DNA shuffling - Factbites

DNA shuffling - Factbites
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Topic: DNA shuffling

Note: these results are not from the primary (high quality) database.

In the News (Tue 22 Dec 09)

Northern Trust

Marvin Harrison

Peter Chernin

Gary Locke

Match Play

Penelope Cruz

Mickey Rourke

AR Rahman

Danny Boyle

Hugh Jackman

	‘Junk’ DNA: evolutionary discards or God’s tools?
		Recombination between similar DNA strands is a necessary process for repair of DNA breaks and allele* shuffling between homologous chromosomes.
		Junk or ‘selfish’ DNA is believed to be largely parasitic in nature, persisting in the genomes of higher organisms as ‘evolutionary remnants’ by their ability to reproduce and spread themselves, or perhaps because they have supposedly mutated into a function the cell can use.
		The ability of DNA sequences to rearrange and/or to move about in the genome or even between genomes, was originally a heretical idea for both evolutionist and creationist, but now is one that is strongly supported as being an integral part of gene regulation.
	www.answersingenesis.org /tj/v14/i2/junk_dna.asp (8575 words)

	Bio-Tech Info - Foreign and Naked DNA
		On the fate of orally ingested foreign DNA in mice: chromosomal association and placental transmission to the fetus, Abstract, Mol Gen Genet (1998) 259: 569-576
		DNA Immunization of Neonates Induces Immunity Despite the Presence of Maternal Antibody, Journal of Clinical Investigation, 100(9):2371-2375, November 1997
		Chromosomal Insertion of Foreign (Adenovirus Type 12, Plasmid, or Bacteriophage) DNA is Associated with Enhanced Methylation of Cellular DNA Segments, Proceedings of the National Academy of Sciences, 92:5515-5519, 1995.
	www.biotech-info.net /FN_DNA.html (354 words)

	FASTA - Wikipedia, the free encyclopedia
		FASTA, described in 1988 (Improved Programs for Biological Sequence Comparison) added the ability to do DNA:DNA searches, translated protein:DNA searches and provided a more sophisticated shuffling program for evaluating statistical significance.
		The current FASTA package programs for protein:protein, DNA:DNA, protein:translated DNA (with frameshifts), and ordered or unordered peptide searches.
		FASTA is a sequence alignment package first described (as FASTP) by David J. Lipman and William R. Pearson in 1985 in the article Rapid and sensitive protein similarity searches.
	en.wikipedia.org /wiki/FASTA (457 words)

	29055.020411&ELEMENT_SET=DECL
		The nucleotides of the present invention may be subjected to DNA shuffling techniques such as
		Techniques for transferring the DNA of the present invention into such organisms are widely known and provided in references such as Sambrook et al.
		The term "transformed cells"includes stably transformed cells in which the inserted DNA is capable of replication either as an autonomously replicating plasmid or as part of the host chromosome, as well as transiently transformed cells which express the inserted DNA or RNA for limited periods of time.
	www.wipo.int /cgi-pct/guest/getbykey5?KEY=02/29055.020411&ELEMENT_SET=DECL (10765 words)

	BBC News Sci/Tech Researchers unravel 'this mortal coil'
		The coil is a coiled piece of DNA which becomes detached and replicates inside a cell until the cell is overwhelmed and dies.
		Eventually the nucleolus is so stuffed with ERC coils that the cell's ability to replicate DNA breaks down and the cell dies.
		In his famous soliloquy, Hamlet speaks of shuffling off "this mortal coil" in a reference to death.
	news.bbc.co.uk /1/hi/sci/tech/42644.stm (452 words)

	DBLP: Masami Hagiya
		John A. Rose, Mitsunori Takano, Masami Hagiya, Akira Suyama : A DNA Computing-based Genetic Program for In Vitro Protein Evolution via Constrained Pseudomodule Shuffling.
		Akio Nishikawa, Masayuki Yamamura, Masami Hagiya: DNA computation simulator based on abstract bases.
		Masanori Arita, Akio Nishikawa, Masami Hagiya, Ken Komiya, Hidetaka Gouzu, Kensaku Sakamoto : Improving Sequence Design for DNA Computing.
	informatik.uni-trier.de /~ley/db/indices/a-tree/h/Hagiya:Masami.html (452 words)

