ライフサイエンスコーパス: astral

1 ts based on PDB chains are newly included in ASTRAL.

2 ttp://www.cs.utexas.edu/users/phylo/datasets/astral.

3 n source form at https://github.com/smirarab/ASTRAL/.

4 ROs data were collected from participants of ASTRAL-2 and ASTRAL-3 studies before, during, and after

5 collected from participants of ASTRAL-2 and ASTRAL-3 studies before, during, and after treatment usi

6 d in a randomised, open-label phase 3 trial (ASTRAL-4) in which patients with HCV-related decompensat

7 virological response rates were sourced from ASTRAL-4, SOLAR-1, and SOLAR-2.

8 l ones by querying a flexible protein in the Astral-40 database (11 154 protein domains).

9 We present ASTRAL, a fast method for estimating species trees from

10 n both retrieval and statistical accuracy on ASTRAL, a SCOP-based test set.

11 e capture via loss of cortical dynein causes astral and cortical microtubules to be greatly reduced i

12 tracking revealed that mEg5 punctae on both astral and midzone microtubules rapidly bind and unbind.

13 by Aurora B-INCENP, led to assembly of mono-astral and monopolar structures instead of bipolar spind

14 indle pole body (SPB) not only organizes the astral and nuclear microtubules but is also associated w

15 EB1, which localized to polymerizing ends of astral and spindle microtubules, was used to track their

16 of the homotetrameric kinesin-5, KLP61F, in astral, centrosome-controlled Drosophila embryo spindles

17 ure prediction program, is used to build the astral compendium for sequence and structure analysis, a

18 than 40% sequence identity as defined by the ASTRAL compendium of protein structures are included.

19 The ASTRAL Compendium provides several databases and tools t

20 The ASTRAL compendium provides several databases and tools t

21 The ASTRAL compendium provides several databases and tools t

22 The ASTRAL compendium provides several databases and tools t

23 ral major improvements have been made to the ASTRAL compendium since its initial release 2 years ago.

24 SCOPe also incorporates and updates the ASTRAL compendium, which provides several databases and

25 These new features are reflected in the ASTRAL compendium.

26 The current release of ASTRAL contains 54,745 domains, more than three times as

27 egative regulation of myosin distribution by astral cues.

28 ery that a plasmid-partitioning ATPase forms astral cytoskeletal structures both unveils a new family

29 SCOPe also incorporates and updates the ASTRAL database.

30 e database, as well as integrated into other ASTRAL databases such as representative subsets.

31 Golgi localization and disrupted the normal astral distribution of microtubules.

32 Hexylene glycol resulted in rapid astral elongation due to decreased MT catastrophe and pr

33 , certain rituals were scheduled by solar or astral events and restricted to initiates/social achieve

34 ld be partially suppressed by disrupting the astral forces that pull spindle poles apart in the 1 cel

35 ASTRAL has undergone major transformations in the past 2

36 tion and multispecies coalescent approaches (ASTRAL-II and SVDquartets).

37 We show that ASTRAL-II has substantial advantages over ASTRAL: it is

38 L's running time is [Formula: see text], and ASTRAL-II's running time is [Formula: see text], where n

39 esent a new version of ASTRAL, which we call ASTRAL-II.

40 ing the number of gene trees required by the ASTRAL inference method, and the approach has potential

41 ASTRAL is available in open source form at https://githu

42 ition to several complete updates each year, ASTRAL is now updated on a weekly basis with preliminary

43 ASTRAL is often more accurate than concatenation using m

44 ASTRAL is statistically consistent, can run on datasets

45 pite the limitation to allowed bipartitions, ASTRAL is statistically consistent.

46 at ASTRAL-II has substantial advantages over ASTRAL: it is faster, can analyze much larger datasets (

47 Astral-like microtubules are not usually prominent in pl

48 The elongated spindle has numerous astral-like microtubules, and aPKCzeta, normally associa

49 ASTRAL may be accessed at http://astral.stanford.edu/.

50 ASTRAL may be accessed at http://astral.stanford.edu/.

51 position in concert with the position of the astral microtubule anchoring complex LGN-NuMA to yield t

52 it as astrin because of its association with astral microtubule arrays assembled in vitro.

