ライフサイエンスコーパス: shuffle

1 contained in different genomic clusters are shuffled.

2 -forming sequences of Ac-MYD and Ac-VIE were shuffled.

3 approach based on a technique known as codon shuffling.

4 reactivity and facilitates efficient proton shuffling.

5 rase and transposase genes suggest past gene shuffling.

6 om a cellulase library created by family DNA shuffling.

7 in vitro recombination methods, such as DNA shuffling.

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

9 used in vitro DNA recombination method, DNA shuffling.

10 ggesting its emergence as a result of domain shuffling.

11 rom discrete structural modules through exon shuffling.

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

13 on to library generation methods such as DNA shuffling.

14 ric gene generated by this mechanism of exon shuffling.

15 eras between multiple Hcr9s in vitro by gene shuffling.

16 enerating chimeras with hASNase1 through DNA shuffling.

17 n diversification of gene function by genome shuffling.

18 three PA-tolerant mutants obtained by genome shuffling.

19 tion mutagenesis, combined at random through shuffling.

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

21 o found to mediate intron retention and exon shuffling.

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

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

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

25 tion-competent viral library composed of DNA-shuffled AAV capsids.

26 of the target bar in the array was randomly shuffled across trials so that it occasionally appeared

27 No shuffling algorithm that simultaneously preserves these

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

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

30 free energy closer to native sequences than shuffled alignments that do not preserve dinucleotide fr

31 are codons from these genes and attempted to shuffle all remaining codons.

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

33 biting small molecules, an aS variant termed shuffled alpha-synuclein (SaS), wherein the first six ps

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

35 e, the linear order of these segments may be shuffled among genomes.

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

37 Protecting group shuffle and oxidation of the primary alcohol enabled the

38 d to the alignment of protein sequences with shuffled and/or repeated domain structure, and allows on

39 est by generating a large number of sequence shuffles and use the distribution of their scores to app

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

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

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

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

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

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

46 DNA shuffling and other in vitro recombination strategies ha

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

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

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

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

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

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

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

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

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

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

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

58 to that of their mutants, their dinucleotide shuffles, and their reverse complement sequences under d

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

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

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

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

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

64 recognition, confirming the validity of the shuffling approach.

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

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

67 s of Ure2p with the prion domain amino acids shuffled are still able to form prions.

68 ionally very expensive, as a large number of shuffles are needed to precisely estimate the score stat

69 ers vector, and possible accompanying atomic shuffles, are extracted.

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

71 Transversal pooling designs involving shuffled BAC arrays were employed for robust mapping eve

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

73 the intra-chromosomal order of genes may be shuffled by inversions and transpositions.

74 genetic barcode cassette whose fragments are shuffled by Rci, a site-specific DNA invertase.

75 Domains can be shuffled by recombination to create proteins with new ar

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

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

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

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

80 bridges was expressed in specialised E. coli SHuffle cells and its activity has been confirmed throug

81 ss-neutralization test revealed that the GP4-shuffled chimera GP4TS14 induced significantly higher cr

82 s FL-12 and NADC20, and similarly that the M-shuffled chimera MTS57 also induced significantly higher

83 Three GP4-shuffled chimeras and five M-shuffled chimeras, each rep

84 Three GP4-shuffled chimeras and five M-shuffled chimeras, each representing sequences from all

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

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

87 A century of climate change significantly shuffles community composition by a basin-wide median va

88 is study, site-directed mutagenesis, plasmid shuffle complementation assays, and primer extension ana

89 networks that were constrained with randomly shuffled constraints.

90 It was absent in phase-shuffled controls with the same power spectrum or empty

91 sely, when b/c </= k or players are randomly shuffled, cooperation decays.

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

93 idal gratings and flashed bars, and computed shuffle-corrected cross-correlograms (CCGs) of spike tra

94 eously recorded neurons were evaluated using shuffle-corrected cross-correlograms.

95 We therefore devised a shuffled correlation procedure to quantify how periodici

96 s were compared to surrogate images of phase shuffled data across patients to reveal clusters of sign

97 ed lower approximate entropy values than the shuffled data, suggesting a temporal organization in the

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

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

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

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

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

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

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

105 ilies and compared this overlap to uniformly shuffled enhancers.

106 ation trials performed on three WT and eight shuffled enzymes revealed two variants that crystallized

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

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

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

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

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

112 As one benchmark, we show that it produces shuffled exonic sequences having folding free energy clo

113 Through in vivo plasmid shuffle experiments, we show that the major characterist

114 The shuffling experiments demonstrate that promiscuous pairi

115 Using domain shuffling experiments, we present evidence showing that

116 Recombination within genes shuffled flanking retrotransposon clusters, creating new

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

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

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

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

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

122 In this scheme, the grouping method of the shuffled frog leaping algorithm (SFLA) is incorporated w

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

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

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

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

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

128 erges despite rearrangements that constantly shuffle gene and operon order.

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

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

131 DNA shuffling generates combinatorial libraries of chimeric

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

133 ffling and iteration of the process, and the shuffled genes were cloned into the backbone of a DNA-la

134 Crossovers (COs) shuffle genetic information and allow balanced segregati

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

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

137 The shuffled GP4 and M genes libraries were each cloned into

138 representative chimeric viruses, DS722 with shuffled GP5 genes and DS5M3 with shuffled GP5-M genes,

139 DS722 with shuffled GP5 genes and DS5M3 with shuffled GP5-M genes, were rescued and shown to replicat

140 ompare this distance against 10,000 randomly shuffled groups made up of the same participants.

