. By using detrended fluctuation analysis (DFA), correlations are quantified by means of the scaling exponent that reflects the type of correlations for a given distance between neighbors note. The following conclusions can be drawn from the analysis: (a) For about 10-25 neighbor note distances, correlations are similar to 1/f-noise. This is an interesting finding since it has been shown that pleasant sounds for humans display a behavior similar to 1/f noise. (b) As the neighbor note distance increases, the long-range correlations decays continuously. For some score sections, the music score behaves like non-correlated (i.e., purely random) noise. Summing up, the results show that the studied Mozart's score contains a certain degree of correlation for relatively small note distances, and becomes close to non-correlated behavior for long note distances. We considered also the sequence constructed by considering the distance between the simultaneously played notes of the two violins. Interestingly, for relatively small neighbor note distances, a scaling behavior similar to that found for individual violins is also displayed. In some sense, this is an expression of the specific structure (palindromes plus upside down construction) used by Mozart in the composition of this music score. Although we focused on a particular high-art music score, our results suggest that modern methods borrowed from statistical physics can be
Single palindromic molecular beacon-based amplification for genetic analysis of cancers.
Li, Feng; Zhao, Hui; Wang, Zheng-Yong; Wu, Zai-Sheng; Yang, Zhe; Li, Cong-Cong; Xu, Huo; Lyu, Jian-Xin; Shen, Zhi-Fa
2017-05-15
The detection of biomarkers is of crucial importance in reducing the morbidity and mortality of complex diseases. Thus, there is a great desire to develop highly efficient and simple sensing methods to fulfill the different diagnostic and therapeutic purposes. Herein, using tumor suppressor p53 gene as model target DNA, we developed a novel palindromic fragment-incorporated molecular beacon (P-MB) that can perform multiple functions, including recognition element, signal reporter, polymerization template and primer. Upon specific hybridization with target DNA, P-MBs can interact with each other and are extended by polymerase without any additional probes. As a result, hybridized targets are peeled off from P-MBs and initiate the next round of reactions, leading to the unique strand displacement amplification (SDA). The newly-proposed enzymatic amplification displays the detection limit as low as 100pM and excellent selectivity in distinguishing single-base mutation with the linear response range from 100pM to 75nM. This is the simplest SDA sensing system so far because of only involving one type of DNA probe. This impressive sensing paradigm is expected to provide new insight into developing new-type of DNA probes that hold tremendous potential with important applications in molecular biology research and clinical diagnosis. Copyright © 2017 Elsevier B.V. All rights reserved.
Sheehan, C; Lynch, M; Cullen, C; Cryan, B; Greer, P; Fanning, S
1995-09-01
Acinetobacter species are important nosocomial pathogens. A rapid and sensitive identification system, capable of providing strain identity at the genetic level, is required to identify outbreak strains and facilitate the early implementation of infection control procedures. Repetitive extragenic palindromic (REP) elements, have been identified in numerous bacteria and these genomic sequences provide useful targets for DNA amplification. A method for amplifying inter-REP DNA sequences, REP-multiple arbitrary amplicon profiling (REP-MAAP), is described and applied to 29 Acinetobacter baumannii from clinical samples. Amplified polymorphic DNA patterns were demonstrated for all isolates and those displaying identical REP-MAAP patterns were considered identical at the genetic level. In the spring of 1993, 10 intensive care unit patients had endotracheal colonization with A. baumannii (five with REP-MAAP I and five with REP-MAAP II patterns). These findings suggested nosocomial transmission of organisms which was terminated by standard infection control measures. No further A. baumannii were detected until the winter of 1993 when isolates of different REP-MAAP groups emerged, suggesting that factors other than nosocomial transmission were implicated.
Regularized Structural Equation Modeling.
Jacobucci, Ross; Grimm, Kevin J; McArdle, John J
A new method is proposed that extends the use of regularization in both lasso and ridge regression to structural equation models. The method is termed regularized structural equation modeling (RegSEM). RegSEM penalizes specific parameters in structural equation models, with the goal of creating easier to understand and simpler models. Although regularization has gained wide adoption in regression, very little has transferred to models with latent variables. By adding penalties to specific parameters in a structural equation model, researchers have a high level of flexibility in reducing model complexity, overcoming poor fitting models, and the creation of models that are more likely to generalize to new samples. The proposed method was evaluated through a simulation study, two illustrative examples involving a measurement model, and one empirical example involving the structural part of the model to demonstrate RegSEM's utility.
Faupin, Jeremy; Møller, Jacob Schach; Skibsted, Erik
2011-01-01
We study regularity of bound states pertaining to embedded eigenvalues of a self-adjoint operator H, with respect to an auxiliary operator A that is conjugate to H in the sense of Mourre. We work within the framework of singular Mourre theory which enables us to deal with confined massless Pauli–......–Fierz models, our primary example, and many-body AC-Stark Hamiltonians. In the simpler context of regular Mourre theory, our results boil down to an improvement of results obtained recently in [8, 9]....
Manifold Regularized Reinforcement Learning.
Li, Hongliang; Liu, Derong; Wang, Ding
2017-01-27
This paper introduces a novel manifold regularized reinforcement learning scheme for continuous Markov decision processes. Smooth feature representations for value function approximation can be automatically learned using the unsupervised manifold regularization method. The learned features are data-driven, and can be adapted to the geometry of the state space. Furthermore, the scheme provides a direct basis representation extension for novel samples during policy learning and control. The performance of the proposed scheme is evaluated on two benchmark control tasks, i.e., the inverted pendulum and the energy storage problem. Simulation results illustrate the concepts of the proposed scheme and show that it can obtain excellent performance.
Annotation of Regular Polysemy
Martinez Alonso, Hector
Regular polysemy has received a lot of attention from the theory of lexical semantics and from computational linguistics. However, there is no consensus on how to represent the sense of underspecified examples at the token level, namely when annotating or disambiguating senses of metonymic words...
Krawczyk, Stefanie; Thurow, Corinna; Niggeweg, Ricarda; Gatz, Christiane
2002-01-01
In higher plants, activation sequence-1 (as-1) of the cauliflower mosaic virus 35S promoter mediates both salicylic acid- and auxin-inducible transcriptional activation. Originally found in viral and T-DNA promoters, as-1-like elements are also functional elements of plant promoters activated in the course of a defence response upon pathogen attack. as-1-like elements are characterised by two imperfect palindromes with the palindromic centres being spaced by 12 bp. They are recognised by plan...
Oude Blenke, Erik; Evers, Martijn J.W.; Mastrobattista, Enrico; Oost, van der John
2016-01-01
The CRISPR-Cas9 gene editing system has taken the biomedical science field by storm, initiating rumors about future Nobel Prizes and heating up a fierce patent war, but also making significant scientific impact. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), together with
Small CRISPR RNAs guide antiviral defense in prokaryotes
Brouns, S.J.J.; Jore, M.M.; Lundgren, M.; Westra, E.R.; Slijkhuis, R.J.; Snijders, A.P.; Dickman, M.J.; Makarova, K.S.; Koonin, E.V.; Oost, van der J.
2008-01-01
Prokaryotes acquire virus resistance by integrating short fragments of viral nucleic acid into clusters of regularly interspaced short palindromic repeats (CRISPRs). Here we show how virus-derived sequences contained in CRISPRs are used by CRISPR-associated (Cas) proteins from the host to mediate an
Oude Blenke, Erik; Evers, Martijn J.W.; Mastrobattista, Enrico; Oost, van der John
2016-01-01
The CRISPR-Cas9 gene editing system has taken the biomedical science field by storm, initiating rumors about future Nobel Prizes and heating up a fierce patent war, but also making significant scientific impact. The Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR), together with
Small CRISPR RNAs guide antiviral defense in prokaryotes
Brouns, S.J.J.; Jore, M.M.; Lundgren, M.; Westra, E.R.; Slijkhuis, R.J.; Snijders, A.P.; Dickman, M.J.; Makarova, K.S.; Koonin, E.V.; Oost, van der J.
2008-01-01
Prokaryotes acquire virus resistance by integrating short fragments of viral nucleic acid into clusters of regularly interspaced short palindromic repeats (CRISPRs). Here we show how virus-derived sequences contained in CRISPRs are used by CRISPR-associated (Cas) proteins from the host to mediate an
CRISPR/Cas system for yeast genome engineering: advances and applications
Stovicek, Vratislav; Holkenbrink, Carina; Borodina, Irina
2017-01-01
The methods based on the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) system have quickly gained popularity for genome editing and transcriptional regulation in many organisms, including yeast. This review aims to provide a comprehensive overview...... of CRISPR application for different yeast species: from basic principles and genetic design to applications....
Application of CRISPR/Cas9 Genome Editing to Improve Recombinant Protein Production in CHO Cells
Grav, Lise Marie; Julie la Cour Karottki, Karen; Lee, Jae Seong
2017-01-01
and yields. In this chapter, we present our protocol on how to use the genome editing tool Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) to knockout engineering target genes in CHO cells. As an example, we refer to the glutamine synthetase (GS...
The Role of CRISPR-Cas Systems in Virulence of Pathogenic Bacteria
Louwen, R.; Staals, R.H.J.; Endtz, H.P.; Baarlen, van P.; Oost, van der J.
2014-01-01
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are present in many bacterial and archaeal genomes. Since the discovery of the typical CRISPR loci in the 1980s, well before their physiological role was revealed, their variable sequences have been
Evolution and classification of the CRISPR-Cas systems
Makarova, K.S.; Brouns, S.J.J.; Oost, van der J.
2011-01-01
The CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) modules are adaptive immunity systems that are present in many archaea and bacteria. These defence systems are encoded by operons that have an extraordinarily diverse architecture and a high rate of
A Golden Gate-based Protocol for Assembly of Multiplexed gRNA Expression Arrays for CRISPR/Cas9
Vad-Nielsen, Johan; Lin, Lin; Jensen, Kristopher Torp
2016-01-01
The CRISPR (clustered regularly interspaced short palindromic repeats)-associated protein 9 (Cas9) has become the most broadly used and powerful tool for genome editing. Many applications of CRISPR-Cas9 require the delivery of multiple small guide RNAs (gRNAs) into the same cell in order to achieve...
Structural biology. Structures of the CRISPR-Cmr complex reveal mode of RNA target positioning
Taylor, D.W.; Zhu, Y.; Staals, R.H.J.; Kornfeld, J.E.; Shinkai, A.; Oost, van der J.; Nogales, E.; Doudna, J.A.
2015-01-01
Adaptive immunity in bacteria involves RNA-guided surveillance complexes that use CRISPR (clustered regularly interspaced short palindromic repeats)-associated (Cas) proteins together with CRISPR RNAs (crRNAs) to target invasive nucleic acids for degradation. Whereas type I and type II CRISPR-Cas
CRISPR interference and priming varies with individual spacer sequences
Xue, Chaoyou; Seetharam, Arun S.; Musharova, Olga; Severinov, Konstantin; Brouns, Stan J.J.; Severin, Andrew J.; Sashital, Dipali G.
2015-01-01
CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring 'spacer' sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for
Wiedenheft, Blake; van Duijn, Esther; Bultema, Jelle; Waghmare, Sakharam; Zhou, Kaihong; Barendregt, Arjan; Westphal, Wiebke; Heck, Albert; Boekema, Egbert; Dickman, Mark; Doudna, Jennifer A.
2011-01-01
Prokaryotes have evolved multiple versions of an RNA-guided adaptive immune system that targets foreign nucleic acids. In each case, transcripts derived from clustered regularly interspaced short palindromic repeats (CRISPRs) are thought to selectively target invading phage and plasmids in a sequenc
Structural basis for CRISPR RNA-guided DNA recognition by Cascade
Jore, Matthijs M.; Lundgren, Magnus; van Duijn, Esther; Bultema, Jelle B.; Westra, Edze R.; Waghmare, Sakharam P.; Wiedenheft, Blake; Pul, Uemit; Wurm, Reinhild; Wagner, Rolf; Beijer, Marieke R.; Barendregt, Arjan; Zhou, Kaihong; Snijders, Ambrosius P. L.; Dickman, Mark J.; Doudna, Jennifer A.; Boekema, Egbert J.; Heck, Albert J. R.; van der Oost, John; Brouns, Stan J. J.; Pul, Ümit
2011-01-01
The CRISPR (clustered regularly interspaced short palindromic repeats) immune system in prokaryotes uses small guide RNAs to neutralize invading viruses and plasmids. In Escherichia coli, immunity depends on a ribonucleoprotein complex called Cascade. Here we present the composition and low-resoluti
Collingro, Astrid; Kostanjšek, Rok; Toenshoff, Elena R; Schulz, Frederik; Schuster, Lisa; Domann, Daryl; Horn, Matthias
2015-08-13
"Candidatus Hepatoplasma crinochetorum" Ps is an extracellular symbiont residing in the hepatopancreas of the terrestrial isopod Porcellio scaber. Its genome is highly similar to that of the close relative "Ca. Hepatoplasma crinochetorum" Av from Armadillidium vulgare. However, instead of a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system, it encodes a type I restriction modification system.
Kostanjšek, Rok; Toenshoff, Elena R.; Schulz, Frederik; Schuster, Lisa; Domann, Daryl; Horn, Matthias
2015-01-01
“Candidatus Hepatoplasma crinochetorum” Ps is an extracellular symbiont residing in the hepatopancreas of the terrestrial isopod Porcellio scaber. Its genome is highly similar to that of the close relative “Ca. Hepatoplasma crinochetorum” Av from Armadillidium vulgare. However, instead of a clustered regularly interspaced short palindromic repeat (CRISPR)-Cas system, it encodes a type I restriction modification system. PMID:26272556
CRISPR interference and priming varies with individual spacer sequences
Xue, Chaoyou; Seetharam, Arun S.; Musharova, Olga; Severinov, Konstantin; Brouns, Stan J.J.; Severin, Andrew J.; Sashital, Dipali G.
2015-01-01
CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated) systems allow bacteria to adapt to infection by acquiring 'spacer' sequences from invader DNA into genomic CRISPR loci. Cas proteins use RNAs derived from these loci to target cognate sequences for destructio
Wiedenheft, Blake; van Duijn, Esther; Bultema, Jelle; Waghmare, Sakharam; Zhou, Kaihong; Barendregt, Arjan; Westphal, Wiebke; Heck, Albert; Boekema, Egbert; Dickman, Mark; Doudna, Jennifer A.
2011-01-01
Prokaryotes have evolved multiple versions of an RNA-guided adaptive immune system that targets foreign nucleic acids. In each case, transcripts derived from clustered regularly interspaced short palindromic repeats (CRISPRs) are thought to selectively target invading phage and plasmids in a sequenc
Who Is in the Driver's Seat : Tracing Cancer Genes Using CRISPR-Barcoding
Drost, Jarno; Clevers, Hans
2016-01-01
Intratumor heterogeneity is thought to be the driving force of tumor evolution and therapy resistance. Yet tools to study these processes are limited. In this issue, Guernet et al. (2016) devised clustered regularly interspaced short palindromic repeats (CRISPR)-barcoding to functionally annotate sp
Evolution and classification of the CRISPR-Cas systems
Makarova, K.S.; Brouns, S.J.J.; Oost, van der J.
2011-01-01
The CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated proteins) modules are adaptive immunity systems that are present in many archaea and bacteria. These defence systems are encoded by operons that have an extraordinarily diverse architecture and a high rate of
Seamless gene editing in Aspergillus species, using CRISPR-Cas9
Nødvig, Christina Spuur; Hoof, Jakob Blæsbjerg; Mortensen, Uffe Hasbro
there are several obstacles slowing down the process. The harnessing of the prokaryotic and archaeal immune mechanism CRISPR (clustered regularly interspaced short palindromic repeats) as a tool for genetic engineering in eukaryotes, has proved to be a powerful technology. CRISPR/Cas9 introduces specific DNA double...
The Role of CRISPR-Cas Systems in Virulence of Pathogenic Bacteria
Louwen, R.; Staals, R.H.J.; Endtz, H.P.; Baarlen, van P.; Oost, van der J.
2014-01-01
Clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) genes are present in many bacterial and archaeal genomes. Since the discovery of the typical CRISPR loci in the 1980s, well before their physiological role was revealed, their variable sequences have been
Lonowski, Lindsey A; Narimatsu, Yoshiki; Riaz, Anjum;
2017-01-01
This protocol describes methods for increasing and evaluating the efficiency of genome editing based on the CRISPR-Cas9 (clustered regularly interspaced short palindromic repeats-CRISPR-associated 9) system, transcription activator-like effector nucleases (TALENs) or zinc-finger nucleases (ZFNs...
Degenerate target sites mediate rapid primed CRISPR adaptation
Fineran, P.C.; Gerritzen, M.J.H.; Suarez Diez, M.; Künne, T.A.; Boekhorst, J.; Hijum, van S.A.F.T.; Staals, R.H.J.; Brouns, S.J.J.
2014-01-01
Prokaryotes encode adaptive immune systems, called CRISPR-Cas (clustered regularly interspaced short palindromic repeats–CRISPR associated), to provide resistance against mobile invaders, such as viruses and plasmids. Host immunity is based on incorporation of invader DNA sequences in a memory locus
Degenerate target sites mediate rapid primed CRISPR adaptation
Fineran, P.C.; Gerritzen, M.J.; Suarez-Diez, M.; Kunne, T.; Boekhorst, J.; Hijum, S.A.F.T. van; Staals, R.H.G.; Brouns, S.J.
2014-01-01
Prokaryotes encode adaptive immune systems, called CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR associated), to provide resistance against mobile invaders, such as viruses and plasmids. Host immunity is based on incorporation of invader DNA sequences in a memory locus
Structural plasticity and in vivo activity of Cas1 from the type I-F CRISPR-Cas system
Wilkinson, Max E.; Nakatani, Yoshio; Staals, Raymond H.J.; Kieper, Sebastian N.; Opel-Reading, Helen K.; McKenzie, Rebecca E.; Fineran, Peter C.; Krause, Kurt L.
2016-01-01
CRISPR-Cas systems are adaptive immune systems in prokaryotes that provide protection against viruses and other foreign DNA. In the adaptation stage, foreign DNA is integrated into CRISPR (clustered regularly interspaced short palindromic repeat) arrays as new spacers. These spacers are used in t
Female to male sex reversal was achieved in an emerging agricultural insect pest, Drosophila suzukii, by creating a temperature-sensitive point mutation in the sex-determination gene, transformer-2 (tra-2) using CRISPR/Cas9 (clustered regularly interspaced palindromic repeats/ CRISPR-associated) hom...
Discovery of "Escherichia coli" CRISPR Sequences in an Undergraduate Laboratory
Militello, Kevin T.; Lazatin, Justine C.
2017-01-01
Clustered regularly interspaced short palindromic repeats (CRISPRs) represent a novel type of adaptive immune system found in eubacteria and archaebacteria. CRISPRs have recently generated a lot of attention due to their unique ability to catalog foreign nucleic acids, their ability to destroy foreign nucleic acids in a mechanism that shares some…
2015-01-01
Hepatitis B virus(HBV)infection remains a major global health problem because current therapies rarely eliminate the replicative template of HBV,which is the covalently closed circular DNA(ccc DNA).As an accurate and efficient genome editing tool,clustered regularly interspaced palindromic repeat(CRISPR)-associated(Cas)9 system represents a very promising potential
Regulatory RNAs in prokaryotes: here, there and everywhere.
Narberhaus, Franz; Vogel, Jörg
2009-10-01
A recent meeting on 'Regulatory RNAs in prokaryotes' reflected the growing interest in this research topic. Almost 200 scientists met to discuss the identification, structure, function and mechanistic details of regulatory RNAs in bacteria and archaea. The topics included small regulatory RNAs, riboswitches, RNA thermosensors and CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) elements.
Salmonella enterica serotype enteritidis in French Polynesia, South Pacific, 2008-2013.
Le Hello, Simon; Maillard, Fiona; Mallet, Henri-Pierre; Daudens, Elise; Levy, Marc; Roy, Valérie; Branaa, Philippe; Bertrand, Sophie; Fabre, Laetitia; Weill, François-Xavier
2015-06-01
Outbreaks of Salmonella enterica serotype Enteritidis infections associated with eggs occurred in French Polynesia during 2008-2013. Molecular analysis of isolates by using clustered regularly interspaced short palindromic repeat polymorphisms and multilocus variable-number tandem-repeat analysis was performed. This subtyping made defining the epidemic strain, finding the source, and decontaminating affected poultry flocks possible.
Sola, Christophe
2015-06-01
The natural history of tuberculosis may be tackled by various means, among which the record of molecular scars that have been registered by the Mycobacterium tuberculosis complex (MTBC) genomes transmitted from patient to patient for tens of thousands years and possibly more. Recently discovered polymorphic loci, the CRISPR sequences, are indirect witnesses of the historical phage-bacteria struggle, and may be related to the time when the ancestor of today's tubercle bacilli were environmental bacteria, i.e. before becoming intracellular parasites. In this article, we present what are CRISPRs and try to summarize almost 20 years of research results obtained using the genetic diversity of the CRISPR loci in MTBC as a perspective for studying new models. We show that the study of the diversity of CRISPR sequences, thanks to «spoligotyping», has played a great role in our global understanding of the population structure of MTBC. Copyright © 2015 Elsevier Ltd. All rights reserved.
Sparse structure regularized ranking
Wang, Jim Jing-Yan
2014-04-17
Learning ranking scores is critical for the multimedia database retrieval problem. In this paper, we propose a novel ranking score learning algorithm by exploring the sparse structure and using it to regularize ranking scores. To explore the sparse structure, we assume that each multimedia object could be represented as a sparse linear combination of all other objects, and combination coefficients are regarded as a similarity measure between objects and used to regularize their ranking scores. Moreover, we propose to learn the sparse combination coefficients and the ranking scores simultaneously. A unified objective function is constructed with regard to both the combination coefficients and the ranking scores, and is optimized by an iterative algorithm. Experiments on two multimedia database retrieval data sets demonstrate the significant improvements of the propose algorithm over state-of-the-art ranking score learning algorithms.
Regularized Reduced Order Models
Wells, David; Xie, Xuping; Iliescu, Traian
2015-01-01
This paper puts forth a regularization approach for the stabilization of proper orthogonal decomposition (POD) reduced order models (ROMs) for the numerical simulation of realistic flows. Two regularized ROMs (Reg-ROMs) are proposed: the Leray ROM (L-ROM) and the evolve-then-filter ROM (EF-ROM). These new Reg-ROMs use spatial filtering to smooth (regularize) various terms in the ROMs. Two spatial filters are used: a POD projection onto a POD subspace (Proj) and a new POD differential filter (DF). The four Reg-ROM/filter combinations are tested in the numerical simulation of the one-dimensional Burgers equation with a small diffusion coefficient and the three-dimensional flow past a circular cylinder at a low Reynolds number (Re = 100). Overall, the most accurate Reg-ROM/filter combination is EF-ROM-DF. Furthermore, the DF generally yields better results than Proj. Finally, the four Reg-ROM/filter combinations are computationally efficient and generally more accurate than the standard Galerkin ROM.
Regularizing portfolio optimization
Still, Susanne; Kondor, Imre
2010-07-01
The optimization of large portfolios displays an inherent instability due to estimation error. This poses a fundamental problem, because solutions that are not stable under sample fluctuations may look optimal for a given sample, but are, in effect, very far from optimal with respect to the average risk. In this paper, we approach the problem from the point of view of statistical learning theory. The occurrence of the instability is intimately related to over-fitting, which can be avoided using known regularization methods. We show how regularized portfolio optimization with the expected shortfall as a risk measure is related to support vector regression. The budget constraint dictates a modification. We present the resulting optimization problem and discuss the solution. The L2 norm of the weight vector is used as a regularizer, which corresponds to a diversification 'pressure'. This means that diversification, besides counteracting downward fluctuations in some assets by upward fluctuations in others, is also crucial because it improves the stability of the solution. The approach we provide here allows for the simultaneous treatment of optimization and diversification in one framework that enables the investor to trade off between the two, depending on the size of the available dataset.
Wen LIU; Jing LIN
2011-01-01
In this paper,we define a class of strongly connected digraph,called the k-walk-regular digraph,study some properties of it,provide its some algebraic characterization and point out that the O-walk-regular digraph is the same as the walk-regular digraph discussed BY Liu and Lin in 2010 and the D-walk-regular digraph is identical with the weakly distance-regular digraph defined by Comellas et al in 2004.
Annotation of Regular Polysemy
Martinez Alonso, Hector
Regular polysemy has received a lot of attention from the theory of lexical semantics and from computational linguistics. However, there is no consensus on how to represent the sense of underspecified examples at the token level, namely when annotating or disambiguating senses of metonymic words...... like “London” (Location/Organization) or “cup” (Container/Content). The goal of this dissertation is to assess whether metonymic sense underspecification justifies incorporating a third sense into our sense inventories, thereby treating the underspecified sense as independent from the literal...
Glass John I
2010-07-01
repeat may be disseminated by HGT and intra-genomic shuffling. Conclusions We describe novel features of PARCELs (Palindromic Amphipathic Repeat Coding ELements, a set of widely distributed repeat protein domains and coding sequences that were likely acquired through HGT by diverse unicellular microbes, further mobilized and diversified within genomes, and co-opted for expression in the membrane proteome of some taxa. Disseminated by multiple gene-centric vehicles, ORFs harboring these elements enhance accessory gene pools as part of the "mobilome" connecting genomes of various clades, in taxa sharing common niches.
Yamamoto, S; Yamamoto, T; Kataoka, T; Kuramoto, E; Yano, O; Tokunaga, T
1992-06-15
Thirty-mer single-stranded oligonucleotides, with a sequence chosen from the known cDNA encoding the 64-kDa protein named Ag A or the MPB-70 protein of Mycobacterium bovis BCG and the human cellular proteins such as complement component 1 inhibitor and Ig rearranged lambda-chain, were used to dissect the capability to induce IFN and to augment NK cell activity of mouse spleen cells by coincubation in vitro. Three with the hexamer palindromic sequence as GACGTC were active, whereas two kinds of oligonucleotides with no palindrome were inactive. The oligonucleotides containing at least one of the different palindromic sequences showed no activity. When a portion of the sequence of the inactive oligonucleotides was substituted with either palindromic sequence of GACGTC, AGCGCT, or AACGTT, the oligonucleotide acquired the ability to augment NK activity. In contrast, the oligonucleotides substituted with another palindromic sequence such as ACCGGT was without effect. Furthermore, exchange of two neighboring mononucleotides within, but not outside, the active palindromic sequence destroyed the ability of the oligonucleotides to augment NK cell activity. Stimulation of spleen cells with the substituted oligonucleotide, A4a-AAC, induced production of significant amounts of IFN-alpha/beta and small amounts of IFN-gamma. Augmentation of NK activity of the cells by the oligonucleotide was ascribed to IFN-alpha/beta production. These results strongly suggest that the presence of the unique palindromic sequences, such as GACGTC, AGCGCT, and AACGTT, but not ACCGGT, is essential for the immunostimulatory activity of oligonucleotides.
Stankovic, Uros; Herk, Marcel van; Ploeger, Lennert S.; Sonke, Jan-Jakob, E-mail: j.sonke@nki.nl [Department of Radiation Oncology, The Netherlands Cancer Institute, Amsterdam 1066 CX (Netherlands)
2014-06-15
Purpose: Medical linear accelerator mounted cone beam CT (CBCT) scanner provides useful soft tissue contrast for purposes of image guidance in radiotherapy. The presence of extensive scattered radiation has a negative effect on soft tissue visibility and uniformity of CBCT scans. Antiscatter grids (ASG) are used in the field of diagnostic radiography to mitigate the scatter. They usually do increase the contrast of the scan, but simultaneously increase the noise. Therefore, and considering other scatter mitigation mechanisms present in a CBCT scanner, the applicability of ASGs with aluminum interspacing for a wide range of imaging conditions has been inconclusive in previous studies. In recent years, grids using fiber interspacers have appeared, providing grids with higher scatter rejection while maintaining reasonable transmission of primary radiation. The purpose of this study was to evaluate the impact of one such grid on CBCT image quality. Methods: The grid used (Philips Medical Systems) had ratio of 21:1, frequency 36 lp/cm, and nominal selectivity of 11.9. It was mounted on the kV flat panel detector of an Elekta Synergy linear accelerator and tested in a phantom and a clinical study. Due to the flex of the linac and presence of gridline artifacts an angle dependent gain correction algorithm was devised to mitigate resulting artifacts. Scan reconstruction was performed using XVI4.5 augmented with inhouse developed image lag correction and Hounsfield unit calibration. To determine the necessary parameters for Hounsfield unit calibration and software scatter correction parameters, the Catphan 600 (The Phantom Laboratory) phantom was used. Image quality parameters were evaluated using CIRS CBCT Image Quality and Electron Density Phantom (CIRS) in two different geometries: one modeling head and neck and other pelvic region. Phantoms were acquired with and without the grid and reconstructed with and without software correction which was adapted for the different
From regular modules to von Neumann regular rings via coordinatization
Leonard Daus
2014-07-01
Full Text Available In this paper we establish a very close link (in terms of von Neu- mann's coordinatization between regular modules introduced by Zel- manowitz, on one hand, and von Neumann regular rings, on the other hand: we prove that the lattice L^{fg}(M of all finitely generated submodules of a finitely generated regular module M, over an arbitrary ring, can be coordinatized as the lattice of all principal right ideals of some von Neumann regular ring S.