53 ntained bipolar spindles with dense and long astral microtubule arrays but with poorly organized kine

54 orylates MISP, thus stabilizing cortical and astral microtubule attachments required for proper mitot

55 e orientation via regulation of actin cortex-astral microtubule attachments.

56 Comparison of astral microtubule behavior in mitosis with microtubule

57 nd positioning around chromosomes depends on astral microtubule connections to a moving cell cortex.

58 Astral microtubule dynamics are critical to the mechanis

59 yeast, Schizosaccharomyces pombe, depend on astral microtubule dynamics that drag the nucleus throug

60 ctility both preceded and was independent of astral microtubule elongation, suggesting that the initi

61 Delta and gfh1Delta cells exhibit defects in astral microtubule formation and anchoring, suggesting t

62 or EB1 in processes that promote equality of astral microtubule function at both poles in a spindle.

63 g that these proteins have specific roles in astral microtubule function.

64 this amino acid, plays a role in a subset of astral microtubule functions during nuclear migration in

65 bly, although it is required for cytoplasmic astral microtubule growth during mitosis.

66 e nucleus moves in the opposite direction of astral microtubule growth in the mother cell, apparently

67 n surrounding the nucleus, which we term the astral microtubule interaction zone (AMIZ).

68 s to regulate cell cycle-specific changes in astral microtubule length to ensure proper spindle align

69 on we found that cenexin depletion decreased astral microtubule length, disrupted astral microtubule

70 equired for proper chromosome separation and astral microtubule length.

71 iated role for the Astrin/SKAP complex as an astral microtubule mediator of mitotic spindle positioni

72 creased astral microtubule length, disrupted astral microtubule minus-end organization, and increased

73 Moreover, astral microtubule number and length correlated with the

74 of SPB maturation, control the asymmetry of astral microtubule organization between the preexisting

75 ove the differential activity of the SPBs in astral microtubule organization rather than intrinsic di

76 icrotubules (aMTs) while the new pole delays astral microtubule organization.

77 NA is involved in negative regulation of the astral microtubule organizing capacity of the spindle po

78 The astral microtubule organizing function of Nud1p is media

79 ), Polo, and Fascetto (Prc1) localize to the astral microtubule overlap region.

80 gly, most of the suppressors that rescue the astral microtubule phenotype also reduce Cdk1-CycB activ

81 by gating the recruitment of dynactin to the astral microtubule plus end, a prerequisite for offloadi

82 Khc-73 localizes to astral microtubule plus ends, and Dlg/Khc-73 and Dlg/Pin

83 ng abnormally stretched or fragmented due to astral microtubule pulling forces.

84 contain mitotic actin bundles, which prevent astral microtubule-actin cortex attachments.

85 ryogenesis is characterized by shifting from astral microtubule-based to central spindle-based positi

86 interactions with mutations that deactivate astral microtubule-dependent nuclear migration.

87 Caenorhabditis elegans one-cell embryo, the astral microtubule-dependent pathway requires anillin, N

88 Reestablishment of astral microtubule-mediated forces align the spindle pol

89 We provide evidence for dynein- and astral microtubule-mediated transport of Galphai/LGN/nuc

90 hem as kinetochore (KMTs), spindle (SMTs) or astral microtubules (AMTs) according to their positions,

91 n, is a dynamic complex whose recruitment to astral microtubules (aMTs) increases dramatically during

92 ll cycle) contacting the bud by its existing astral microtubules (aMTs) while the new pole delays ast

93 -300 nuclear ring and a polarized network of astral microtubules (aMTs).

94 in to the cell cortex followed by capture of astral microtubules (aMTs).

95 al imaging microscopy to examine cytoplasmic astral microtubules (Mts) and spindle dynamics during th

96 they grow, their minus ends are captured by astral microtubules (MTs) and transported poleward throu

97 Astral microtubules (MTs) are known to be important for

98 Contacts between cytoplasmic dynein and astral microtubules (MTs) at the cell cortex generate pu

99 cess begins with the capture of pole-derived astral microtubules (MTs) by the polarity determinant Bu

100 Astral microtubules (MTs) emanating from the mitotic app

101 e positioning in budding yeast by pulling on astral microtubules (MTs) from the cell cortex.

