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PubMed2007

Importance of interfacial adsorption in the biphasic hydroformylation of higher olefins promoted by cyclodextrins: a molecular dynamics study at the decene/water interface.

We report herein a molecular dynamics study of the main species involved in the hydroformylation of higher olefins promoted by cyclodextrins in 1-decene/water biphasic systems at a temperature of 350 K. The two liquids form a well-defined sharp interface of approximately 7 A width in the absence of solute; the decene molecules are generally oriented "parallel" to the interface where they display transient contacts with water. We first focused on rhodium complexes bearing water-soluble TPPTS(3-) ligands (where TPPTS(3-) represents tris(m-sulfonatophenyl)phosphine) involved in the early steps of the reaction. The most important finding concerned the surface activity of the "active" form of the catalyst [RhH(CO)(TPPTS)(2)](6-), the [RhH(CO)(2)(TPPTS)(2)](6-) complex, and the key reaction intermediate [RhH(CO)(TPPTS)(2)(decene)](6-) (with the olefin pi-coordinated to the metal center) which are adsorbed at the water side of the interface in spite of their -6 charge. The free TPPTS(3-) ligands themselves are also surface-active, whereas the -9 charged catalyst precursor [RhH(CO)(TPPTS)(3)](9-) prefers to be solubilized in water. The role of cyclodextrins was then investigated by performing simulations on 2,6-dimethyl-beta-cyclodextrin ("CD") and its inclusion complexes with the reactant (1-decene), a reaction product (undecanal), and the corresponding key reaction intermediate [RhH(CO)(TPPTS)(2)(decene)](6-) as guests; they were all shown to be surface-active and prefer the interface over the bulk aqueous phase. These results suggest that the biphasic hydroformylation of higher olefins takes place "right" at the interface and that the CDs promote the "meeting" of the olefin and the catalyst in this peculiar region of the solution by forming inclusion complexes "preorganized" for the reaction. Our results thus point to the importance of adsorption at the liquid/liquid interface in this important phase-transfer-catalyzed reaction.

Journal Article↗
PubMed2002

Evolution of transcription factor binding sites in Mammalian gene regulatory regions: conservation and turnover.

Comparisons between human and rodent DNA sequences are widely used for the identification of regulatory regions (phylogenetic footprinting), and the importance of such intergenomic comparisons for promoter annotation is expanding. The efficacy of such comparisons for the identification of functional regulatory elements hinges on the evolutionary dynamics of promoter sequences. Although it is widely appreciated that conservation of sequence motifs may provide a suggestion of function, it is not known as to what proportion of the functional binding sites in humans is conserved in distant species. In this report, we present an analysis of the evolutionary dynamics of transcription factor binding sites whose function had been experimentally verified in promoters of 51 human genes and compare their sequence to homologous sequences in other primate species and rodents. Our results show that there is extensive divergence within the nucleotide sequence of transcription factor binding sites. Using direct experimental data from functional studies in both human and rodents for 20 of the regulatory regions, we estimate that 32%-40% of the human functional sites are not functional in rodents. This is evidence that there is widespread turnover of transcription factor binding sites. These results have important implications for the efficacy of phylogenetic footprinting and the interpretation of the pattern of evolution in regulatory sequences.

Animals↗
PubMed2004

Highly specific interactions between bHLH transcription factors and chromatin during retina development.

Basic helix-loop-helix (bHLH) transcription factors such as atonal homolog 5 (ATH5) and neurogenin 2 (NGN2) determine crucial events in retinogenesis. Using chromatin immunoprecipitation, we demonstrate that their interactions with target promoters undergo dynamic changes as development proceeds in the chick embryo. Chick ATH5 associates with its own promoter and with the promoter of the beta3 nicotinic receptor specifically in retinal ganglion cells and their precursors. NGN2 binds to the ATH5 promoter in retina but not in optic tectum, suggesting that interactions between bHLH factors and chromatin are highly tissue specific. The transcriptional activations of both promoters correlate with dimethylation of lysine 4 on histone H3. Inactivation of the ATH5 promoter in differentiated neurons is accompanied by replication-independent chromatin de-methylation. This report is one of the first demonstrations of correlation between gene expression, binding of transcription factors and chromatin modification in a developing neural tissue.

Animals↗
PubMed1995

Evolution of a dynamic cytoskeleton.