Modular Regularization Algorithms
Jacobsen, Michael
2004-01-01
The class of linear ill-posed problems is introduced along with a range of standard numerical tools and basic concepts from linear algebra, statistics and optimization. Known algorithms for solving linear inverse ill-posed problems are analyzed to determine how they can be decomposed into indepen......The class of linear ill-posed problems is introduced along with a range of standard numerical tools and basic concepts from linear algebra, statistics and optimization. Known algorithms for solving linear inverse ill-posed problems are analyzed to determine how they can be decomposed...... into independent modules. These modules are then combined to form new regularization algorithms with other properties than those we started out with. Several variations are tested using the Matlab toolbox MOORe Tools created in connection with this thesis. Object oriented programming techniques are explained...... and used to set up the illposed problems in the toolbox. Hereby, we are able to write regularization algorithms that automatically exploit structure in the ill-posed problem without being rewritten explicitly. We explain how to implement a stopping criteria for a parameter choice method based upon...
Structure for Regular Inclusions
Pitts, David R
2012-01-01
We study pairs (C,D) of unital C*-algebras where D is an abelian C*-subalgebra of C which is regular in C. When D is a MASA in C, there exists a unique completely positive unital map E of C into the injective envelope I(D) of D whose restriction to D is the identity on D. We show that the left kernel of E is the unique closed two-sided ideal of C maximal with respect to having trivial intersection with D. We introduce a new class of well behaved state extensions, the compatible states; we identify compatible states when D is a MASA in C in terms of groups constructed from local dynamics near a pure state on D. When C is separable, D is a MASA in C, and the pair (C,D) is regular, the set of pure states on D with unique state extensions to C is dense in D. The map E can be used as a substitute for a conditional expectation in the construction of coordinates for C relative to D. We show that certain classes of compatible states have natural groupoid operations, and we show that constructions of Kumjian and Renau...
Evolutionary internalized regularities.
Schwartz, R
2001-08-01
Roger Shepard's proposals and supporting experiments concerning evolutionary internalized regularities have been very influential in the study of vision and in other areas of psychology and cognitive science. This paper examines issues concerning the need, nature, explanatory role, and justification for postulating such internalized constraints. In particular, I seek further clarification from Shepard on how best to understand his claim that principles of kinematic geometry underlie phenomena of motion perception. My primary focus is on the ecological validity of Shepard's kinematic constraint in the context of ordinary motion perception. First, I explore the analogy Shepard draws between internalized circadian rhythms and the supposed internalization of kinematic geometry. Next, questions are raised about how to interpret and justify applying results from his own and others' experimental studies of apparent motion to more everyday cases of motion perception in richer environments. Finally, some difficulties with Shepard's account of the evolutionary development of his kinematic constraint are considered.
Adaptive Regularization of Neural Classifiers
Andersen, Lars Nonboe; Larsen, Jan; Hansen, Lars Kai
1997-01-01
We present a regularization scheme which iteratively adapts the regularization parameters by minimizing the validation error. It is suggested to use the adaptive regularization scheme in conjunction with optimal brain damage pruning to optimize the architecture and to avoid overfitting. Furthermo...
Lavrov, Dennis V
2010-04-01
Animal mitochondrial DNA (mtDNA) is a remarkably compact molecule largely because of the scarcity of noncoding "selfish" DNA. Recently, however, we found that mitochondrial genomes of several phylogenetically diverse species of demosponges contain small repetitive palindromic sequences, interspersed within intergenic regions and fused in protein and ribosomal RNA genes. Here, I report and analyze the proliferation of such elements in the mitochondrial genome of the endemic sponge of Lake Baikal Lubomirskia baicalensis. Because Baikal sponges are closely related to the circumglobally distributed freshwater sponge Ephydatia muelleri with which they shared a common ancestor approximately 3-10 Ma, both the rate of single nucleotide substitutions and the rate of palindromic repeat insertions can be calculated in this system. I found the rate of nucleotide substitutions in mtDNA of freshwater sponges to be extremely low (0.5-1.6 x 10(-9) per site per year), more similar to that in plants than bilaterian animals. By contrast, the per/nucleotide rate of insertions of repetitive elements is at least four times higher. This rapid rate of proliferation combined with the broad phylogenetic distribution of hairpin elements can make them a defining force in the evolution of mitochondrial genomes of demosponges.
Bendtsen, Kirstine L; Xu, Kehan; Luckmann, Majbritt
2017-01-01
for binding and inactivation of the VapC1 toxin dimer. Sequence analysis of 4127 orthologous VapB sequences reveals that such palindromic protein sequences are widespread and unique to bacterial and archaeal VapB antitoxins suggesting a general principle governing regulation of VapBC TA systems. Finally......Expression of bacterial type II toxin-antitoxin (TA) systems is regulated at the transcriptional level through direct binding of the antitoxin to pseudo-palindromic sequences on operator DNA. In this context, the toxin functions as a co-repressor by stimulating DNA binding through direct...... architectural rearrangement of conserved TA interactions in which C-terminal extended structures of the antitoxin VapB1 swap positions to interlock the complex in the DNA-bound state. We further show that a pseudo-palindromic protein sequence in the antitoxin is responsible for this interaction and required...
Bambi, Cosimo
2013-01-01
The formation of spacetime singularities is a quite common phenomenon in General Relativity and it is regulated by specific theorems. It is widely believed that spacetime singularities do not exist in Nature, but that they represent a limitation of the classical theory. While we do not yet have any solid theory of quantum gravity, toy models of black hole solutions without singularities have been proposed. So far, there are only non-rotating regular black holes in the literature. These metrics can be hardly tested by astrophysical observations, as the black hole spin plays a fundamental role in any astrophysical process. In this letter, we apply the Newman-Janis algorithm to the Hayward and to the Bardeen black hole metrics. In both cases, we obtain a family of rotating solutions. Every solution corresponds to a different matter configuration. Each family has one solution with special properties, which can be written in Kerr-like form in Boyer-Lindquist coordinates. These special solutions are of Petrov type ...
Bambi, Cosimo, E-mail: bambi@fudan.edu.cn; Modesto, Leonardo, E-mail: lmodesto@fudan.edu.cn
2013-04-25
The formation of spacetime singularities is a quite common phenomenon in General Relativity and it is regulated by specific theorems. It is widely believed that spacetime singularities do not exist in Nature, but that they represent a limitation of the classical theory. While we do not yet have any solid theory of quantum gravity, toy models of black hole solutions without singularities have been proposed. So far, there are only non-rotating regular black holes in the literature. These metrics can be hardly tested by astrophysical observations, as the black hole spin plays a fundamental role in any astrophysical process. In this Letter, we apply the Newman–Janis algorithm to the Hayward and to the Bardeen black hole metrics. In both cases, we obtain a family of rotating solutions. Every solution corresponds to a different matter configuration. Each family has one solution with special properties, which can be written in Kerr-like form in Boyer–Lindquist coordinates. These special solutions are of Petrov type D, they are singularity free, but they violate the weak energy condition for a non-vanishing spin and their curvature invariants have different values at r=0 depending on the way one approaches the origin. We propose a natural prescription to have rotating solutions with a minimal violation of the weak energy condition and without the questionable property of the curvature invariants at the origin.
Ensemble manifold regularization.
Geng, Bo; Tao, Dacheng; Xu, Chao; Yang, Linjun; Hua, Xian-Sheng
2012-06-01
We propose an automatic approximation of the intrinsic manifold for general semi-supervised learning (SSL) problems. Unfortunately, it is not trivial to define an optimization function to obtain optimal hyperparameters. Usually, cross validation is applied, but it does not necessarily scale up. Other problems derive from the suboptimality incurred by discrete grid search and the overfitting. Therefore, we develop an ensemble manifold regularization (EMR) framework to approximate the intrinsic manifold by combining several initial guesses. Algorithmically, we designed EMR carefully so it 1) learns both the composite manifold and the semi-supervised learner jointly, 2) is fully automatic for learning the intrinsic manifold hyperparameters implicitly, 3) is conditionally optimal for intrinsic manifold approximation under a mild and reasonable assumption, and 4) is scalable for a large number of candidate manifold hyperparameters, from both time and space perspectives. Furthermore, we prove the convergence property of EMR to the deterministic matrix at rate root-n. Extensive experiments over both synthetic and real data sets demonstrate the effectiveness of the proposed framework.
Regular Bisimple ω2-semigroups
汪立民; 商宇
2008-01-01
@@ The regular semigroups S with an idempotent set Es = {e0,e1,…,en,…} such that e0 ＞ e1 ＞…＞ en ＞… is called a regular ω-semigroup. In [5] Reilly determined the structure of a regular bisimple ω-semigroup as BR(G,θ),which is the classical Bruck-Reilly extension of a group G.
Completely regular fuzzifying topological spaces
A. K. Katsaras
2005-12-01
Full Text Available Some of the properties of the completely regular fuzzifying topological spaces are investigated. It is shown that a fuzzifying topology ÃÂ„ is completely regular if and only if it is induced by some fuzzy uniformity or equivalently by some fuzzifying proximity. Also, ÃÂ„ is completely regular if and only if it is generated by a family of probabilistic pseudometrics.
On regular rotating black holes
Torres, R.; Fayos, F.
2017-01-01
Different proposals for regular rotating black hole spacetimes have appeared recently in the literature. However, a rigorous analysis and proof of the regularity of this kind of spacetimes is still lacking. In this note we analyze rotating Kerr-like black hole spacetimes and find the necessary and sufficient conditions for the regularity of all their second order scalar invariants polynomial in the Riemann tensor. We also show that the regularity is linked to a violation of the weak energy conditions around the core of the rotating black hole.
Constrained and regularized system identification
Tor A. Johansen
1998-04-01
Full Text Available Prior knowledge can be introduced into system identification problems in terms of constraints on the parameter space, or regularizing penalty functions in a prediction error criterion. The contribution of this work is mainly an extension of the well known FPE (Final Production Error statistic to the case when the system identification problem is constrained and contains a regularization penalty. The FPECR statistic (Final Production Error with Constraints and Regularization is of potential interest as a criterion for selection of both regularization parameters and structural parameters such as order.
On regular rotating black holes
Torres, Ramon
2016-01-01
Different proposals for regular rotating black hole spacetimes have appeared recently in the literature. However, a rigorous analysis and proof of the regularity of this kind of spacetimes is still lacking. In this note we analyze rotating Kerr-like black hole spacetimes and find the necessary and sufficient conditions for the regularity of all their second order scalar invariants polynomial in the Riemann tensor. We also show that the regularity is linked to a violation of the weak energy conditions around the core of the rotating black hole.
CHEN Huan Yin; LI Fu An
2002-01-01
In this paper, we investigate ideals of regular rings and give several characterizations for an ideal to satisfy the comparability. In addition, it is shown that, if Ⅰ is a minimal two-sided ideal of a regular ring R, then Ⅰ satisfies the comparability if and only if Ⅰ is separative. Furthermore, we prove that, for ideals with stable range one, Roth's problem has an affirmative solution. These extend the corresponding results on unit-regularity and one-sided unit-regularity.
Crystal Structure of the Dimeric Oct6 (Pou3fl) POU Domain Bound to Palindromic MORE DNA
R Jauch; S Choo; C Ng; P Kolatkar
2011-12-31
POU domains (named after their identification in Pit1, Oct1 unc86) are found in around 15 transcription factors encoded in mammalian genomes many of which feature prominently as key regulators at development bifurcations. For example, the POU III class Octamer binding protein 6 (Oct6) is expressed in embryonic stem cells and during neural development and drives the differentia5tion of myelinated cells in the central and peripheral nervous system. Defects in oct6 expression levels are linked to neurological disorders such as schizophrenia. POU proteins contain a bi-partite DNA binding domain that assembles on various DNA motifs with differentially configured subdomains. Intriguingly, alternative configurations of POU domains on different DNA sites were shown to affect the subsequent recruitment of transcriptional coactivators. Namely, binding of Oct1 to a Palindromic Oct-factor Recognition Element (PORE) was shown to facilitate the recruitment of the OBF1 coactivator whereas More of PORE (MORE) bound Oct1 does not. Moreover, Pit1 was shown to recruit the corepressor N-CoR only when bound to a variant MORE motif with a 2 bp half-site spacing. Therefore, POU proteins are seen as a paradigm for DNA induced allosteric effects on transcription factors modulating their regulatory potential. However, a big unresolved conundrum for the POU class and for most if not all other transcription factor classes is how highly similar proteins regulate different sets of genes causing fundamentally different biological responses. Ultimately, there must be subtle features enabling those factors to engage in contrasting molecular interactions in the cell. Thus, the dissection of the molecular details of the transcription-DNA recognition in general, and the formation of multimeric regulatory complexes, in particular, is highly desirable. To contribute to these efforts they solved the 2.05 {angstrom} crystal structure of Oct6 bound as a symmetrical homodimer to palindromic MORE DNA.
Emad, Yasser; Anbar, Ashraf; Abo-Elyoun, Ihab; El Shaarawy, Nashwa; Al-Hanafi, Hadeel; Darwish, Hatem; Gamil, Mona; Rasker, Hans J.
2014-01-01
This study aimed to determine the frequency of rheumatoid factor (RF) and cyclic citrullinated peptide (CCP) antibodies in a cohort of patients with palindromic rheumatism (PR) and to find determinants for progression to rheumatoid arthritis (RA). All new cases of PR (n = 90) were included
Emad, Yasser; Anbar, Ashraf; Abo-Elyoun, Ihab; El-Shaarawy, Nashwa; Al-Hanafi, Hadeel; Darwish, Hatem; Gamil, Mona; Rasker, Johannes J.
2014-01-01
This study aimed to determine the frequency of rheumatoid factor (RF) and cyclic citrullinated peptide (CCP) antibodies in a cohort of patients with palindromic rheumatism (PR) and to find determinants for progression to rheumatoid arthritis (RA). All new cases of PR (n = 90) were included prospecti
Regularly timed events amid chaos
Blakely, Jonathan N.; Cooper, Roy M.; Corron, Ned J.
2015-11-01
We show rigorously that the solutions of a class of chaotic oscillators are characterized by regularly timed events in which the derivative of the solution is instantaneously zero. The perfect regularity of these events is in stark contrast with the well-known unpredictability of chaos. We explore some consequences of these regularly timed events through experiments using chaotic electronic circuits. First, we show that a feedback loop can be implemented to phase lock the regularly timed events to a periodic external signal. In this arrangement the external signal regulates the timing of the chaotic signal but does not strictly lock its phase. That is, phase slips of the chaotic oscillation persist without disturbing timing of the regular events. Second, we couple the regularly timed events of one chaotic oscillator to those of another. A state of synchronization is observed where the oscillators exhibit synchronized regular events while their chaotic amplitudes and phases evolve independently. Finally, we add additional coupling to synchronize the amplitudes, as well, however in the opposite direction illustrating the independence of the amplitudes from the regularly timed events.
Online co-regularized algorithms
Ruijter, T. de; Tsivtsivadze, E.; Heskes, T.
2012-01-01
We propose an online co-regularized learning algorithm for classification and regression tasks. We demonstrate that by sequentially co-regularizing prediction functions on unlabeled data points, our algorithm provides improved performance in comparison to supervised methods on several UCI benchmarks
Online co-regularized algorithms
Ruijter, T. de; Tsivtsivadze, E.; Heskes, T.
2012-01-01
We propose an online co-regularized learning algorithm for classification and regression tasks. We demonstrate that by sequentially co-regularizing prediction functions on unlabeled data points, our algorithm provides improved performance in comparison to supervised methods on several UCI benchmarks
Nonconvex Regularization in Remote Sensing
Tuia, Devis; Flamary, Remi; Barlaud, Michel
2016-11-01
In this paper, we study the effect of different regularizers and their implications in high dimensional image classification and sparse linear unmixing. Although kernelization or sparse methods are globally accepted solutions for processing data in high dimensions, we present here a study on the impact of the form of regularization used and its parametrization. We consider regularization via traditional squared (2) and sparsity-promoting (1) norms, as well as more unconventional nonconvex regularizers (p and Log Sum Penalty). We compare their properties and advantages on several classification and linear unmixing tasks and provide advices on the choice of the best regularizer for the problem at hand. Finally, we also provide a fully functional toolbox for the community.
Conservative regularization of compressible flow
Krishnaswami, Govind S; Thyagaraja, Anantanarayanan
2015-01-01
Ideal Eulerian flow may develop singularities in vorticity w. Navier-Stokes viscosity provides a dissipative regularization. We find a local, conservative regularization - lambda^2 w times curl(w) of compressible flow and compressible MHD: a three dimensional analogue of the KdV regularization of the one dimensional kinematic wave equation. The regulator lambda is a field subject to the constitutive relation lambda^2 rho = constant. Lambda is like a position-dependent mean-free path. Our regularization preserves Galilean, parity and time-reversal symmetries. We identify locally conserved energy, helicity, linear and angular momenta and boundary conditions ensuring their global conservation. Enstrophy is shown to remain bounded. A swirl velocity field is identified, which transports w/rho and B/rho generalizing the Kelvin-Helmholtz and Alfven theorems. A Hamiltonian and Poisson bracket formulation is given. The regularized equations are used to model a rotating vortex, channel flow, plane flow, a plane vortex ...
Approximate Sparse Regularized Hyperspectral Unmixing
Chengzhi Deng
2014-01-01
Full Text Available Sparse regression based unmixing has been recently proposed to estimate the abundance of materials present in hyperspectral image pixel. In this paper, a novel sparse unmixing optimization model based on approximate sparsity, namely, approximate sparse unmixing (ASU, is firstly proposed to perform the unmixing task for hyperspectral remote sensing imagery. And then, a variable splitting and augmented Lagrangian algorithm is introduced to tackle the optimization problem. In ASU, approximate sparsity is used as a regularizer for sparse unmixing, which is sparser than l1 regularizer and much easier to be solved than l0 regularizer. Three simulated and one real hyperspectral images were used to evaluate the performance of the proposed algorithm in comparison to l1 regularizer. Experimental results demonstrate that the proposed algorithm is more effective and accurate for hyperspectral unmixing than state-of-the-art l1 regularizer.
ZOU Zhi-Yun; MAO Bao-Hua; HAO Hai-Ming; GAO Jian-Zhi; YANG Jie-Jiao
2009-01-01
According to the deficiencies in Watts and Strogatz's small-world network model, we present a new regular model to establish the small-world network. Besides the property of the small-world, this model has other properties such as accuracy in controlling the average shortest path length L, and the average clustering coefficient C, also regular network topology as well as enhanced network robustness. This method improves the construction of the small-world network essentially, so that the regular small-world network closely resembles the actual network. We also present studies on the relationships among the quantities of a variety of edges, L and C in regular small-world network in detail. This research lays the foundation for the establishment of the regular small-world network and acts as a good guidance for further research of this model and its applications.
A Criterion for Regular Sequences
D P Patil; U Storch; J Stückrad
2004-05-01
Let be a commutative noetherian ring and $f_1,\\ldots,f_r \\in R$. In this article we give (cf. the Theorem in $\\mathcal{x}$2) a criterion for $f_1,\\ldots,f_r$ to be regular sequence for a finitely generated module over which strengthens and generalises a result in [2]. As an immediate consequence we deduce that if $V(g_1,\\ldots,g_r) \\subseteq V(f_1,\\ldots,f_r)$ in Spec and if $f_1,\\ldots,f_r$ is a regular sequence in , then $g_1,\\ldots,g_r$ is also a regular sequence in .
Huanyin CHEN
2009-01-01
The necessary and sufficient conditions under which a ring satisfies regular power-substitution are investigated. It is shown that a ring R satisfies regular power-substitution if and only if a(-～)b in R implies that there exist n ∈ N and a U ∈ GLn(R) such that aU =Ub if and only if for any regular x ∈ R there exist m,n ∈ N and U ∈ GLn(R) such that xmIn = xmUxm, where a(-～)b means that there exists x, y, z ∈ R such that a = ybx, b = xaz and x = xyx = xzx. It is proved that every directly finite simple ring satisfies regular power-substitution. Some applications for stably free R-modules are also obtained.
NONCONVEX REGULARIZATION FOR SHAPE PRESERVATION
CHARTRAND, RICK [Los Alamos National Laboratory
2007-01-16
The authors show that using a nonconvex penalty term to regularize image reconstruction can substantially improve the preservation of object shapes. The commonly-used total-variation regularization, {integral}|{del}u|, penalizes the length of the object edges. They show that {integral}|{del}u|{sup p}, 0 < p < 1, only penalizes edges of dimension at least 2-p, and thus finite-length edges not at all. We give numerical examples showing the resulting improvement in shape preservation.
Regularization with a pruning prior
Goutte, Cyril; Hansen, Lars Kai
1997-01-01
We investigate the use of a regularization priorthat we show has pruning properties. Analyses areconducted both using a Bayesian framework and withthe generalization method, on a simple toyproblem. Results are thoroughly compared withthose obtained with a traditional weight decay.......We investigate the use of a regularization priorthat we show has pruning properties. Analyses areconducted both using a Bayesian framework and withthe generalization method, on a simple toyproblem. Results are thoroughly compared withthose obtained with a traditional weight decay....
Regular and Periodic Tachyon Kinks
Bazeia, D.; Menezes, R.; Ramos, J. G.
2004-01-01
We search for regular tachyon kinks in an extended model, which includes the tachyon action recently proposed to describe the tachyon field. The extended model that we propose adds a new contribution to the tachyon action, and seems to enrich the present scenario for the tachyon field. We have found stable tachyon kinks of regular profile, which may appropriately lead to the singular kink found by Sen sometime ago. Also, under specific conditions we may find periodic array of kink-antikink co...
Shervin Sahebi
2014-05-01
Full Text Available $R$ is called commuting regular ring (resp. semigroupif for each $x,y\\in R$ there exists $a\\in R$ such that$xy=yxayx$. In this paper, we introduce the concept ofcommuting $\\pi$-regular rings (resp. semigroups andstudy various properties of them.
Condition Number Regularized Covariance Estimation.
Won, Joong-Ho; Lim, Johan; Kim, Seung-Jean; Rajaratnam, Bala
2013-06-01
Estimation of high-dimensional covariance matrices is known to be a difficult problem, has many applications, and is of current interest to the larger statistics community. In many applications including so-called the "large p small n" setting, the estimate of the covariance matrix is required to be not only invertible, but also well-conditioned. Although many regularization schemes attempt to do this, none of them address the ill-conditioning problem directly. In this paper, we propose a maximum likelihood approach, with the direct goal of obtaining a well-conditioned estimator. No sparsity assumption on either the covariance matrix or its inverse are are imposed, thus making our procedure more widely applicable. We demonstrate that the proposed regularization scheme is computationally efficient, yields a type of Steinian shrinkage estimator, and has a natural Bayesian interpretation. We investigate the theoretical properties of the regularized covariance estimator comprehensively, including its regularization path, and proceed to develop an approach that adaptively determines the level of regularization that is required. Finally, we demonstrate the performance of the regularized estimator in decision-theoretic comparisons and in the financial portfolio optimization setting. The proposed approach has desirable properties, and can serve as a competitive procedure, especially when the sample size is small and when a well-conditioned estimator is required.
Condition Number Regularized Covariance Estimation*
Won, Joong-Ho; Lim, Johan; Kim, Seung-Jean; Rajaratnam, Bala
2012-01-01
Estimation of high-dimensional covariance matrices is known to be a difficult problem, has many applications, and is of current interest to the larger statistics community. In many applications including so-called the “large p small n” setting, the estimate of the covariance matrix is required to be not only invertible, but also well-conditioned. Although many regularization schemes attempt to do this, none of them address the ill-conditioning problem directly. In this paper, we propose a maximum likelihood approach, with the direct goal of obtaining a well-conditioned estimator. No sparsity assumption on either the covariance matrix or its inverse are are imposed, thus making our procedure more widely applicable. We demonstrate that the proposed regularization scheme is computationally efficient, yields a type of Steinian shrinkage estimator, and has a natural Bayesian interpretation. We investigate the theoretical properties of the regularized covariance estimator comprehensively, including its regularization path, and proceed to develop an approach that adaptively determines the level of regularization that is required. Finally, we demonstrate the performance of the regularized estimator in decision-theoretic comparisons and in the financial portfolio optimization setting. The proposed approach has desirable properties, and can serve as a competitive procedure, especially when the sample size is small and when a well-conditioned estimator is required. PMID:23730197
Quotient Complexity of Regular Languages
Janusz Brzozowski
2009-07-01
Full Text Available The past research on the state complexity of operations on regular languages is examined, and a new approach based on an old method (derivatives of regular expressions is presented. Since state complexity is a property of a language, it is appropriate to define it in formal-language terms as the number of distinct quotients of the language, and to call it "quotient complexity". The problem of finding the quotient complexity of a language f(K,L is considered, where K and L are regular languages and f is a regular operation, for example, union or concatenation. Since quotients can be represented by derivatives, one can find a formula for the typical quotient of f(K,L in terms of the quotients of K and L. To obtain an upper bound on the number of quotients of f(K,L all one has to do is count how many such quotients are possible, and this makes automaton constructions unnecessary. The advantages of this point of view are illustrated by many examples. Moreover, new general observations are presented to help in the estimation of the upper bounds on quotient complexity of regular operations.
Ratanpal B S; Sharma Jaita
2016-03-01
The charged anisotropic star on paraboloidal space-time is reported by choosing a particular form of radial pressure and electric field intensity. The non-singular solution of Einstein–Maxwell system of equation has been derived and it is shown that the model satisfies all the physical plausibility conditions. It is observed that in the absence of electric field intensity, the model reducesto a particular case of uncharged Sharma and Ratanpal model. It is also observed that the parameter used in the electric field intensity directly affects mass of the star.
Efficient Hyperelastic Regularization for Registration
Darkner, Sune; Hansen, Michael Sass; Larsen, Rasmus;
2011-01-01
For most image registration problems a smooth one-to-one mapping is desirable, a diffeomorphism. This can be obtained using priors such as volume preservation, certain kinds of elasticity or both. The key principle is to regularize the strain of the deformation which can be done through penalizat......For most image registration problems a smooth one-to-one mapping is desirable, a diffeomorphism. This can be obtained using priors such as volume preservation, certain kinds of elasticity or both. The key principle is to regularize the strain of the deformation which can be done through...... penalization of the eigen values of the stress tensor. We present a computational framework for regularization of image registration for isotropic hyper elasticity. We formulate an efficient and parallel scheme for computing the principal stain based for a given parameterization by decomposing the left Cauchy...
Regular algebra and finite machines
Conway, John Horton
2012-01-01
World-famous mathematician John H. Conway based this classic text on a 1966 course he taught at Cambridge University. Geared toward graduate students of mathematics, it will also prove a valuable guide to researchers and professional mathematicians.His topics cover Moore's theory of experiments, Kleene's theory of regular events and expressions, Kleene algebras, the differential calculus of events, factors and the factor matrix, and the theory of operators. Additional subjects include event classes and operator classes, some regulator algebras, context-free languages, communicative regular alg
Regularized Statistical Analysis of Anatomy
Sjöstrand, Karl
2007-01-01
This thesis presents the application and development of regularized methods for the statistical analysis of anatomical structures. Focus is on structure-function relationships in the human brain, such as the connection between early onset of Alzheimer’s disease and shape changes of the corpus cal...
Regularization in Matrix Relevance Learning
Schneider, Petra; Bunte, Kerstin; Stiekema, Han; Hammer, Barbara; Villmann, Thomas; Biehl, Michael
2010-01-01
A In this paper, we present a regularization technique to extend recently proposed matrix learning schemes in learning vector quantization (LVQ). These learning algorithms extend the concept of adaptive distance measures in LVQ to the use of relevance matrices. In general, metric learning can displa
Singularities of slice regular functions
Stoppato, Caterina
2010-01-01
Beginning in 2006, G. Gentili and D.C. Struppa developed a theory of regular quaternionic functions with properties that recall classical results in complex analysis. For instance, in each Euclidean ball centered at 0 the set of regular functions coincides with that of quaternionic power series converging in the same ball. In 2009 the author proposed a classification of singularities of regular functions as removable, essential or as poles and studied poles by constructing the ring of quotients. In that article, not only the statements, but also the proving techniques were confined to the special case of balls centered at 0. In a subsequent paper, F. Colombo, G. Gentili, I. Sabadini and D.C. Struppa (2009) identified a larger class of domains, on which the theory of regular functions is natural and not limited to quaternionic power series. The present article studies singularities in this new context, beginning with the construction of the ring of quotients and of Laurent-type expansions at points other than ...
Regular inference as vertex coloring
Costa Florêncio, C.; Verwer, S.
2012-01-01
This paper is concerned with the problem of supervised learning of deterministic finite state automata, in the technical sense of identification in the limit from complete data, by finding a minimal DFA consistent with the data (regular inference). We solve this problem by translating it in its enti
Regularized Generalized Structured Component Analysis
Hwang, Heungsun
2009-01-01
Generalized structured component analysis (GSCA) has been proposed as a component-based approach to structural equation modeling. In practice, GSCA may suffer from multi-collinearity, i.e., high correlations among exogenous variables. GSCA has yet no remedy for this problem. Thus, a regularized extension of GSCA is proposed that integrates a ridge…
Regular inference as vertex coloring
Costa Florêncio, C.; Verwer, S.