102 A), proteins that generate pulling forces on astral microtubules (MTs) through cytoplasmic dynein.

103 ynactin was sufficient to generate forces on astral microtubules (MTs) to orient the spindle, with Nu

104 nuclear complex (PNC) and its two associated astral microtubules (MTs).

105 ates MF-dependent cortical forces applied to astral microtubules (MTs).

106 Finally, dynein-dependent sliding of astral microtubules along the cortex and oscillation of

107 Astral microtubules also inhibit RhoA accumulation at th

108 rk in mitotic cells with an extension of the astral microtubules and a reduction of kinetochore micro

109 rnover of LGN relies, at least partially, on astral microtubules and DYNC1H1.

110 nted spindles were associated with disrupted astral microtubules and near complete loss of a unique s

111 (TCJs) localize force generators, pulling on astral microtubules and orienting cell division via the

112 e involved in generating forces that pull on astral microtubules and position the spindle asymmetrica

113 CLASPs act partially redundantly to regulate astral microtubules and position the spindle during asym

114 microtubules with a significant increase in astral microtubules and reduction in K-fiber fluorescenc

115 l deposition of new furrow membrane requires astral microtubules and release of internal stores of Ca

116 centrin-gamma TuRC interaction and perturbed astral microtubules and spindle bipolarity.

117 howed that spindle orientation required both astral microtubules and the actin cytoskeleton.

118 ed to be governed by the interaction between astral microtubules and the cell cortex and involve cort

119 itioning depends on interactions between the astral microtubules and the cell cortex.

120 enter to the cortex, a process that requires astral microtubules and the microtubule-based motor dyne

121 Cytokinesis is regulated by both astral microtubules and the midzone microtubules of the

122 molecular mechanism for the organization of astral microtubules and the mitotic spindle through Rab1

123 As centrosome integrity and astral microtubules appeared unperturbed by (+)-1,2-bis(

124 The majority of astral microtubules are dynamically unstable.

125 Although astral microtubules are known to play roles in these pro

126 Our results indicate that astral microtubules are required for establishing bipola

127 physical centrosome removal demonstrate that astral microtubules are required for such spindle elonga

128 In addition, dynein-mediated forces on astral microtubules are sufficient to segregate a 2N chr

129 racted to form spindles joined in series via astral microtubules as revealed by live cell imaging.

130 he stabilization of cortical associations of astral microtubules at cell-cell adhesions to orient the

131 to examine the residence time of individual astral microtubules at the cell cortex of developing emb

132 raction at SPBs compromises the anchorage of astral microtubules at the SPB and surprisingly also inf

133 lin and late stage embryos often do not have astral microtubules at their spindle poles.

134 f, while making contact with the cortex, the astral microtubules buckle as they exert compressive, pu

135 h MUG and normal mitosis, chromatin attracts astral microtubules but cannot induce spindle assembly.

136 ugh the capture and subsequent shortening of astral microtubules by a site in the cortex.

137 absence of a functional exclusion mechanism, astral microtubules can associate with Pins over the ent

138 Remarkably, cells depleted of astral microtubules conduct accurate, complete cytokines

139 These forces act before astral microtubules contact the cortex; thus, dynein mus

140 During mitosis, spindle poles align so the astral microtubules contact the lateral cortex.

141 cortical dynein-generated pulling forces on astral microtubules contribute to anaphase spindle elong

142 same cytokinetic signaling ensemble-opposed astral microtubules decorated with Ect2 and Cyk4.