Actin filaments and microtubules form the cytoskeleton of all eukaryotic cells, and they are responsible for organizing the cytoplasm and supporting motile processes. Both polymers are highly dynamic, and their polymerization dynamics are central to their organization. Though their evolutionary origins appear to be distinct, actin and tubulin have a similar mechanism for promoting polymerization dynamics in which the energy of nucleotide triphosphate hydrolysis during polymerization is used to weaken the bonds between subunits, thus promoting subsequent depolymerization. The evolutionary origins of actin and tubulin are unclear. It is likely that motile mechanisms driven by reversible polymerization, termed thermal ratchets, are older than those based on ATPase motor proteins. Such mechanisms are still important in modern eukaryotes, and may have powered early versions of the critical motile processes of phagocytosis and chromosome segregation in primitive cells. Thus evolution of dynamic cytoskeletal polymers may have been one of the earliest and most important steps leading to the evolution of eukaryotes. Plausible evolutionary pathways can be constructed leading from simple enzymes to dynamic cytoskeletal polymers.

Actins↗
PubMed2006

Hypoxic regulation of telomerase gene expression by transcriptional and post-transcriptional mechanisms.

Basal telomerase activity is dependent on expression of the hTERT and hTR genes and upregulation of telomerase gene expression is associated with tumour development. It is therefore possible that signal transduction pathways involved in tumour development and features of the tumour environment itself may influence telomerase gene regulation. The majority of solid tumours contain regions of hypoxia and it has recently been demonstrated that hypoxia can increase telomerase activity by mechanisms that are still poorly defined. Here, we show that hypoxia induces the transcriptional activity of both hTR and hTERT gene promoters. While endogenous hTR expression is regulated at the transcriptional level, hTERT is subject to regulation by alternative splicing under hypoxic conditions, which involves a switch in the splice pattern in favour of the active variant. Furthermore, analysis of the chromatin landscape of the telomerase promoters reveals dynamic recruitment of a transcriptional complex involving the hypoxia-inducible factor-1 transcription factor, p300, RNA polymerase II and TFIIB, to both promoters during hypoxia, which traffics along and remains associated with the hTERT gene as transcription proceeds. These studies show that hTERT and hTR are subject to similar controls under hypoxia and highlight the rapid and dynamic regulation of the telomerase genes in vivo.

Alternative Splicing↗
PubMed2001

CREM and ICER are differentially implicated in trans-synaptic induction of tyrosine hydroxylase gene expression in adrenal medulla and sympathetic ganglia of rat.

Reserpine treatment leads to a trans-synaptic increase of the tyrosine hydroxylase (TH) gene transcription rate, mRNA and protein levels in catecholaminergic tissues including the adrenal medulla (AM) and the superior cervical ganglia (SCG). The TPA-responsive element plays an important role in the trans-synaptically-induced transcription of the TH gene in the AM, whereas it does not appear to be involved in the SCG (Trocmé et al. [1997] J. Neurosci. Res. 48:489-498). In this study, we show that another regulatory sequence of the TH proximal promoter, the cAMP-responsive element (CRE), binds different factors in the AM and in the SCG. To elucidate the dynamics of promoter regulation a complete time course analysis was conducted. Reserpine treatment enhances, between 1 hr and 8 hr after the injection, the expression and the binding of the repressor ICER in the AM, whereas in the SCG it enhances the binding of CREM factors. These results suggest that the mechanisms mediating trans-synaptic induction of the TH gene are different in the AM and SCG. The interplay between positive and negative transcription factors and their kinetics of action are responsive of the long-term regulation of the TH gene.

Adrenal Medulla↗
PubMed2006

Adsorption at the liquid-liquid interface in the biphasic rhodium catalyzed hydroformylation of olefins promoted by cyclodextrins: a molecular dynamics study.