2012-01-01
This paper is concerned with the problem of supervised learning of deterministic finite state automata, in the technical sense of identification in the limit from complete data, by finding a minimal DFA consistent with the data (regular inference). We solve this problem by translating it in its
2011-01-20
... meeting of the Board will be held at the offices of the Farm Credit Administration in McLean, Virginia, on...Lean, Virginia 22102. SUPPLEMENTARY INFORMATION: This meeting of the Board will be open to the ] public... CORPORATION Farm Credit System Insurance Corporation Board Regular Meeting SUMMARY: Notice is hereby given of...
Recursively-regular subdivisions and applications
Rafel Jaume
2016-05-01
Full Text Available We generalize regular subdivisions (polyhedral complexes resulting from the projection of the lower faces of a polyhedron introducing the class of recursively-regular subdivisions. Informally speaking, a recursively-regular subdivision is a subdivision that can be obtained by splitting some faces of a regular subdivision by other regular subdivisions (and continue recursively. We also define the finest regular coarsening and the regularity tree of a polyhedral complex. We prove that recursively-regular subdivisions are not necessarily connected by flips and that they are acyclic with respect to the in-front relation. We show that the finest regular coarsening of a subdivision can be efficiently computed, and that whether a subdivision is recursively regular can be efficiently decided. As an application, we also extend a theorem known since 1981 on illuminating space by cones and present connections of recursive regularity to tensegrity theory and graph-embedding problems.
Lin, Ching-Heng; Chen, Der-Yuan; Chao, Wen-Cheng; Liao, Tsai-Ling; Chen, Yi-Ming; Chen, Hsin-Hua
2017-01-01
To estimate the association between a history of periodontitis (PD) and the risk of incident palindromic rheumatism (PR). Using a nationwide, administrative database, this study identified 4,421 newly-diagnosed PR cases from 2007 to 2012 and randomly selected 44,210 non-PR controls matched (1:10) for sex, age and the year of the index date. After adjusting for comorbid diabetes mellitus, we estimated the odds ratios (ORs) with 95% confidence intervals (CIs) using conditional logistic regression analysis to quantify the association between a history of PD and the risk of PR. The influences of the lag time and severity of PD were examined by calculating ORs for subgroups of patients based on the time interval between the last PD-related visit and the index date and PD-related cumulative cost and number of visit. This study showed an association between a history of PD and incident PR (OR, 1.51; 95% CI, 1.41-1.61). The association remained significant after variation of PD definitions. The magnitude of the association was greater in those with shorter lag time between the latest date of PD diagnosis and PR index date and those who had a higher number of visits for PD or a greater cumulative cost for PD-related visits. After excluding 569 PR patients who developed rheumatoid arthritis after the index date, we found a consistent time- and dose-dependent association between PD and PR risk. This study demonstrated a time- and dose-dependent association between PD exposure and PR risk.
Tucker, Colin; McHugh, Theresa A.; Howell, Armin; Gill, Richard; Weber, Bettina; Belnap, Jayne; Grote, Ed; Reed, Sasha C.
2017-01-01
Carbon cycling associated with biological soil crusts, which occupy interspaces between vascular plants in drylands globally, may be an important part of the coupled climate-carbon cycle of the Earth system. A major challenge to understanding CO2 fluxes in these systems is that much of the biotic and biogeochemical activity occurs in the upper few mm of the soil surface layer (i.e., the ‘mantle of fertility’), which exhibits highly dynamic and difficult to measure temperature and moisture fluctuations. Here, we report a multi-sensor approach to simultaneously measuring temperature and moisture of this biocrust surface layer (0–2 mm), and the deeper soil profile, concurrent with automated measurement of surface soil CO2effluxes. Our results illuminate robust relationships between biocrust water content and field CO2 pulses that have previously been difficult to detect and explain. All observed CO2 pulses over the measurement period corresponded to surface wetting events, including when the wetting events did not penetrate into the soil below the biocrust layer (0–2 mm). The variability of temperature and moisture of the biocrust surface layer was much greater than even in the 0–5 cm layer of the soil beneath the biocrust, or deeper in the soil profile. We therefore suggest that coupling surface measurements of biocrust moisture and temperature to automated CO2flux measurements may greatly improve our understanding of the climatic sensitivity of carbon cycling in biocrusted interspaces in our study region, and that this method may be globally relevant and applicable.
General inverse problems for regular variation
Damek, Ewa; Mikosch, Thomas Valentin; Rosinski, Jan
2014-01-01
Regular variation of distributional tails is known to be preserved by various linear transformations of some random structures. An inverse problem for regular variation aims at understanding whether the regular variation of a transformed random object is caused by regular variation of components ...
Regular Motions of Resonant Asteroids
Ferraz-Mello, S.
1990-11-01
RESUMEN. Se revisan resultados analiticos relativos a soluciones regulares del problema asteroidal eliptico promediados en la vecindad de una resonancia con jupiten Mencionamos Ia ley de estructura para libradores de alta excentricidad, la estabilidad de los centros de liberaci6n, las perturbaciones forzadas por la excentricidad de jupiter y las 6rbitas de corotaci6n. ABSTRAC This paper reviews analytical results concerning the regular solutions of the elliptic asteroidal problem averaged in the neighbourhood of a resonance with jupiter. We mention the law of structure for high-eccentricity librators, the stability of the libration centers, the perturbations forced by the eccentricity ofjupiter and the corotation orbits. Key words: ASThROIDS
Energy functions for regularization algorithms
Delingette, H.; Hebert, M.; Ikeuchi, K.
1991-01-01
Regularization techniques are widely used for inverse problem solving in computer vision such as surface reconstruction, edge detection, or optical flow estimation. Energy functions used for regularization algorithms measure how smooth a curve or surface is, and to render acceptable solutions these energies must verify certain properties such as invariance with Euclidean transformations or invariance with parameterization. The notion of smoothness energy is extended here to the notion of a differential stabilizer, and it is shown that to void the systematic underestimation of undercurvature for planar curve fitting, it is necessary that circles be the curves of maximum smoothness. A set of stabilizers is proposed that meet this condition as well as invariance with rotation and parameterization.
Physical model of dimensional regularization
Schonfeld, Jonathan F.
2016-12-15
We explicitly construct fractals of dimension 4-ε on which dimensional regularization approximates scalar-field-only quantum-field theory amplitudes. The construction does not require fractals to be Lorentz-invariant in any sense, and we argue that there probably is no Lorentz-invariant fractal of dimension greater than 2. We derive dimensional regularization's power-law screening first for fractals obtained by removing voids from 3-dimensional Euclidean space. The derivation applies techniques from elementary dielectric theory. Surprisingly, fractal geometry by itself does not guarantee the appropriate power-law behavior; boundary conditions at fractal voids also play an important role. We then extend the derivation to 4-dimensional Minkowski space. We comment on generalization to non-scalar fields, and speculate about implications for quantum gravity. (orig.)
Maximum mutual information regularized classification
Wang, Jim Jing-Yan
2014-09-07
In this paper, a novel pattern classification approach is proposed by regularizing the classifier learning to maximize mutual information between the classification response and the true class label. We argue that, with the learned classifier, the uncertainty of the true class label of a data sample should be reduced by knowing its classification response as much as possible. The reduced uncertainty is measured by the mutual information between the classification response and the true class label. To this end, when learning a linear classifier, we propose to maximize the mutual information between classification responses and true class labels of training samples, besides minimizing the classification error and reducing the classifier complexity. An objective function is constructed by modeling mutual information with entropy estimation, and it is optimized by a gradient descend method in an iterative algorithm. Experiments on two real world pattern classification problems show the significant improvements achieved by maximum mutual information regularization.
Central charges in regular mechanics
Cabo-Montes de Oca, Alejandro; Villanueva, V M
1997-01-01
We consider the algebra associated to a group of transformations which are symmetries of a regular mechanical system (i.e. system free of constraints). For time dependent coordinate transformations we show that a central extension may appear at the classical level which is coordinate and momentum independent. A cochain formalism naturally arises in the argument and extends the usual configuration space cochain concepts to phase space.
Fast regularized image interpolation method
Hongchen Liu; Yong Feng; Linjing Li
2007-01-01
The regularized image interpolation method is widely used based on the vector interpolation model in which down-sampling matrix has very large dimension and needs large storage consumption and higher computation complexity. In this paper, a fast algorithm for image interpolation based on the tensor product of matrices is presented, which transforms the vector interpolation model to matrix form. The proposed algorithm can extremely reduce the storage requirement and time consumption. The simulation results verify their validity.
Efficient Hyperelastic Regularization for Registration
Darkner, Sune; Hansen, Michael S; Larsen, Rasmus;
2011-01-01
For most image registration problems a smooth one-to-one mapping is desirable, a diffeomorphism. This can be obtained using priors such as volume preservation, certain kinds of elasticity or both. The key principle is to regularize the strain of the deformation which can be done through penalizat......For most image registration problems a smooth one-to-one mapping is desirable, a diffeomorphism. This can be obtained using priors such as volume preservation, certain kinds of elasticity or both. The key principle is to regularize the strain of the deformation which can be done through...... penalization of the eigen values of the stress tensor. We present a computational framework for regularization of image registration for isotropic hyper elasticity. We formulate an efficient and parallel scheme for computing the principal stain based for a given parameterization by decomposing the left Cauchy...... elastic priors such at the Saint Vernant Kirchoff model, the Ogden material model or Riemanian elasticity. We exemplify the approach through synthetic registration and special tests as well as registration of different modalities; 2D cardiac MRI and 3D surfaces of the human ear. The artificial examples...
From Dimensional to Cut-Off Regularization
Dillig, M
2006-01-01
We extent the standard approach of dimensional regularization of Feynman diagrams: we replace the transition to lower dimensions by a 'natural' cut-off regulator. Introducing an external regulator of mass Lambda^(2e), we regain in the limit e -> 0 and e > 0 the results of dimensional and cut-off regularization, respectively. We demonstrate the versatility and adequacy of the different regularization schemes for practical examples (such as non covariant regularization, the axial anomaly or regularization in effective field theories).
Palindromic random trigonometric polynomials
Conrey, J. Brian; Farmer, David W.; Imamoglu, Özlem
2008-01-01
We show that if a real trigonometric polynomial has few real roots, then the trigonometric polynomial obtained by writing the coefficients in reverse order must have many real roots. This is used to show that a class of random trigonometric polynomials has, on average, many real roots. In the case that the coefficients of a real trigonometric polynomial are independently and identically distributed, but with no other assumptions on the distribution, the expected fraction of real zeros is at l...
System-level perturbations of cell metabolism using CRISPR/Cas9
Jakociunas, Tadas; Jensen, Michael Krogh; Keasling, Jay
2017-01-01
CRISPR/Cas9 (clustered regularly interspaced palindromic repeats and the associated protein Cas9) techniques have made genome engineering and transcriptional reprogramming studies more advanced and cost-effective. For metabolic engineering purposes, the CRISPR-based tools have been applied...... previously possible. In this mini-review we highlight recent studies adopting CRISPR/Cas9 for systems-level perturbations and model-guided metabolic engineering....
In Vivo Delivery of CRISPR/Cas9 for Therapeutic Gene Editing: Progress and Challenges.
Mout, Rubul; Ray, Moumita; Lee, Yi-Wei; Scaletti, Federica; Rotello, Vincent M
2017-03-17
The successful use of clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-based gene editing for therapeutics requires efficient in vivo delivery of the CRISPR components. There are, however, major challenges on the delivery front. In this Topical Review, we will highlight recent developments in CRISPR delivery, and we will present hurdles that still need to be overcome to achieve effective in vivo editing.
A High Excision Potential of TALENs for Integrated DNA of HIV-Based Lentiviral Vector
Hirotaka Ebina; Yuka Kanemura; Naoko Misawa; Tetsushi Sakuma; Tomoko Kobayashi; Takashi Yamamoto; Yoshio Koyanagi
2015-01-01
DNA-editing technology has made it possible to rewrite genetic information in living cells. Human immunodeficiency virus (HIV) provirus, an integrated form of viral complementary DNA in host chromosomes, could be a potential target for this technology. We recently reported that HIV proviral DNA could be excised from the chromosomal DNA of HIV-based lentiviral DNA-transduced T cells after multiple introductions of a clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 endonuc...
A Versatile Two-Step CRISPR- and RMCE-Based Strategy for Efficient Genome Engineering in Drosophila
Zhang, X.; Koolhaas, W.; Schnorrer, F.
2014-01-01
The development of clustered, regularly interspaced, short palindromic repeats (CRISPR)/CRISPR-associated (Cas) technologies promises a quantum leap in genome engineering of model organisms. However, CRISPR-mediated gene targeting reports in Drosophila melanogaster are still restricted to a few genes, use variable experimental conditions, and vary in efficiency, questioning the universal applicability of the method. Here, we developed an efficient two-step strategy to flexibly engineer the fl...
Programming Native CRISPR Arrays for the Generation of Targeted Immunity
Hynes, Alexander P.; Labrie, Simon J.
2016-01-01
ABSTRACT The adaptive immune system of prokaryotes, called CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated genes), results in specific cleavage of invading nucleic acid sequences recognized by the cell’s “memory” of past encounters. Here, we exploited the properties of native CRISPR-Cas systems to program the natural “memorization” process, efficiently generating immunity not only to a bacteriophage or plasmid but to any specifically chosen DNA sequence. PMID:27143383
Biotechnology: An Era of Hopes and Fears
2016-01-01
molecular signals and receptors that open and close gates in the cell’s membrane , allowing a change in the electrical potential. As the ability to...0120152. 34. Clustered regularly interspaced short palindromic repeats (CRISPR, pronounced crisper) are segments of prokaryotic DNA containing short...repetitions of base sequences. The CRISPR/Cas9 system is a prokaryotic “immune system” in that it is a genetic/protein combi- nation which is able to
Bioinformatic prediction and functional characterization of human KIAA0100 gene
He Cui; Xi Lan; Shemin Lu; Fujun Zhang; Wanggang Zhang
2017-01-01
Our previous study demonstrated that human KIAA0100 gene was a novel acute monocytic leukemia-associated antigen (MLAA) gene. But the functional characterization of human KIAA0100 gene has remained unknown to date. Here, firstly, bioinformatic prediction of human KIAA0100 gene was carried out using online softwares; Secondly, Human KIAA0100 gene expression was downregulated by the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) 9 system in U937 cells...
Mouse genome engineering using designer nucleases
Hermann, Mario; Cermak, Tomas; Daniel F Voytas; Pelczar, Pawel
2014-01-01
Transgenic mice carrying site-specific genome modifications (knockout, knock-in) are of vital importance for dissecting complex biological systems as well as for modeling human diseases and testing therapeutic strategies. Recent advances in the use of designer nucleases such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) 9 system for site-specific geno...
Using engineered endonucleases to create knockout and knockin zebrafish models
Bedell, Victoria M.; Ekker, Stephen C.
2015-01-01
Over the last few years, the technology to create targeted knockout and knockin zebrafish animals has exploded. We have gained the ability to create targeted knockouts through the use of zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/CRISPR associated system (CRISPR/Cas). Furthermore, using the high-efficiency TALEN system, we were able to create knockin zebrafish using a single-stranded DNA ...
CRISPR-Cas9: tool for qualitative and quantitative plant genome editing
Ali Noman; Muhammad Aqeel; Shuilin He
2016-01-01
Recent developments in genome editing techniques have aroused substantial excitement among agricultural scientists. These techniques offer new opportunities for developing improved plant lines with addition of important traits or removal of undesirable traits. Increased adoption of genome editing has been geared by swiftly developing Clustered regularly interspaced short palindromic repeats (CRISPR). This is appearing as driving force for innovative utilization in diverse branches of plant bi...
Diversity, Activity, and Evolution of CRISPR Loci in Streptococcus thermophilus▿ †
Horvath, Philippe; Romero, Dennis A.; Coûté-Monvoisin, Anne-Claire; Richards, Melissa; Deveau, Hélène; Moineau, Sylvain; Boyaval, Patrick; Fremaux, Christophe; Barrangou, Rodolphe
2007-01-01
Clustered regularly interspaced short palindromic repeats (CRISPR) are hypervariable loci widely distributed in prokaryotes that provide acquired immunity against foreign genetic elements. Here, we characterize a novel Streptococcus thermophilus locus, CRISPR3, and experimentally demonstrate its ability to integrate novel spacers in response to bacteriophage. Also, we analyze CRISPR diversity and activity across three distinct CRISPR loci in several S. thermophilus strains. We show that both ...
Multidrug-Resistant Enterococci Lack CRISPR-cas
Palmer, Kelli L.; Michael S Gilmore
2010-01-01
Clustered, regularly interspaced short palindromic repeats (CRISPR) provide bacteria and archaea with sequence-specific, acquired defense against plasmids and phage. Because mobile elements constitute up to 25% of the genome of multidrug-resistant (MDR) enterococci, it was of interest to examine the codistribution of CRISPR and acquired antibiotic resistance in enterococcal lineages. A database was built from 16 Enterococcus faecalis draft genome sequences to identify commonalities and polymo...
汪加兴; 张淑君
2015-01-01
CRISPR(clustered regularly interspaced short palindromic repeats)/Cas(CRISPR-associated) 、TALENs (Transcription Activator-Like Effector Nucleases)作为分子生物学工具,在基因编辑和改造、药物打靶等方面具有非常重要的应用和发展前景.本文就CRISPR/Cas、TALEN的技术进行介绍.
The CRISPR/Cas Genome-Editing Tool: Application in Improvement of Crops
2016-01-01
The Clustered Regularly Interspaced Short Palindromic Repeats associated Cas9/sgRNA system is a novel targeted genome-editing technique derived from bacterial immune system. It is an inexpensive, easy, most user friendly and rapidly adopted genome editing tool transforming to revolutionary paradigm. This technique enables precise genomic modifications in many different organisms and tissues. Cas9 protein is an RNA guided endonuclease utilized for creating targeted double-stranded breaks with ...
Site-Specific Integration of Exogenous Genes Using Genome Editing Technologies in Zebrafish
Atsuo Kawahara; Yu Hisano; Satoshi Ota; Kiyohito Taimatsu
2016-01-01
The zebrafish (Danio rerio) is an ideal vertebrate model to investigate the developmental molecular mechanism of organogenesis and regeneration. Recent innovation in genome editing technologies, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR associated protein 9 (Cas9) system, have allowed researchers to generate diverse genomic modifications in whole animals and i...
Genome Editing and Its Applications in Model Organisms
Dongyuan Ma; Feng Liu
2015-01-01
Technological advances are important for innovative biological research. Development of molecular tools for DNA manipulation, such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and the clustered regularly-interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas), has revolutionized genome editing. These approaches can be used to develop potential therapeutic strategies to effectively treat heritable diseases. In the last few years, subs...
Efficient Editing of Malaria Parasite Genome Using the CRISPR/Cas9 System
2014-01-01
ABSTRACT Malaria parasites are unicellular organisms residing inside the red blood cells, and current methods for editing the parasite genes have been inefficient. The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats and Cas9 endonuclease-mediated genome editing) system is a new powerful technique for genome editing and has been widely employed to study gene function in various organisms. However, whether this technique can be applied to modify the genomes of malaria par...
Genome Sequence of Borrelia garinii Strain SZ, Isolated in China
Wu, Qiong; Liu, Zhijie; Li, Youquan; Guan, Guiquan; Niu, Qingli; Chen, Ze; Luo, Jianxun; Yin, Hong
2014-01-01
We announce the genome sequence of Borrelia garinii strain SZ, isolated from Dermacentor ticks collected in northeastern China. B. garinii strain SZ carries numerous plasmids, both 10 circular and 9 linear plasmids. The 902,487-bp linear chromosome (28.2% GC content) contains 820 open reading frames, 33 tRNAs, and 4 complete rRNAs. The plasmid cp32-10 contains one clustered regularly interspaced short palindromic repeat (CRISPR) with four repeats.
Programming Native CRISPR Arrays for the Generation of Targeted Immunity
Alexander P. Hynes
2016-05-01
Full Text Available The adaptive immune system of prokaryotes, called CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated genes, results in specific cleavage of invading nucleic acid sequences recognized by the cell’s “memory” of past encounters. Here, we exploited the properties of native CRISPR-Cas systems to program the natural “memorization” process, efficiently generating immunity not only to a bacteriophage or plasmid but to any specifically chosen DNA sequence.
Vergnaud Gilles; Grissa Ibtissem; Pourcel Christine
2007-01-01
Abstract Background In Archeae and Bacteria, the repeated elements called CRISPRs for "clustered regularly interspaced short palindromic repeats" are believed to participate in the defence against viruses. Short sequences called spacers are stored in-between repeated elements. In the current model, motifs comprising spacers and repeats may target an invading DNA and lead to its degradation through a proposed mechanism similar to RNA interference. Analysis of intra-species polymorphism shows t...
Genome Sequence of the Urethral Isolate Pseudomonas aeruginosa RN21
Wibberg, Daniel; Tielen, Petra; Narten, Maike; Schobert, Max; Blom, Jochen; Schatschneider, Sarah; Meyer, Ann-Kathrin; Neubauer, Rüdiger; Albersmeier, Andreas; Albaum, Stefan; Jahn, Martina; Goesmann, Alexander; Vorhölter, Frank-Jörg; Pühler, Alfred; Jahn, Dieter
2015-01-01
Pseudomonas aeruginosa is known to cause complicated urinary tract infections (UTI). The improved 7.0-Mb draft genome sequence of P. aeruginosa RN21, isolated from a patient with an acute UTI, was determined. It carries three (pro)phage genomes, genes for two restriction/modification systems, and a clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated (Cas) system.
CRISPR-Cas9: Tool for Qualitative and Quantitative Plant Genome Editing
Ali Noman; Muhammad Aqeel; Shuilin He
2016-01-01
Recent developments in genome editing techniques have aroused substantial excitement among agricultural scientists. These techniques offer new opportunities for developing improved plant lines with addition of important traits or removal of undesirable traits. Increased adoption of genome editing has been geared by swiftly developing Clustered regularly interspaced short palindromic repeats (CRISPR). This is appearing as driving force for innovative utilization in diverse branches of plant bi...
CRISPR-Cpf1: A New Tool for Plant Genome Editing
Zaidi, Syed Shan-e-Ali
2017-05-19
Clustered regularly interspaced palindromic repeats (CRISPR)-CRISPR-associated proteins (CRISPR-Cas), a groundbreaking genome-engineering tool, has facilitated targeted trait improvement in plants. Recently, CRISPR-CRISPR from Prevotella and Francisella 1 (Cpf1) has emerged as a new tool for efficient genome editing, including DNA-free editing in plants, with higher efficiency, specificity, and potentially wider applications than CRISPR-Cas9.
The genetic engineering system, clustered regularly interspaced short palindromic repeats (CRISPR), has conventionally been used to inactivate genes by making targeted double stranded cuts in DNA. While CRISPR is a useful tool, it can only be used to create loss-of-function modifications and often causes off-target effects due to the disruptive mechanism by which it works. CTD2 researchers at the University of California, San Francisco recently addressed these shortcomings in a publication in Cell.
Biased and Unbiased Methods for the Detection of Off-Target Cleavage by CRISPR/Cas9: An Overview
Francisco Martin; Sabina Sánchez-Hernández; Alejandra Gutiérrez-Guerrero; Javier Pinedo-Gomez; Karim Benabdellah
2016-01-01
The clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein 9 endonuclease (Cas9) derived from bacterial adaptive immune systems is a revolutionary tool used in both basic and applied science. It is a versatile system that enables the genome of different species to be modified by generating double strand breaks (DSBs) at specific locations. However, all of the CRISPR/Cas9 systems can also produce DSBs at off-target sites that differ substantially from on-target si...
Application Progress of CRISPR/Cas9 System for Gene Editing in Tumor Research
Liu, Chao; Li, Zhiwei; Zhang, Yanqiao
2015-01-01
TCRISPR/Cas9 (Clustered Regularly Interspaced Short Palindromic Repeat/CRISPR-associated nuclease 9) gene editing system is a new type of gene editing technology developed based on the immune mechanism of archaea resisting the invasion of exogenous nucleic acid. Compared with traditional gene editing system, CRISPR/Cas9 system is more efficient, easier operating, and less cytotoxic. Currently, CRISPR/Cas9 gene editing technology has been applied to many aspects of cancer research, including r...
Bendtsen, Kirstine L; Xu, Kehan; Luckmann, Majbritt; Winther, Kristoffer S; Shah, Shiraz A; Pedersen, Christian N S; Brodersen, Ditlev E
2017-03-17
Expression of bacterial type II toxin-antitoxin (TA) systems is regulated at the transcriptional level through direct binding of the antitoxin to pseudo-palindromic sequences on operator DNA. In this context, the toxin functions as a co-repressor by stimulating DNA binding through direct interaction with the antitoxin. Here, we determine crystal structures of the complete 90 kDa heterooctameric VapBC1 complex from Caulobacter crescentus CB15 both in isolation and bound to its cognate DNA operator sequence at 1.6 and 2.7 Å resolution, respectively. DNA binding is associated with a dramatic architectural rearrangement of conserved TA interactions in which C-terminal extended structures of the antitoxin VapB1 swap positions to interlock the complex in the DNA-bound state. We further show that a pseudo-palindromic protein sequence in the antitoxin is responsible for this interaction and required for binding and inactivation of the VapC1 toxin dimer. Sequence analysis of 4127 orthologous VapB sequences reveals that such palindromic protein sequences are widespread and unique to bacterial and archaeal VapB antitoxins suggesting a general principle governing regulation of VapBC TA systems. Finally, a structure of C-terminally truncated VapB1 bound to VapC1 reveals discrete states of the TA interaction that suggest a structural basis for toxin activation in vivo. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.
Regularized degenerate multi-solitons
Correa, Francisco
2016-01-01
We report complex PT-symmetric multi-soliton solutions to the Korteweg de-Vries equation that asymptotically contain one-soliton solutions, with each of them possessing the same amount of finite real energy. We demonstrate how these solutions originate from degenerate energy solutions of the Schroedinger equation. Technically this is achieved by the application of Darboux-Crum transformations involving Jordan states with suitable regularizing shifts. Alternatively they may be constructed from a limiting process within the context Hirota's direct method or on a nonlinear superposition obtained from multiple Baecklund transformations. The proposed procedure is completely generic and also applicable to other types of nonlinear integrable systems.
Academic Training Lecture - Regular Programme
PH Department
2011-01-01
Regular Lecture Programme 9 May 2011 ACT Lectures on Detectors - Inner Tracking Detectors by Pippa Wells (CERN) 10 May 2011 ACT Lectures on Detectors - Calorimeters (2/5) by Philippe Bloch (CERN) 11 May 2011 ACT Lectures on Detectors - Muon systems (3/5) by Kerstin Hoepfner (RWTH Aachen) 12 May 2011 ACT Lectures on Detectors - Particle Identification and Forward Detectors by Peter Krizan (University of Ljubljana and J. Stefan Institute, Ljubljana, Slovenia) 13 May 2011 ACT Lectures on Detectors - Trigger and Data Acquisition (5/5) by Dr. Brian Petersen (CERN) from 11:00 to 12:00 at CERN ( Bldg. 222-R-001 - Filtration Plant )
Regularization methods in Banach spaces
Schuster, Thomas; Hofmann, Bernd; Kazimierski, Kamil S
2012-01-01
Regularization methods aimed at finding stable approximate solutions are a necessary tool to tackle inverse and ill-posed problems. Usually the mathematical model of an inverse problem consists of an operator equation of the first kind and often the associated forward operator acts between Hilbert spaces. However, for numerous problems the reasons for using a Hilbert space setting seem to be based rather on conventions than on an approprimate and realistic model choice, so often a Banach space setting would be closer to reality. Furthermore, sparsity constraints using general Lp-norms or the B
Robust integral stabilization of regular linear systems
XU Chengzheng; FENG Dexing
2004-01-01
We consider regular systems with control and observation. We prove some necessary and sufficient condition for an exponentially stable regular system to admit an integral stabilizing controller. We propose also some robust integral controllers when they exist.
Generalization performance of regularized neural network models
Larsen, Jan; Hansen, Lars Kai
1994-01-01
Architecture optimization is a fundamental problem of neural network modeling. The optimal architecture is defined as the one which minimizes the generalization error. This paper addresses estimation of the generalization performance of regularized, complete neural network models. Regularization...
A FAST CONVERGENT METHOD OF ITERATED REGULARIZATION
Huang Xiaowei; Wu Chuansheng; Wu Di
2009-01-01
This article presents a fast convergent method of iterated regularization based on the idea of Landweber iterated regularization, and a method for a-posteriori choice by the Morozov discrepancy principle and the optimum asymptotic convergence order of the regularized solution is obtained. Numerical test shows that the method of iterated regu-larization can quicken the convergence speed and reduce the calculation burden efficiently.
Weakly and Strongly Regular Near-rings
N.Argac; N.J.Groenewald
2005-01-01
In this paper, we prove some basic properties of left weakly regular near-rings.We give an affirmative answer to the question whether a left weakly regular near-ring with left unity and satisfying the IFP is also right weakly regular. In the last section, we use among others left 0-prime and left completely prime ideals to characterize strongly regular near-rings.