143 We show that reducing astral microtubules decreases the frequency of spindle m

144 Before cellularization, astral microtubules determine metaphase furrow position

145 ow the cortex causes the depolymerization of astral microtubules during asymmetric spindle positionin

146 held assumptions that the centrosome and the astral microtubules emanating from it are essential for

147 The distance between astral microtubules ends and the anterior cortex was sig

148 contact geometry from "end-on" to "side-on." Astral microtubules engage cortically anchored motors al

149 Simultaneous contact of astral microtubules from both poles with the AMIZ direct

150 hate-bound Ran, stimulated polymerization of astral microtubules from centrosomes assembled on Xenopu

151 Astral microtubules from one pole only then contact the

152 Astral microtubules grow out from the two spindle poles,

153 g that Ect2 migrates from spindle midzone to astral microtubules in anaphase and that Ect2 shapes the

154 port a role for both the central spindle and astral microtubules in cytokinesis in animal cells.

155 sh embryos, where cells are unusually large, astral microtubules in metaphase are too short to positi

156 dundantly to suppress the formation of basal astral microtubules in neuroblasts.

157 robably a direct result of a failure to form astral microtubules in parthenogenetic embryos lacking c

158 r RNAi leads to a reduction in the length of astral microtubules in syncytial embryos, larval neurobl

159 the actomyosin cytoskeleton to plus ends of astral microtubules in the equatorial region of the cell

160 Because the plus-ends of many astral microtubules in the spindle point to the cell cor

161 es delayed development and a failure to form astral microtubules in the zygote.

162 000, consistent with the several thousand of astral microtubules in these cells.

163 absence of Cdc28-Clb4 activity (G1/S phase), astral microtubules interact with the bud tip in a manne

164 Dynamic plus ends of astral microtubules interact with the shmoo tip in matin

165 ctin cables are important for either guiding astral microtubules into the bud or anchoring them in th

166 eavage plane geometry in which the length of astral microtubules is limited by interaction with these

167 ted at the cell cortex to generate forces on astral microtubules is not clear.

168 Rather, confinement increases numbers of astral microtubules laterally contacting the cortex, shi

169 Disruption of astral microtubules leads to misalignment of the spindle

170 l release and transport of LGN complex along astral microtubules may contribute to spindle positionin

171 Transport on astral microtubules may provide a general mechanism for

172 In contrast, mEg5 punctae on astral microtubules moved transiently toward microtubule

173 though these cells lack the radial arrays of astral microtubules normally associated with each spindl

174 process thought to include direct capture by astral microtubules of kinetochores and/or noncentrosoma

175 yeast spindle pole body [SPB]) nucleate more astral microtubules on one of the two spindle poles than

176 Loss of either astral microtubules or Lis1/dynactin leads to spindle/co

177 primed to form furrows at either overlapping astral microtubules or the central spindle.

178 As nuclei divide, continued transport on astral microtubules partitions germ plasm to daughter nu

179 Cortical pulling on astral microtubules positions the mitotic spindle in res

180 mal in these embryos, but reduced numbers of astral microtubules reach all regions of the cortex at t

181 A subset of astral microtubules stabilizes during anaphase, becoming

182 the most dramatic effect on the lifetimes of astral microtubules that extend toward the cell cortex.

183 le treatment revealed a population of stable astral microtubules that formed during anaphase; among t

184 The long astral microtubules that occur in the absence of Kif18B

185 However, mitotic C377S tub1 cells displayed astral microtubules that often appeared excessive in num

186 phases due to a tethering force, mediated by astral microtubules that reach the anterior cell cortex.

187 brane, where dynein captures and walks along astral microtubules to help orient the mitotic spindle.

188 The dynein/dynactin motor complex pulls astral microtubules to orient the spindle.

189 ar mitotic apparatus protein (NuMA)-positive astral microtubules to orientate the mitotic spindle.

190 chromosomes during anaphase, cooperates with astral microtubules to position the cleavage furrow.

191 anchored dynein generates pulling forces on astral microtubules to position the mitotic spindle acro

192 c delay and prevents appropriate assembly of astral microtubules to promote spindle misorientation.

193 However, the motors that pull astral microtubules toward these actin structures are no

194 one spindle pole body the task of organizing astral microtubules towards the mother cell.

195 eted embryos, but the polymerization rate of astral microtubules was not slower than in wild type.

196 eation rate in LLCPK cells and the number of astral microtubules was similar in stathmin +/+ and -/-

197 rosome and a subset of differentially stable astral microtubules were also observed.