	MacDevCenter.com: Bioinformatics and Comparative Genomics
		The DNA sequence is the most complete representation of a genome that we have available, and it is the form of the data that we actually compare and align, using the BLAST software tools, for example.
		The complete DNA sequence of the Human Genome is a remarkable achievement for molecular biology and represents the work of many people in a number of large sequencing centers.
		Perhaps more striking than the "shuffling" of blocks between the species are the large blocks of sequence that are common to both, and in particular the complete conservation, at this level of resolution, in the sex chromosomes X and Y. Image credit: U.S. Department of Energy Human Genome Program
	www.macdevcenter.com /pub/a/mac/2004/06/29/bioinformatics.html (452 words)

	Message 0124+1
		Reva, A. Finkelstein, J. Skolnick 11:00 am Break 11:15 am Modeling DNA Shuffling F.
		Koonin, R. Tatusov, M. Galperin, M. Rozanov 11:00 am Break Session 2, Chair: Gene Myers 11:15 am Non-Adjoining Correlations Within Signals in DNA P.
		Sankoff, M. Blanchette 12:05 pm Lunch 1:30 pm Invited Lecture Session Eugene Koonin, Chair Ruben Abagyan Challenges of biomolecular structure prediction 2:30 pm Break Session 5, Chair: Martin Farach 2:40 pm From Four-taxon Trees to Phylogenies: The Case of Mammalian Evolution A.
	www.ccl.net /cca/info/conferencelist/mess0125.html (1127 words)

	Natural selection - Wikipedia, the free encyclopedia
		Such variation is generated by the shuffling of genetic material (crossing over) during meiosis and syngamy, by random alterations of the genetic material like point mutations, insertions, and deletions, and by the insertion and deletion of self-replicating genetic elements like transposons as well as of viruses that integrate their genomes in that of their hosts.
		Modern genetics has characterized several mechanisms that generate heritable genetic differences: Permanent alterations of the genetic material (DNA) can result from errors during DNA replication, or from damage during the transcription of genes and genetic recombination, or be caused by chemicals and physical agents (e.g.
		Natural Selection is the phrase Charles Darwin used in 1859 in his book The Origin of Species to name the natural process he proposed to be responsible for the origin of new species and the adaptation of organisms to their environments.
	en.wikipedia.org /wiki/Natural_selection (3939 words)

	12782.html
		For directed evolution studies, DNA libraries will be generated using established methods (mutagenic PCR, DNA shuffling) followed by colony screening.
		HDHs are, at most, weakly active towards fluoroalkanes and in decontaminating these substrates, an improvement in the enzymatic catalysis of their turnover is essential to further their bioremediation application.
		The second component of the project (as part of a larger research group effort) will apply the methods of protein engineering and directed evolution to an investigation of the structural factors that determine substrate specificity (cap domain of the protein) and efficiency of halide binding/release for the three enzymes.
	www.ucd.ie /ofrss/html/science/chemist/12782.html (3939 words)

	Introns and Exons
		Over evolutionary time the demands of regulation of gene expression would have been imposed upon this primitive arrangement, so that low FORS-D values might be present in regions of DNA where regulatory proteins bind (except, perhaps, where the regulatory proteins recognize DNA palindromes).
		" might have been imposed by mobile genetic elements and recombinations accompanying exon shuffling (Gilbert and Glynias 1993).
		The positions of exon-intron junctions are held to have been determined by the need to form stem loops and are not necessarily related to protein domains (Gilbert and Glynias 1993).
	post.queensu.ca /~forsdyke/introns.htm (8863 words)