MAXIMAL POINTS OF A REGULAR TRUTH FUNCTION
Every canonical linearly separable truth function is a regular function, but not every regular truth function is linearly separable. The most...promising method of determining which of the regular truth functions are linearly separable r quires finding their maximal and minimal points. In this...report is developed a quick, systematic method of finding the maximal points of any regular truth function in terms of its arithmetic invariants. (Author)
Natural frequency of regular basins
Tjandra, Sugih S.; Pudjaprasetya, S. R.
2014-03-01
Similar to the vibration of a guitar string or an elastic membrane, water waves in an enclosed basin undergo standing oscillatory waves, also known as seiches. The resonant (eigen) periods of seiches are determined by water depth and geometry of the basin. For regular basins, explicit formulas are available. Resonance occurs when the dominant frequency of external force matches the eigen frequency of the basin. In this paper, we implement the conservative finite volume scheme to 2D shallow water equation to simulate resonance in closed basins. Further, we would like to use this scheme and utilizing energy spectra of the recorded signal to extract resonant periods of arbitrary basins. But here we first test the procedure for getting resonant periods of a square closed basin. The numerical resonant periods that we obtain are comparable with those from analytical formulas.
Regularized degenerate multi-solitons
Correa, Francisco; Fring, Andreas
2016-09-01
We report complex {P}{T} -symmetric multi-soliton solutions to the Korteweg de-Vries equation that asymptotically contain one-soliton solutions, with each of them possessing the same amount of finite real energy. We demonstrate how these solutions originate from degenerate energy solutions of the Schrödinger equation. Technically this is achieved by the application of Darboux-Crum transformations involving Jordan states with suitable regularizing shifts. Alternatively they may be constructed from a limiting process within the context Hirota's direct method or on a nonlinear superposition obtained from multiple Bäcklund transformations. The proposed procedure is completely generic and also applicable to other types of nonlinear integrable systems.
Modeling polycrystals with regular polyhedra
Paulo Rangel Rios
2006-06-01
Full Text Available Polycrystalline structure is of paramount importance to materials science and engineering. It provides an important example of a space-filling irregular network structure that also occurs in foams as well as in certain biological tissues. Therefore, seeking an accurate description of the characteristics of polycrystals is of fundamental importance. Recently, one of the authors (MEG published a paper in which a method was devised of representation of irregular networks by regular polyhedra with curved faces. In Glicksman's method a whole class of irregular polyhedra with a given number of faces, N, is represented by a single symmetrical polyhedron with N curved faces. This paper briefly describes the topological and metric properties of these special polyhedra. They are then applied to two important problems of irregular networks: the dimensionless energy 'cost' of irregular networks, and the derivation of a 3D analogue of the von Neumann-Mullins equation for the growth rate of grains in a polycrystal.
REGULARITY FOR CERTAIN QUASILINEARELLIPTIC SYSTEMS OF DIVERGENCESTRUCTURE
周树清; 冉启康
2001-01-01
The regularity of the gradient of H lder continuous solutions of quasi-linear elliptic systems of the form -Dj(aij(x, u, Du)Diuk) = -Difik + gkis investigated. Partial regularity and ε-regularity are shown to hold under the structural assumption-Dj(aij(x,u, Du)) = hi ∈ L∞.
Technology Corner: A Regular Expression Training App
Nick Flor
2012-12-01
Full Text Available Regular expressions enable digital forensic analysts to find information in files. The best way for an analyst to become proficient in writing regular expressions is to practice. This paper presents the code for an app that allows an analyst to practice writing regular expressions.
Counting Rooted Nearly 2-regular Planar Maps
郝荣霞; 蔡俊亮
2004-01-01
The number of rooted nearly 2-regular maps with the valency of rootvertex, the number of non-rooted vertices and the valency of root-face as three parameters is obtained. Furthermore, the explicit expressions of the special cases including loopless nearly 2-regular maps and simple nearly 2-regular maps in terms of the above three parameters are derived.
On the Construction of Regular Orthocryptogroups
Xiang Zhi KONG
2002-01-01
The aim of this paper is to study regular orthocryptogroups. After obtaining some charac-terizations of such semigroups, we establish the construction theorem of regular orthocryptogroups. Asan application, we give the construction theorem of right quasi-normal orthocryptogroups and studyhomomorphisms between two regular orthocryptogroups.
REGULAR RELATIONS AND MONOTONE NORMAL ORDERED SPACES
XU XIAOQUAN; LIU YINGMING
2004-01-01
In this paper the classical theorem of Zareckii about regular relations is generalized and an intrinsic characterization of regularity is obtained. Based on the generalized Zareckii theorem and the intrinsic characterization of regularity, the authors give a characterization of monotone normality of ordered spaces. A new proof of the UrysohnNachbin lemma is presented which is quite different from the classical one.
Regular Pentagons and the Fibonacci Sequence.
French, Doug
1989-01-01
Illustrates how to draw a regular pentagon. Shows the sequence of a succession of regular pentagons formed by extending the sides. Calculates the general formula of the Lucas and Fibonacci sequences. Presents a regular icosahedron as an example of the golden ratio. (YP)
Willwand, Kurt; Moroianu, Adela; Hörlein, Rita; Stremmel, Wolfgang; Rommelaere, Jean
2002-07-01
The linear single-stranded DNA genome of minute virus of mice (MVM) is replicated via a double-stranded replicative form (RF) intermediate DNA. Amplification of viral RF DNA requires the structural transition of the right-end palindrome from a linear duplex into a double-hairpin structure, which serves for the repriming of unidirectional DNA synthesis. This conformational transition was found previously to be induced by the MVM nonstructural protein NS1. Elimination of the cognate NS1-binding sites, [ACCA](2), from the central region of the right-end palindrome next to the axis of symmetry was shown to markedly reduce the efficiency of hairpin-primed DNA replication, as measured in a reconstituted in vitro replication system. Thus, [ACCA](2) sequence motifs are essential as NS1-binding elements in the context of the structural transition of the right-end MVM palindrome.
Effect of regularization parameters on geophysical reconstruction
Zhou Hui; Wang Zhaolei; Qiu Dongling; Li Guofa; Shen Jinsong
2009-01-01
In this paper we discuss the edge-preserving regularization method in the reconstruction of physical parameters from geophysical data such as seismic and ground-penetrating radar data.In the regularization method a potential function of model parameters and its corresponding functions are introduced.This method is stable and able to preserve boundaries, and protect resolution.The effect of regularization depends to a great extent on the suitable choice of regularization parameters.The influence of the edge-preserving parameters on the reconstruction results is investigated and the relationship between the regularization parameters and the error of data is described.
Regular Black Holes with Cosmological Constant
MO Wen-Juan; CAI Rong-Gen; SU Ru-Keng
2006-01-01
We present a class of regular black holes with cosmological constant Λ in nonlinear electrodynamics. Instead of usual singularity behind black hole horizon, all fields and curvature invariants are regular everywhere for the regular black holes. Through gauge invariant approach, the linearly dynamical stability of the regular black hole is studied. In odd-parity sector, we find that the Λ term does not appear in the master equations of perturbations, which shows that the regular black hole is stable under odd-parity perturbations. On the other hand, for the even-parity sector, the master equations are more complicated than the case without the cosmological constant. We obtain the sufficient conditions for stability of the regular black hole. We also investigate the thermodynamic properties of the regular black hole, and find that those thermodynamic quantities do not satisfy the differential form of first law of black hole thermodynamics. The reason for violating the first law is revealed.
Learning regularized LDA by clustering.
Pang, Yanwei; Wang, Shuang; Yuan, Yuan
2014-12-01
As a supervised dimensionality reduction technique, linear discriminant analysis has a serious overfitting problem when the number of training samples per class is small. The main reason is that the between- and within-class scatter matrices computed from the limited number of training samples deviate greatly from the underlying ones. To overcome the problem without increasing the number of training samples, we propose making use of the structure of the given training data to regularize the between- and within-class scatter matrices by between- and within-cluster scatter matrices, respectively, and simultaneously. The within- and between-cluster matrices are computed from unsupervised clustered data. The within-cluster scatter matrix contributes to encoding the possible variations in intraclasses and the between-cluster scatter matrix is useful for separating extra classes. The contributions are inversely proportional to the number of training samples per class. The advantages of the proposed method become more remarkable as the number of training samples per class decreases. Experimental results on the AR and Feret face databases demonstrate the effectiveness of the proposed method.
Ideal regularization for learning kernels from labels.
Pan, Binbin; Lai, Jianhuang; Shen, Lixin
2014-08-01
In this paper, we propose a new form of regularization that is able to utilize the label information of a data set for learning kernels. The proposed regularization, referred to as ideal regularization, is a linear function of the kernel matrix to be learned. The ideal regularization allows us to develop efficient algorithms to exploit labels. Three applications of the ideal regularization are considered. Firstly, we use the ideal regularization to incorporate the labels into a standard kernel, making the resulting kernel more appropriate for learning tasks. Next, we employ the ideal regularization to learn a data-dependent kernel matrix from an initial kernel matrix (which contains prior similarity information, geometric structures, and labels of the data). Finally, we incorporate the ideal regularization to some state-of-the-art kernel learning problems. With this regularization, these learning problems can be formulated as simpler ones which permit more efficient solvers. Empirical results show that the ideal regularization exploits the labels effectively and efficiently.
Regularity extraction from non-adjacent sounds
Alexandra eBendixen
2012-05-01
Full Text Available The regular behavior of sound sources helps us to make sense of the auditory environment. Regular patterns may, for instance, convey information on the identity of a sound source (such as the acoustic signature of a train moving on the rails. Yet typically, this signature overlaps in time with signals emitted from other sound sources. It is generally assumed that auditory regularity extraction cannot operate upon this mixture of signals because it only finds regularities between adjacent sounds. In this view, the auditory environment would be grouped into separate entities by means of readily available acoustic cues such as separation in frequency and location. Regularity extraction processes would then operate upon the resulting groups. Our new experimental evidence challenges this view. We presented two interleaved sound sequences which overlapped in frequency range and shared all acoustic parameters. The sequences only differed in their underlying regular patterns. We inserted deviants into one of the sequences to probe whether the regularity was extracted. In the first experiment, we found that these deviants elicited the mismatch negativity (MMN component. Thus the auditory system was able to find the regularity between the non-adjacent sounds. Regularity extraction was not influenced by sequence cohesiveness as manipulated by the relative duration of tones and silent inter-tone-intervals. In the second experiment, we showed that a regularity connecting non-adjacent sounds was discovered only when the intervening sequence also contained a regular pattern, but not when the intervening sounds were randomly varying. This suggests that separate regular patterns are available to the auditory system as a cue for identifying signals coming from distinct sound sources. Thus auditory regularity extraction is not necessarily confined to a processing stage after initial sound grouping, but may precede grouping when other acoustic cues are unavailable.
New Regularization Method in Electrical Impedance Tomography
侯卫东; 莫玉龙
2002-01-01
Image reconstruction in elecrical impedance tomography(EIT)is a highly ill-posed inverse problem,Regularization techniques must be used in order to solve the problem,In this paper,a new regularization method based on the spatial filtering theory is proposed.The new regularized reconstruction for EIT is independent of the estimation of impedance distribution,so it can be implemented more easily than the maxiumum a posteriori(MAP) method.The regularization level in our proposed method varies spatially so as to be suited to the correlation character of the object's impedance distribution.We implemented our regularization method with two dimensional computer simulations.The experimental results indicate that the quality of the reconstructed impedance images with the descibed regularization method based on spatial filtering theory is better than that with Tikhonov method.
Regularized Laplacian Estimation and Fast Eigenvector Approximation
Perry, Patrick O
2011-01-01
Recently, Mahoney and Orecchia demonstrated that popular diffusion-based procedures to compute a quick \\emph{approximation} to the first nontrivial eigenvector of a data graph Laplacian \\emph{exactly} solve certain regularized Semi-Definite Programs (SDPs). In this paper, we extend that result by providing a statistical interpretation of their approximation procedure. Our interpretation will be analogous to the manner in which $\\ell_2$-regularized or $\\ell_1$-regularized $\\ell_2$-regression (often called Ridge regression and Lasso regression, respectively) can be interpreted in terms of a Gaussian prior or a Laplace prior, respectively, on the coefficient vector of the regression problem. Our framework will imply that the solutions to the Mahoney-Orecchia regularized SDP can be interpreted as regularized estimates of the pseudoinverse of the graph Laplacian. Conversely, it will imply that the solution to this regularized estimation problem can be computed very quickly by running, e.g., the fast diffusion-base...
Total variation regularization with bounded linear variations
Makovetskii, Artyom; Voronin, Sergei; Kober, Vitaly
2016-09-01
One of the most known techniques for signal denoising is based on total variation regularization (TV regularization). A better understanding of TV regularization is necessary to provide a stronger mathematical justification for using TV minimization in signal processing. In this work, we deal with an intermediate case between one- and two-dimensional cases; that is, a discrete function to be processed is two-dimensional radially symmetric piecewise constant. For this case, the exact solution to the problem can be obtained as follows: first, calculate the average values over rings of the noisy function; second, calculate the shift values and their directions using closed formulae depending on a regularization parameter and structure of rings. Despite the TV regularization is effective for noise removal; it often destroys fine details and thin structures of images. In order to overcome this drawback, we use the TV regularization for signal denoising subject to linear signal variations are bounded.
Hidden Regular Variation: Detection and Estimation
Mitra, Abhimanyu
2010-01-01
Hidden regular variation defines a subfamily of distributions satisfying multivariate regular variation on $\\mathbb{E} = [0, \\infty]^d \\backslash \\{(0,0, ..., 0) \\} $ and models another regular variation on the sub-cone $\\mathbb{E}^{(2)} = \\mathbb{E} \\backslash \\cup_{i=1}^d \\mathbb{L}_i$, where $\\mathbb{L}_i$ is the $i$-th axis. We extend the concept of hidden regular variation to sub-cones of $\\mathbb{E}^{(2)}$ as well. We suggest a procedure of detecting the presence of hidden regular variation, and if it exists, propose a method of estimating the limit measure exploiting its semi-parametric structure. We exhibit examples where hidden regular variation yields better estimates of probabilities of risk sets.
A multiplicative regularization for force reconstruction
Aucejo, M.; De Smet, O.
2017-02-01
Additive regularizations, such as Tikhonov-like approaches, are certainly the most popular methods for reconstructing forces acting on a structure. These approaches require, however, the knowledge of a regularization parameter, that can be numerically computed using specific procedures. Unfortunately, these procedures are generally computationally intensive. For this particular reason, it could be of primary interest to propose a method able to proceed without defining any regularization parameter beforehand. In this paper, a multiplicative regularization is introduced for this purpose. By construction, the regularized solution has to be calculated in an iterative manner. In doing so, the amount of regularization is automatically adjusted throughout the resolution process. Validations using synthetic and experimental data highlight the ability of the proposed approach in providing consistent reconstructions.
Regular Disjunction-Free Default Theories
Xi-ShunZhao
2004-01-01
In this paper, the class of regular disjunction-free default theories is introduced and investigated. A transformation from regular default theories to normal default theories is established. The initial theory and the transformed theory have the same extensions when restricted to old variables. Hence, regular default theories enjoy some similar properties (e.g., existence of extensions, semi-monotonicity) as normal default theories. Then, a new algorithm for credulous reasoning of regular theories is developed. This algorithm runs in a time not more than O(1.45n), where n is the number of defaults. In case of regular prerequisite-free or semi-2CNF default theories, the credulous reasoning can be solved in polynomial time. However, credulous reasoning for semi-Horn default theories is shown to be NP-complete although it is tractable for Horn default theories. Moreover, skeptical reasoning for regular unary default theories is co-NP-complete.
Regular Disjunction-Free Default Theories
Xi-Shun Zhao
2004-01-01
In this paper, the class of regular disjunction-free default theories is introduced and investigated.A transformation from regular default theories to normal default theories is established. The initial theory and the transformed theory have the same extensions when restricted to old variables. Hence, regular default theories enjoy some similar properties (e.g., existence of extensions, semi-monotonicity) as normal default theories. Then,a new algorithm for credulous reasoning of regular theories is developed. This algorithm runs in a time not more than O(1.45n), where n is the number of defaults. In case of regular prerequisite-free or semi-2CNF default theories, the credulous reasoning can be solved in polynomial time. However, credulous reasoning for semi-Horn default theories is shown to be NP-complete although it is tractable for Horn default theories. Moreover, skeptical reasoning for regular unary default theories is co-NP-complete.
Regularity effect in prospective memory during aging
Geoffrey Blondelle
2016-10-01
Full Text Available Background: Regularity effect can affect performance in prospective memory (PM, but little is known on the cognitive processes linked to this effect. Moreover, its impacts with regard to aging remain unknown. To our knowledge, this study is the first to examine regularity effect in PM in a lifespan perspective, with a sample of young, intermediate, and older adults. Objective and design: Our study examined the regularity effect in PM in three groups of participants: 28 young adults (18–30, 16 intermediate adults (40–55, and 25 older adults (65–80. The task, adapted from the Virtual Week, was designed to manipulate the regularity of the various activities of daily life that were to be recalled (regular repeated activities vs. irregular non-repeated activities. We examine the role of several cognitive functions including certain dimensions of executive functions (planning, inhibition, shifting, and binding, short-term memory, and retrospective episodic memory to identify those involved in PM, according to regularity and age. Results: A mixed-design ANOVA showed a main effect of task regularity and an interaction between age and regularity: an age-related difference in PM performances was found for irregular activities (older < young, but not for regular activities. All participants recalled more regular activities than irregular ones with no age effect. It appeared that recalling of regular activities only involved planning for both intermediate and older adults, while recalling of irregular ones were linked to planning, inhibition, short-term memory, binding, and retrospective episodic memory. Conclusion: Taken together, our data suggest that planning capacities seem to play a major role in remembering to perform intended actions with advancing age. Furthermore, the age-PM-paradox may be attenuated when the experimental design is adapted by implementing a familiar context through the use of activities of daily living. The clinical
Ambiguities in Pauli-Villars regularization
Kleiss, Ronald H P
2014-01-01
We investigate regularization of scalar one-loop integrals in the Pauli- Villars subtraction scheme. The results depend on the number of sub- tractions, in particular the finite terms that survive after the diver- gences have been absorbed by renormalization. Therefore the process of Pauli-Villars regularization is ambiguous. We discuss how these am- biguities may be resolved by applying an asymptotically large number of subtractions, which results in a regularization that is automatically valid in any number of dimensions.
Regularized brain reading with shrinkage and smoothing
Wehbe, Leila; Ramdas, Aaditya; Steorts, Rebecca C.; Shalizi, Cosma Rohilla
2014-01-01
Functional neuroimaging measures how the brain responds to complex stimuli. However, sample sizes are modest, noise is substantial, and stimuli are high dimensional. Hence, direct estimates are inherently imprecise and call for regularization. We compare a suite of approaches which regularize via shrinkage: ridge regression, the elastic net (a generalization of ridge regression and the lasso), and a hierarchical Bayesian model based on small area estimation (SAE). We contrast regularization w...
Branch Processes of Regular Magnetic Monopole
MO Shu-Fan; REN Ji-Rong; ZHU Tao
2009-01-01
In this paper, by making use of Duan's topological current theory, the branch process of regular magnetic monopoles is discussed in detail Regular magnetic monopoles are found generating or annihilating at the limit point and encountering, splitting, or merging at the bifurcation point and the degenerate point systematically of the vector order parameter field φ(x).Furthermore, it is also shown that when regular magnetic monopoles split or merge at the degenerate point of field function φ, the total topological charges of the regular magnetic monopoles axe still unchanged.
Iterative Regularization with Minimum-Residual Methods
Jensen, Toke Koldborg; Hansen, Per Christian
2007-01-01
We study the regularization properties of iterative minimum-residual methods applied to discrete ill-posed problems. In these methods, the projection onto the underlying Krylov subspace acts as a regularizer, and the emphasis of this work is on the role played by the basis vectors of these Krylov...... subspaces. We provide a combination of theory and numerical examples, and our analysis confirms the experience that MINRES and MR-II can work as general regularization methods. We also demonstrate theoretically and experimentally that the same is not true, in general, for GMRES and RRGMRES their success...... as regularization methods is highly problem dependent....
Iterative regularization with minimum-residual methods
Jensen, Toke Koldborg; Hansen, Per Christian
2006-01-01
We study the regularization properties of iterative minimum-residual methods applied to discrete ill-posed problems. In these methods, the projection onto the underlying Krylov subspace acts as a regularizer, and the emphasis of this work is on the role played by the basis vectors of these Krylov...... subspaces. We provide a combination of theory and numerical examples, and our analysis confirms the experience that MINRES and MR-II can work as general regularization methods. We also demonstrate theoretically and experimentally that the same is not true, in general, for GMRES and RRGMRES - their success...... as regularization methods is highly problem dependent....
Ideal-comparability over Regular Rings
Huan Yin CHEN; Miao Sen CHEN
2006-01-01
We introduce the concept of ideal-comparability condition for regular rings. Let I be an ideal of a regular ring R. If R satisfies the Ⅰ-comparability condition, then R is one-sided unit-regular if and only if so is R/I. Also, we show that a regular ring R satisfies the general comparability if and only if the following hold: (1) R/I satisfies the general comparability; (2) R satisfies the general Ⅰ-comparability condition; (3) The natural map B(R) → B(R/I) is surjective.
Local and Nonlocal Regularization to Image Interpolation
Yi Zhan
2014-01-01
Full Text Available This paper presents an image interpolation model with local and nonlocal regularization. A nonlocal bounded variation (BV regularizer is formulated by an exponential function including gradient. It acts as the Perona-Malik equation. Thus our nonlocal BV regularizer possesses the properties of the anisotropic diffusion equation and nonlocal functional. The local total variation (TV regularizer dissipates image energy along the orthogonal direction to the gradient to avoid blurring image edges. The derived model efficiently reconstructs the real image, leading to a natural interpolation which reduces blurring and staircase artifacts. We present experimental results that prove the potential and efficacy of the method.
Regularization and error assignment to unfolded distributions
Zech, Gunter
2011-01-01
The commonly used approach to present unfolded data only in graphical formwith the diagonal error depending on the regularization strength is unsatisfac-tory. It does not permit the adjustment of parameters of theories, the exclusionof theories that are admitted by the observed data and does not allow the com-bination of data from different experiments. We propose fixing the regulariza-tion strength by a p-value criterion, indicating the experimental uncertaintiesindependent of the regularization and publishing the unfolded data in additionwithout regularization. These considerations are illustrated with three differentunfolding and smoothing approaches applied to a toy example.
Bit-coded regular expression parsing
Nielsen, Lasse; Henglein, Fritz
2011-01-01
Regular expression parsing is the problem of producing a parse tree of a string for a given regular expression. We show that a compact bit representation of a parse tree can be produced efficiently, in time linear in the product of input string size and regular expression size, by simplifying...... the DFA-based parsing algorithm due to Dub ´e and Feeley to emit the bits of the bit representation without explicitly materializing the parse tree itself. We furthermore show that Frisch and Cardelli’s greedy regular expression parsing algorithm can be straightforwardly modified to produce bit codings...
The regularity of quotient paratopological groups
Banakh, Taras
2010-01-01
Let $H$ be a closed subgroup of a regular abelian paratopological group $G$. The group reflexion $G^\\flat$ of $G$ is the group $G$ endowed with the strongest group topology, weaker that the original topology of $G$. We show that the quotient $G/H$ is Hausdorff (and regular) if $H$ is closed (and locally compact) in $G^\\flat$. On the other hand, we construct an example of a regular abelian paratopological group $G$ containing a closed discrete subgroup $H$ such that the quotient $G/H$ is Hausdorff but not regular.
Pille Hallast
Full Text Available The male-specific region of the human Y chromosome (MSY includes eight large inverted repeats (palindromes in which arm-to-arm similarity exceeds 99.9%, due to gene conversion activity. Here, we studied one of these palindromes, P6, in order to illuminate the dynamics of the gene conversion process. We genotyped ten paralogous sequence variants (PSVs within the arms of P6 in 378 Y chromosomes whose evolutionary relationships within the SNP-defined Y phylogeny are known. This allowed the identification of 146 historical gene conversion events involving individual PSVs, occurring at a rate of 2.9-8.4×10(-4 events per generation. A consideration of the nature of nucleotide change and the ancestral state of each PSV showed that the conversion process was significantly biased towards the fixation of G or C nucleotides (GC-biased, and also towards the ancestral state. Determination of haplotypes by long-PCR allowed likely co-conversion of PSVs to be identified, and suggested that conversion tract lengths are large, with a mean of 2068 bp, and a maximum in excess of 9 kb. Despite the frequent formation of recombination intermediates implied by the rapid observed gene conversion activity, resolution via crossover is rare: only three inversions within P6 were detected in the sample. An analysis of chimpanzee and gorilla P6 orthologs showed that the ancestral state bias has existed in all three species, and comparison of human and chimpanzee sequences with the gorilla outgroup confirmed that GC bias of the conversion process has apparently been active in both the human and chimpanzee lineages.
Continuum regularization of quantum field theory
Bern, Z.
1986-04-01
Possible nonperturbative continuum regularization schemes for quantum field theory are discussed which are based upon the Langevin equation of Parisi and Wu. Breit, Gupta and Zaks made the first proposal for new gauge invariant nonperturbative regularization. The scheme is based on smearing in the ''fifth-time'' of the Langevin equation. An analysis of their stochastic regularization scheme for the case of scalar electrodynamics with the standard covariant gauge fixing is given. Their scheme is shown to preserve the masslessness of the photon and the tensor structure of the photon vacuum polarization at the one-loop level. Although stochastic regularization is viable in one-loop electrodynamics, two difficulties arise which, in general, ruins the scheme. One problem is that the superficial quadratic divergences force a bottomless action for the noise. Another difficulty is that stochastic regularization by fifth-time smearing is incompatible with Zwanziger's gauge fixing, which is the only known nonperturbaive covariant gauge fixing for nonabelian gauge theories. Finally, a successful covariant derivative scheme is discussed which avoids the difficulties encountered with the earlier stochastic regularization by fifth-time smearing. For QCD the regularized formulation is manifestly Lorentz invariant, gauge invariant, ghost free and finite to all orders. A vanishing gluon mass is explicitly verified at one loop. The method is designed to respect relevant symmetries, and is expected to provide suitable regularization for any theory of interest. Hopefully, the scheme will lend itself to nonperturbative analysis. 44 refs., 16 figs.
Regular Decompositions for H(div) Spaces
Kolev, Tzanio [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Center for Applied Scientific Computing; Vassilevski, Panayot [Lawrence Livermore National Lab. (LLNL), Livermore, CA (United States). Center for Applied Scientific Computing
2012-01-01
We study regular decompositions for H(div) spaces. In particular, we show that such regular decompositions are closely related to a previously studied “inf-sup” condition for parameter-dependent Stokes problems, for which we provide an alternative, more direct, proof.
Adaptive regularization of noisy linear inverse problems
Hansen, Lars Kai; Madsen, Kristoffer Hougaard; Lehn-Schiøler, Tue
2006-01-01
In the Bayesian modeling framework there is a close relation between regularization and the prior distribution over parameters. For prior distributions in the exponential family, we show that the optimal hyper-parameter, i.e., the optimal strength of regularization, satisfies a simple relation: T...
12 CFR 725.3 - Regular membership.
2010-01-01
... 12 Banks and Banking 6 2010-01-01 2010-01-01 false Regular membership. 725.3 Section 725.3 Banks and Banking NATIONAL CREDIT UNION ADMINISTRATION REGULATIONS AFFECTING CREDIT UNIONS NATIONAL CREDIT UNION ADMINISTRATION CENTRAL LIQUIDITY FACILITY § 725.3 Regular membership. (a) A natural person...
Fast and compact regular expression matching
Bille, Philip; Farach-Colton, Martin
2008-01-01
We study 4 problems in string matching, namely, regular expression matching, approximate regular expression matching, string edit distance, and subsequence indexing, on a standard word RAM model of computation that allows logarithmic-sized words to be manipulated in constant time. We show how...
Regularity of harmonic maps with the potential
CHU; Yuming
2006-01-01
The aim of this work is to prove the partial regularity of the harmonic maps with potential. The main difficulty caused by the potential is how to find the equation satisfied by the scaling function. Under the assumption on the potential we can obtain the equation, however, for a general potential, even if it is smooth, the partial regularity is still open.
On the Equivalence of Regularization Schemes
YANG Ji-Feng
2002-01-01
We illustrate via the sunset diagram that dimensional regularization ‘deforms' the nonlocal contentsof multi-loop diagrams with its equivalence to cutoff regularization scheme recovered only after sub-divergence wassubtracted. Then we employed a differential equation approach for calculating loop diagrams to verify that dimensionalare argued especially in nonperturbativc perspective.
Regular Event Structures and Finite Petri Nets
Nielsen, M.; Thiagarajan, P.S.
2002-01-01
We present the notion of regular event structures and conjecture that they correspond exactly to finite 1-safe Petri nets. We show that the conjecture holds for the conflict-free case. Even in this restricted setting, the proof is non-trivial and involves a natural subclass of regular event...
