ライフサイエンスコーパス: shuffling

1 atterning on phase behavior through sequence shuffling.

2 rase and transposase genes suggest past gene shuffling.

3 ical EGFD AspH substrates to avoid disulfide shuffling.

4 om a cellulase library created by family DNA shuffling.

5 in vitro recombination methods, such as DNA 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 ds based on surrogate spike trains and trial shuffling.

13 nalyze chimeric DNA libraries created by DNA shuffling.

14 protein was subjected to mutagenesis and DNA shuffling.

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

16 ed alternative to sexual PCR for gene family shuffling.

17 show how the splice frame rules govern exon shuffling.

18 approach based on a technique known as codon shuffling.

19 reactivity and facilitates efficient proton shuffling.

20 ggesting its emergence as a result of domain shuffling.

21 enerating chimeras with hASNase1 through DNA shuffling.

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

23 n diversification of gene function by genome shuffling.

24 three PA-tolerant mutants obtained by genome shuffling.

25 tion mutagenesis, combined at random through shuffling.

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

27 o found to mediate intron retention and exon shuffling.

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

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

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

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

32 No shuffling algorithm that simultaneously preserves these

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

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

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

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

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

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

39 We describe synthetic shuffling, an evolutionary protein engineering technolog

40 e used a method that combined antibody chain shuffling and a staggered-extension process to produce u

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

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

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

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

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

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

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

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

49 DNA shuffling and other in vitro recombination strategies ha

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

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

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

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

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

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

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

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

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

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

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

61 ased avidity via a series of constant region shuffling and subdomain swapping approaches to create im

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

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

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

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

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

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

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

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

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

71 recognition, confirming the validity of the shuffling approach.

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

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

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

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

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

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

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

79 n generated by recombination-mediated domain shuffling between ppzA-1 and ppzA-2, resulting in the pp

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

81 nce for the evolution of proteins via domain shuffling, but literature in the field has so far strugg

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

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

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

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

86 Results indicate that shuffling can occur in a canonically 'stable' symbiosis,

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

104 The shuffling experiments demonstrate that promiscuous pairi

105 Using domain shuffling experiments, we present evidence showing that

106 ssessing the generation of crossovers in DNA shuffling experiments.

107 DNA shuffling facilitated the evolution of a human immunodef

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

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

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

111 a source of natural diversity, we used gene shuffling for library generation and screened for novel

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

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

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

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

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

117 eover, traditional measures fail to consider shuffling from independent assortment of homologous chro

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

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

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

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

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

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

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

125 DNA shuffling generates combinatorial libraries of chimeric

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

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

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

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

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

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

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

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

134 ificity and that gene duplication and domain shuffling have resulted in diversification of secondary

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

136 Constant region shuffling identified a major CH3 and a minor CH2 contrib

137 DNA shuffling identified the beneficial NagAc mutation G407S

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

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

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

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

142 Using synthetic shuffling in combination with a restricted tetranomial d

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

144 y offspring and supports the hypothesis that shuffling in microbial communities may serve as a mechan

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

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

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

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

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

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

151 Permutations are performed by shuffling individual IDs of the genotype vector for this

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

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

154 alue of 1/2 and that (ii) this high level of shuffling is due almost entirely to independent assortme

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

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

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

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

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

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

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

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

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

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

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

166 Tetrahymena species have used a massive exon-shuffling mechanism, involving unequal crossing over pos

167 ons, and thus the possible mechanism of gene shuffling mediated by this type of mobile element.

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

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

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

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

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

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

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

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

176 Shuffling of binding sites has been suggested to lie beh

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

178 lify them by PCR, which avoids unintentional shuffling of complementary determining regions.

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

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

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

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

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

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

185 iversification, gene repertoire changes, and shuffling of expression domains.

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

187 the complex multidomain architecture and the shuffling of functional domains in many protein families

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

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

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

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

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

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

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

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

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

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

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

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

200 DNA shuffling of NDO nagAcAd also generated the NagAc varian

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

202 Systematic shuffling of polymorphic sites between Gpa2 and Rx1 show

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

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

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

206 omolog of kinesin-3 KIF1A known for its fast shuffling of synaptic vesicle protein transport vesicles

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 Hence, acclimatory changes like shuffling of the Symbiodiniaceae community are not limit

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

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

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

216 hineries was interlinked by the simultaneous shuffling of two components (metal and ligand) requiring

217 alyses demonstrated these classes arose from shuffling of two different subdomains within the Ag43 pa

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

219 Recursive shuffling of whole genomes has recently been demonstrate

220 ble-strand breaks have been shown to enable "shuffling" of antigen-encoding gene sequences to vastly

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

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

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

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

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

226 By shuffling our repertoire of modified zinc finger domains

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

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

229 nd sequenced the year before to characterize shuffling potential in these M. digitata colonies and de

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

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

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

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

234 l, this reaction is achieved via a molecular shuffling process involving an alkyne, an alpha,beta-uns

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

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

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

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

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

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

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

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

243 nases has elucidated important biases in the shuffling reaction.

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

245 onent Analysis (CHPCA) and Rotational Random Shuffling (RRS).

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

247 Genome shuffling seems broadly useful for the rapid evolution o

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

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

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

251 Consensus shuffling should facilitate the rapid and accurate synth

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

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

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

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

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

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

258 ineering by conventional, homology-dependent shuffling techniques.

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

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

261 oward the middle of a chromosome causes more shuffling than a crossover toward the tip.

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

263 we present a rigorous measure of genome-wide shuffling that does not suffer from these limitations.

264 on evaluation of the total amount of genetic shuffling that occurs during gamete production.

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

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

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

268 thways in different Brassicaceae lineages by shuffling the genes encoding a core palette of triterpen

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

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

271 nts blend, either by synthetic manipulation (shuffling the organic cations or inorganic elements) or

272 The device operates by shuffling the smallest cation, the proton, in a three-te

273 tly increased phase separation propensity by shuffling the wild-type sequence, which contains well-mi

274 These results suggest that, more than merely shuffling their spatial code following threat exposure,

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

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

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

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

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

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

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

286 After shuffling trials, destroying noise correlations, informa

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

288 e/Propagate/Terminate, Fragment-Based Domain Shuffling, Two-Directional Synthesis, and Successive Rin

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

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

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

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

293 Using DNA shuffling, we isolated specific amino acids combinations

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

297 These expansions are accompanied by domain shuffling, which suggests roles for pseudokinases in pla

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