Analysis of epigenetic stability and conversions in Saccharomyces cerevisiae reveals a novel role of CAF-I in position-effect variegation

Position-effect variegation (PEV) phenotypes are characterized by the robust multigenerational repression of a gene located at a certain locus (often called gene silencing) and occasional conversions to fully active state. Consequently, the active state then persists with occasional conversions to the repressed state. These effects are mediated by the establishment and maintenance of heterochromatin or euchromatin structures, respectively. In this study, we have addressed an important but often neglected aspect of PEV: the frequency of conversions at such loci. We have developed a model and have projected various PEV scenarios based on various rates of conversions. We have also enhanced two existing assays for gene silencing in Saccharomyces cerevisiae to measure the rate of switches from repressed to active state and vice versa. We tested the validity of our methodology in Δsir1 cells and in several mutants with defects in gene silencing. The assays have revealed that the histone chaperone Chromatin Assembly Factor I is involved in the control of epigenetic conversions. Together, our model and assays provide a comprehensive methodology for further investigation of epigenetic stability and position effects.     

Location and timing of Asian carp spawning in the Lower Missouri River

We sampled for eggs of Asian carps, (bighead carp Hypophthalmichthys nobilis, silver carp H. molitrix, and grass carp Ctenopharyngodon idella) in 12 sites on the Lower Missouri River and in six tributaries from the months of May through July 2005 and May through June 2006 to examine the spatial and temporal dynamics of spawning activity. We categorized eggs into thirty developmental stages, but usually they could not be identified to species. We estimated spawning times and locations based on developmental stage, temperature dependent rate of development and water velocity. Spawning rate was higher in the daytime between 05:00 and 21:00 h than at night. Spawning was not limited to a few sites, as has been reported for the Yangtze River, where these fishes are native, but more eggs were spawned in areas of high sinuosity. We employ a sediment transport model to estimate vertical egg concentration profiles and total egg fluxes during spawning periods on the Missouri River. We did not identify substantial spawning activity within tributaries or at tributary confluences examined in this study.     

Molecular simulation study of the assembly of DNA-functionalised nanoparticles: Effect of DNA strand sequence and composition

DNA functionalisation is a proven route to program an assembly of nanoparticles into a vast array of nanostructures. In this paper, we used coarse-grained molecular dynamics simulations to study DNA-functionalised nanoparticles and demonstrate the effect of grafted DNA strand composition, specifically the placement and number of contiguous G/C bases in the grafted DNA single strands, on the thermodynamics and structure of nanoparticle assembly at varying grafting densities and particle sizes. At a constant G/C content, nanoparticles assemble more readily when the G/C bases are placed on the outer or middle portions of the strands than on the inner portion. In addition, the number of neighbours within the assembled cluster decreases as the placement of the G/C bases goes from the outer to middle to inner sections of the strand. As the G/C content decreases, the cluster dissociation temperature, T_d, decreases, as the enthalpic drive to assemble decreases. At a high G/C content (number of grafts and G/C placement are held constant), as particle size decreases, T_d increases. This is because the smaller particles experience a lower entropic loss than do larger particles upon assembly. On the other hand, at a low G/C content, small changes in particle size lead to negligible changes in T_d.     

An N-terminal Nuclear Export Signal Regulates Trafficking and Aggregation of Huntingtin (Htt) Protein Exon 1

Huntington disease is a dominantly inherited neurodegenerative condition caused by polyglutamine expansion in the N terminus of the huntingtin protein (Htt). The first 17 amino acids (N17) of Htt play a key role in regulating its toxicity and aggregation. Both nuclear export and cytoplasm retention functions have been ascribed to N17. We have determined that N17 acts as a nuclear export sequence (NES) within Htt exon and when fused to yellow fluorescent protein. We have defined amino acids within N17 that constitute the nuclear export sequence (NES). Mutation of any of the conserved residues increases nuclear accumulation of Htt exon 1. Nuclear export of Htt is sensitive to leptomycin B and is reduced by knockdown of exportin 1. In HEK293 cells, NES mutations decrease overall Htt aggregation but increase the fraction of cells with nuclear inclusions. In primary cultured neurons, NES mutations increase nuclear accumulation and increase overall aggregation. This work defines a bona fide nuclear export sequence within N17 and links it to effects on protein aggregation. This may help explain the important role of N17 in controlling Htt toxicity.     

