ライフサイエンスコーパス: shuffling

1 approach based on a technique known as codon shuffling.

2 reactivity and facilitates efficient proton shuffling.

3 om a cellulase library created by family DNA shuffling.

4 in vitro recombination methods, such as DNA shuffling.

5 R-retroposition as a novel mechanism of exon shuffling.

6 used in vitro DNA recombination method, DNA shuffling.

7 rom discrete structural modules through exon shuffling.

8 s) at positions not accessible by DNA family shuffling.

9 on to library generation methods such as DNA shuffling.

10 ric gene generated by this mechanism of exon shuffling.

11 eras between multiple Hcr9s in vitro by gene shuffling.

12 ggesting its emergence as a result of domain shuffling.

13 n diversification of gene function by genome shuffling.

14 ds based on surrogate spike trains and trial shuffling.

15 nalyze chimeric DNA libraries created by DNA shuffling.

16 protein was subjected to mutagenesis and DNA shuffling.

17 a major role in the origin of genes by exon shuffling.

18 ed alternative to sexual PCR for gene family shuffling.

19 show how the splice frame rules govern exon shuffling.

20 ons by intronic recombination is called exon shuffling.

21 rated by local sequence variation and domain shuffling.

22 n for the creation of hybrid enzymes and DNA shuffling.

23 provide very efficient mechanism for genomic shuffling.

24 sover statistics and draws contrast with DNA shuffling.

25 g a specific DNA recombination protocol, DNA shuffling.

26 ins and enzymes have been improved using DNA shuffling.

27 c murine leukemia virus (MLV) strains by DNA shuffling.

28 N-alpha2a was obtained in the first cycle of shuffling.

29 enerating chimeras with hASNase1 through DNA shuffling.

30 three PA-tolerant mutants obtained by genome shuffling.

31 tion mutagenesis, combined at random through shuffling.

32 ion model built on the theory of exon/domain shuffling.

33 o found to mediate intron retention and exon shuffling.

34 rase and transposase genes suggest past gene shuffling.

35 Exon shuffling, a major mechanism of gene evolution, scramble

36 ltiple rounds of cycling mutagenesis and DNA shuffling, a more efficient nuclease variant (Sharkey) w

37 pline was galvanized by the invention of DNA shuffling, a procedure that randomly recombines point mu

38 We describe here whole-genome shuffling; a process that combines the advantage of mult

39 No shuffling algorithm that simultaneously preserves these

40 We present here a random shuffling algorithm, Multiperm, that preserves not only

41 Using codon-shuffling algorithms that preserve amino acid sequence,

42 onstrate that there exists an unusual atomic shuffling along the tilt axis, which greatly assists SCM

43 ences, chimeric proteins were constructed by shuffling amino-terminal, central, and carboxy-terminal

44 pendent "reentry" mechanism that allows CFTR shuffling among different open states by undergoing mult

45 Thus, we have revealed a 'function shuffling' among genes of paralogue group 1 during the e

46 We describe synthetic shuffling, an evolutionary protein engineering technolog

47 roup is developing in vitro formats for exon shuffling and applying these to the directed evolution o

48 like a and a' domains mediate disulfide bond shuffling and b and b' domains are substrate binding.

49 r into extinction (clonal interference); DNA shuffling and combinatorial cassette mutagenesis led ins

50 , we introduce a new method termed consensus shuffling and demonstrate its use to significantly reduc

51 s show a modular organization with extensive shuffling and displacement of the constituent domains; h

52 n the human genome, and the extent of domain shuffling and domain sharing among proteins.

53 Eight rounds of DNA shuffling and in vivo selection followed by a backcross

54 t PRRSV strains were molecularly bred by DNA shuffling and iteration of the process, and the shuffled

55 Our results suggest that combined DNA shuffling and mutagenesis of libraries of Flp variants a

56 DNA shuffling and other in vitro recombination strategies ha

57 More specifically, DNA shuffling and other methods of genetic recombination and

58 racellular receptor domains by in vitro exon shuffling and phage display, generating multidomain prot

59 novel strategy that utilizes directed domain shuffling and rapid cell-based selections.