Using molecular dynamics (MD) simulations, we investigate the interfacial distribution of partners involved in the phase transfer rhodium catalyzed hydroformylation of olefins promoted by beta-cyclodextrins (beta-CDs). The beta-CDs, the reactant (alkene), product (aldehyde), several rhodium complexes (the catalyst, its precursor, and its alkene adduct) are simulated at the water-"oil" interface, where oil is represented by chloroform or hexane. It is shown that unsubstituted beta-CD and its 6-methylated and 2,6-dimethylated analogues adsorb at the interface, whereas the liposoluble permethylated CD does not. The precursor of the catalyst [RhH(CO)(TPPTS)3]9- (with triphenylphosphine trisulfonated TPPTS3- ligands) sits in water, but the less charged [RhH(CO)(TPPTS)2]6- catalyst and the [RhH(CO)(TPPTS)2(alkene)]6- reaction intermediate are clearly surface active. The TPPTS3- anions also concentrate at the interface, where they adopt an amphiphilic conformation, forming an electrical double layer with their Na+ counterions. Thus, the most important key partners involved in the hydroformylation reaction concentrate at the interface, thereby facilitating the reaction, a process which may be further facilitated upon complexation by CDs. These results point to the importance of adsorption at the liquid-liquid interface in the two-phase hydroformylation reaction of olefins promoted by beta-CDs and provide microscopic pictures of this peculiar region of the solution.

Journal Article↗
PubMed2004

Characterization of a 200 kDa microtubule-associated protein of tobacco BY-2 cells, a member of the XMAP215/MOR1 family.

A microtubule-associated protein composed of a 200 kDa polypeptide (MAP200) was isolated from tobacco-cultured BY-2 cells. Analysis of the partial amino acid sequence showed that MAP200 was identical to TMBP200, the tobacco MOR1/XMAP215 homolog. Although several homolog proteins in animal and yeast cells have been reported to promote MT dynamics in vitro, no such function has been reported for plant homologs. Turbidity measurements of tubulin solution suggested that MAP200 promoted tubulin polymerization, and analysis by dark-field microscopy revealed that this MAP increased both the number and length of microtubules (MTs). Electron microscopy and experiments using a chemical crosslinker demonstrated that MAP200 forms a complex with tubulin. Throughout the cell cycle, some MAP200 colocalized with MT structures, including cortical MTs, the preprophase band, spindle and phragmoplast, while some MAP200 was localized in areas lacking MTs. Based on our biochemical and immunofluorescence findings, the function of MAP200 in MT polymerization is discussed.

Biopolymers↗
PubMed2005

Critical mass hypothesis revisited: role of dynamical wave stability in spontaneous termination of cardiac fibrillation.

The tendency of atrial or ventricular fibrillation to terminate spontaneously in finite-sized tissue is known as the critical mass hypothesis. Previous studies have shown that dynamical instabilities play an important role in creating new wave breaks that maintain cardiac fibrillation, but its role in self-termination, in relation to tissue size and geometry, is not well understood. This study used computer simulations of two- and three-dimensional tissue models to investigate qualitatively how, in relation to tissue size and geometry, dynamical instability affects the spontaneous termination of cardiac fibrillation. The major findings are as follows: 1) Dynamical instability promotes wave breaks, maintaining fibrillation, but it also causes the waves to extinguish, facilitating spontaneous termination of fibrillation. The latter effect predominates as dynamical instability increases, so that fibrillation is more likely to self-terminate in a finite-sized tissue. 2) In two-dimensional tissue, the average duration of fibrillation increases exponentially as tissue area increases. In three-dimensional tissue, the average duration of fibrillation decreases initially as tissue thickness increases as a result of thickness-induced instability but then increases after a critical thickness is reached. Therefore, in addition to tissue mass and geometry, dynamical instability is an important factor influencing the maintenance of cardiac fibrillation.

Atrial Fibrillation↗
PubMed2006

Visualizing dynamic E2F-mediated repression in vivo.

Although many E2F target genes have been identified recently, very little is known about how any single E2F site controls the expression of an E2F target gene in vivo. To test the requirement for a single E2F site in vivo and to learn how E2F-mediated repression is regulated during development and tumorigenesis, we have constructed a novel series of wild-type and mutant Rb promoter-LacZ transgenic reporter lines that allow us to visualize the activity of a crucial E2F target in vivo, the retinoblastoma tumor suppressor gene (Rb). Two mutant Rb promoter-LacZ constructs were used to evaluate the importance of a single E2F site or a nearby activator (Sp1/Ets) site that is found mutated in low-penetrance retinoblastomas. The activity of the wild-type Rb promoter is dynamic, varying spatially and temporally within the developing nervous system. While loss of the activator site silences the Rb promoter, loss of the E2F site stimulates its activity in the neocortex, retina, and trigeminal ganglion. Surprisingly, E2F-mediated repression of Rb does not act globally or in a static manner but, instead, is a highly dynamic process in vivo. Using neocortical extracts, we detected GA-binding protein alpha (GABPalpha, an Ets family member) bound to the activator site and both E2F1 and E2F4 bound to the repressor site of the Rb promoter in vitro. Additionally, we detected binding of both E2F1 and E2F4 to the Rb promoter in vivo using chromatin immunoprecipitation analysis on embryonic day 13.5 brain. Unexpectedly, we detect no evidence for Rb promoter autoregulation in neuroendocrine tumors from Rb+/-; RbP-LacZ mice that undergo loss of heterozygosity at the Rb locus, in contrast to the situation in human retinoblastomas where high RB mRNA levels are found. In summary, this study provides the first demonstration that loss of an E2F site is critical for target gene repression in vivo and underscores the complexity of the Rb and E2F family network in vivo.