	Refereed Journal Publications (Including Books and Book Chapters)
		Suyama, ``A DNA Computing-based Genetic Program for in vitro Protein Evolution via Constrained Pseudomodule Shuffling", invited paper: Journal of Genetic Programming and Evolvable machines 4, 139-152 (2003).
		Rose, M. Hagiya, A. Suyama, ``Whiplash ”½‰ž", in (‰¡�X‹M�C”‹’J�¹ŒÈ, Eds.)�C DNAƒRƒ“ƒsƒ…�ƒ^ �A�i‚Q‚O‚O‚P�A“Œ‹ž�A”•—ŠÙ�j, ‘æ‚S�Í‚Q�ß, translator: Akio Nishikawa, in press.
		Rose and A. Suyama, "Physical modeling of biomolecular computers: Models, limitations, and experimental validation", invited paper: Int'l Journal of Natural Computing 3, pp.
	nicosia.is.s.u-tokyo.ac.jp /~johnrose/Pub1.htm (8863 words)

	Directed evolution of thymidine kinase for AZT phosphorylation using DNA family shuffling.
		The thymidine kinase (TK) genes from herpes simplex virus (HSV) types 1 and 2 were recombined in vitro with a technique called DNA family shuffling.
		Directed evolution of thymidine kinase for AZT phosphorylation using DNA family shuffling.
		Both clones are hybrids derived from several crossover events between the two parental genes and carry several additional amino acid substitutions not found in either parent, including active site mutations.
	www.aegis.com /aidsline/1999/sep/A9990668.html (479 words)

	A second-generation system for unbiased reading frame selection -- Gerth et al. 17 (7): 595 -- Protein Engineering Design and Selection
		(C) The in-frame hybrids are re-amplified and recombined by DNA shuffling, yielding a library of multi-crossover hybrids in which all clones must retain a correct reading frame.
		be eliminated in the course of pre-selection for reading frame.
		Reading frame selection for both GPX libraries was performed
	peds.oxfordjournals.org /cgi/content/full/17/7/595 (4005 words)

	Medigenomix GmbH: Gene Synthesis Services
		Synthetic genes are valuable tools for various types of projects, such as adjusting the codon usage of genes, domain / epitope shuffling experiments, construction of hybrid genes, etc.
		Each synthetic gene is verified by double strand DNA sequencing to ensure 100 % accuracy of gene synthesis.
		The synthetic gene will be cloned in a suitable vector chosen by the customer.
	www.medigenomix.de /en/molbio1E.html (4005 words)

	Novozymes Inc.'s Research and Publications
		J. DNA shuffling of subgenomic sequences of subtilisn.
		Xu, F., Golightly, E.J., Schneider, P., Berka, R.M., Brown, K.M., Johnstone, J.A., Baker, D.H., Fuglsang, C.C., Brown, S.H., and Klotz, A.V. Expression and characterization of a recombinant Fusarium spp.
		Rey, M.W., Brown, K.M., Golightly, E.J., Fuglsang, C., C., Nielson, B.R., Hendricksen, H.V., Butterworth, A., and Xu, F. "Cloning, heterologous expression and characterization of Thielavia terrestris glucoamylase" Appl.
	www.novozymesbiotech.com /publications.htm (2233 words)

	Simultaneous Enhancement of Thermostability and Catalytic Activity of Phospholipase A1 by Evolutionary Molecular Engineering -- Song and Rhee 66 (3): 890 -- Applied and Environmental Microbiology
		Stemmer, W. DNA shuffling by random fragmentation and reassembly: in vitro recombination for molecular evolution.
		Molecular characterization of enterobacterial pldA genes encoding outer membrane phospholipase A. Bacteriol.
		Engineering of a cold-adapted protease by sequential random mutagenesis and a screening system.
	aem.asm.org /cgi/content/full/66/3/890 (3445 words)