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

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

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

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

145 ) HA is a reversible event whereby TSG-6 can shuffle HCs from one HA molecule to another.

146 des can be used, with TSG-6, to irreversibly shuffle HCs from pathological, HMW HC-HA to HA oligosacc

147 nsfer in the context of the proposed "domain shuffle hypothesis" for intraprotein electron transfer i

148 DNA shuffling identified the beneficial NagAc mutation G407S

149 The regrading of the shuffled image set was performed by 3 graders, 3 weeks l

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

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

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

153 Two scFvs that share 89.8% homology were shuffled in vivo by homologous recombination, and chimer

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

155 Using synthetic shuffling in combination with a restricted tetranomial d

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

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

158 DsbD provides reducing power to DsbC that shuffles incorrect disulfide bond in misfolded proteins

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

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

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

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

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

164 tography indicated the presence of disulfide shuffled isomers, containing the non-native 61-73 disulf

165 We present Shuffle-LAGAN, a glocal alignment algorithm that is base

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

167 y stringent selections from these new "chain-shuffled" libraries.

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

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

170 Although recombinant viruses bearing the shuffled M2-2 gene were recovered and expressed higher l

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

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

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

174 ucleation of fcc-Ti is accomplished via pure-shuffle mechanism with a minimum stable thickness of thr

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

176 ugh gliding two-layer disconnections or pure-shuffle mechanisms through gliding four-layer disconnect

177 hree atomic layers, and the growth via shear-shuffle mechanisms through gliding two-layer disconnecti

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

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

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

181 flexibility of ZFN design and the ability to shuffle monomers of different ZFNs for the digestion of

182 e at a local minimum compared with surrogate shuffled networks.

183 s (NS) than from Gaussian white-noise (GWN), shuffled-NS or Gaussian-1/f stimuli; integrating larger

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

202 DNA shuffling of NDO nagAcAd also generated the NagAc varian

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

204 Systematic shuffling of polymorphic sites between Gpa2 and Rx1 show

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

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

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

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

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

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

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

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

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

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

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

216 Recursive shuffling of whole genomes has recently been demonstrate

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

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

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

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

221 By shuffling our repertoire of modified zinc finger domains

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

223 Meiotic crossovers shuffle parental genetic information, providing novel co

224 as Lagrangian coherent structures (LCSs) may shuffle plant pathogens along highways in the sky.

225 value close to the 50% expected from a fully shuffled population.

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

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

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

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

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

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

232 -fold overrepresented compared with a window-shuffled random model.

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

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

235 inter-spike interval sequences with that of shuffled representations of the same data.

236 t physically indistinguishable from randomly shuffled RNAs.

237 lts indicate that RNase ES is a structurally shuffled RNase E homologue showing evolutionary conserva

238 Complementation with codon-shuffled RTA constructs did not yield any WT revertant v

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

240 s (ScFvs) representing the original Fabs and shuffled ScFvs in which heavy chains were recombined wit

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

242 utation test should be used, with phenotypes shuffled separately within the genotyped and ungenotyped

243 Indeed, a single shuffled sequence could give rise to several prion varia

244 ovided evidence that extensive recombination shuffles sequence motifs sufficiently to evade CRISPR sp

245 Randomly shuffled sequences are routinely used in sequence analys

246 The shuffled sequences were computationally predicted to hav

247 re for all 13 tested ncRNA sets, compared to shuffled sequences.

248 ignificance thresholds being calculated from shuffled sequences.

249 , we recently used offset recombinant PCR to shuffle seven artificially constructed representatives o

250 chnique, known as offset recombinant PCR, to shuffle seven homologues that encode a broad range of na

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

252 Consensus shuffling should facilitate the rapid and accurate synth

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

254 These partially folded, disulfide shuffled species are largely responsible for the pronoun

255 that Y131, one of the yeast histone H2A/H2B shuffle strains widely used for the last decade in the f

256 nificantly differed between the parental and shuffled strains.

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

258 sequences that are composed of repeated and shuffled subsequences.

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

260 ta indicate the same conclusion for a single shuffled Sup35 prion domain.

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

262 ineering by conventional, homology-dependent shuffling techniques.

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

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

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

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

267 ns inactivate genes by direct disruption and shuffle the genome through recombination, they can also

268 s CO (a reversible inhibitor of the enzyme), shuffle the intrinsic CO ligands, and even destroy the H

269 utilizing an in vitro selection process that shuffles the order of deoxy- and ribonucleotides in each

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

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

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

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

274 n the same slit-dependent shape slivers were shuffled, thereby preventing their spatiotemporal integr

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

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

277 he Vibrio cholera vibriobactin cluster, were shuffled to produce a new siderophore biosynthetic pathw

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

283 Using DNA shuffling to introduce functional sequence variability i

284 agments that can be readily interchanged or "shuffled" to produce subtly different variants with dist

285 L/I219L/C248I variant coexpressed with a DNA-shuffled toluene ortho-monooxygenase, which initiates at

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

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

288 Sexual reproduction enables organisms to shuffle two parental genomes to produce recombinant prog

289 We demonstrate that two shuffled Ure2 prion domains capable of being prions form

290 minal 86 amino acids fused to an insensitive shuffled variant of maize (Zea mays) 4-hydroxyphenylpyru

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

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

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

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

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

296 ommunity appears poised for marked shift and shuffle, which may have broad effects on food webs and b

297 amino acids in the prion domain was randomly shuffled while keeping the amino acid composition and C-

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

299 The Pto gene was shuffled with four of its paralogs from a resistant hapl

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