On birds: scale effects in the neognath hindlimb and differences in the gross morphology of wings and hindlimbs

Scale effects on whole limb morphology (i.e. bones together with in situ overlying muscles) are well understood for the neognath forelimb. However, scale effects on neognath gross hindlimb morphology remain largely unexplored. To broaden our understanding of avian whole limb morphology, I investigated the scaling of hindlimb inertial properties in neognath birds, testing empirical scaling relationships against the model of geometric similarity. Inertial property data – mass, moment of inertia, centre of mass distance, and radius of gyration – were collected from 22 neognath species representing a wide range of locomotor specializations. When scaled against body mass, hindlimb inertial properties scale with positive allometry. Thus, in terms of morphology, larger bodied neognaths possess hindlimbs requiring disproportionately more energy to accelerate and decelerate relative to body mass than smaller bodied birds. When scaled against limb length, hindlimb inertial properties scale according to isometry. In the subclade Land Birds (sensu Hackett et al.), hindlimb inertial properties largely scale according to positive allometry. The contrasting results of positive allometry vs. isometry in neognaths are due to how hindlimb length scales against body mass. Negative allometry of hindlimb inertial properties, which would reduce terrestrial locomotion costs, would probably make the hindlimb susceptible to mechanical failure or too diminutive for its many ecological functions. Comparing the scaling relationships of wings and hindlimbs highlights how locomotor costs influence the scaling of limb inertial properties. © 2013 The Linnean Society of London, Biological Journal of the Linnean Society, 2013, 110 , 14–31.     

Vps1 in the late endosome-to-vacuole traffic

Vacuolar protein sorting 1 (Vps1), the yeast homolog to human dynamin, is a GTP hydrolyzing protein, which plays an important role in protein sorting and targeting between the Golgi and late endosomal compartments. In this study, we assessed the functional significance of Vps1 in the membrane traffic towards the vacuole. We show here that vps1Δ cells accumulated FM4-64 to a greater extent than wild-type (WT) cells, suggesting slower endocytic degradation traffic toward the vacuole. In addition, we observed that two endosome-to-vacuole traffic markers, DsRed-FYVE and Ste2-GFP, were highly accumulated in Vps1-deficient cells, further supporting Vps1’s implication in efficient trafficking of endocytosed materials to the vacuole. Noteworthy, a simultaneous imaging analysis in conjunction with FM4-64 pulse-chase experiment further revealed that Vps1 plays a role in late endosome to the vacuole transport. Consistently, our subcellular localization analysis showed that Vps1 is present at the late endosome. The hyperaccumulation of endosomal intermediates in the vps1 mutant cells appears to be caused by the disruption of integrity of HOPS tethering complexes, manifested by mislocalization of Vps39 to the cytoplasm. Finally, we postulate that Vps1 functions together with the Endosomal Sorting Complex Required for Transport (ESCRT) complex at the late endosomal compartments, based on the observation that the double mutants, in which VPS1 along with singular ESCRT I, II and III genes have been disrupted, exhibited synthetic lethality. Together, we propose that Vps1 is required for correct and efficient trafficking from the late endosomal compartments to the vacuole.     

THE EVOLUTION OF LOCOMOTOR RHYTHMICITY IN TETRAPODS

Differences in rhythmicity (relative variance in cycle period) among mammal, fish, and lizard feeding systems have been hypothesized to be associated with differences in their sensorimotor control systems. We tested this hypothesis by examining whether the locomotion of tachymetabolic tetrapods (birds and mammals) is more rhythmic than that of bradymetabolic tetrapods (lizards, alligators, turtles, salamanders). Species averages of intraindividual coefficients of variation in cycle period were compared while controlling for gait and substrate. Variance in locomotor cycle periods is significantly lower in tachymetabolic than in bradymetabolic animals for datasets that include treadmill locomotion, non‐treadmill locomotion, or both. When phylogenetic relationships are taken into account the pooled analyses remain significant, whereas the non‐treadmill and the treadmill analyses become nonsignificant. The co‐occurrence of relatively high rhythmicity in both feeding and locomotor systems of tachymetabolic tetrapods suggests that the anatomical substrate of rhythmicity is in the motor control system, not in the musculoskeletal components.     

Design,synthesis, and evaluation of curcumin-derived arylheptanoids for glioblastoma and neuroblastoma cytotoxicity

Using an innovative approach toward multiple carbon–carbon bond-formations that relies on the multifaceted catalytic properties of titanocene complexes we constructed a series of C1–C7 analogs of curcumin for evaluation as brain and peripheral nervous system anti-cancer agents. C2-Arylated analogs proved efficacious against neuroblastoma (SK-N-SH & SK-N-FI) and glioblastoma multiforme (U87MG) cell lines. Similar inhibitory activity was also evident in p53 knockdown U87MG GBM cells. Furthermore, lead compounds showed limited growth inhibition in vitro against normal primary human CD34+hematopoietic progenitor cells. Taken together, the present findings indicate that these curcumin analogs are viable lead compounds for the development of new central and peripheral nervous system cancer chemotherapeutics with the potential for little effects on normal hematopoietic progenitor cells.