Animals↗
PubMed2001

Control of microtubule dynamics by Stu2p is essential for spindle orientation and metaphase chromosome alignment in yeast.

Stu2p is a member of a conserved family of microtubule-binding proteins and an essential protein in yeast. Here, we report the first in vivo analysis of microtubule dynamics in cells lacking a member of this protein family. For these studies, we have used a conditional Stu2p depletion strain expressing alpha-tubulin fused to green fluorescent protein. Depletion of Stu2p leads to fewer and less dynamic cytoplasmic microtubules in both G1 and preanaphase cells. The reduction in cytoplasmic microtubule dynamics is due primarily to decreases in both the catastrophe and rescue frequencies and an increase in the fraction of time microtubules spend pausing. These changes have significant consequences for the cell because they impede the ability of cytoplasmic microtubules to orient the spindle. In addition, recovery of fluorescence after photobleaching indicates that kinetochore microtubules are no longer dynamic in the absence of Stu2p. This deficiency is correlated with a failure to properly align chromosomes at metaphase. Overall, we provide evidence that Stu2p promotes the dynamics of microtubule plus-ends in vivo and that these dynamics are critical for microtubule interactions with kinetochores and cortical sites in the cytoplasm.

Animals↗
PubMed2005

Origins of extrinsic variability in eukaryotic gene expression.

Variable gene expression within a clonal population of cells has been implicated in a number of important processes including mutation and evolution, determination of cell fates and the development of genetic disease. Recent studies have demonstrated that a significant component of expression variability arises from extrinsic factors thought to influence multiple genes simultaneously, yet the biological origins of this extrinsic variability have received little attention. Here we combine computational modelling with fluorescence data generated from multiple promoter-gene inserts in Saccharomyces cerevisiae to identify two major sources of extrinsic variability. One unavoidable source arising from the coupling of gene expression with population dynamics leads to a ubiquitous lower limit for expression variability. A second source, which is modelled as originating from a common upstream transcription factor, exemplifies how regulatory networks can convert noise in upstream regulator expression into extrinsic noise at the output of a target gene. Our results highlight the importance of the interplay of gene regulatory networks with population heterogeneity for understanding the origins of cellular diversity.

Eukaryotic Cells↗
PubMed2004

Biological role and structural mechanism of twinfilin-capping protein interaction.

Twinfilin and capping protein (CP) are highly conserved actin-binding proteins that regulate cytoskeletal dynamics in organisms from yeast to mammals. Twinfilin binds actin monomer, while CP binds the barbed end of the actin filament. Remarkably, twinfilin and CP also bind directly to each other, but the mechanism and role of this interaction in actin dynamics are not defined. Here, we found that the binding of twinfilin to CP does not affect the binding of either protein to actin. Furthermore, site-directed mutagenesis studies revealed that the CP-binding site resides in the conserved C-terminal tail region of twinfilin. The solution structure of the twinfilin-CP complex supports these conclusions. In vivo, twinfilin's binding to both CP and actin monomer was found to be necessary for twinfilin's role in actin assembly dynamics, based on genetic studies with mutants that have defined biochemical functions. Our results support a novel model for how sequential interactions between actin monomers, twinfilin, CP, and actin filaments promote cytoskeletal dynamics.

Actin Depolymerizing Factors↗
PubMed2002

[Soybean proteins in correction of coronary risk factors in patients with cardiovascular diseases].