60 altered by stochastic mutations based on DNA shuffling and rationally tailored by structure-based red

61 of flagellar genes have undergone extensive shuffling and rearrangement among lineages, and based on

62 ity to change sequence specificity by domain shuffling and rearrangements.

63 ative and denatured (scrambled) proteins via shuffling and reshuffling of disulfide bonds.

64 t, TG-15, was subjected to iterations of DNA shuffling and screened for enzyme variants with up-regul

65 Here we use two cycles of DNA shuffling and screening in Escherichia coli to obtain ev

66 a more potent version of IL-12 by using DNA shuffling and screening to improve its expression in hum

67 ng 32 clones isolated in three rounds of DNA shuffling and screening were mapped to the active site.

68 After four rounds of shuffling and screening, two clones were isolated that s

69 bstrate) were evolved in seven rounds of DNA shuffling and screening.

70 monkey, baboon, cat, cow, and rabbit by DNA shuffling and screening.

71 Further rounds of evolution using DNA shuffling and staggered extension process (StEP) resulte

72 y expanded in the human genome due to domain shuffling and that 1-1 symmetrical domains and domain fa

73 (RTRS) could potentially contribute to exon shuffling and the genesis of some primordial SINEs.

74 Our study validates DNA family shuffling and viral peptide display as two powerful and

75 requires fewer PCR cycles than in vitro DNA shuffling and, unlike site-specific recombination method

76 ly because this domain may undergo disulfide shuffling and/or conformational changes during handling.

77 zymes resulting from random mutagenesis, DNA shuffling, and combinatorial saturation mutagenesis were

78 air may play a role in genetic disease, exon shuffling, and mammalian evolution.

79 f error-prone polymerase chain reaction, DNA shuffling, and multiple-site-directed mutagenesis to aff

80 ns revealed that loop length diversity, loop shuffling, and recursive mutagenesis of diverse populati

81 isolated after three rounds of mutation, DNA shuffling, and screening.

82 rn in a de novo fashion, to detect disulfide shuffling, and to provide information on heterogeneity,

83 recognition, confirming the validity of the shuffling approach.

84 Our CODNS (cross-over optimization for DNA shuffling) approach employs polynomial-time dynamic prog

85 CD277 knockdown and domain-shuffling approaches confirm the key implication of the

86 ic recombination and, in particular, genetic shuffling are at odds with sequence comparison by alignm

87 ns with novel functions were created by exon shuffling around the time of the metazoan radiation.

88 We propose complementation by codon shuffling as a means to produce replication-defective or

89 We describe a computational model of DNA shuffling based on the thermodynamics and kinetics of th

90 etaalphaalphabeta fold, suggestive of module shuffling between different homing endonuclease families

91 icking itinerary characterized by continuous shuffling between the plasma membrane and the Rab11 recy

92 mammalian mutation caused by germ line exon shuffling between unrelated genes.

93 We also find that an intriguing function 'shuffling' between paralogues has occurred, such that on

94 Thus, genome shuffling by Alu-mediated rearrangements has contributed

95 strongly supports a complex history of gene shuffling by recombination and multiple horizontal trans

96 Domain duplication and shuffling by recombination are probably the most importa

97 Molecular breeding via DNA shuffling can direct the evolution of viruses with desir

98 A second stage of disulfide shuffling catalyzed by isomerase converts X-Hir to the n

99 Yet, genomes are more than ever-shuffling collections of genes.

100 HeV G, was affinity maturated by light-chain shuffling combined with random mutagenesis of its heavy-

101 In addition, two iterations of consensus shuffling corrected a population of GFPuv clones where a

102 hologous genes frequently showed cis-element shuffling, demonstrating that compositional similarity c

103 , removing spike count correlations by trial shuffling did not impact decoding performance or bias.