Regularity Re-Revisited: Modality Matters
Tsapkini, Kyrana; Jarema, Gonia; Kehayia, Eva
2004-01-01
The issue of regular-irregular past tense formation was examined in a cross-modal lexical decision task in Modern Greek, a language where the orthographic and phonological overlap between present and past tense stems is the same for both regular and irregular verbs. The experiment described here is a follow-up study of previous visual lexical…
Regularization algorithms based on total least squares
Hansen, Per Christian; O'Leary, Dianne P.
1996-01-01
Discretizations of inverse problems lead to systems of linear equations with a highly ill-conditioned coefficient matrix, and in order to compute stable solutions to these systems it is necessary to apply regularization methods. Classical regularization methods, such as Tikhonov's method or trunc...
A regularized stationary mean-field game
Yang, Xianjin
2016-04-19
In the thesis, we discuss the existence and numerical approximations of solutions of a regularized mean-field game with a low-order regularization. In the first part, we prove a priori estimates and use the continuation method to obtain the existence of a solution with a positive density. Finally, we introduce the monotone flow method and solve the system numerically.
Minimal regular 2-graphs and applications
FAN; Hongbing; LIU; Guizhen; LIU; Jiping
2006-01-01
A 2-graph is a hypergraph with edge sizes of at most two. A regular 2-graph is said to be minimal if it does not contain a proper regular factor. Let f2(n) be the maximum value of degrees over all minimal regular 2-graphs of n vertices. In this paper, we provide a structure property of minimal regular 2-graphs, and consequently, prove that f2(n) = n+3-i/3where 1 ≤i≤6, i=n (mod 6) andn≥ 7, which solves a conjecture posed by Fan, Liu, Wu and Wong. As applications in graph theory, we are able to characterize unfactorable regular graphs and provide the best possible factor existence theorem on degree conditions. Moreover, f2(n) and the minimal 2-graphs can be used in the universal switch box designs, which originally motivated this study.
Regular Expression Matching and Operational Semantics
Rathnayake, Asiri; 10.4204/EPTCS.62.3
2011-01-01
Many programming languages and tools, ranging from grep to the Java String library, contain regular expression matchers. Rather than first translating a regular expression into a deterministic finite automaton, such implementations typically match the regular expression on the fly. Thus they can be seen as virtual machines interpreting the regular expression much as if it were a program with some non-deterministic constructs such as the Kleene star. We formalize this implementation technique for regular expression matching using operational semantics. Specifically, we derive a series of abstract machines, moving from the abstract definition of matching to increasingly realistic machines. First a continuation is added to the operational semantics to describe what remains to be matched after the current expression. Next, we represent the expression as a data structure using pointers, which enables redundant searches to be eliminated via testing for pointer equality. From there, we arrive both at Thompson's lock...
A linear functional strategy for regularized ranking.
Kriukova, Galyna; Panasiuk, Oleksandra; Pereverzyev, Sergei V; Tkachenko, Pavlo
2016-01-01
Regularization schemes are frequently used for performing ranking tasks. This topic has been intensively studied in recent years. However, to be effective a regularization scheme should be equipped with a suitable strategy for choosing a regularization parameter. In the present study we discuss an approach, which is based on the idea of a linear combination of regularized rankers corresponding to different values of the regularization parameter. The coefficients of the linear combination are estimated by means of the so-called linear functional strategy. We provide a theoretical justification of the proposed approach and illustrate them by numerical experiments. Some of them are related with ranking the risk of nocturnal hypoglycemia of diabetes patients.
On regularizations of the Dirac delta distribution
Hosseini, Bamdad; Nigam, Nilima; Stockie, John M.
2016-01-01
In this article we consider regularizations of the Dirac delta distribution with applications to prototypical elliptic and hyperbolic partial differential equations (PDEs). We study the convergence of a sequence of distributions SH to a singular term S as a parameter H (associated with the support size of SH) shrinks to zero. We characterize this convergence in both the weak-* topology of distributions and a weighted Sobolev norm. These notions motivate a framework for constructing regularizations of the delta distribution that includes a large class of existing methods in the literature. This framework allows different regularizations to be compared. The convergence of solutions of PDEs with these regularized source terms is then studied in various topologies such as pointwise convergence on a deleted neighborhood and weighted Sobolev norms. We also examine the lack of symmetry in tensor product regularizations and effects of dissipative error in hyperbolic problems.
Quantitative regularities in floodplain formation
Nevidimova, O.
2009-04-01
Quantitative regularities in floodplain formation Modern methods of the theory of complex systems allow to build mathematical models of complex systems where self-organizing processes are largely determined by nonlinear effects and feedback. However, there exist some factors that exert significant influence on the dynamics of geomorphosystems, but hardly can be adequately expressed in the language of mathematical models. Conceptual modeling allows us to overcome this difficulty. It is based on the methods of synergetic, which, together with the theory of dynamic systems and classical geomorphology, enable to display the dynamics of geomorphological systems. The most adequate for mathematical modeling of complex systems is the concept of model dynamics based on equilibrium. This concept is based on dynamic equilibrium, the tendency to which is observed in the evolution of all geomorphosystems. As an objective law, it is revealed in the evolution of fluvial relief in general, and in river channel processes in particular, demonstrating the ability of these systems to self-organization. Channel process is expressed in the formation of river reaches, rifts, meanders and floodplain. As floodplain is a periodically flooded surface during high waters, it naturally connects river channel with slopes, being one of boundary expressions of the water stream activity. Floodplain dynamics is inseparable from the channel dynamics. It is formed at simultaneous horizontal and vertical displacement of the river channel, that is at Y=Y(x, y), where х, y - horizontal and vertical coordinates, Y - floodplain height. When dу/dt=0 (for not lowering river channel), the river, being displaced in a horizontal plane, leaves behind a low surface, which flooding during high waters (total duration of flooding) changes from the maximum during the initial moment of time t0 to zero in the moment tn. In a similar manner changed is the total amount of accumulated material on the floodplain surface
Multiple graph regularized protein domain ranking
Wang, Jim Jing-Yan
2012-11-19
Background: Protein domain ranking is a fundamental task in structural biology. Most protein domain ranking methods rely on the pairwise comparison of protein domains while neglecting the global manifold structure of the protein domain database. Recently, graph regularized ranking that exploits the global structure of the graph defined by the pairwise similarities has been proposed. However, the existing graph regularized ranking methods are very sensitive to the choice of the graph model and parameters, and this remains a difficult problem for most of the protein domain ranking methods.Results: To tackle this problem, we have developed the Multiple Graph regularized Ranking algorithm, MultiG-Rank. Instead of using a single graph to regularize the ranking scores, MultiG-Rank approximates the intrinsic manifold of protein domain distribution by combining multiple initial graphs for the regularization. Graph weights are learned with ranking scores jointly and automatically, by alternately minimizing an objective function in an iterative algorithm. Experimental results on a subset of the ASTRAL SCOP protein domain database demonstrate that MultiG-Rank achieves a better ranking performance than single graph regularized ranking methods and pairwise similarity based ranking methods.Conclusion: The problem of graph model and parameter selection in graph regularized protein domain ranking can be solved effectively by combining multiple graphs. This aspect of generalization introduces a new frontier in applying multiple graphs to solving protein domain ranking applications. 2012 Wang et al; licensee BioMed Central Ltd.
J-regular rings with injectivities
Shen, Liang
2010-01-01
A ring $R$ is called a J-regular ring if R/J(R) is von Neumann regular, where J(R) is the Jacobson radical of R. It is proved that if R is J-regular, then (i) R is right n-injective if and only if every homomorphism from an $n$-generated small right ideal of $R$ to $R_{R}$ can be extended to one from $R_{R}$ to $R_{R}$; (ii) R is right FP-injective if and only if R is right (J, R)-FP-injective. Some known results are improved.
Low power implementation of datapath using regularity
LAI Li-ya; LIU Peng
2005-01-01
Datapath accounts for a considerable part of power consumption in VLSI circuit design. This paper presents a method for physical implementation of datapath to achieve low power consumption. Regularity is a characteristic of datapath and the key of the proposed method, where synthesis is tightly combined with placement to make full use of regularity, so that low power consumption is achieved. In This paper, a new concept of Synthesis In Relative Placement (SIRP) is given to deal with the semi-regularity in some datapath. Experimental results of a sample circuit validated the proposed method.
REGULARIZATION OF SINGULAR SYSTEMS BY OUTPUT FEEDBACK
De-lin Chu; Da-yong Cai
2000-01-01
Problem of regularization of a singular system by derivative and proportional output feedback is studied. Necessary and sufficient conditions are obtained under which a singular system can be regularized into a closed-loop system that is regular and of index at most one. The reduced form is given that can easily explore the system properties as well as the feedback to be determined. The main results of the present paper are based on orthogonal transformations. Therefore, they can be implemented by numerically stable ways.
Limitations on Dimensional Regularization in Renyi Entropy
Bao, Ning
2016-01-01
Dimensional regularization is a common method used to regulate the UV divergence of field theoretic quantities. When it is used in the context of Renyi entropy, however, it is important to consider whether such a procedure eliminates the statistical interpretation thereof as a measure of entanglement of states living on a Hilbert space. We therefore examine the dimensionally regularized Renyi entropy of a 4d unitary CFT and show that it admits no underlying Hilbert space in the state-counting sense. This gives a concrete proof that dimensionally regularized Renyi entropy cannot always be obtained as a limit of the Renyi entropy of some finite-dimensional quantum system.
Iterative Regularization with Minimum-Residual Methods
Jensen, Toke Koldborg; Hansen, Per Christian
2007-01-01
We study the regularization properties of iterative minimum-residual methods applied to discrete ill-posed problems. In these methods, the projection onto the underlying Krylov subspace acts as a regularizer, and the emphasis of this work is on the role played by the basis vectors of these Krylov...... subspaces. We provide a combination of theory and numerical examples, and our analysis confirms the experience that MINRES and MR-II can work as general regularization methods. We also demonstrate theoretically and experimentally that the same is not true, in general, for GMRES and RRGMRES their success...
Could Regular Pot Smoking Harm Vision?
... fullstory_162441.html Could Regular Pot Smoking Harm Vision? Study suggests that it might slow signaling among ... may be linked to a limited degree of vision impairment, a new French study suggests. The finding ...
Regular-fat dairy and human health
Astrup, Arne; Bradley, Beth H Rice; Brenna, J Thomas
2016-01-01
In recent history, some dietary recommendations have treated dairy fat as an unnecessary source of calories and saturated fat in the human diet. These assumptions, however, have recently been brought into question by current research on regular fat dairy products and human health. In an effort...... dairy foods have on human health. The emerging scientific evidence indicates that the consumption of regular fat dairy foods is not associated with an increased risk of cardiovascular disease and inversely associated with weight gain and the risk of obesity. Dairy foods, including regular-fat milk...... to disseminate, explore and discuss the state of the science on the relationship between regular fat dairy products and health, symposia were programmed by dairy industry organizations in Europe and North America at The Eurofed Lipids Congress (2014) in France, The Dairy Nutrition Annual Symposium (2014...
The regularization of Old English weak verbs
Marta Tío Sáenz
2015-07-01
Full Text Available This article deals with the regularization of non-standard spellings of the verbal forms extracted from a corpus. It addresses the question of what the limits of regularization are when lemmatizing Old English weak verbs. The purpose of such regularization, also known as normalization, is to carry out lexicological analysis or lexicographical work. The analysis concentrates on weak verbs from the second class and draws on the lexical database of Old English Nerthus, which has incorporated the texts of the Dictionary of Old English Corpus. As regards the question of the limits of normalization, the solution adopted are, in the first place, that when it is necessary to regularize, normalization is restricted to correspondences based on dialectal and diachronic variation and, secondly, that normalization has to be unidirectional.
On π-regularity of General Rings
CHEN WEI-XING; CUI SHU-YING
2010-01-01
A general ring means an associative ring with or without identity. An idempotent e in a general ring I is called left (right) semicentral if for every x∈ I,xe = exe (ex = exe). And I is called semiabelian ff every idempotent in I is left or right semicentral. It is proved that a semiabelian general ring I is π-regular if and only ff the set N(I) of nilpotent elements in I is an ideal of I and I/N(I) is regular. It follows that if I is a semiabelian general ring and K is an ideal of I,then I is π-regular if and only if both K and I/K are r-regular. Based on this we prove that every semiabelian GVNL-ring is an SGVNL-ring. These generalize several known results on the relevant subject. Furthermore we give a characterization of a semiabelian GVNL-ring.
A Biordered Set Representation of Regular Semigroups
Bing Jun YU; Mang XU
2005-01-01
In this paper, for an arbitrary regular biordered set E, by using biorder-isomorphisms between the ω-ideals of E, we construct a fundamental regular semigroup WE called NH-semigroup of E, whose idempotent biordered set is isomorphic to E. We prove further that WE can be used to give a new representation of general regular semigroups in the sense that, for any regular semigroup S with the idempotent biordered set isomorphic to E, there exists a homomorphism from S to WE whose kernel is the greatest idempotent-separating congruence on S and the image is a full symmetric subsemigroup of WE. Moreover, when E is a biordered set of a semilattice E0, WE is isomorphic to the Munn-semigroup TE0; and when E is the biordered set of a band B, WE is isomorphic to the Hall-semigroup WB.
Regularities and Radicals in Near-rings
N.J. Groenewald
2002-01-01
Let F be a regularity for near-rings and F(R) the largest FR-regular ideal in R. In the first part of this paper, we introduce the concepts of maximal Fmodular ideals and F-primitive near-rings to characterize F(R) for any near-ring regularity F. Under certain conditions, F(R) is equal to the intersection of all the maximal F-modular ideals of R. As examples, we apply this to the different analogs of the Brown-McCoy radicals and also the Behrens radicals. In the last part of this paper, we show that for certain regularities, the class of F-primitive near-rings forms a special class.
Spectral partitioning of random regular blockmodels
Barucca, Paolo
2016-01-01
Graph partitioning problems emerge in a wide variety of complex systems, ranging from biology to finance, but can be rigorously analyzed and solved only for a few graph ensembles. Here, an ensemble of random graphs with regular block structure is introduced, for which analytical results can be obtained. In particular, the spectral density of such random regular blockmodels is computed exactly for a modular, bipartite and core-periphery structure. McKay's law for random regular graphs is found analytically to apply also for regular modular and bipartite structures when blocks are homogeneous. In core-periphery structures, where blocks are intrinsically heterogeneous, a new law is found to apply for the spectral density. Exact solution to the inference problem is provided for the models discussed. All analytical results show perfect agreement with numerical experiments. Final discussion summarizes results and outlines the relevance of the results for the solution of graph partitioning problems in other graph en...
Comparability for ideals of regular rings
CHEN Huanyin
2005-01-01
In this paper we investigate necessary and sufficient conditions under which the ideals possess comparability structure. For regular rings, we prove that every square matrix over ideals satisfying general comparability admits a diagonal reduction by quasi invertible matrices.
Regularity of optimal transport maps and applications
Philippis, Guido
2013-01-01
In this thesis, we study the regularity of optimal transport maps and its applications to the semi-geostrophic system. The first two chapters survey the known theory, in particular there is a self-contained proof of Brenier’ theorem on existence of optimal transport maps and of Caffarelli’s Theorem on Holder continuity of optimal maps. In the third and fourth chapter we start investigating Sobolev regularity of optimal transport maps, while in Chapter 5 we show how the above mentioned results allows to prove the existence of Eulerian solution to the semi-geostrophic equation. In Chapter 6 we prove partial regularity of optimal maps with respect to a generic cost functions (it is well known that in this case global regularity can not be expected). More precisely we show that if the target and source measure have smooth densities the optimal map is always smooth outside a closed set of measure zero.
On Comparison of Adaptive Regularization Methods
Sigurdsson, Sigurdur; Larsen, Jan; Hansen, Lars Kai
2000-01-01
, a very flexible regularization may substitute the need for selection procedures. This paper investigates recently suggested adaptive regularization schemes. Some methods focus directly on minimizing an estimate of the generalization error (either algebraic or empirical), whereas others start from...... different criteria, e.g., the Bayesian evidence. The evidence expresses basically the probability of the model, which is conceptually different from generalization error; however, asymptotically for large training data sets they will converge. First the basic model definition, training and generalization...
The mechanisms of palindrome-stimulated mutation and related human diseases%回文序列诱导突变的机制及人类相关疾病
陈旭; 肖飞; 郭健
2013-01-01
In prokaryotic and eukaryotic genomes, the palindrome regions are highly variable and instable. The reason for this instability is that palindrome can form a hairpin or cruciform structure, which can result in deletions or chromosomal translocations by certain mechanisms, such as slipped mispairing, single-strand annealing and non-homologous end joining. In human genomes, palindromes commonly exist in the essential elements which can regulate the expressions of different genes, and the mutations stimulated by palindromes are also closely associated with the occurrences and progressions of certain human diseases such as male infertility and thalassemia. Based on recent studies, we briefly summarize the types of mutations caused by palindromes and their possible mechanisms, as well as the related human diseases. This review would provide some information for the following researches about the roles and functions of palindromes in gene expression,regulation,mutation and related human diseases.%在原核和真核生物基因组中,含有回文序列的区域高度可变且稳定性差,主要原因是回文序列能形成发 卡或十字形二级结构,然后通过滑动错配、单链复性以及非同源末端连接(Non-homologous end joining,NHEJ) 等机制导致缺失突变或染色体易位的发生.在人类基因组中,回文序列较普遍存在于基因表达调控的重要作用 元件中,它诱导的缺失和易位突变还与男性不育、地中海贫血等多种疾病的发生、发展密切相关.文章综合近 几年国内外相关文献,初步阐释回文序列诱导突变的类型和可能机制,及其与人类疾病的关系,为进一步探讨 回文序列在基因表达调控、基因突变及人类疾病中的作用及功能等相关研究提供参考.
*-Regular Leavitt Path Algebras of Arbitrary Graphs
Gonzalo ARANDA PINO; Kulumani RANGASWAMY; Lia VA(S)
2012-01-01
If K is a field with involution and E an arbitrary graph,the involution from K naturally induces an involution of the Leavitt path algebra LK(E).We show that the involution on LK(E) is proper if the involution on K is positive-definite,even in the case when the graph E is not necessarily finite or row-finite.It has been shown that the Leavitt path algebra LK(E) is regular if and only if E is acyclic.We give necessary and sufficient conditions for LK(E) to be *-regular (i.e.,regular with proper involution).This characterization of *-regularity of a Leavitt path algebra is given in terms of an algebraic property of K,not just a graph-theoretic property of E.This differs from the.known characterizations of various other algebraic properties of a Leavitt path algebra in terms of graphtheoretic properties of E alone.As a corollary,we show that Handelman's conjecture (stating that every *-regular ring is unit-regular) holds for Leavitt path algebras.Moreover,its generalized version for rings with local units also continues to hold for Leavitt path algebras over arbitrary graphs.
张淼; 顾苏俊
2009-01-01
OBJECTIVE Research the therapeutic effectiveness of combination Imipenem and teicoplanin to treat septicemia due to interspace of lumbar vertebrae Infection complicated pulmonary abscess and the method of diagnosis, prevention and cure of Secondary interspace of lumbar vertebrae Injection. METHODS The successful cure case-report that severe postoperative interspace of lumbar vertebrae infection complicated blood-borne pulmonary abscess used small needle knife to treat Lumbar intervertebral disc protrusion (LIDP) were reviewed.RESULTS Unstandard asepsis technique and invasive operation long time operation, too mang damage of tissue in operation, patient weak, diabetes, glucocorticoid, lacking postoperative anti infection therapy etc. Lumbocrural pain were found aggravated, high fever, blood sedimentation increased, CRP heightened. CONCLUSIONS Strict asepsis,sufficient preoperotive preparation, Standard operation, less damage, can reduce interspace of lumbar vertebrae infection rate. Strict asepsis and less damage in the operation can reduce the incidence of intervertebral disc space infection.%目的 探讨亚胺培南/西司他丁与替考拉宁联合应用治疗腰椎间隙感染后败血症合并肺脓肿的疗效以及继发件腰椎间隙感染的发病特点、诊断及防治方法.方法 通过对1例小针刀治疗腰椎间盘突出后导致重度腰椎间隙感染合并血源性肺脓肿患者的成功救治进行同顾性总结分析.结果 无菌观念不严格、介入性操作不规范、手术时间长、术中组织损伤多、患者基础条件差、糖尿病、应用糖皮质激素、术后抗炎不足等因素有关;患者术后3 d腰腿痛加剧.高热,血沉增快,C-反应蛋白增高.结论 严格无菌观念,充分术前准备,术中操作规范减少损伤可减少腰椎间隙感染的发生.
Solomon, K
2011-08-01
A repetitive-extragenic palindromic PCR (rep-PCR) subtyping method (DiversiLab) in conjunction with ribotyping, toxinotyping and antimicrobial-susceptibility testing was used to detect subtypes within Clostridium difficile ribotypes 027 and 078. Clinical isolates of ribotypes 027 (toxinotype III) (n = 30) and 078 (toxinotype V) (n = 23) were provided by health-care facilities across the Republic of Ireland over 2 months in 2006 and 1 month in 2009. Ribotype 027 isolates were significantly more related to each other (9 different subtype profiles) when compared to ribotype 078 isolates (14 different profiles) (P = 0.001; cut-off >90 % similarity). Almost half of ribotype 078 isolates (45.5 %) showed no relationship to each other. The clonality of ribotype 027 isolates suggests effective adaptation to the human niche, whereas the considerable genetic diversity within ribotype 078 isolates suggests that they may have originated from a variety of sources. Subtyping correlated well with antimicrobial susceptibility, in particular clindamycin susceptibility for ribotype 027, but diverse antimicrobial-susceptibility profiles were seen in ribotype 078 isolates, even within a single health-care facility. Between 2006 and 2009, a change in the predominant subtype of ribotype 027 was seen, with the recent clone representing half of all ribotype 027 isolates studied. This strain exhibited 89 % similarity to a rep-PCR profile of the North American NAP-1 strain.
Castro-Chavez, Fernando
2012-02-01
Palindromati, the massive host-edited synthetic palindromic contamination found in GenBank, is illustrated and exemplified. Millions of contaminated sequences with portions or tandems of such portions derived from the ZAP adaptor or related linkers are shown (1) by the 12-bp sequence reported elsewhere, exon Xb, 5' CCCGAATTCGGG 3', (2) by a 22-bp related sequence 5' CTCGTGCCGAATTCGGCACGAG 3', and (3) by a longer 44-bp related sequence: 5' CTCGTGCCGAATTCGGCACGAGCTCGTGCCGAATTCGGCACGAG 3'. Possible reasons for why those long contaminating sequences continue in the databases are presented here: (1) the recognition site for the plus strand (+) is single-strand self-annealed; (2) the recognition site for the minus strand (-) is not only single-strand self-annealed but also located far away from the single-strand self-annealed plus strand, rendering impossible the formation of the active EcoRI enzyme dimer to cut on 5' G/AATTC 3', its target sequence. As a possible solution, it is suggested to rely on at least two or three independent results, such as sequences obtained by independent laboratories with the use, preferably, of independent sequencing methodologies. This information may help to develop tools for bioinformatics capable to detect/remove these contaminants and to infer why some damaged sequences which cause genetic diseases escape detection by the molecular quality control mechanism of cells and organisms, being undesirably transferred unchecked through the generations.
The Least Regular Order with Respect to a Regular Congruence on Ordered Γ-Semigroups
Manoj SIRIPITUKDET; Aiyared IAMPAN
2012-01-01
The motivation mainly comes from the conditions of congruences to be regular that are of importance and interest in ordered semigroups.In 1981,Sen has introduced the concept of the Γ-semigroups.We can see that any semigroup can be considered as a Γ-semigroup.In this paper,we introduce and characterize the concept of the regular congruences on ordered Γ-semigroups and prove the following statements on an ordered Γ-semigroup M:(1) Every ordered semilattice congruences is a regular congruence.(2) There exists the least regular order on the T-semigroup M/p with respect to a regular congruence p on M.(3) The regular congruences are not ordered semilattice congruences in general.
A Construction for P-Regular Semigroups
无
2000-01-01
@@A regular semigroup S with a special involution *, i.e., a unaryoperation on S satisfying (x*)*=x, xx*x=x, (xy)*=y*x* x, y S, is called a regular *-semigroup［1］. It has been shown by Yamada［2］ that a regular semigroup S is a regular *-semigroup if and only if ithas a P-system, that is to say, there is a subset P ofE(S) such that (c.1) (1) ( p, q P) pq E(S), pqp P; (2) ( a S) ( | a+ V(a)) aP1a+, a+P1a P.As a generalization of regular *-semigroup and orthodox semigroup,Yamada［3］ defined P-regular semigroup. Let S be a regularsemigroup. A subset P of E(S) is called a C-set in S if (c.2) (1) ( p, q P) pq E(S), pqp P; (2) ( a S) ( a+ V(a)) aP1a+, a+P1a P. In this case, (S,P) forms a P-regular semigroup, innotation S(P). The element a+ in(c.2) (2) is called a P-inverse of a. The set of all P-inverses of a is denoted by VP(a). S(P) is said to bestrongly, meanwhile P is called a strong C-set in S, ifVP(p) P for all p P. A partial groupoid E as well as its partial subgroupoid Pforms a P-regular partial band and is denoted by E(P) if itis exactly the subalgebra of the idempotents in some P-regularsemigroup S(P). In this case, S(P) is called an adjacentsemigroup E(P). All P-regular partial bands are obtained inZhang and He［4］.
Counting colorings of a regular graph
Galvin, David
2012-01-01
At most how many (proper) q-colorings does a regular graph admit? Galvin and Tetali conjectured that among all n-vertex, d-regular graphs with 2d|n, none admits more q-colorings than the disjoint union of n/2d copies of the complete bipartite graph K_{d,d}. In this note we give asymptotic evidence for this conjecture, giving an upper bound on the number of proper q-colorings admitted by an n-vertex, d-regular graph of the form a^n b^{n(1+o(1))/d} (where a and b depend on q and where o(1) goes to 0 as d goes to infinity) that agrees up to the o(1) term with the count of q-colorings of n/2d copies of K_{d,d}. An auxiliary result is an upper bound on the number of colorings of a regular graph in terms of its independence number. For example, we show that for all even q and fixed \\epsilon > 0 there is \\delta=\\delta(\\epsilon,q) such that the number of proper q-colorings admitted by an n-vertex, d-regular graph with no independent set of size n(1-\\epsilon)/2 is at most (a-\\delta)^n.
Modified sparse regularization for electrical impedance tomography.
Fan, Wenru; Wang, Huaxiang; Xue, Qian; Cui, Ziqiang; Sun, Benyuan; Wang, Qi
2016-03-01
Electrical impedance tomography (EIT) aims to estimate the electrical properties at the interior of an object from current-voltage measurements on its boundary. It has been widely investigated due to its advantages of low cost, non-radiation, non-invasiveness, and high speed. Image reconstruction of EIT is a nonlinear and ill-posed inverse problem. Therefore, regularization techniques like Tikhonov regularization are used to solve the inverse problem. A sparse regularization based on L1 norm exhibits superiority in preserving boundary information at sharp changes or discontinuous areas in the image. However, the limitation of sparse regularization lies in the time consumption for solving the problem. In order to further improve the calculation speed of sparse regularization, a modified method based on separable approximation algorithm is proposed by using adaptive step-size and preconditioning technique. Both simulation and experimental results show the effectiveness of the proposed method in improving the image quality and real-time performance in the presence of different noise intensities and conductivity contrasts.
Regular Expression Matching and Operational Semantics
Asiri Rathnayake
2011-08-01
Full Text Available Many programming languages and tools, ranging from grep to the Java String library, contain regular expression matchers. Rather than first translating a regular expression into a deterministic finite automaton, such implementations typically match the regular expression on the fly. Thus they can be seen as virtual machines interpreting the regular expression much as if it were a program with some non-deterministic constructs such as the Kleene star. We formalize this implementation technique for regular expression matching using operational semantics. Specifically, we derive a series of abstract machines, moving from the abstract definition of matching to increasingly realistic machines. First a continuation is added to the operational semantics to describe what remains to be matched after the current expression. Next, we represent the expression as a data structure using pointers, which enables redundant searches to be eliminated via testing for pointer equality. From there, we arrive both at Thompson's lockstep construction and a machine that performs some operations in parallel, suitable for implementation on a large number of cores, such as a GPU. We formalize the parallel machine using process algebra and report some preliminary experiments with an implementation on a graphics processor using CUDA.
Regularities, Natural Patterns and Laws of Nature
Stathis Psillos
2014-02-01
Full Text Available The goal of this paper is to sketch an empiricist metaphysics of laws of nature. The key idea is that there are regularities without regularity-enforcers. Differently put, there are natural laws without law-makers of a distinct metaphysical kind. This sketch will rely on the concept of a natural pattern and more significantly on the existence of a network of natural patterns in nature. The relation between a regularity and a pattern will be analysed in terms of mereology. Here is the road map. In section 2, I will briefly discuss the relation between empiricism and metaphysics, aiming to show that an empiricist metaphysics is possible. In section 3, I will offer arguments against stronger metaphysical views of laws. Then, in section 4 I will motivate nomic objectivism. In section 5, I will address the question ‘what is a regularity?’ and will develop a novel answer to it, based on the notion of a natural pattern. In section 6, I will raise the question: ‘what is a law of nature?’, the answer to which will be: a law of nature is a regularity that is characterised by the unity of a natural pattern.