	Metabolic Pathway Engineering Team
		Protein engineering of xylose-transporting permeases by DNA shuffling is another approach for improved xylose uptake.
		Xylose metabolism of the overexpression strains was studied in anaerobic batch fermentations (manuscript in preparation).
		Effective and reliable analytical methods for the measurement of intracellular and extracellular metabolites are a fundamental prerequisite of metabolic engineering.
	www.vtt.fi /bel/coe/patheng.htm (3445 words)

	Lecture VI - BMO 520
		Probably genes for large proteins evolved by the accidental juxtaposition of exons coding for specific functions or structural motifs or domains; this process is sometimes referred to as exon shuffling.
		[This structure is prominent in influenza hemagglutinin, the bacterial DNA binding protein CAP (catabolite gene activating protein) and coat proteins of small spherical viruses (picorna, T=3 plant).]
		Several examples of this structure are found among glycolytic enzymes, a classical case being triose phosphate isomerase after which the structure also is called the TIM barrel (show).
	www.sunysb.edu /biochem/courses/lectures/6bmo520.html (3445 words)

	Bacillus thuringiensis, is a gram-positive soil bacterium that forms spores and parasporal crystal during the stationary phase of its growth cycle
		It was found that the sequence space for searching for this method was very less when compared to the sequence space available in DNA family shuffling.
		The first step of this method is to randomly fragment a population of related genes using DNAse I. This produces fragments of various lengths that, after denaturation, hybridize to form an equal mixture of 5' and 3' overhangs.
		The high level of synthesis and coordination with the stationary phase are controlled by a variety of mechanisms occurring at the transcriptional, posttranscriptional and posttranslational levels.
	www.geocities.com /madanm2/dnashuff.htm (3445 words)

	Untitled Document
		Végh, Z., Vincze, É., Kadirov, R., Tóth, G. and Kiss, G. The nucleotide sequence of a nodule specific gene, Nms-25 of Medicago sativa: its primary evolution via exon-shuffling and retrotransposon mediated DNA rearrangements.
		(1987) Nucleotide sequence of a cDNA clone encoding leghemoglobin III (LbIII) from Medicago sativa.
		Kaló, P., Endre, G., Zimányi, L., Csanádi, G., Kiss, G.B. Construction of an improved linkage map of diploid alfalfa (Medicago sativa).
	www.szbk.u-szeged.hu /~alfi/refs.html (3445 words)

	A protozoan undergoes "binary fission" - with some help!
		Sexual reproduction allows for the mixing of DNA among the various strains (asexual daughters) of a local protozoan population.
		Shuffling the deck in this manner produces cells which are genetically different from each other, an important characteristic as genetic make-up determines how cells respond to their environment.
		These images, captured from video using a Snappy video grabber, illustrate the final stages of protozoan asexual reproduction (a process known as "binary fission").
	www.microscopy-uk.org.uk /mag/art98/celldiv.html (3445 words)

	The Scientist :: DNA Detection Without PCR; Sequence-Analysis Beerware; Shuffling the Genome Deck, Mar.24, 2003
		The Scientist :: DNA Detection Without PCR; Sequence-Analysis Beerware; Shuffling the Genome Deck, Mar.24, 2003
		DNA Detection Without PCR; Sequence-Analysis Beerware; Shuffling the Genome Deck
	www.the-scientist.com /yr2003/mar/labcon_030324.html (3445 words)

	Bio-Tech Info - Ecological Risks
		Monitoring field releases of genetically modified sugar beets for persistence of transgenic plant DNA and horizontal gene transfer, FEMS Microbiology Ecology, 28(3):261-272, March 1, 1999.
		Can such rampant unregulated gene shuffling be safe?: New artificial genetic constructs pose even greater threats to health and biodiversity, ISIS News, Issue 4, April 2000.
		Impact of gene flow from cultivated beet on genetic diversity of wild sea beet populations, Detlef Bartsch, Aachen University of Technology RWTH, Germany, November 1999
	www.biotech-info.net /risks.html (2600 words)