198 ligned in latrunculin-treated cells and that astral microtubules were misoriented, confirming a role

199 l and cellular events, perhaps by nucleating astral microtubules which mediate interactions with othe

200 e alignment by regulating the interaction of astral microtubules with subdomains of the bud cortex.

201 tioned and oriented by interactions of their astral microtubules with the cellular cortex, followed b

202 rotation is dependent on the interaction of astral microtubules with the cortical actin cytoskeleton

203 elial cells resulted in the disappearance of astral microtubules, and dividing spindle fiber formatio

204 short mitotic spindles, increased numbers of astral microtubules, and require the presence of the kin

205 om the cell cortex through interactions with astral microtubules, but neither the mechanism governing

206 bules nucleated along the length of existing astral microtubules, but this increase negatively affect

207 tic centrosomes and has few or no detectable astral microtubules, can develop into an adult fly.

208 entrosomes lose gamma-tubulin, spindles lose astral microtubules, chromosomes fail to reach a metapha

209 dominant-negative Rab11 expression disrupts astral microtubules, delays mitosis, and redistributes s

210 We show that astral microtubules, kinesin Khc-73, and Discs large (Dl

211 otic cells, including a drastic reduction in astral microtubules, malformed mitotic spindles, defocus

212 We report that even in the absence of astral microtubules, metaphase spindles in MDCK and HeLa

213 cally, constitutively active Rab11 increases astral microtubules, restores gamma-tubulin spindle pole

214 Second, astral microtubules, structures that undergo similar pat

215 e at approximately 11 microm/min, similar to astral microtubules, suggesting polymerization velocity

216 ely associated with both the cell cortex and astral microtubules, suggesting that it may directly int

217 ocess is likely driven by interactions among astral microtubules, the motor protein dynein, and the c

218 ed through a cortical machinery by capturing astral microtubules, thereby generating pushing/pulling

219 er to move from this SPB to the plus ends of astral microtubules, where Cdc28-Clb4 regulates the inte

220 nhibition of dynein blocked mEg5 movement on astral microtubules, whereas depletion of the Eg5-bindin

221 gamma-tubulin complex organizes spindle and astral microtubules, which, in turn, separate replicated

222 rst, Peg1 was required to form a spindle and astral microtubules, yet destabilized interphase microtu

223 rganize in vitro into asters, which resemble astral microtubules.

224 ion plane and a reduced number and length of astral microtubules.

225 ioles and are not anchored to the cortex via astral microtubules.

226 tic polarization via the central spindle and astral microtubules.

227 parallel with a second pathway that involves astral microtubules.

228 cal machine that mediates a pulling force on astral microtubules.

229 nents of the signaling pathway downstream of astral microtubules.

230 recruited, and thus modulate the behavior of astral microtubules.

231 proteins and large sizes, rely primarily on astral microtubules.

232 latter delivered cytoplasmic aurora B along astral microtubules.

233 endent pulling forces exerted on the tips of astral microtubules.

234 tained collapsed spindles with numerous long astral microtubules.

235 ruption of the organization of dynein and/or astral microtubules.

236 d also suggested a possible interaction with astral microtubules.

237 tor complex, which exerts a pulling force on astral microtubules.

238 xplained by the conventional model involving astral microtubules.

239 plus-end tracking, including localization to astral microtubules.

240 bule organization and a dramatic increase in astral microtubules.

241 rients the spindle through interactions with astral microtubules.

242 nisms of mitotic spindle orientation rely on astral microtubules.

243 determined site of cytokinesis by pulling on astral microtubules.

244 g by affecting the stability and dynamics of astral microtubules.

245 rces that act between the cell periphery and astral microtubules.

246 ndle misorientation accompanied by shortened astral microtubules.

247 teractions of cortical molecular motors with astral microtubules.