Mining High Utility Itemsets with Regular Occurrence
Komate Amphawan
2016-09-01
Full Text Available High utility itemset mining (HUIM plays an important role in the data mining community and in a wide range of applications. For example, in retail business it is used for finding sets of sold products that give high profit, low cost, etc. These itemsets can help improve marketing strategies, make promotions/ advertisements, etc. However, since HUIM only considers utility values of items/itemsets, it may not be sufficient to observe product-buying behavior of customers such as information related to “regular purchases of sets of products having a high profit margin”. To address this issue, the occurrence behavior of itemsets (in the term of regularity simultaneously with their utility values was investigated. Then, the problem of mining high utility itemsets with regular occurrence (MHUIR to find sets of co-occurrence items with high utility values and regular occurrence in a database was considered. An efficient single-pass algorithm, called MHUIRA, was introduced. A new modified utility-list structure, called NUL, was designed to efficiently maintain utility values and occurrence information and to increase the efficiency of computing the utility of itemsets. Experimental studies on real and synthetic datasets and complexity analyses are provided to show the efficiency of MHUIRA combined with NUL in terms of time and space usage for mining interesting itemsets based on regularity and utility constraints.
On a correspondence between regular and non-regular operator monotone functions
Gibilisco, P.; Hansen, Frank; Isola, T.
2009-01-01
We prove the existence of a bijection between the regular and the non-regular operator monotone functions satisfying a certain functional equation. As an application we give a new proof of the operator monotonicity of certain functions related to the Wigner-Yanase-Dyson skew information.......We prove the existence of a bijection between the regular and the non-regular operator monotone functions satisfying a certain functional equation. As an application we give a new proof of the operator monotonicity of certain functions related to the Wigner-Yanase-Dyson skew information....
M.I. Hiyane
2006-03-01
Full Text Available Cloning of the T-cell receptor genes is a critical step when generating T-cell receptor transgenic mice. Because T-cell receptor molecules are clonotypical, isolation of their genes requires reverse transcriptase-assisted PCR using primers specific for each different Valpha or Vß genes or by the screening of cDNA libraries generated from RNA obtained from each individual T-cell clone. Although feasible, these approaches are laborious and costly. The aim of the present study was to test the application of the non-palindromic adaptor-PCR method as an alternative to isolate the genes encoding the T-cell receptor of an antigen-specific T-cell hybridoma. For this purpose, we established hybridomas specific for trans-sialidase, an immunodominant Trypanosoma cruzi antigen. These T-cell hybridomas were characterized with regard to their ability to secrete interferon-gamma, IL-4, and IL-10 after stimulation with the antigen. A CD3+, CD4+, CD8- interferon-gamma-producing hybridoma was selected for the identification of the variable regions of the T-cell receptor by the non-palindromic adaptor-PCR method. Using this methodology, we were able to rapidly and efficiently determine the variable regions of both T-cell receptor chains. The results obtained by the non-palindromic adaptor-PCR method were confirmed by the isolation and sequencing of the complete cDNA genes and by the recognition with a specific antibody against the T-cell receptor variable ß chain. We conclude that the non-palindromic adaptor-PCR method can be a valuable tool for the identification of the T-cell receptor transcripts of T-cell hybridomas and may facilitate the generation of T-cell receptor transgenic mice.
Shadow of rotating regular black holes
Abdujabbarov, Ahmadjon; Ahmedov, Bobomurat; Ghosh, Sushant G
2016-01-01
We study the shadows cast by the different types of rotating regular black holes viz. Ay\\'on-Beato-Garc\\'ia {(ABG)}, Hayward, and Bardeen. These black holes have in addition to the total mass ($M$) and rotation parameter ($a$), different parameters as electric charge ($Q$), deviation parameter ($g$), and magnetic charge ($g_{*}$), respectively. Interestingly, the size of the shadow is affected by these parameters in addition to the rotation parameter. We found that the radius of the shadow in each case decreases monotonically and the distortion parameter increases when the value of these parameters increase. A comparison with the standard Kerr case is also investigated. We have also studied the influence of the plasma environment around regular black holes to discuss its shadow. The presence of the plasma affects the apparent size of the regular black hole's shadow to be increased due to two effects (i) gravitational redshift of the photons and (ii) radial dependence of plasma density.
Fractional Regularization Term for Variational Image Registration
Rafael Verdú-Monedero
2009-01-01
Full Text Available Image registration is a widely used task of image analysis with applications in many fields. Its classical formulation and current improvements are given in the spatial domain. In this paper a regularization term based on fractional order derivatives is formulated. This term is defined and implemented in the frequency domain by translating the energy functional into the frequency domain and obtaining the Euler-Lagrange equations which minimize it. The new regularization term leads to a simple formulation and design, being applicable to higher dimensions by using the corresponding multidimensional Fourier transform. The proposed regularization term allows for a real gradual transition from a diffusion registration to a curvature registration which is best suited to some applications and it is not possible in the spatial domain. Results with 3D actual images show the validity of this approach.
Obregón, O; Ryan, M P; Obregon, Octavio; Quevedo, Hernando; Ryan, Michael P.
2004-01-01
We construct a family of time and angular dependent, regular S-brane solutions which corresponds to a simple analytical continuation of the Zipoy-Voorhees 4-dimensional vacuum spacetime. The solutions are asymptotically flat and turn out to be free of singularities without requiring a twist in space. They can be considered as the simplest non-singular generalization of the singular S0-brane solution. We analyze the properties of a representative of this family of solutions and show that it resembles to some extent the asymptotic properties of the regular Kerr S-brane. The R-symmetry corresponds, however, to the general Lorentzian symmetry. Several generalizations of this regular solution are derived which include a charged S-brane and an additional dilatonic field.
Landweber iterative regularization for nearfield acoustic holography
BI Chuanxing; CHEN Xinzhao; ZHOU Rong; CHEN Jian
2006-01-01
On the basis of the distributed source boundary point method (DSBPM)-based nearfield acoustic holography (NAH), Landweber iterative regularization method is proposed to stabilize the NAH reconstruction process, control the influence of measurement errors on the reconstructed results and ensure the validity of the reconstructed results. And a new method, the auxiliary surface method, is proposed to determine the optimal iterative number for optimizing the regularization effect. Here, the optimal number is determined by minimizing the relative error between the calculated pressure on the auxiliary surface corresponding to each iterative number and the measured pressure. An experiment on a speaker is investigated to demonstrate the high sensitivity of the reconstructed results to measurement errors and to validate the chosen method of the optimal iterative number and the Landweber iterative regularization method for controlling the influence of measurement errors on the reconstructed results.
Robust super-resolution without regularization
Pham, T Q [Canon Information Systems Research Australia, 1 Thomas Holt drive, North Ryde, NSW 2113 (Australia); Vliet, L J v [Quantitative Imaging Group, Department of Imaging Science and Technology, Faculty of Applied Sciences, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft (Netherlands); Schutte, K [Electro-Optics Group, TNO Defence, Security and Safety, PO Box 96864, 2509 JG The Hague (Netherlands)
2008-07-15
Super-resolution restoration is the problem of restoring a high-resolution scene from multiple degraded low-resolution images under motion. Due to imaging blur and noise, this problem is ill-posed. Additional constraints such as smoothness of the solution (i.e. regularization) is often required to obtain a stable solution. While regularizing the cost function is a standard practice in image restoration, we propose a restoration algorithm that does not require this extra regularization term. The robustness of the algorithm is achieved by a robust error norm that does not response to intensity outliers. With the outliers suppressed, our solution behaves similarly to a maximum-likelihood solution under the presence of Gaussian noise. The effectiveness of our algorithm is demonstrated with super-resolution restoration of real infrared image sequences under severe aliasing and intensity outliers.
Implementing regularization implicitly via approximate eigenvector computation
Mahoney, Michael W
2010-01-01
Regularization is a powerful technique for extracting useful information from noisy data. Typically, it is implemented by adding some sort of norm constraint to an objective function and then exactly optimizing the modified objective function. This procedure typically leads to optimization problems that are computationally more expensive than the original problem, a fact that is clearly problematic if one is interested in large-scale applications. On the other hand, a large body of empirical work has demonstrated that heuristics, and in some cases approximation algorithms, developed to speed up computations sometimes have the side-effect of performing regularization implicitly. Thus, we consider the question: What is the regularized optimization objective that an approximation algorithm is exactly optimizing? We address this question in the context of computing approximations to the smallest nontrivial eigenvector of a graph Laplacian; and we consider three random-walk-based procedures: one based on the heat ...
Nonlinear electrodynamics and regular black holes
Sajadi, S. N.; Riazi, N.
2017-03-01
In this work, an exact regular black hole solution in General Relativity is presented. The source is a nonlinear electromagnetic field with the algebraic structure T00=T11 for the energy-momentum tensor, partially satisfying the weak energy condition but not the strong energy condition. In the weak field limit, the EM field behaves like the Maxwell field. The solution corresponds to a charged black hole with q≤0.77 m. The metric, the curvature invariants, and the electric field are regular everywhere. The BH is stable against small perturbations of spacetime and using the Weinhold metric, geometrothermodynamical stability has been investigated. Finally we investigate the idea that the observable universe lives inside a regular black hole. We argue that this picture might provide a viable description of universe.
Regularization and Migration Policy in Europe
Philippe de Bruycker
2001-05-01
Full Text Available The following pages present, in a general way, the contents of Regularization of illegal immigrants in the European Union, which includes a comparative synthesis and statistical information for each of the eight countries involved; a description of actions since the beginning of the year 2000; and a systematic analysis of the different categories of foreigners, the types of regularization carried out, and the rules that have governed these actions.In relation to regularization, the author considers the political coherence of the actions taken by the member states as well as how they relate to two ever more crucial aspects of immigration policy –the integration of legal resident immigrants and the fight againstillegal immigration in the context of a control of migratory flows.
Width Distributions for Convex Regular Polyhedra
Finch, Steven R
2011-01-01
The mean width is a measure on three-dimensional convex bodies that enjoys equal status with volume and surface area [Rota]. As the phrase suggests, it is the mean of a probability density f. We verify formulas for mean widths of the regular tetrahedron and the cube. Higher-order moments of f_tetra and f_cube have not been examined until now. Assume that each polyhedron has edges of unit length. We deduce that the mean square width of the regular tetrahedron is 1/3+(3+sqrt(3))/(3*pi) and the mean square width of the cube is 1+4/pi.
Stability Analysis for Regularized Least Squares Regression
Rudin, Cynthia
2005-01-01
We discuss stability for a class of learning algorithms with respect to noisy labels. The algorithms we consider are for regression, and they involve the minimization of regularized risk functionals, such as L(f) := 1/N sum_i (f(x_i)-y_i)^2+ lambda ||f||_H^2. We shall call the algorithm `stable' if, when y_i is a noisy version of f*(x_i) for some function f* in H, the output of the algorithm converges to f* as the regularization term and noise simultaneously vanish. We consider two flavors of...
Interaction of Regular and Chaotic States
De Pace, A; Weidenmüller, H A
2006-01-01
Modelling the chaotic states in terms of the Gaussian Orthogonal Ensemble of random matrices (GOE), we investigate the interaction of the GOE with regular bound states. The eigenvalues of the latter may or may not be embedded in the GOE spectrum. We derive a generalized form of the Pastur equation for the average Green's function. We use that equation to study the average and the variance of the shift of the regular states, their spreading width, and the deformation of the GOE spectrum non-perturbatively. We compare our results with various perturbative approaches.
Regular transport dynamics produce chaotic travel times.
Villalobos, Jorge; Muñoz, Víctor; Rogan, José; Zarama, Roberto; Johnson, Neil F; Toledo, Benjamín; Valdivia, Juan Alejandro
2014-06-01
In the hope of making passenger travel times shorter and more reliable, many cities are introducing dedicated bus lanes (e.g., Bogota, London, Miami). Here we show that chaotic travel times are actually a natural consequence of individual bus function, and hence of public transport systems more generally, i.e., chaotic dynamics emerge even when the route is empty and straight, stops and lights are equidistant and regular, and loading times are negligible. More generally, our findings provide a novel example of chaotic dynamics emerging from a single object following Newton's laws of motion in a regularized one-dimensional system.
No finite $5$-regular matchstick graph exists
2014-01-01
A graph $G=(V,E)$ is called a unit-distance graph in the plane if there is an injective embedding of $V$ in the plane such that every pair of adjacent vertices are at unit distance apart. If additionally the corresponding edges are non-crossing and all vertices have the same degree $r$ we talk of a regular matchstick graph. Due to Euler's polyhedron formula we have $r\\le 5$. The smallest known $4$-regular matchstick graph is the so called Harborth graph consisting of $52$ vertices. In this ar...
Learning Rates for -Regularized Kernel Classifiers
Hongzhi Tong
2013-01-01
Full Text Available We consider a family of classification algorithms generated from a regularization kernel scheme associated with -regularizer and convex loss function. Our main purpose is to provide an explicit convergence rate for the excess misclassification error of the produced classifiers. The error decomposition includes approximation error, hypothesis error, and sample error. We apply some novel techniques to estimate the hypothesis error and sample error. Learning rates are eventually derived under some assumptions on the kernel, the input space, the marginal distribution, and the approximation error.
Estrada, Ernesto; de la Pena, Jose A.
2013-01-01
Let G be a graph with set of vertices 1,...,n and adjacency matrix A of size nxn. Let d(i,j)=d, we say that f_d:N->N is a d-function on G if for every pair of vertices i,j and k>=d, we have a_ij^(k)=f_d(k). If this function f_d exists on G we say that G is d-walk regular. We prove that G is d-walk regular if and only if for every pair of vertices i,j at distance
刘佳玮; 徐晖; 张海员; 白静; 傅松滨; 周春水
2014-01-01
基因组不稳定是肿瘤细胞的特征性标志,基因扩增是一种特殊的基因组不稳定性的表现形式,其在激活原癌基因引发癌症的过程中起着重要的作用.基因扩增将导致细胞加速生长增殖或耐药生长等表型.人们已经广泛注意到其在癌症的诊断和治疗等方面的重要临床意义.但是,人们对基因扩增的分子机制的认识仍然十分有限,本文综述了回文序列介导的基因扩增的分子机制,提出在DNA断点处以无模板形式、新合成小回文序列可能是一部分肿瘤细胞中基因扩增的关键机制,为进一步探索基因扩增的分子机制提供理论参考.%Gene amplification is a common chromosomal aberration which is often the result of tumor genome instability,and plays a crucial role in the process of activating oncogenes and leading to cancers.As gene amplification often is evident in advanced stages of cancer,its clinical importance in diagnosis and treatment has been popularly recognized.However,the underlying mechanisms governing gene amplification are still not fully understood.Herein,we reviewed one of the well-defined gene amplification mechanisms:DNA double-strand breaks-triggered,palindromes or short DNA inverted repeatsmediated gene amplification model,which was established and validated in a variety of research organisms including T.thermophila,fission yeast,budding yeast and rodent cells.Based on the recent published reports,we put forward a new model for the palindromes mediated gene amplification mechanism,that is de novo synthesis of small palindromic sequences (usually several hundred base pairs in length or shorter) at the DNA breakpoints in a template-free manner is the key determinant for gene amplification in certain tumor genomes.Elucidating the potential mechanism and involved enzymes for the regulation and creation of novel palindromic sequences should shed more light onto the palindromes mediated gene amplification and the
Dynamic stabilization of regular linear systems
Weiss, G; Curtain, RF
We consider a general class of infinite-dimensional linear systems, called regular linear systems, for which convenient representations are known to exist both in time and in frequency domain, For this class of systems, we investigate the concepts of stabilizability and detectability, in particular,
Regular and context-free nominal traces
Mezzetti, Gianluca
2016-01-01
Two kinds of automata are presented, for recognising new classes of regular and context-free nominal languages. We compare their expressive power with analogous proposals in the literature, showing that they express novel classes of languages. Although many properties of classical languages hold ...
Neural Classifier Construction using Regularization, Pruning
Hintz-Madsen, Mads; Hansen, Lars Kai; Larsen, Jan;
1998-01-01
In this paper we propose a method for construction of feed-forward neural classifiers based on regularization and adaptive architectures. Using a penalized maximum likelihood scheme, we derive a modified form of the entropic error measure and an algebraic estimate of the test error. In conjunction...
Deconvolution and Regularization with Toeplitz Matrices
Hansen, Per Christian
2002-01-01
of these discretized deconvolution problems, with emphasis on methods that take the special structure of the matrix into account. Wherever possible, analogies to classical DFT-based deconvolution problems are drawn. Among other things, we present direct methods for regularization with Toeplitz matrices, and we show...
The moduli space of regular stable maps
Robbin, Joel; Salamon, Dietmar; 10.1007/s00209-007-0237-x
2012-01-01
The moduli space of regular stable maps with values in a complex manifold admits naturally the structure of a complex orbifold. Our proof uses the methods of differential geometry rather than algebraic geometry. It is based on Hardy decompositions and Fredholm intersection theory in the loop space of the target manifold.
Regular conformal system for Einstein equations
Choquet-Bruhat, Y.; Novello, M.
1987-06-21
We give a system of partial differential equations satisfied by a metric g conformal to an Einstein metric and by the conformal factor ..omega.., regular system in the sense that it does not contain negative powers of ..omega... We use the ideas of Friedrich but we obtain here a hyperbolic system in the sense of Leray, by a different method.
Optimal Regularizing Effect for Scalar Conservation Laws
Golse, François
2011-01-01
We investigate the regularity of bounded weak solutions of scalar conservation laws with uniformly convex flux in space dimension one, satisfying an entropy condition with entropy production term that is a signed Radon measure. The proof is based on the kinetic formulation of scalar conservation laws and on an interaction estimate in physical space.
Bayesian regularization of diffusion tensor images
Frandsen, Jesper; Hobolth, Asger; Østergaard, Leif;
2007-01-01
several directions. The measured diffusion coefficients and thereby the diffusion tensors are subject to noise, leading to possibly flawed representations of the three dimensional fibre bundles. In this paper we develop a Bayesian procedure for regularizing the diffusion tensor field, fully utilizing...
Regularity of rotational travelling water waves.
Escher, Joachim
2012-04-13
Several recent results on the regularity of streamlines beneath a rotational travelling wave, along with the wave profile itself, will be discussed. The survey includes the classical water wave problem in both finite and infinite depth, capillary waves and solitary waves as well. A common assumption in all models to be discussed is the absence of stagnation points.
Contour Propagation With Riemannian Elasticity Regularization
Bjerre, Troels; Hansen, Mads Fogtmann; Sapru, W.;
2011-01-01
the planning CT onto the rescans and correcting to reflect actual anatomical changes. For deformable registration, a free-form, multi-level, B-spline deformation model with Riemannian elasticity, penalizing non-rigid local deformations, and volumetric changes, was used. Regularization parameters was defined...
NOTE ON REGULAR D-OPTIMAL MATRICES
李乔良
2003-01-01
Let A be aj ×d (0,1) matrix. It is known that ifj = 2k-1is odd, then det(AAT) ≤(j+1)((j+1)d/4j)j; ifj is even, then det(AAT) ≤ (j+1)((j+2)d/4(j+1))j. A is called a regularD-optimal matrix if it satisfies the equality of the above bounds. In this note, it is proved thatifj = 2k - 1 is odd, then A is a regular D-optimal matrix if and only if A is the adjacent matrixof a (2k - 1, k, (j + 1)d/4j)-BIBD; if j ＝ 2k is even, then A is a regular D-optimal matrix ifand only if A can be obtained from the adjacent matrix B of a (2k + 1, k + 1, (j + 2)d/4(j + 1))-BIBD by deleting any one row from B. Three 21 × 42 regular D-optimal matrices, which wereunknown in [11], are also provided.
A Note on Left Regular Semiring
N. Sulochana
2016-08-01
Full Text Available In this paper we have focused on the additive and multiplicative identity „e‟ and determine the additive and multiplicative semigroups. Here we established that, A semiring S in which (S, + and (S, • are left singular semigroups, then S is a left regular semiring. We have framed an example for this proposition by considering a two element set
Tikhonov Regularization and Total Least Squares
Golub, G. H.; Hansen, Per Christian; O'Leary, D. P.
2000-01-01
formulation involves a least squares problem, can be recast in a total least squares formulation suited for problems in which both the coefficient matrix and the right-hand side are known only approximately. We analyze the regularizing properties of this method and demonstrate by a numerical example that...
Creativity Workshops in the Regular Classroom.
Mildrum, Nancy King
2000-01-01
This article describes implementation of a creativity curriculum, Ten Lessons in Creativity, with gifted and typical students in elementary and middle school settings. It discusses creativity instruction as a bridge between gifted and regular education, ways that creativity workshops affirm the highly creative child, creativity and self-esteem,…
Regularization of turbulence - a comprehensive modeling approach
Geurts, B. J.
2011-12-01
Turbulence readily arises in numerous flows in nature and technology. The large number of degrees of freedom of turbulence poses serious challenges to numerical approaches aimed at simulating and controlling such flows. While the Navier-Stokes equations are commonly accepted to precisely describe fluid turbulence, alternative coarsened descriptions need to be developed to cope with the wide range of length and time scales. These coarsened descriptions are known as large-eddy simulations in which one aims to capture only the primary features of a flow, at considerably reduced computational effort. Such coarsening introduces a closure problem that requires additional phenomenological modeling. A systematic approach to the closure problem, know as regularization modeling, will be reviewed. Its application to multiphase turbulent will be illustrated in which a basic regularization principle is enforced to physically consistently approximate momentum and scalar transport. Examples of Leray and LANS-alpha regularization are discussed in some detail, as are compatible numerical strategies. We illustrate regularization modeling to turbulence under the influence of rotation and buoyancy and investigate the accuracy with which particle-laden flow can be represented. A discussion of the numerical and modeling errors incurred will be given on the basis of homogeneous isotropic turbulence.
Coprime factorization for regular linear systems
Curtain, R; Weiss, G; Weiss, M
1996-01-01
Mild sufficient conditions are given for the existence of a doubly coprime factorization of the transfer function of a regular linear system, as well as formulae for such a factorization. The results are illustrated by two examples of delay systems, one of which has infinitely many unstable poles. C
Dynamic stabilization of regular linear systems
Weiss, G; Curtain, RF
1997-01-01
We consider a general class of infinite-dimensional linear systems, called regular linear systems, for which convenient representations are known to exist both in time and in frequency domain, For this class of systems, we investigate the concepts of stabilizability and detectability, in particular,
Annotation of regular polysemy and underspecification
Martínez Alonso, Héctor; Pedersen, Bolette Sandford; Bel, Núria
2013-01-01
We present the result of an annotation task on regular polysemy for a series of seman- tic classes or dot types in English, Dan- ish and Spanish. This article describes the annotation process, the results in terms of inter-encoder agreement, and the sense distributions obtained with two methods...
Strategies of Teachers in the Regular Classroom
De Leeuw, Renske Ria; De Boer, Anke Aaltje
2016-01-01
It is known that regular schoolteachers have difficulties in educating students with social, emotional and behavioral difficulties (SEBD), mainly because of their disruptive behavior. In order to manage the disruptive behavior of students with SEBD many advices and strategies are provided in educational literature. However, very little is known…
Strategies of teachers in the regular classroom
de Leeuw, Renske Ria; de Boer, Anke Aaltje
2016-01-01
It is known that regular schoolteachers have difficulties in educating students with social, emotional and behavioral difficulties (SEBD), mainly because of their disruptive behavior. In order to manage the disruptive behavior of students with SEBD many advices and strategies are provided in educati
On the regularity in some variational problems
Ragusa, Maria Alessandra; Tachikawa, Atsushi
2017-01-01
Our main goal is the study some regularity results where are considered estimates in Morrey spaces for the derivatives of local minimizers of variational integrals of the form 𝒜 (u ,Ω )= ∫Ω F (x ,u ,D u ) dx where Ω is a bounded domain in ℝm and the integrand F have some different forms.
Regular-fat dairy and human health
Astrup, Arne; Bradley, Beth H Rice; Brenna, J Thomas;
2016-01-01
to disseminate, explore and discuss the state of the science on the relationship between regular fat dairy products and health, symposia were programmed by dairy industry organizations in Europe and North America at The Eurofed Lipids Congress (2014) in France, The Dairy Nutrition Annual Symposium (2014...
Regular Submanifolds in Conformal Space Qnp
Changxiong NIE; Chuanxi WU
2012-01-01
The authors study the regular submanifolds in the conformal space Qnp and introduce the submanifold theory in the conformal space Qnp.The first variation formula of the Willmore volume functional of pseudo-Riemannian submanifolds in the conformal space Qnp is given.Finally,the conformal isotropic submanifolds in the conformal space Qnp are classified.
On the regularization procedure in classical electrodynamics
Yaremko, Yu
2003-01-01
We consider the self-action problem in classical electrodynamics. A strict geometrical sense of commonly used renormalization of mass is made. A regularization procedure is proposed which relies on energy-momentum and angular momentum balance equations. We correct the expression for angular momentum tensor obtained by us in a previous paper (2002 J. Phys. A: Math. Gen. 35 831).
The canonical controller and its regularity
Willems, Jan C.; Belur, Madhu N.; Anak Agung Julius, A.A.J.; Trentelman, Harry L.
2003-01-01
This paper deals with properties of canonical controllers. We first specify the behavior that they implement. It follows that a canonical controller implements the desired controlled behavior if and only if the desired behavior is implementable. We subsequently investigate the regularity of the cont
Stabilization, Pole Placement, and Regular Implementability
Belur, Madhu N.; Trentelman, H.L.
2002-01-01
In this paper, we study control by interconnection of linear differential systems. We give necessary and sufficient conditions for regular implementability of a given linear differential system. We formulate the problems of stabilization and pole placement as problems of finding a suitable, regularl
Generalisation of Regular and Irregular Morphological Patterns.
Prasada, Sandeep; and Pinker, Steven
1993-01-01
When it comes to explaining English verbs' patterns of regular and irregular generalization, single-network theories have difficulty with the former, rule-only theories with the latter process. Linguistic and psycholinguistic evidence, based on observation during experiments and simulations in morphological pattern generation, independently call…
Liu, Jinzhen; Ling, Lin; Li, Gang
2013-07-01
A Tikhonov regularization method in the inverse problem of electrical impedance tomography (EIT) often results in a smooth distribution reconstruction, with which we can barely make a clear separation between the inclusions and background. The recently popular total variation (TV)regularization method including the lagged diffusivity (LD) method can sharpen the edges, and is robust to noise in a small convergence region. Therefore, in this paper, we propose a novel regularization method combining the Tikhonov and LD regularization methods. Firstly, we clarify the implementation details of the Tikhonov, LD and combined methods in two-dimensional open EIT by performing the current injection and voltage measurement on one boundary of the imaging object. Next, we introduce a weighted parameter to the Tikhonov regularization method aiming to explore the effect of the weighted parameter on the resolution and quality of reconstruction images with the inclusion at different depths. Then, we analyze the performance of these algorithms with noisy data. Finally, we evaluate the effect of the current injection pattern on reconstruction quality and propose a modified current injection pattern.The results indicate that the combined regularization algorithm with stable convergence is able to improve the reconstruction quality with sharp contrast and more robust to noise in comparison to the Tikhonov and LD regularization methods solely. In addition, the results show that the current injection pattern with a bigger driver angle leads to a better reconstruction quality.
ZHANG; Xiaoxia; GUO; Maozheng
2005-01-01
In this paper, it is shown that the regular representation and regular covariant representation of the crossed products A×α G correspond to the twisted multiplicative unitary operators, where A is a Woronowicz C*-algebra acted upon by a discrete group G. Meanwhile, it is also shown that the regular covariant C*-algebra is the Woronowicz C*-algebra which corresponds to a multiplicative unitary. Finally, an explicit description of the multiplicative unitary operator for C(SUq(2))×α Z is given in terms of those of the Woronowicz C*-algebra C(SUq(2)) and the discrete group G.
Regularization and Iterative Methods for Monotone Variational Inequalities
Xiubin Xu
2010-01-01
Full Text Available We provide a general regularization method for monotone variational inequalities, where the regularizer is a Lipschitz continuous and strongly monotone operator. We also introduce an iterative method as discretization of the regularization method. We prove that both regularization and iterative methods converge in norm.
Power-law regularities in human language
Mehri, Ali; Lashkari, Sahar Mohammadpour
2016-11-01
Complex structure of human language enables us to exchange very complicated information. This communication system obeys some common nonlinear statistical regularities. We investigate four important long-range features of human language. We perform our calculations for adopted works of seven famous litterateurs. Zipf's law and Heaps' law, which imply well-known power-law behaviors, are established in human language, showing a qualitative inverse relation with each other. Furthermore, the informational content associated with the words ordering, is measured by using an entropic metric. We also calculate fractal dimension of words in the text by using box counting method. The fractal dimension of each word, that is a positive value less than or equal to one, exhibits its spatial distribution in the text. Generally, we can claim that the Human language follows the mentioned power-law regularities. Power-law relations imply the existence of long-range correlations between the word types, to convey an especial idea.