104 es is an irreversible event where subsequent shuffling does not occur, i.e. HA oligosaccharides from

105 Tube growth, eruption, and shuffling droplets are subsequently observed, depending

106 heir genes has allowed extensive exon/domain shuffling during evolution to generate hundreds of ECM p

107 The sequence diversity introduced through shuffling efficiently samples crystal packing space by m

108 Surprisingly, shuffling either prion domain, leaving amino acid conten

109 on shuffling-like process, which we call MDS shuffling, enables ciliates to generate novel genetic ma

110 A single round of shuffling envelope sequences from six murine leukaemia v

111 s across gene boundaries in conjunction with shuffling events have at least as much potential to cont

112 e assays, and two potential L1-mediated exon shuffling events have been identified in the genome.

113 e, while have undergone different degrees of shuffling events in other investigated cucurbit genomes.

114 Here we show that two gene shuffling events led to two independent acquisitions of

115 and gene duplication and triplication, exon shuffling, exon accretion, and fusion/fission events.

116 The shuffling experiments demonstrate that promiscuous pairi

117 Gene shuffling experiments generated a mutant protein (MRD(E5

118 Using domain shuffling experiments, we present evidence showing that

119 ssessing the generation of crossovers in DNA shuffling experiments.

120 DNA shuffling facilitated the evolution of a human immunodef

121 d metazoans, suggesting that abundant domain shuffling followed the separation of the choanoflagellat

122 r homeologous regions derived from segmental shuffling following polyploid formation.

123 lus licheniformis that was optimized by gene shuffling for acetylation of the broad spectrum herbicid

124 ein production and demonstrated the power of shuffling for plant virus vector improvement.

125 To bridge this gap, we invented Megaprimer Shuffling for Tandem Affinity Reagents (MegaSTAR) to ide

126 source-intensive and more effective than DNA shuffling for this particular evolutionary pathway.

127 vities of JGW evolved extensively after exon-shuffling from a preexisting enzyme.

128 The effects of proton shuffling from Asp82 to Glu78 and from Glu32 to Asp82 ar

129 ations rather than merely reduced acyl group shuffling from PC in the mutant.

130 egative LRs, 0.30 to 0.44), and a history of shuffling gait (range of positive LRs, 3.3 to 15; range

131 halus and MASA (Mental retardation, Aphasia, Shuffling gait, Adducted thumbs) syndrome.

132 remor, rigidity, bradykinesia, micrographia, shuffling gait, and difficulty with the tasks of turning

133 ing such as spontaneous unilateral rotation, shuffling gait, and stereotypy.

134 xpand rapidly under the joint forces of exon shuffling, gene duplication, and natural selection.

135 several mechanisms of origin including exon shuffling, gene fission/fusion, retrotransposition, dupl

136 DNA shuffling generates combinatorial libraries of chimeric

137 functional primate Siglec (Siglec-13); exon shuffling, generating hybrid genes; accelerated accumula

138 c crossovers (COs) have two important roles, shuffling genetic information and ensuring proper chromo

139 g gametes, and promotes genetic diversity by shuffling genetic material between parental chromosomes.

140 While DNA shuffling has been applied quite successfully, it is lim

141 the ligand-binding domain suggests that exon shuffling has played a role in the evolution of this fam

142 This suggests that exon shuffling has primarily involved rearrangement of struct

143 ro recombination of homologous genes (family shuffling) has been proposed as an effective search stra

144 roaches to solve this problem based on codon-shuffling have been limited to exploring only an infinit

145 tagenesis, site-directed mutagenesis and DNA shuffling, have been widely used to generate variants of

146 DNA shuffling identified the beneficial NagAc mutation G407S

147 We show that two iterations of consensus shuffling improved a population of synthetic green fluor

148 Eleven iterations of DNA shuffling improved enzyme efficiency by nearly four orde

149 Furthermore, DNA shuffling improved the level of expression and homogenei

150 h is best explained by the two motor domains shuffling in an alternating manner between rear and forw

151 These studies demonstrate the utility of DNA shuffling in breeding viral strains with improved charac

152 Using synthetic shuffling in combination with a restricted tetranomial d

153 tatistical significance by doing Monte Carlo shuffling in fixed-length sequence windows, thus elimina

154 As a result of disulfide shuffling in its terminal domains, hPDI exists in two ox

155 To elucidate the role of exon shuffling in shaping the complexity of the human genome/

156 protein and can lead to quirks such as some shuffling in the order of the normal modes when applied

157 ble with the suggestion of primordial domain shuffling in the progenote.