248 are thought to be organized differently from astral mitotic spindles, but the field lacks the basic s

249 To investigate the effect of excess astral MT activity, we depleted the MT depolymerizer mit

250 ally assemble a connected pair of polarized, astral MT arrays--termed an amphiaster ("a star on both

251 Our findings indicate that astral MT contact with the cortex is necessary for furro

252 importazole treatment results in defects in astral MT dynamics, as well as in mislocalization of LGN

253 etween EB1 and p150glued suppressed anaphase astral MT elongation and resulted in a delay of cytokine

254 Analysis of astral MT growth rates during anaphase shows that MTs co

255 per LGN and NuMA localization but stabilizes astral MT interactions with the cortex.

256 y protein that interacts with EB1 to control astral MT length.

257 8 Kif18B functions during mitosis to control astral MT organization.

258 the nucleus in interphase and is enriched at astral MT plus ends during early mitosis.

259 Astral MT shrinkage linked to Bud6p involves its direct

260 ortening velocities typical of free plus end astral Mts (approximately 0.5 micrometer/min).

261 protein She1 regulates dynein activity along astral MTs and directs spindle movements toward the bud

262 ndle MTs are partially destabilized, whereas astral MTs are dramatically destabilized.

263 and their interaction promotes elongation of astral MTs at anaphase onset.

264 of HIs between the MTs, the cytoplasm-filled astral MTs behave like a porous medium, with its permeab

265 row initiation but that the dynamic state of astral MTs does not affect their competency to stimulate

266 MCAK) from HeLa cells to produce ultra-long, astral MTs during mitosis.

267 ng normal contractile activity and that long astral MTs enlarge the blebs.

268 duction and spindle positioning, and loss of astral MTs has been reported to increase cortical contra

269 To maintain SPOC-mediated anaphase arrest, astral MTs must maintain persistent interactions with an

270 The data demonstrate that dynamic astral Mts search the cytoplasm for other Mts, as well a

271 ve role by serving as an attachment site for astral MTs to pull centrosomes apart [3-6].

272 n but did not prevent elongation of anaphase astral MTs toward the cortex, suggesting that EB1 and dy

273 Dynamically unstable astral Mts were captured at the shmoo tip forming a bund

274 monstrated that both motors decorated single astral MTs with dynein persisting at the plus end in ass

275 Urethane resulted in short, highly dynamic astral MTs with increased catastrophe that also stimulat

276 e cooperative activity of MSP-300, Klar, and astral MTs, and demonstrate its physiological significan

277 by nocodazole treatment, which depolymerizes astral MTs, or by overexpression of CLASP1, which does n

278 In addition to localizing to astral MTs, She1 also targets to the spindle, but its ro

279 shmoo tip forming a bundle of three or four astral Mts.

280 These results demonstrate that astral overlap in equilaterally dividing cells not only

281 In particular, we conclude that the astral pathway for cleavage-furrow formation involves th

282 ged nonmuscle myosin, we have found that the astral pathway for furrow formation involves the negativ

283 We tested the classical hypothesis that astral, prometaphase bipolar mitotic spindles are mainta

284 affected the assembly of microtubules in the astral region and impaired microtubule nucleation at the

285 ASTRAL runs in polynomial time, by constraining the sear

286 ASTRAL's running time is [Formula: see text], and ASTRAL

287 of proteins in SCOP provide the basis of the ASTRAL sequence libraries that can be used as a source o

288 lex, which regulates cortical attachments of astral spindle microtubules.

289 ssociate with centrosomes and play a role in astral spindle pole integrity in mitotic systems.

290 bryo, GFP-Pav-KLP cyclically associates with astral, spindle, and midzone microtubules and also to ac

291 ndles, and perhaps also to interpolar MTs in astral spindles.

292 Previously reported astral spreading during embryonic micromere formation su

293 ASTRALmay be accessed at http://astral.stanford.edu/

294 ASTRAL may be accessed at http://astral.stanford.edu/.

295 ASTRAL may be accessed at http://astral.stanford.edu/.

296 Several search tools have been added to ASTRAL to facilitate retrieval of data by individual use

297 To enhance the utility of ASTRAL to structural biologists, all SCOP domains are no

298 In this analysis of the ASTRAL trials (non-opioid substitution therapy [OST], n

299 ecently developed a coalescent-based method, ASTRAL, which is statistically consistent under the mult

300 We present a new version of ASTRAL, which we call ASTRAL-II.