Towards lattice-regularized Quantum Gravity
Diakonov, Dmitri
2011-01-01
Using the Cartan formulation of General Relativity, we construct a well defined lattice-regularized theory capable to describe large non-perturbative quantum fluctuations of the frame field (or the metric) and of the spin connection. To that end we need to present the tetrad by a composite field built as a bilinear combination of fermion fields. The theory is explicitly invariant under local Lorentz transformations and, in the continuum limit, under general covariant transformations, or diffeomorphisms. Being well defined for large and fast varying fields at the ultraviolet cutoff, the theory simultaneously has chances of reproducing standard General Relativity in the infrared continuum limit. The present regularization of quantum gravity opens new possibilities of its unification with the Standard Model.
Basic analysis of regularized series and products
Jorgenson, Jay A
1993-01-01
Analytic number theory and part of the spectral theory of operators (differential, pseudo-differential, elliptic, etc.) are being merged under amore general analytic theory of regularized products of certain sequences satisfying a few basic axioms. The most basic examples consist of the sequence of natural numbers, the sequence of zeros with positive imaginary part of the Riemann zeta function, and the sequence of eigenvalues, say of a positive Laplacian on a compact or certain cases of non-compact manifolds. The resulting theory is applicable to ergodic theory and dynamical systems; to the zeta and L-functions of number theory or representation theory and modular forms; to Selberg-like zeta functions; andto the theory of regularized determinants familiar in physics and other parts of mathematics. Aside from presenting a systematic account of widely scattered results, the theory also provides new results. One part of the theory deals with complex analytic properties, and another part deals with Fourier analys...
Extreme values, regular variation and point processes
Resnick, Sidney I
1987-01-01
Extremes Values, Regular Variation and Point Processes is a readable and efficient account of the fundamental mathematical and stochastic process techniques needed to study the behavior of extreme values of phenomena based on independent and identically distributed random variables and vectors It presents a coherent treatment of the distributional and sample path fundamental properties of extremes and records It emphasizes the core primacy of three topics necessary for understanding extremes the analytical theory of regularly varying functions; the probabilistic theory of point processes and random measures; and the link to asymptotic distribution approximations provided by the theory of weak convergence of probability measures in metric spaces The book is self-contained and requires an introductory measure-theoretic course in probability as a prerequisite Almost all sections have an extensive list of exercises which extend developments in the text, offer alternate approaches, test mastery and provide for enj...
Tracking magnetogram proper motions by multiscale regularization
Jones, Harrison P.
1995-01-01
Long uninterrupted sequences of solar magnetograms from the global oscillations network group (GONG) network and from the solar and heliospheric observatory (SOHO) satellite will provide the opportunity to study the proper motions of magnetic features. The possible use of multiscale regularization, a scale-recursive estimation technique which begins with a prior model of how state variables and their statistical properties propagate over scale. Short magnetogram sequences are analyzed with the multiscale regularization algorithm as applied to optical flow. This algorithm is found to be efficient, provides results for all the spatial scales spanned by the data and provides error estimates for the solutions. It is found that the algorithm is less sensitive to evolutionary changes than correlation tracking.
Chiral Perturbation Theory With Lattice Regularization
Ouimet, P P A
2005-01-01
In this work, alternative methods to regularize chiral perturbation theory are discussed. First, Long Distance Regularization will be considered in the presence of the decuplet of the lightest spin 32 baryons for several different observables. This serves motivation and introduction to the use of the lattice regulator for chiral perturbation theory. The mesonic, baryonic and anomalous sectors of chiral perturbation theory will be formulated on a lattice of space time points. The consistency of the lattice as a regulator will be discussed in the context of the meson and baryon masses. Order a effects will also be discussed for the baryon masses, sigma terms and magnetic moments. The work will close with an attempt to derive an effective Wess-Zumino-Witten Lagrangian for Wilson fermions at non-zero a. Following this discussion, there will be a proposal for a phenomenologically useful WZW Lagrangian at non-zero a.
Testing the Equivalence of Regular Languages
Marco Almeida
2009-07-01
Full Text Available The minimal deterministic finite automaton is generally used to determine regular languages equality. Antimirov and Mosses proposed a rewrite system for deciding regular expressions equivalence of which Almeida et al. presented an improved variant. Hopcroft and Karp proposed an almost linear algorithm for testing the equivalence of two deterministic finite automata that avoids minimisation. In this paper we improve the best-case running time, present an extension of this algorithm to non-deterministic finite automata, and establish a relationship between this algorithm and the one proposed in Almeida et al. We also present some experimental comparative results. All these algorithms are closely related with the recent coalgebraic approach to automata proposed by Rutten.
Least square regularized regression in sum space.
Xu, Yong-Li; Chen, Di-Rong; Li, Han-Xiong; Liu, Lu
2013-04-01
This paper proposes a least square regularized regression algorithm in sum space of reproducing kernel Hilbert spaces (RKHSs) for nonflat function approximation, and obtains the solution of the algorithm by solving a system of linear equations. This algorithm can approximate the low- and high-frequency component of the target function with large and small scale kernels, respectively. The convergence and learning rate are analyzed. We measure the complexity of the sum space by its covering number and demonstrate that the covering number can be bounded by the product of the covering numbers of basic RKHSs. For sum space of RKHSs with Gaussian kernels, by choosing appropriate parameters, we tradeoff the sample error and regularization error, and obtain a polynomial learning rate, which is better than that in any single RKHS. The utility of this method is illustrated with two simulated data sets and five real-life databases.
Effort variation regularization in sound field reproduction
Stefanakis, Nick; Jacobsen, Finn; Sarris, Ioannis
2010-01-01
. Specifically, it is suggested that the phase differential of the source driving signals should be in agreement with the phase differential of the desired sound pressure field. The performance of the suggested method is compared with that of conventional effort regularization, wave field synthesis (WFS......In this paper, active control is used in order to reproduce a given sound field in an extended spatial region. A method is proposed which minimizes the reproduction error at a number of control positions with the reproduction sources holding a certain relation within their complex strengths......), and adaptive wave field synthesis (AWFS), both under free-field conditions and in reverberant rooms. It is shown that effort variation regularization overcomes the problems associated with small spaces and with a low ratio of direct to reverberant energy, improving thus the reproduction accuracy...
Totally Corrective Boosting for Regularized Risk Minimization
Shen, Chunhua; Barnes, Nick
2010-01-01
Consideration of the primal and dual problems together leads to important new insights into the characteristics of boosting algorithms. In this work, we propose a general framework that can be used to design new boosting algorithms. A wide variety of machine learning problems essentially minimize a regularized risk functional. We show that the proposed boosting framework, termed CGBoost, can accommodate various loss functions and different regularizers in a totally-corrective optimization fashion. We show that, by solving the primal rather than the dual, a large body of totally-corrective boosting algorithms can actually be efficiently solved and no sophisticated convex optimization solvers are needed. We also demonstrate that some boosting algorithms like AdaBoost can be interpreted in our framework--even their optimization is not totally corrective. We empirically show that various boosting algorithms based on the proposed framework perform similarly on the UCIrvine machine learning datasets [1] that we hav...
Regular black hole in three dimensions
Myung, Yun Soo; Yoon, Myungseok
2008-01-01
We find a new black hole in three dimensional anti-de Sitter space by introducing an anisotropic perfect fluid inspired by the noncommutative black hole. This is a regular black hole with two horizons. We compare thermodynamics of this black hole with that of non-rotating BTZ black hole. The first-law of thermodynamics is not compatible with the Bekenstein-Hawking entropy.
A short proof of increased parabolic regularity
Stephen Pankavich
2015-08-01
Full Text Available We present a short proof of the increased regularity obtained by solutions to uniformly parabolic partial differential equations. Though this setting is fairly introductory, our new method of proof, which uses a priori estimates and an inductive method, can be extended to prove analogous results for problems with time-dependent coefficients, advection-diffusion or reaction diffusion equations, and nonlinear PDEs even when other tools, such as semigroup methods or the use of explicit fundamental solutions, are unavailable.
Regular aspirin use and lung cancer risk
Cummings K
2002-11-01
Full Text Available Abstract Background Although a large number of epidemiological studies have examined the role of aspirin in the chemoprevention of colon cancer and other solid tumors, there is a limited body of research focusing on the association between aspirin and lung cancer risk. Methods We conducted a hospital-based case-control study to evaluate the role of regular aspirin use in lung cancer etiology. Study participants included 868 cases with primary, incident lung cancer and 935 hospital controls with non-neoplastic conditions who completed a comprehensive epidemiological questionnaire. Participants were classified as regular aspirin users if they had taken the drug at least once a week for at least one year. Results Results indicated that lung cancer risk was significantly lower for aspirin users compared to non-users (adjusted OR = 0.57; 95% CI 0.41–0.78. Although there was no clear evidence of a dose-response relationship, we observed risk reductions associated with greater frequency of use. Similarly, prolonged duration of use and increasing tablet years (tablets per day × years of use was associated with reduced lung cancer risk. Risk reductions were observed in both sexes, but significant dose response relationships were only seen among male participants. When the analyses were restricted to former and current smokers, participants with the lowest cigarette exposure tended to benefit most from the potential chemopreventive effect of aspirin. After stratification by histology, regular aspirin use was significantly associated with reduced risk of small cell lung cancer and non-small cell lung cancer. Conclusions Overall, results from this hospital-based case-control study suggest that regular aspirin use may be associated with reduced risk of lung cancer.
Bouncing cosmology inspired by regular black holes
Neves, J. C. S.
2017-09-01
In this article, we present a bouncing cosmology inspired by a family of regular black holes. This scale-dependent cosmology deviates from the cosmological principle by means of a scale factor which depends on the time and the radial coordinate as well. The model is isotropic but not perfectly homogeneous. That is, this cosmology describes a universe almost homogeneous only for large scales, such as our observable universe.
Regular black hole in three dimensions
Myung, Yun Soo; Yoon, Myungseok
2008-01-01
We find a new black hole in three dimensional anti-de Sitter space by introducing an anisotropic perfect fluid inspired by the noncommutative black hole. This is a regular black hole with two horizons. We compare thermodynamics of this black hole with that of non-rotating BTZ black hole. The first-law of thermodynamics is not compatible with the Bekenstein-Hawking entropy.
Stream Processing Using Grammars and Regular Expressions
Rasmussen, Ulrik Terp
Kleenex, a language for expressing high-performance streaming string processing programs as regular grammars with embedded semantic actions, and its compilation to streaming string transducers with worst-case linear-time performance. Its underlying theory is based on transducer decomposition into oracle...... is based on a bottom-up tabulation algorithm reformulated using least fixed points and evaluated using an instance of the chaotic iteration scheme by Cousot and Cousot....
Sparse regularization for force identification using dictionaries
Qiao, Baijie; Zhang, Xingwu; Wang, Chenxi; Zhang, Hang; Chen, Xuefeng
2016-04-01
The classical function expansion method based on minimizing l2-norm of the response residual employs various basis functions to represent the unknown force. Its difficulty lies in determining the optimum number of basis functions. Considering the sparsity of force in the time domain or in other basis space, we develop a general sparse regularization method based on minimizing l1-norm of the coefficient vector of basis functions. The number of basis functions is adaptively determined by minimizing the number of nonzero components in the coefficient vector during the sparse regularization process. First, according to the profile of the unknown force, the dictionary composed of basis functions is determined. Second, a sparsity convex optimization model for force identification is constructed. Third, given the transfer function and the operational response, Sparse reconstruction by separable approximation (SpaRSA) is developed to solve the sparse regularization problem of force identification. Finally, experiments including identification of impact and harmonic forces are conducted on a cantilever thin plate structure to illustrate the effectiveness and applicability of SpaRSA. Besides the Dirac dictionary, other three sparse dictionaries including Db6 wavelets, Sym4 wavelets and cubic B-spline functions can also accurately identify both the single and double impact forces from highly noisy responses in a sparse representation frame. The discrete cosine functions can also successfully reconstruct the harmonic forces including the sinusoidal, square and triangular forces. Conversely, the traditional Tikhonov regularization method with the L-curve criterion fails to identify both the impact and harmonic forces in these cases.
Computational Topology for Regular Closed Sets
project, The I-TANGO; :; Peters, T J; Bisceglio, J.; Ferguson, D. R.; Hoffmann, C.M.; Maekawa, T.; Patrikalakis, N.M.; Sakkalis, T.; N F Stewart
2004-01-01
The Boolean algebra of regular closed sets is prominent in topology, particularly as a dual for the Stone-Cech compactification. This algebra is also central for the theory of geometric computation, as a representation for combinatorial operations on geometric sets. However, the issue of computational approximation introduces unresolved subtleties that do not occur within "pure" topology. One major effort towards reconciling this mathematical theory with computational practice is our ongoing ...
Hyperspectral Image Recovery via Hybrid Regularization
Arablouei, Reza; de Hoog, Frank
2016-12-01
Natural images tend to mostly consist of smooth regions with individual pixels having highly correlated spectra. This information can be exploited to recover hyperspectral images of natural scenes from their incomplete and noisy measurements. To perform the recovery while taking full advantage of the prior knowledge, we formulate a composite cost function containing a square-error data-fitting term and two distinct regularization terms pertaining to spatial and spectral domains. The regularization for the spatial domain is the sum of total-variation of the image frames corresponding to all spectral bands. The regularization for the spectral domain is the l1-norm of the coefficient matrix obtained by applying a suitable sparsifying transform to the spectra of the pixels. We use an accelerated proximal-subgradient method to minimize the formulated cost function. We analyze the performance of the proposed algorithm and prove its convergence. Numerical simulations using real hyperspectral images exhibit that the proposed algorithm offers an excellent recovery performance with a number of measurements that is only a small fraction of the hyperspectral image data size. Simulation results also show that the proposed algorithm significantly outperforms an accelerated proximal-gradient algorithm that solves the classical basis-pursuit denoising problem to recover the hyperspectral image.
Charge-regularization effects on polyelectrolytes
Muthukumar, Murugappan
2012-02-01
When electrically charged macromolecules are dispersed in polar solvents, their effective net charge is generally different from their chemical charges, due to competition between counterion adsorption and the translational entropy of dissociated counterions. The effective charge changes significantly as the experimental conditions change such as variations in solvent quality, temperature, and the concentration of added small electrolytes. This charge-regularization effect leads to major difficulties in interpreting experimental data on polyelectrolyte solutions and challenges in understanding the various polyelectrolyte phenomena. Even the most fundamental issue of experimental determination of molar mass of charged macromolecules by light scattering method has been difficult so far due to this feature. We will present a theory of charge-regularization of flexible polyelectrolytes in solutions and discuss the consequences of charge-regularization on (a) experimental determination of molar mass of polyelectrolytes using scattering techniques, (b) coil-globule transition, (c) macrophase separation in polyelectrolyte solutions, (c) phase behavior in coacervate formation, and (d) volume phase transitions in polyelectrolyte gels.
Regularization Parameter Selections via Generalized Information Criterion.
Zhang, Yiyun; Li, Runze; Tsai, Chih-Ling
2010-03-01
We apply the nonconcave penalized likelihood approach to obtain variable selections as well as shrinkage estimators. This approach relies heavily on the choice of regularization parameter, which controls the model complexity. In this paper, we propose employing the generalized information criterion (GIC), encompassing the commonly used Akaike information criterion (AIC) and Bayesian information criterion (BIC), for selecting the regularization parameter. Our proposal makes a connection between the classical variable selection criteria and the regularization parameter selections for the nonconcave penalized likelihood approaches. We show that the BIC-type selector enables identification of the true model consistently, and the resulting estimator possesses the oracle property in the terminology of Fan and Li (2001). In contrast, however, the AIC-type selector tends to overfit with positive probability. We further show that the AIC-type selector is asymptotically loss efficient, while the BIC-type selector is not. Our simulation results confirm these theoretical findings, and an empirical example is presented. Some technical proofs are given in the online supplementary material.
Yildiz, Cemil; ABBAS, Fadhil
2011-01-01
The concepts of fuzzy regular-I-closed set and fuzzy semi-I-regular set in fuzzy ideal topological spaces are investigated and some of their properties are obtained. Key words: Topological, Spaces, Fuzzy, Regular, Sets
Convergence and fluctuations of Regularized Tyler estimators
Kammoun, Abla
2015-10-26
This article studies the behavior of regularized Tyler estimators (RTEs) of scatter matrices. The key advantages of these estimators are twofold. First, they guarantee by construction a good conditioning of the estimate and second, being a derivative of robust Tyler estimators, they inherit their robustness properties, notably their resilience to the presence of outliers. Nevertheless, one major problem that poses the use of RTEs in practice is represented by the question of setting the regularization parameter p. While a high value of p is likely to push all the eigenvalues away from zero, it comes at the cost of a larger bias with respect to the population covariance matrix. A deep understanding of the statistics of RTEs is essential to come up with appropriate choices for the regularization parameter. This is not an easy task and might be out of reach, unless one considers asymptotic regimes wherein the number of observations n and/or their size N increase together. First asymptotic results have recently been obtained under the assumption that N and n are large and commensurable. Interestingly, no results concerning the regime of n going to infinity with N fixed exist, even though the investigation of this assumption has usually predated the analysis of the most difficult N and n large case. This motivates our work. In particular, we prove in the present paper that the RTEs converge to a deterministic matrix when n → ∞ with N fixed, which is expressed as a function of the theoretical covariance matrix. We also derive the fluctuations of the RTEs around this deterministic matrix and establish that these fluctuations converge in distribution to a multivariate Gaussian distribution with zero mean and a covariance depending on the population covariance and the parameter.
Regular physical exercise: way to healthy life.
Siddiqui, N I; Nessa, A; Hossain, M A
2010-01-01
Any bodily activity or movement that enhances and maintains overall health and physical fitness is called physical exercise. Habit of regular physical exercise has got numerous benefits. Exercise is of various types such as aerobic exercise, anaerobic exercise and flexibility exercise. Aerobic exercise moves the large muscle groups with alternate contraction and relaxation, forces to deep breath, heart to pump more blood with adequate tissue oxygenation. It is also called cardiovascular exercise. Examples of aerobic exercise are walking, running, jogging, swimming etc. In anaerobic exercise, there is forceful contraction of muscle with stretching, usually mechanically aided and help to build up muscle strength and muscle bulk. Examples are weight lifting, pulling, pushing, sprinting etc. Flexibility exercise is one type of stretching exercise to improve the movements of muscles, joints and ligaments. Walking is a good example of aerobic exercise, easy to perform, safe, effective, does not require any training or equipment and less chance of injury. Regular 30 minutes brisk walking in the morning with 150 minutes per week is a good exercise. Regular exercise improves the cardiovascular status, reduces the risk of cardiac disease, high blood pressure and cerebrovascular disease. It reduces body weight, improves insulin sensitivity, helps in glycemic control, prevents obesity and diabetes mellitus. It is helpful for relieving anxiety, stress, brings a sense of well being and overall physical fitness. Global trend is mechanization, labor savings and leading to epidemic of long term chronic diseases like diabetes mellitus, cardiovascular diseases etc. All efforts should be made to create public awareness promoting physical activity, physically demanding recreational pursuits and providing adequate facilities.
Invariant Regularization of Supersymmetric Chiral Gauge Theory
Suzuki, H
1999-01-01
We present a regularization scheme which respects the supersymmetry and the maximal background gauge covariance in supersymmetric chiral gauge theories. When the anomaly cancellation condition is satisfied, the effective action in the superfield background field method automatically restores the gauge invariance without counterterms. The scheme also provides a background gauge covariant definition of composite operators that is especially useful in analyzing anomalies. We present several applications: The minimal consistent gauge anomaly; the super-chiral anomaly and the superconformal anomaly; as the corresponding anomalous commutators, the Konishi anomaly and an anomalous supersymmetric transformation law of the supercurrent (the ``central extension'' of N=1 supersymmetry algebra) and of the R-current.
Total-variation regularization with bound constraints
Chartrand, Rick [Los Alamos National Laboratory; Wohlberg, Brendt [Los Alamos National Laboratory
2009-01-01
We present a new algorithm for bound-constrained total-variation (TV) regularization that in comparison with its predecessors is simple, fast, and flexible. We use a splitting approach to decouple TV minimization from enforcing the constraints. Consequently, existing TV solvers can be employed with minimal alteration. This also makes the approach straightforward to generalize to any situation where TV can be applied. We consider deblurring of images with Gaussian or salt-and-pepper noise, as well as Abel inversion of radiographs with Poisson noise. We incorporate previous iterative reweighting algorithms to solve the TV portion.
Regularizing mappings of Lévy measures
Barndorff-Nielsen, Ole Eiler; Thorbjørnsen, Steen
2006-01-01
In this paper we introduce and study a regularizing one-to-one mapping from the class of one-dimensional Lévy measures into itself. This mapping appeared implicitly in our previous paper [O.E. Barndorff-Nielsen, S. Thorbjørnsen, A connection between free and classical infinite divisibility, Inf....... Dim. Anal. Quant. Probab. 7 (2004) 573–590], where we introduced a one-to-one mapping from the class of one-dimensional infinitely divisible probability measures into itself. Based on the investigation of in the present paper, we deduce further properties of . In particular it is proved that maps...
Multichannel image regularization using anisotropic geodesic filtering
Grazzini, Jacopo A [Los Alamos National Laboratory
2010-01-01
This paper extends a recent image-dependent regularization approach introduced in aiming at edge-preserving smoothing. For that purpose, geodesic distances equipped with a Riemannian metric need to be estimated in local neighbourhoods. By deriving an appropriate metric from the gradient structure tensor, the associated geodesic paths are constrained to follow salient features in images. Following, we design a generalized anisotropic geodesic filter; incorporating not only a measure of the edge strength, like in the original method, but also further directional information about the image structures. The proposed filter is particularly efficient at smoothing heterogeneous areas while preserving relevant structures in multichannel images.
Homology of powers of regular ideals
2003-01-01
For a commutative ring R with an ideal I, generated by a finite regular sequence, we construct differential graded algebras which provide R-free resolutions of I^s and of R/I^s for s>0 and which generalise the Koszul resolution. We derive these from a certain multiplicative double complex. By means of a Cartan-Eilenberg spectral sequence we express Tor_*^R(R/I,R/I^s) and Tor_*^R(R/I, I^s) in terms of exact sequences and find that they are free as R/I-modules. Except for R/I, their product str...
The regular state in higher order gravity
Cotsakis, Spiros; Kadry, Seifedine; Trachilis, Dimitrios
2016-08-01
We consider the higher-order gravity theory derived from the quadratic Lagrangian R + 𝜖R2 in vacuum as a first-order (ADM-type) system with constraints, and build time developments of solutions of an initial value formulation of the theory. We show that all such solutions, if analytic, contain the right number of free functions to qualify as general solutions of the theory. We further show that any regular analytic solution which satisfies the constraints and the evolution equations can be given in the form of an asymptotic formal power series expansion.
Regular collision of dilatonic inflating branes
Leeper, E; Maartens, R
2005-01-01
We demonstrate that a two brane system with a bulk scalar field driving power-law inflation on the branes has an instability in the radion. We solve for the resulting trajectory of the brane, and find that the instability can lead to collision. Brane quantities such as the scale factor are shown to be regular at this collision. In addition we describe the system using a low energy expansion. The low energy expansion accurately reproduces the known exact solution, but also identifies an alternative solution for the bulk metric and brane trajectory.
Limit cycle walking on a regularized ground
Jacobs, Henry O
2012-01-01
The singular nature of contact problems, such as walking, makes them difficult to analyze mathematically. In this paper we will "regularize" the contact problem of walking by approximating the ground with a smooth repulsive potential energy and a smooth dissipative friction force. Using this model we are able to prove the existence of a limit cycle for a periodically perturbed system which consists of three masses connected by springs. In particular, this limit cycle exists in a symmetry reduced phase. In the unreduced phase space, the motion of the masses resembles walking.
Two-pass greedy regular expression parsing
Grathwohl, Niels Bjørn Bugge; Henglein, Fritz; Nielsen, Lasse;
2013-01-01
We present new algorithms for producing greedy parses for regular expressions (REs) in a semi-streaming fashion. Our lean-log algorithm executes in time O(mn) for REs of size m and input strings of size n and outputs a compact bit-coded parse tree representation. It improves on previous algorithms......-based prototype indicates that the superior performance of our lean-log algorithm can also be observed in practice; it is also surprisingly competitive with RE tools not performing full parsing, such as Grep....
Accretion onto some well-known regular black holes
Jawad, Abdul; Shahzad, M.U. [COMSATS Institute of Information Technology, Department of Mathematics, Lahore (Pakistan)
2016-03-15
In this work, we discuss the accretion onto static spherically symmetric regular black holes for specific choices of the equation of state parameter. The underlying regular black holes are charged regular black holes using the Fermi-Dirac distribution, logistic distribution, nonlinear electrodynamics, respectively, and Kehagias-Sftesos asymptotically flat regular black holes. We obtain the critical radius, critical speed, and squared sound speed during the accretion process near the regular black holes. We also study the behavior of radial velocity, energy density, and the rate of change of the mass for each of the regular black holes. (orig.)
Accretion onto Some Well-Known Regular Black Holes
Jawad, Abdul
2016-01-01
In this work, we discuss the accretion onto static spherical symmetric regular black holes for specific choices of equation of state parameter. The underlying regular black holes are charged regular black hole using Fermi-Dirac Distribution, logistic distribution, nonlinear electrodynamics, respectively and Kehagias-Sftesos asymptotically flat regular black hole. We obtain the critical radius, critical speed and squared sound speed during the accretion process near the regular black holes. We also study the behavior of radial velocity, energy density and rate of change of mass for each regular black holes.
Multiple graph regularized nonnegative matrix factorization
Wang, Jim Jing-Yan
2013-10-01
Non-negative matrix factorization (NMF) has been widely used as a data representation method based on components. To overcome the disadvantage of NMF in failing to consider the manifold structure of a data set, graph regularized NMF (GrNMF) has been proposed by Cai et al. by constructing an affinity graph and searching for a matrix factorization that respects graph structure. Selecting a graph model and its corresponding parameters is critical for this strategy. This process is usually carried out by cross-validation or discrete grid search, which are time consuming and prone to overfitting. In this paper, we propose a GrNMF, called MultiGrNMF, in which the intrinsic manifold is approximated by a linear combination of several graphs with different models and parameters inspired by ensemble manifold regularization. Factorization metrics and linear combination coefficients of graphs are determined simultaneously within a unified object function. They are alternately optimized in an iterative algorithm, thus resulting in a novel data representation algorithm. Extensive experiments on a protein subcellular localization task and an Alzheimer\\'s disease diagnosis task demonstrate the effectiveness of the proposed algorithm. © 2013 Elsevier Ltd. All rights reserved.
Regularized Semiparametric Estimation for Ordinary Differential Equations.
Li, Yun; Zhu, Ji; Wang, Naisyin
2015-07-01
Ordinary differential equations (ODEs) are widely used in modeling dynamic systems and have ample applications in the fields of physics, engineering, economics and biological sciences. The ODE parameters often possess physiological meanings and can help scientists gain better understanding of the system. One key interest is thus to well estimate these parameters. Ideally, constant parameters are preferred due to their easy interpretation. In reality, however, constant parameters can be too restrictive such that even after incorporating error terms, there could still be unknown sources of disturbance that lead to poor agreement between observed data and the estimated ODE system. In this paper, we address this issue and accommodate short-term interferences by allowing parameters to vary with time. We propose a new regularized estimation procedure on the time-varying parameters of an ODE system so that these parameters could change with time during transitions but remain constants within stable stages. We found, through simulation studies, that the proposed method performs well and tends to have less variation in comparison to the non-regularized approach. On the theoretical front, we derive finite-sample estimation error bounds for the proposed method. Applications of the proposed method to modeling the hare-lynx relationship and the measles incidence dynamic in Ontario, Canada lead to satisfactory and meaningful results.
Tomographic laser absorption spectroscopy using Tikhonov regularization.
Guha, Avishek; Schoegl, Ingmar
2014-12-01
The application of tunable diode laser absorption spectroscopy (TDLAS) to flames with nonhomogeneous temperature and concentration fields is an area where only few studies exist. Experimental work explores the performance of tomographic reconstructions of species concentration and temperature profiles from wavelength-modulated TDLAS measurements within the plume of an axisymmetric McKenna burner. Water vapor transitions at 1391.67 and 1442.67 nm are probed using calibration-free wavelength modulation spectroscopy with second harmonic detection (WMS-2f). A single collimated laser beam is swept parallel to the burner surface, where scans yield pairs of line-of-sight (LOS) data at multiple radial locations. Radial profiles of absorption data are reconstructed using Tikhonov regularized Abel inversion, which suppresses the amplification of experimental noise that is typically observed for reconstructions with high spatial resolution. Based on spectral data reconstructions, temperatures and mole fractions are calculated point-by-point. Here, a least-squares approach addresses difficulties due to modulation depths that cannot be universally optimized due to a nonuniform domain. Experimental results show successful reconstructions of temperature and mole fraction profiles based on two-transition, nonoptimally modulated WMS-2f and Tikhonov regularized Abel inversion, and thus validate the technique as a viable diagnostic tool for flame measurements.