	DNA Mutation Rates and Evolution
		Beyond this, it has been generally assumed that mitochondria are always passed on from the mother to the offspring without being involved with genetic shuffling and recombining of mtDNA with the mtDNA of the father.
		Human mtDNA has been completely mapped and all the coding regions are known (As well as the proteins or RNA for which they code).
		Mitochondrial DNA (mtDNA) is generally assumed to be inherited exclusively from the mother.
	naturalselection.0catch.com /Files/dnamutationrates.html (2600 words)

	Shuffling viral tropism - Nature Biotechnology
		The researchers combined DNA encoding the envelopes from six strains of a virus in nearly one million configurations, and tested whether the recombinant viruses could infect a cell type that none of the six strains would normally infect.
		Using in vitro molecular breeding to mimic genetic variation and recombination, followed by selection, they "evolved" a virus for new tropism toward a specific target cell.
		Nay-Wei Soong and colleagues now have developed a general strategy for creating "better" viruses (Nat.
	www.nature.com /nbt/journal/v18/n9/full/nbt0900_913a.html (193 words)

	Bioinformatics, Computational Molecular Biology - Alignment, Strings, Sequences, Trees, Maps
		Fewer false positives, fewer false negatives, can (and should) change rank-order of alignments, applicable to more general models than the "shuffling" correction for non-uniform populations of sequences, identifies correct population model(s).
		Seminars: (DNA) Sequence Complexity and Alignment, to the Walter and Eliza Hall (WEHI) Bioinformatics Group,
		Whatever they are called, they are useful in pattern and structure discovery, compression, alignment of pair of sequences, etc..
	www.csse.monash.edu.au /~lloyd/tildeStrings (1848 words)

	The effect of substrate binding on the conformation and structural stability of Herpes simplex virus type 1 thymidine kinase -- Wurth et al. 10 (1): 63 -- Protein Science
		Christians, F.C., Scapozza, L., Crameri, A., Folkers, G., and Stemmer, W.P. Directed evolution of thymidine kinase for AZT phosphorylation using DNA family shuffling.
		Wild, K., Bohner, T., Folkers, G., and Schulz, G.E. The structures of thymidine kinase from herpes simplex virus type 1 in complex with substrates and a substrate analogue.
		Caruso, M. and Bank, A. Efficient retroviral gene transfer of a Tat-regulated herpes simplex virus thymidine kinase gene for HIV gene therapy.
	protsci.highwire.org /cgi/content/full/10/1/63 (1848 words)

	Nucleotide shuffling and ssDNA recognition in Oxytricha nova telomere end-binding protein complexes
		Otherwise, the molecular conformations of the cognate and non-cognate complexes are nearly identical, including the portions of the DNA backbone that flank the flipped-out nucleotide Tel+T T8 (Figure 2C).
		Phases were generated from two complementary models derived from the cognate OnTEBP:Tel complex structures (1OTC and 1JB7): an OnTEBP:Tel model containing the ssDNA and one omitting the ssDNA.
		Previous work has shown that various non-specific ssDNAs give an
	www.nature.com /emboj/journal/v22/n16/full/7590826a.html (7284 words)

	Expression and nucleotide sequence of the Clostridium acetobutylicum beta-galactosidase gene cloned in Escherichia coli. -- Hancock et al. 173 (10): 3084 -- The Journal of Bacteriology
		Zhang, J.-H., Dawes, G., Stemmer, W. Directed evolution of a fucosidase from a galactosidase by DNA shuffling and screening.
		Roth, N. J., Huber, R. The beta -Galactosidase (Escherichia coli) Reaction Is Partly Facilitated by Interactions of His-540 with the C6 Hydroxyl of Galactose.
		Strey, J., Wittchen, K. D., Meinhardt, F. Regulation of beta -Galactosidase Expression in Bacillus megaterium DSM319 by a XylS/AraC-Type Transcriptional Activator.
	jb.asm.org /cgi/lookup?vol=173&fp=3084&view=abstract (352 words)

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In the News (Tue 22 Dec 09)