158 abundance of domains in the proteome, domain shuffling increases versatility, i.e. the number of dist

159 Light chain shuffling indicated that non-stochastically paired L cha

160 Surprisingly, we also show that shuffling individual disease histories only marginally d

161 ter the shears, and the excess reverse shear-shuffling induced gamma necks in the epsilon martensite

162 is that ancient genes were assembled by exon shuffling involving compact modules.

163 ence of synergistic reassembly in family DNA shuffling is obtained.

164 uggests that de novo recruitment rather than shuffling is the major route by which exons are added to

165 Exon shuffling is thought to be an important mechanism for ev

166 or, alpha-lactalbumin (alphaLA) denatures by shuffling its four native disulfide bonds and converts t

167 ce of thiol initiator, alpha-LA denatures by shuffling its four native disulfide bonds and converts t

168 thiol initiator, the native PCI denatures by shuffling its native disulfide bonds and converts to for

169 Transforming BW5Delta with the shuffling libraries allowed for the identification of se

170 isplay selection strategy from a 'mini-exon' shuffling library generated from the yeast genome and fr

171 This suggests that an exon shuffling-like process, which we call MDS shuffling, ena

172 new transcripts by exon exaptation and exon shuffling, many of which are primarily expressed in the

173 autonomous and suggest that genomic enhancer shuffling may have contributed to the evolution of compl

174 d, and the results indicate that such proton shuffling may not play an important role in the stabiliz

175 This phenomenon, termed nucleotide shuffling, may be of general importance in protein recog

176 in-binding protein formed by an unusual exon-shuffling mechanism in hominoid primates and represents

177 We used a novel gene shuffling method called synthetic template shuffling to

178 We present an overhang-based DNA block shuffling method to create a customized random DNA libra

179 At a molecular level, DNA shuffling mimics, yet accelerates, evolutionary processe

180 network provides evidence for a conformation shuffling model, in which exchange between rotamer state

181 The in vitro process of DNA shuffling (molecular breeding) mimics this mechanism on

182 sequences for recombination, we combined DNA shuffling mutagenesis and a forward selection strategy t

183 We performed synthetic shuffling of 15 subtilisin genes and obtained active and

184 strains, whose major recombination effect is shuffling of a relatively conserved set of amino acid mo

185 s (AJs), intracellular formation and nuclear shuffling of beta-catenin/MUC1-CT complexes, and, ultima

186 Shuffling of binding sites has been suggested to lie beh

187 We conclude that despite the tremendous shuffling of chromosomes during the course of mammalian

188 to the evolution of new proteins through the shuffling of conserved protein domains.

189 ing and assembly by catalyzing formation and shuffling of cysteine disulfide bonds in the endoplasmic

190 terest, production of potential biofuels and shuffling of disease-resistance traits between crop spec

191 a thiol catalyst in promoting the disulfide shuffling of diverse non-native intermediates accumulate

192 Four rounds of random mutagenesis and DNA shuffling of Drosophila melanogaster 2'-deoxynucleoside

193 The shuffling of Et 743-DNA adducts to the more stable alkyl

194 We show that shuffling of existing enhancer elements both within and

195 tion as a result of insertions, deletions or shuffling of fragments of underlying gene sequences, and

196 reservation of synteny, we found substantial shuffling of gene order along corresponding chromosome a

197 tric inversions, thereby contributing to the shuffling of gene order in the D. pseudoobscura lineage.

198 n vitro and in vivo, indicating that the DNA shuffling of GP4 and M genes did not significantly impai

199 II, which is controlled through the cyclical shuffling of Hg(2+) ions between the solution phase and

200 es, Rad51 and Dmc1, catalyze the pairing and shuffling of homologous DNA sequences in eukaryotic cell

201 C transposons to mediate the duplication and shuffling of host genes in bacteria and maize, it is tem

202 For example, exon shuffling of human pharmaceutical proteins can generate

203 Furthermore, shuffling of HV regions may result in novel HSPG recepto

204 g either a common origin of these introns or shuffling of intron structural elements.