Regularized multiple criteria linear programs for classification
SHI Yong; TIAN YingJie; CHEN XiaoJun; ZHANG Peng
2009-01-01
Although multiple criteria mathematical program (MCMP), as an alternative method of classification, has been used in various real-life data mining problems, its mathematical structure of solvability is still challengeable. This paper proposes a regularized multiple criteria linear program (RMCLP) for two classes of classification problems. It first adds some regularization terms in the objective function of the known multiple criteria linear program (MCLP) model for possible existence of solution. Then the paper describes the mathematical framework of the solvability. Finally, a series of experimental tests are conducted to illustrate the performance of the proposed RMCLP with the existing methods: MCLP, multiple criteria quadratic program (MCQP), and support vector machine (SVM). The results of four publicly available datasets and a real-life credit dataset all show that RMCLP is a competitive method in classification. Furthermore, this paper explores an ordinal RMCLP (ORMCLP) model for ordinal multi-group problems. Comparing ORMCLP with traditional methods such as One-Against-One, One-Against-The rest on large-scale credit card dataset, experimental results show that both ORMCLP and RMCLP perform well.
Supporting Regularized Logistic Regression Privately and Efficiently.
Wenfa Li
Full Text Available As one of the most popular statistical and machine learning models, logistic regression with regularization has found wide adoption in biomedicine, social sciences, information technology, and so on. These domains often involve data of human subjects that are contingent upon strict privacy regulations. Concerns over data privacy make it increasingly difficult to coordinate and conduct large-scale collaborative studies, which typically rely on cross-institution data sharing and joint analysis. Our work here focuses on safeguarding regularized logistic regression, a widely-used statistical model while at the same time has not been investigated from a data security and privacy perspective. We consider a common use scenario of multi-institution collaborative studies, such as in the form of research consortia or networks as widely seen in genetics, epidemiology, social sciences, etc. To make our privacy-enhancing solution practical, we demonstrate a non-conventional and computationally efficient method leveraging distributing computing and strong cryptography to provide comprehensive protection over individual-level and summary data. Extensive empirical evaluations on several studies validate the privacy guarantee, efficiency and scalability of our proposal. We also discuss the practical implications of our solution for large-scale studies and applications from various disciplines, including genetic and biomedical studies, smart grid, network analysis, etc.
Supporting Regularized Logistic Regression Privately and Efficiently.
Li, Wenfa; Liu, Hongzhe; Yang, Peng; Xie, Wei
2016-01-01
As one of the most popular statistical and machine learning models, logistic regression with regularization has found wide adoption in biomedicine, social sciences, information technology, and so on. These domains often involve data of human subjects that are contingent upon strict privacy regulations. Concerns over data privacy make it increasingly difficult to coordinate and conduct large-scale collaborative studies, which typically rely on cross-institution data sharing and joint analysis. Our work here focuses on safeguarding regularized logistic regression, a widely-used statistical model while at the same time has not been investigated from a data security and privacy perspective. We consider a common use scenario of multi-institution collaborative studies, such as in the form of research consortia or networks as widely seen in genetics, epidemiology, social sciences, etc. To make our privacy-enhancing solution practical, we demonstrate a non-conventional and computationally efficient method leveraging distributing computing and strong cryptography to provide comprehensive protection over individual-level and summary data. Extensive empirical evaluations on several studies validate the privacy guarantee, efficiency and scalability of our proposal. We also discuss the practical implications of our solution for large-scale studies and applications from various disciplines, including genetic and biomedical studies, smart grid, network analysis, etc.
Supporting Regularized Logistic Regression Privately and Efficiently
Li, Wenfa; Liu, Hongzhe; Yang, Peng; Xie, Wei
2016-01-01
As one of the most popular statistical and machine learning models, logistic regression with regularization has found wide adoption in biomedicine, social sciences, information technology, and so on. These domains often involve data of human subjects that are contingent upon strict privacy regulations. Concerns over data privacy make it increasingly difficult to coordinate and conduct large-scale collaborative studies, which typically rely on cross-institution data sharing and joint analysis. Our work here focuses on safeguarding regularized logistic regression, a widely-used statistical model while at the same time has not been investigated from a data security and privacy perspective. We consider a common use scenario of multi-institution collaborative studies, such as in the form of research consortia or networks as widely seen in genetics, epidemiology, social sciences, etc. To make our privacy-enhancing solution practical, we demonstrate a non-conventional and computationally efficient method leveraging distributing computing and strong cryptography to provide comprehensive protection over individual-level and summary data. Extensive empirical evaluations on several studies validate the privacy guarantee, efficiency and scalability of our proposal. We also discuss the practical implications of our solution for large-scale studies and applications from various disciplines, including genetic and biomedical studies, smart grid, network analysis, etc. PMID:27271738
Xiangyu, Fan; Yanping, Lin; Guojian, Liao; Jianping, Xie
2015-12-01
Zinc finger nuclease, transcription activator-like effector nuclease, and clustered regularly interspaced short palindromic repeats/Cas9 nuclease are important targeted genome editing technologies. They have great significance in scientific research and applications on aspects of functional genomics research, species improvement, disease prevention and gene therapy. There are past or ongoing disputes over ownership of the intellectual property behind every technology. In this review, we summarize the patents on these three targeted genome editing technologies in order to provide some reference for developing genome editing technologies with self-owned intellectual property rights and some implications for current innovation and entrepreneurship education in universities.
CRISPR-Cas9: a promising tool for gene editing on induced pluripotent stem cells.
Kim, Eun Ji; Kang, Ki Ho; Ju, Ji Hyeon
2017-01-01
Recent advances in genome editing with programmable nucleases have opened up new avenues for multiple applications, from basic research to clinical therapy. The ease of use of the technology-and particularly clustered regularly interspaced short palindromic repeats (CRISPR)-will allow us to improve our understanding of genomic variation in disease processes via cellular and animal models. Here, we highlight the progress made in correcting gene mutations in monogenic hereditary disorders and discuss various CRISPR-associated applications, such as cancer research, synthetic biology, and gene therapy using induced pluripotent stem cells. The challenges, ethical issues, and future prospects of CRISPR-based systems for human research are also discussed.
CRISPR/Cas9 technology for targeted genome editing
Lomov N. A.
2015-08-01
Full Text Available CRISPRs (Clustered Regularly Interspaced Short Palindromic Repeats are the segments of prokaryotic DNA containing short repeats in its nucleotide sequence. Today we know that this is a bacterial protection system against viral DNA. The molecular components of CRISPR/Cas9 system have been used for a gene editing in eukaryotes since 2013. But as any other method it also has the limitations and drawbacks. Here we are going to review the history of CRISPR biology and to discuss the possibilities that this new technology provides to researchers as well as the prospects for its use in the medical research and treatment.
Bakondi, Benjamin; Lv, Wenjian; Lu, Bin; Jones, Melissa K; Tsai, Yuchun; Kim, Kevin J; Levy, Rachelle; Akhtar, Aslam Abbasi; Breunig, Joshua J; Svendsen, Clive N; Wang, Shaomei
2016-03-01
Reliable genome editing via Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/Cas9 may provide a means to correct inherited diseases in patients. As proof of principle, we show that CRISPR/Cas9 can be used in vivo to selectively ablate the rhodopsin gene carrying the dominant S334ter mutation (Rho(S334)) in rats that model severe autosomal dominant retinitis pigmentosa. A single subretinal injection of guide RNA/Cas9 plasmid in combination with electroporation generated allele-specific disruption of Rho(S334), which prevented retinal degeneration and improved visual function.
Harnessing type I and type III CRISPR-Cas systems for genome editing
Li, Yingjun; Pan, Saifu; Zhang, Yan
2016-01-01
report on harnessing a Type I or Type III system for genome editing. Here, a method was developed to repurpose both CRISPR-Cas systems for genetic manipulation in Sulfolobus islandicus, a thermophilic archaeon. A novel type of genome-editing plasmid (pGE) was constructed, carrying an artificial mini......CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems are widespread in archaea and bacteria, and research on their molecular mechanisms has led to the development of genome-editing techniques based on a few Type II systems. However, there has not been any...
CRISPR adaptation in Escherichia coli subtypeI-E system.
Kiro, Ruth; Goren, Moran G; Yosef, Ido; Qimron, Udi
2013-12-01
The CRISPRs (clustered regularly interspaced short palindromic repeats) and their associated Cas (CRISPR-associated) proteins are a prokaryotic adaptive defence system against foreign nucleic acids. The CRISPR array comprises short repeats flanking short segments, called 'spacers', which are derived from foreign nucleic acids. The process of spacer insertion into the CRISPR array is termed 'adaptation'. Adaptation allows the system to rapidly evolve against emerging threats. In the present article, we review the most recent studies on the adaptation process, and focus primarily on the subtype I-E CRISPR-Cas system of Escherichia coli.
The Power of CRISPR-Cas9-Induced Genome Editing to Speed Up Plant Breeding
Hieu X. Cao
2016-01-01
Full Text Available Genome editing with engineered nucleases enabling site-directed sequence modifications bears a great potential for advanced plant breeding and crop protection. Remarkably, the RNA-guided endonuclease technology (RGEN based on the clustered regularly interspaced short palindromic repeats (CRISPR and CRISPR-associated protein 9 (Cas9 is an extremely powerful and easy tool that revolutionizes both basic research and plant breeding. Here, we review the major technical advances and recent applications of the CRISPR-Cas9 system for manipulation of model and crop plant genomes. We also discuss the future prospects of this technology in molecular plant breeding.
CRISPR-Cas: Revolutionising genome engineering.
Nicholson, Samantha Anne; Pepper, Michael Sean
2016-08-01
The ability to permanently alter or repair the human genome has been the subject of a number of science fiction films, but with the recent advent of several customisable sequence-specific endonuclease technologies, genome engineering looks set to become a clinical reality in the near future. This article discusses recent advancements in the technology called 'clustered regularly interspaced palindromic repeat (CRISPR)-associated genes' (CRISPR-Cas), the potential of CRISPR-Cas to revolutionise molecular medicine, and the ethical and regulatory hurdles facing its application.
The Power of CRISPR-Cas9-Induced Genome Editing to Speed Up Plant Breeding
Wang, Wenqin; Le, Hien T. T.
2016-01-01
Genome editing with engineered nucleases enabling site-directed sequence modifications bears a great potential for advanced plant breeding and crop protection. Remarkably, the RNA-guided endonuclease technology (RGEN) based on the clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated protein 9 (Cas9) is an extremely powerful and easy tool that revolutionizes both basic research and plant breeding. Here, we review the major technical advances and recent applications of the CRISPR-Cas9 system for manipulation of model and crop plant genomes. We also discuss the future prospects of this technology in molecular plant breeding. PMID:28097123
Duda, Katarzyna; Lonowski, Lindsey A; Kofoed-Nielsen, Michael
2014-01-01
Targeted endonucleases including zinc finger nucleases (ZFNs) and clustered regularly interspaced short palindromic repeats (CRISPRs)/Cas9 are increasingly being used for genome editing in higher species. We therefore devised a broadly applicable and versatile method for increasing editing...... were minimal, and when occurring, our data suggest that they may be counteracted by selecting intermediate nuclease levels where off-target mutagenesis is low, but on-target mutagenesis remains relatively high. The method was also applicable to the CRISPR/Cas9 system, including CRISPR/Cas9 mutant...
Archaeal CRISPR-based immune systems
Garrett, Roger A; Vestergaard, Gisle Alberg; Shah, Shiraz Ali
2011-01-01
CRISPR (clustered regularly interspaced short palindromic repeats)-based immune systems are essentially modular with three primary functions: the excision and integration of new spacers, the processing of CRISPR transcripts to yield mature CRISPR RNAs (crRNAs), and the targeting and cleavage...... of foreign nucleic acid. The primary target appears to be the DNA of foreign genetic elements, but the CRISPR/Cmr system that is widespread amongst archaea also specifically targets and cleaves RNA in vitro. The archaeal CRISPR systems tend to be both diverse and complex. Here we examine evidence...... of CRISPR loci and the evidence for intergenomic exchange of CRISPR systems....
Gene regulation by engineered CRISPR-Cas systems.
Fineran, Peter C; Dy, Ron L
2014-04-01
The clustered regularly interspaced short palindromic repeat (CRISPR) arrays and their CRISPR associated (Cas) proteins constitute adaptive immune systems in bacteria and archaea that provide protection from bacteriophages, plasmids and other mobile genetic elements (MGEs). Recently, the ability to direct these systems to DNA in a sequence-specific manner has led to the emergence of new technologies for engineered gene regulation in bacteria and eukaryotes. These systems have the potential to enable facile high-throughput functional genomics studies aimed at identifying gene function and will be a crucial tool for synthetic biology. Here, we review the recent engineering of these systems for controlling gene expression.
Kim, Jin-Soo
2016-09-01
Genome editing harnesses programmable nucleases to cut and paste genetic information in a targeted manner in living cells and organisms. Here, I review the development of programmable nucleases, including zinc finger nucleases (ZFNs), TAL (transcription-activator-like) effector nucleases (TALENs) and CRISPR (cluster of regularly interspaced palindromic repeats)-Cas9 (CRISPR-associated protein 9) RNA-guided endonucleases (RGENs). I specifically highlight the key advances that set the foundation for the rapid and widespread implementation of CRISPR-Cas9 genome editing approaches that has revolutionized the field.
HEK293T Cells Are Heterozygous for CCR5 Delta 32 Mutation
2016-01-01
C-C chemokine receptor 5 (CCR5) is a receptor for chemokines and a co-receptor for HIV-1 entry into the target CD4+ cells. CCR5 delta 32 deletion is a loss-of-function mutation, resistant to HIV-1 infection. We tried to induce the CCR5 delta 32 mutation harnessing the genome editing technique, CRISPR-Cas9 (Clustered Regularly Interspaced Short Palindromic Repeats, CRISPR and CRISPR associated protein 9, Cas9) in the commonly used cell line human embryonic kidney HEK 293T cells. Surprisingly, ...
Using engineered endonucleases to create knockout and knockin zebrafish models.
Bedell, Victoria M; Ekker, Stephen C
2015-01-01
Over the last few years, the technology to create targeted knockout and knockin zebrafish animals has exploded. We have gained the ability to create targeted knockouts through the use of zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeats/CRISPR associated system (CRISPR/Cas). Furthermore, using the high-efficiency TALEN system, we were able to create knockin zebrafish using a single-stranded DNA (ssDNA) protocol described here. Through the use of these technologies, the zebrafish has become a valuable vertebrate model and an excellent bridge between the invertebrate and mammalian model systems for the study of human disease.
Lin, Lin; Petersen, Trine Skov; Jensen, Kristopher Torp
2017-01-01
Mammalian cells repair double-strand DNA breaks (DSB) by a range of different pathways following DSB induction by the engineered clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein Cas9. While CRISPR-Cas9 thus enables predesigned modifications of the genome......, applications of CRISPR-Cas9-mediated genome-editing are frequently hampered by the unpredictable and varying pathways for DSB repair in mammalian cells. Here we present a strategy of fusing Cas9 to recombinant proteins for fine-tuning of the DSB repair preferences in mammalian cells. By fusing Streptococcus...
Applications of CRISPR-Cas9 mediated genome engineering
Xiao Yang
2015-01-01
Targeted mutagenesis based on homologous recombination has been a powerful tool for understanding the mechanisms underlying development, normal physiology, and disease. A recent breakthrough in genome engineering technology based on the class of RNA-guided endonucleases, such as clustered regularly interspaced short palindromic repeats (CRISPR)-associated Cas9, is further revolutionizing biology and medical studies. The simplicity of the CRISPR-Cas9 system has enabled its widespread applications in generating germline animal models, somatic genome engineering, and functional genomic screening and in treating genetic and infectious diseases. This technology will likely be used in all fields of biomedicine, ranging from basic research to human gene therapy.
Duda, Katarzyna; Lonowski, Lindsey A; Kofoed-Nielsen, Michael
2014-01-01
Targeted endonucleases including zinc finger nucleases (ZFNs) and clustered regularly interspaced short palindromic repeats (CRISPRs)/Cas9 are increasingly being used for genome editing in higher species. We therefore devised a broadly applicable and versatile method for increasing editing...... were minimal, and when occurring, our data suggest that they may be counteracted by selecting intermediate nuclease levels where off-target mutagenesis is low, but on-target mutagenesis remains relatively high. The method was also applicable to the CRISPR/Cas9 system, including CRISPR/Cas9 mutant...
CRISPR-Cas系统在生物学研究中的应用%Application of CRISPR-Cas System in Biology Research
康峰; 卢胜明; 张海峰
2014-01-01
成簇的规律间隔的短回文重复序列(clustered regularly interspaced short palindromic repeats,简称为CRISPR)系统是一种新的基因修饰技术,具有制作周期短、成本低和作用高效等优点.本文从结构、研究历史、分类和分布、作用机制和其在生物学研究中的应用等方面介绍CRISPR-Cas系统.
Augmenting CRISPR applications in Drosophila with tRNA-flanked sgRNAs.
Port, Fillip; Bullock, Simon L
2016-10-01
We present tRNA-based vectors for producing multiple clustered regularly interspaced short palindromic repeats (CRISPR) single guide RNAs (sgRNAs) from a single RNA polymerase II or III transcript in Drosophila. The system, which is based on liberation of sgRNAs by processing flanking tRNAs, permits highly efficient multiplexing of Cas9-based mutagenesis. We also demonstrate that the tRNA-sgRNA system markedly increases the efficacy of conditional gene disruption by Cas9 and can promote editing by the recently discovered RNA-guided endonuclease Cpf1.
Expanding the Biologist's Toolkit with CRISPR-Cas9.
Sternberg, Samuel H; Doudna, Jennifer A
2015-05-21
Few discoveries transform a discipline overnight, but biologists today can manipulate cells in ways never possible before, thanks to a peculiar form of prokaryotic adaptive immunity mediated by clustered regularly interspaced short palindromic repeats (CRISPR). From elegant studies that deciphered how these immune systems function in bacteria, researchers quickly uncovered the technological potential of Cas9, an RNA-guided DNA cleaving enzyme, for genome engineering. Here we highlight the recent explosion in visionary applications of CRISPR-Cas9 that promises to usher in a new era of biological understanding and control.
Applications of CRISPR-Cas systems in neuroscience.
Heidenreich, Matthias; Zhang, Feng
2016-01-01
Genome-editing tools, and in particular those based on CRISPR-Cas (clustered regularly interspaced short palindromic repeat (CRISPR)-CRISPR-associated protein) systems, are accelerating the pace of biological research and enabling targeted genetic interrogation in almost any organism and cell type. These tools have opened the door to the development of new model systems for studying the complexity of the nervous system, including animal models and stem cell-derived in vitro models. Precise and efficient gene editing using CRISPR-Cas systems has the potential to advance both basic and translational neuroscience research.
Utilization of TALEN and CRISPR/Cas9 technologies for gene targeting and modification.
Pu, Jiali; Frescas, David; Zhang, Baorong; Feng, Jian
2015-08-01
The capability to modify the genome precisely and efficiently offers an extremely useful tool for biomedical research. Recent developments in genome editing technologies such as transcription activator-like effector nuclease and the clustered regularly interspaced short palindromic repeats system have made genome modification available for a number of organisms with relative ease. Here, we introduce these genome editing techniques, compare and contrast each technical approach and discuss their potential to study the underlying mechanisms of human disease using patient-derived induced pluripotent stem cells.
D'Andrea, Marco Maria; Giani, Tommaso; Henrici De Angelis, Lucia; Ciacci, Nagaia; Gniadkowski, Marek; Miriagou, Vivi; Torricelli, Francesca; Rossolini, Gian Maria
2016-02-11
Proteus mirabilis NO-051/03, representative of a multidrug-resistant clone expressing the CMY-16 AmpC-type β-lactamase and circulating in Europe since 2003, was sequenced by a MiSeq platform using a paired-end approach. The genome was assembled in 100 scaffolds with a total length of 4,197,318 bp. Analysis of the draft genome sequence revealed the presence of several acquired resistance determinants to β-lactams, aminoglycosides, phenicols, tetracyclines, trimethoprim, and sulfonamides, of one plasmid replicon, and of a type I-E clustered regularly interspaced short palindromic repeat (CRISPR)-associated protein (Cas) adaptive immune system.
Harnessing type I and type III CRISPR-Cas systems for genome editing
Li, Yingjun; Pan, Saifu; Zhang, Yan;
2016-01-01
CRISPR-Cas (clustered regularly interspaced short palindromic repeats-CRISPR-associated) systems are widespread in archaea and bacteria, and research on their molecular mechanisms has led to the development of genome-editing techniques based on a few Type II systems. However, there has not been any...... report on harnessing a Type I or Type III system for genome editing. Here, a method was developed to repurpose both CRISPR-Cas systems for genetic manipulation in Sulfolobus islandicus, a thermophilic archaeon. A novel type of genome-editing plasmid (pGE) was constructed, carrying an artificial mini...
DNA-free genome editing methods for targeted crop improvement.
Kanchiswamy, Chidananda Nagamangala
2016-07-01
Evolution of the next-generation clustered, regularly interspaced, short palindromic repeat/Cas9 (CRISPR/Cas9) genome editing tools, ribonucleoprotein (RNA)-guided endonuclease (RGEN) RNPs, is paving the way for developing DNA-free genetically edited crop plants. In this review, I discuss the various methods of RGEN RNPs tool delivery into plant cells and their limitations to adopt this technology to numerous crop plants. Furthermore, focus is given on the importance of developing DNA-free genome edited crop plants, including perennial crop plants. The possible regulation on the DNA-free, next-generation genome-edited crop plants is also highlighted.
CRISPR/Cas9 for plant genome editing: accomplishments, problems and prospects.
Paul, Joseph W; Qi, Yiping
2016-07-01
The increasing burden of the world population on agriculture requires the development of more robust crops. Dissecting the basic biology that underlies plant development and stress responses will inform the design of better crops. One powerful tool for studying plants at the molecular level is the RNA-programmed genome editing system composed of a clustered regularly interspaced short palindromic repeats (CRISPR)-encoded guide RNA and the nuclease Cas9. Here, some of the recent advances in CRISPR/Cas9 technology that have profound implications for improving the study of plant biology are described. These tools are also paving the way towards new horizons for biotechnologies and crop development.
[The application of CRISPR/Cas9 genome editing technology in cancer research].
Wang, Dayong; Ma, Ning; Hui, Yang; Gao, Xu
2016-01-01
The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR-associated protein-9 nuclease) genome editing technology has become more and more popular in gene editing because of its simple design and easy operation. Using the CRISPR/Cas9 system, researchers can perform site-directed genome modification at the base level. Moreover, it has been widely used in genome editing in multiple species and related cancer research. In this review, we summarize the application of the CRISPR/Cas9 system in cancer research based on the latest research progresses as well as our understanding of cancer research and genome editing techniques.
CRISPR-Cas immunity in prokaryotes.
Marraffini, Luciano A
2015-10-01
Prokaryotic organisms are threatened by a large array of viruses and have developed numerous defence strategies. Among these, only clustered, regularly interspaced short palindromic repeat (CRISPR)-Cas systems provide adaptive immunity against foreign elements. Upon viral injection, a small sequence of the viral genome, known as a spacer, is integrated into the CRISPR locus to immunize the host cell. Spacers are transcribed into small RNA guides that direct the cleavage of the viral DNA by Cas nucleases. Immunization through spacer acquisition enables a unique form of evolution whereby a population not only rapidly acquires resistance to its predators but also passes this resistance mechanism vertically to its progeny.
System-level perturbations of cell metabolism using CRISPR/Cas9
Jakočiūnas, Tadas [Technical Univ. of Denmark, Lyngby (Denmark); Jensen, Michael K. [Technical Univ. of Denmark, Lyngby (Denmark); Keasling, Jay D. [Technical Univ. of Denmark, Lyngby (Denmark); Joint BioEnergy Inst. (JBEI), Emeryville, CA (United States); Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States); Univ. of California, Berkeley, CA (United States)
2017-03-30
CRISPR/Cas9 (clustered regularly interspaced palindromic repeats and the associated protein Cas9) techniques have made genome engineering and transcriptional reprogramming studies much more advanced and cost-effective. For metabolic engineering purposes, the CRISPR-based tools have been applied to single and multiplex pathway modifications and transcriptional regulations. The effectiveness of these tools allows researchers to implement genome-wide perturbations, test model-guided genome editing strategies, and perform transcriptional reprogramming perturbations in a more advanced manner than previously possible. In this mini-review we highlight recent studies adopting CRISPR/Cas9 for systems-level perturbations and model-guided metabolic engineering.
SSFinder: High Throughput CRISPR-Cas Target Sites Prediction Tool
Santosh Kumar Upadhyay
2014-01-01
Full Text Available Clustered regularly interspaced short palindromic repeats (CRISPR and CRISPR-associated protein (Cas system facilitates targeted genome editing in organisms. Despite high demand of this system, finding a reliable tool for the determination of specific target sites in large genomic data remained challenging. Here, we report SSFinder, a python script to perform high throughput detection of specific target sites in large nucleotide datasets. The SSFinder is a user-friendly tool, compatible with Windows, Mac OS, and Linux operating systems, and freely available online.
A male-determining factor in the mosquito Aedes aegypti
Hall, Andrew Brantley; Basu, Sanjay; Jiang, Xiaofang; Qi, Yumin; Timoshevskiy, Vladimir A.; Biedler, James K.; Sharakhova, Maria V; Elahi, Rubayet; Michelle A E Anderson; Chen, Xiao-Guang; Sharakhov, Igor V.; Adelman, Zach N.; Tu, Zhijian
2015-01-01
Sex determination in the mosquito Aedes aegypti is governed by a dominant male-determining factor (M factor) located within a Y chromosome–like region called the M locus. Here, we show that an M-locus gene, Nix, functions as an M factor in A. aegypti. Nix exhibits persistent M linkage and early embryonic expression, two characteristics required of an M factor. Nix knockout with clustered regularly interspaced short palindromic repeats (CRISPR)–Cas9 resulted in largely feminized genetic males ...
Engineering Synthetic Gene Circuits in Living Cells with CRISPR Technology.
Jusiak, Barbara; Cleto, Sara; Perez-Piñera, Pablo; Lu, Timothy K
2016-07-01
One of the goals of synthetic biology is to build regulatory circuits that control cell behavior, for both basic research purposes and biomedical applications. The ability to build transcriptional regulatory devices depends on the availability of programmable, sequence-specific, and effective synthetic transcription factors (TFs). The prokaryotic clustered regularly interspaced short palindromic repeat (CRISPR) system, recently harnessed for transcriptional regulation in various heterologous host cells, offers unprecedented ease in designing synthetic TFs. We review how CRISPR can be used to build synthetic gene circuits and discuss recent advances in CRISPR-mediated gene regulation that offer the potential to build increasingly complex, programmable, and efficient gene circuits in the future.
van Wijk, Xander M.; Döhrmann, Simon; Hallstrom, Bjorn
2017-01-01
To understand the role of glycosaminoglycans in bacterial cellular invasion, xylosyltransferase-deficient mutants of Chinese hamster ovary (CHO) cells were created using clustered regularly interspaced short palindromic repeat (CRISPR) and CRISPR-associated gene 9 (CRISPR-cas9) gene targeting. When...... cells. Whole-genome sequencing and transcriptome sequencing (RNA-Seq) uncovered a deletion in the gene encoding the laminin subunit α2 (Lama2) that eliminated much of domain L4a. Silencing of the long Lama2 isoform in wild-type cells strongly reduced bacterial invasion, whereas transfection with human...
2016-01-01
A Pseudorabies virus (PRV) variant has emerged in China since 2011 that is not protected by commercial vaccines, and has not been well studied. The PRV genome is large and difficult to manipulate, but it is feasible to use clustered, regularly interspaced short palindromic repeats (CRISPR)/Cas9 technology. However, identification of single guide RNA (sgRNA) through screening is critical to the CRISPR/Cas9 system, and is traditionally time and labor intensive, and not suitable for rapid and hi...
CRISPR-Cas9-guided Genome Engineering in C. elegans
Kim, Hyun-Min; Colaiácovo, Monica P.
2016-01-01
The CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) system is successfully being used for efficient and targeted genome editing in various organisms including the nematode C. elegans. Recent studies developed various CRISPR-Cas9 approaches to enhance genome engineering via two major DNA double-strand break repair pathways: non-homologous end joining and homologous recombination. Here we describe a protocol for Cas9-mediated C. elegans genome editing together with single guide RNA (sgRNA) and repair template cloning and injection methods required for delivering Cas9, sgRNAs and repair template DNA into the C. elegans germline. PMID:27366893
Application of CRISPR/Cas9 system in virus research
ZHENG Qingfen
2016-01-01
Full Text Available To date, the clustered regularly interspaced short palindromic repeat (CRISPR/Cas9 system has been widely used to edit the genome in many species and cells. The system is the third generation of artificial endonuclease, which can edit DNA by recognizing short DNA sequences. This paper reviews the structural features of the system and its application in virus research, such as the functional studies of virus-related genes and the exploration of antiviral therapies (including HIV, HBV, and EB virus, looking forward to the future direction of virus research.
Control of gene expression by CRISPR-Cas systems
2013-01-01
Clustered regularly interspaced short palindromic repeats (CRISPR) loci and their associated cas (CRISPR-associated) genes provide adaptive immunity against viruses (phages) and other mobile genetic elements in bacteria and archaea. While most of the early work has largely been dominated by examples of CRISPR-Cas systems directing the cleavage of phage or plasmid DNA, recent studies have revealed a more complex landscape where CRISPR-Cas loci might be involved in gene regulation. In this review, we summarize the role of these loci in the regulation of gene expression as well as the recent development of synthetic gene regulation using engineered CRISPR-Cas systems. PMID:24273648