At 95 patients with coronary artery disease and high blood pressure studied influence of a diet with low lipid by a directedness including yields of processing soy, on dynamics(changes) of clinical symptoms, indexes lipid of the status and coronary risk factors. The application of a diet, 50% of fiber in which was replaced on soy protein isolate, promoted positive dynamics(changes) of clinical manifestations of disease on a hum noise of improving of indexes lipid of a spectrum and coronary risk factors. The research has shown, that the use in the treat-preventive purposes soy protein isolate is rather perspective.

Adult↗
PubMed2006

Origin of the dynamic transition upon pressurization of crystalline proteins.

We study the role of hydration water in the dynamic transition of low-hydrated proteins upon pressurization found recently (Meinhold, L.; Smith, J. C. Phys. Rev. E 2005, 72, 061908). Clustering and percolation of water in the hydration shells of protein molecules in crystalline Staphylococcal nuclease are analyzed at various pressures. The number of water molecules in the hydration shell increases and the hydrogen-bonded network of hydration water spans with increasing pressure. The dynamic transition of protein occurs when the spanning water network exists with the probability of about 50% and hydration water shows large density fluctuations. Formation of a spanning water network upon pressurization promotes protein dynamics as in the case of the dynamic transition with increasing hydration. Properties of hydration water in various thermodynamic states and their influence on biological function are discussed.

Biophysics↗
PubMed2006

Cdc42 participates in the regulation of ADF/cofilin and retinal growth cone filopodia by brain derived neurotrophic factor.

Rho family GTPases have important roles in mediating the effects of guidance cues and growth factors on the motility of neuronal growth cones. We previously showed that the neurotrophin BDNF regulates filopodial dynamics on growth cones of retinal ganglion cell axons through activation of the actin regulatory proteins ADF and cofilin by inhibiting a RhoA-dependent pathway that phosphorylates (inactivates) ADF/cofilin. The GTPase Cdc42 has also been implicated in mediating the effects of positive guidance cues. In this article we investigated whether Cdc42 is involved in the effects of BDNF on filopodial dynamics. BDNF treatment increases Cdc42 activity in retinal neurons, and neuronal incorporation of constitutively active Cdc42 mimics the increases in filopodial number and length. Furthermore, constitutively active and dominant negative Cdc42 decreased and increased, respectively, the activity of RhoA in retinal growth cones, indicating crosstalk between these GTPases in retinal growth cones. Constitutively active Cdc42 mimicked the activation of ADF/cofilin that resulted from BDNF treatment, while dominant negative Cdc42 blocked the effects of BDNF on filopodia and ADF/cofilin. The inability of dominant negative Cdc42 to block ADF/cofilin activation and stimulation of filopodial dynamics by the ROCK inhibitor Y-27632 indicate interaction between Cdc42 and RhoA occurs upstream of ROCK. Our results demonstrate crosstalk occurs between GTPases in mediating the effects of BDNF on growth cone motility, and Cdc42 activity can promote actin dynamics via activation of ADF/cofilin.

Actin Depolymerizing Factors↗
PubMed1998

On the stabilizing role of stage structure in piscene consumer-resource interactions.

A stage-structured consumer-resource model is investigated using plausible biological parameter estimates. The model, developed from patterns in energy allocation across fish life-history strategies, explicitly considers the effects of delays in maturation on juvenile growth and mortality. It is found that stage structure in the consumer fish population tends to locally stabilize consumer-resource dynamics for realistic parameters. Additionally, it is shown that stage structure bounds nonequilibrium behavior relative to the case without stage structure. Finally, it is shown that the increased stability and bounding of solutions has the seemingly paradoxical consequence of promoting nonequilibrium dynamics when even small amounts of noise are added to the system.

Age Factors↗
PubMed2001

Evidence for the role of MAP1B in axon formation.

Cultured neurons obtained from a hypomorphous MAP1B mutant mouse line display a selective and significant inhibition of axon formation that reflects a delay in axon outgrowth and a reduced rate of elongation. This phenomenon is paralleled by decreased microtubule formation and dynamics, which is dramatic at the distal axonal segment, as well as in growth cones, where the more recently assembled microtubule polymer normally predominates. These neurons also have aberrant growth cone formation and increased actin-based protrusive activity. Taken together, this study provides direct evidence showing that by promoting microtubule dynamics and regulating cytoskeletal organization MAP1B has a crucial role in axon formation.

Animals↗