205 are involved in Mg(II) binding, suggesting a shuffling of Mg(II) ligands in the active site.

206 n sex, is important for population genetics--shuffling of minor variants, but relatively insignifican

207 were used to construct ancient genes by exon shuffling of modules at the earliest stages of evolution

208 A cell-cycle-dependent shuffling of multiple centromeric units results in the f

209 s as well as homologous recombination-driven shuffling of mutagenized loops.

210 DNA shuffling of mutations from the various screens and reco

211 DNA shuffling of NDO nagAcAd also generated the NagAc varian

212 ngineered proteins suggested that fusion and shuffling of OB folds can lead to well-folded polypeptid

213 Systematic shuffling of polymorphic sites between Gpa2 and Rx1 show

214 ns from a library generated by combinatorial shuffling of polypeptide segments and to convert a parti

215 SA11 sequence, revealing a complex patchwork shuffling of segments not explained by a simple transloc

216 ge to the circuit diagram resulting from the shuffling of synaptic partners.

217 esponding distributions, arising from random shuffling of the charged side chains.

218 ween the different populations must take the shuffling of the genomic segments into account.

219 study we molecularly bred PRRSV through DNA shuffling of the GP4 and M genes, separately, from six g

220 The results suggest that DNA shuffling of the GP4 or M genes from different parental

221 Here, random mutagenesis and DNA shuffling of the single-chain variable fragment of the n

222 the virus was achieved in this study by DNA shuffling of the viral envelope genes from multiple stra

223 omology in the PCR insertion products drives shuffling of these genes in vivo by yeast homologous rec

224 design for new sequence targets via modular shuffling of these units.

225 study reveals a unique approach through DNA shuffling of viral envelope genes to attenuate a positiv

226 Recursive shuffling of whole genomes has recently been demonstrate

227 to "flipping a fair coin," a thorough-random-shuffling-of-the-genes explanation, via mutations, does

228 r rates of gene gain and loss, elevated gene shuffling on the X chromosome, and more intron losses, r

229 d as beneficial by random mutagenesis or DNA shuffling or seen in any of the naturally occurring TEM

230 rsity than that obtained by canonical family shuffling or with conventional SCRATCHY.

231 hGSTT1-1 constructed by error-prone PCR, DNA shuffling, or saturation mutagenesis were screened for i

232 By shuffling our repertoire of modified zinc finger domains

233 en phenotypes and variation generated by DNA shuffling paralleled natural variation observed between

234 L1 exon shuffling potential has been reported in cell culture as

235 nal change, whereas inhibition of this redox shuffling prevents gp41 from assuming the fusogenic 6-he

236 Three aspects of the DNA shuffling procedure are modeled: the fragment size distr

237 Four different shuffling procedures were used to control for the popula

238 arity for any pair of sequences early in the shuffling process and thus save on the search time.

239 splay vector pC3C followed by a tandem chain shuffling process designed for minimal deviation from na

240 himeric sections are then subjected to a DNA shuffling process generating an enhanced crossover SCRAT

241 led to several unique insights into the DNA shuffling process.

242 Two subsequent rounds of DNA shuffling produced additional clones that showed further

243 versity targets are investigated for the DNA shuffling protocol to showcase the utility of the eCodon

244 se of degenerate oligonucleotides, synthetic shuffling provides a direct route from database sequence

245 mmunoprecipitation can be generated by chain shuffling, providing a scalable approach to mapping prot

246 ve been subject to Post-transcriptional exon shuffling (PTES), have an exon order inconsistent with t

247 will therefore aid in the design of optimal shuffling reaction conditions.

248 and records their states at every stage of a shuffling reaction.

249 nases has elucidated important biases in the shuffling reaction.

250 e intergenic, or generated synthetically by 'shuffling' real sequences.

251 Pairwise analysis with random shuffling revealed that the multiple lipoproteins (Mlp;

252 Besides extensive allele shuffling, SARB strains showed notably larger recombinag

253 Genome shuffling seems broadly useful for the rapid evolution o

254 we used sound quilts, stimuli constructed by shuffling segments of a natural sound, approximately pre

255 We previously used DNA shuffling (sexual recombination) and a histochemical scr

256 Our less biased approach to DNA shuffling should be useful for the engineering of a wide

257 Consensus shuffling should facilitate the rapid and accurate synth

258 me sequence variability and extensive domain shuffling, signal transduction proteins are difficult to

259 eldom detect gross rearrangements ('promoter shuffling') since such analyses usually employ relativel

260 ncy rates was observed for both viruses when shuffling single sequence elements.

261 sequence; (ii) minimizing bias in family DNA shuffling so that each of the parental sequence pair con

262 artificial family is then subjected to a DNA-shuffling step to augment the number of crossovers.

263 Using a plasmid-shuffling strategy in haploid Saccharomyces cerevisiae,

264 e duplication-divergence hypothesis and exon shuffling, suggesting an important role in both genome a

265 Here we describe a facile plasmid-chromosome shuffling technique for generating and analyzing non-del

266 ineering by conventional, homology-dependent shuffling techniques.

267 atural AAV isolates by an adapted DNA family shuffling technology to create a complex library of hybr

268 is under elevated temperatures, we used gene shuffling technology to generate several Arabidopsis tha

269 genome that has undergone less gene loss and shuffling than previously sequenced arthropods, and many

270 protein engineer with a new approach to DNA shuffling that supports substantially more diverse paren

271 recombination has not played a large role in shuffling the bfpA and perA loci between separate EAF pl

272 m library of adeno-associated virus (AAV) by shuffling the capsid genes of AAV serotypes 1 to 9, and

273 t may also destroy high-fitness genotypes by shuffling the genes of a fit parent with a genetically d

274 versions serve as the dominant mechanism for shuffling the order of genes along a chromosome.

275 roblems where the cutoff can be proved (card shuffling, the Ehrenfests' urn).

276 ptive morphological variation was created by shuffling these cis-regulatory modules through recombina

277 By exon shuffling, this mechanism leads to the production of bis

278 We previously used DNA shuffling to direct the evolution of Escherichia coli be

279 We used DNA shuffling to explore and confirm the hypothesis that one

280 which indicated gene duplication and domain shuffling to generate the observed diversity in the enco

281 efficient methods to extend the scope of DNA shuffling to handle significantly more diverse parents a

282 Here we describe the use of genome shuffling to improve the acid tolerance of a poorly char

283 e shuffling method called synthetic template shuffling to introduce 62 differentially conserved amino

284 Using DNA shuffling to introduce functional sequence variability i

285 pectrum, we used rounds of selection and DNA shuffling to obtain GroEL/S variants that dramatically e

286 e a method of in vitro recombination or "DNA shuffling" to generate libraries of evolved enzymes.

287 In many cases, biologists need sophisticated shuffling tools that preserve not only the counts of dis

288 These include gene shuffling, truncation of the cytoplasmic tail of the G p

289 Utilizing activity-shuffling validation methods, we have demonstrated the r

290 DNA shuffling was used as a combinatorial in vitro genetic a

291 Plasmid shuffling was used for ectopic expression of altered b s

292 mutagenesis and in vitro recombination (DNA shuffling) was used to generate mutant libraries, which

293 binatorial random mutagenesis technique (DNA shuffling), we have isolated an IE(ME)-specific hyperact

294 re whether there might be limits to such DNA shuffling, we have mapped the termini of mitochondrial m

295 an explicit water molecule to mediate proton shuffling were significantly more successful, with rate

296 ditionally, newer tools such as Whole Genome Shuffling (WGS), Scalar Analysis of Library Enrichments

297 process suggests that the mechanism of exon shuffling, which can generate protein-coding genes, also

298 information benefit from refinements such as shuffling, while being highly efficient.

299 ge of multi-parental crossing allowed by DNA shuffling with the recombination of entire genomes norma

300 A single round of DNA back-shuffling with wild-type aspartate aminotransferase on t