Tunable-slip boundaries for coarse-grained simulations of fluid flow

On the micro- and nanoscale, classical hydrodynamic boundary conditions such as the no-slip condition no longer apply. Instead, the flow profiles exhibit "slip" at the surface, which is characterized by a finite slip length (partial slip). We present a new, systematic way of implementing partial-slip boundary conditions with arbitrary slip length in coarse-grained computer simulations. The main idea is to represent the complex microscopic interface structure by a spatially varying effective viscous force. An analytical equation for the resulting slip length can be derived for planar and for curved surfaces. The comparison with computer simulations of a DPD (dissipative particle dynamics) fluid shows that this expression is valid from full slip to no slip.

Forces between elongated particles in a nematic colloid

Using molecular dynamics simulations we study the interactions between elongated colloidal particles (length to breath ratio >>1) in a nematic host. The simulation results are compared to the results of a Landau-de Gennes elastic free energy. We find that depletion forces dominate for the sizes of the colloidal particles studied. The tangential component of the force, however, allows us to resolve the elastic contribution to the total interaction. We find that this contribution differs from the quadrupolar interaction predicted at large separations. The difference is due to the presence of nonlinear effects, namely, the change in the positions and structure of the defects and their annihilation at small separations.

Dynamical precursor of nematic order in a dense fluid of hard ellipsoids of revolution

We investigate hard ellipsoids of revolution in a parameter regime where no long range nematic order is present but already finite-size domains are formed which show orientational order. Domain formation leads to a substantial slowing down of a collective rotational mode which separates well from the usual microscopic frequency regime. A dynamic coupling of this particular mode into all other modes provides a general mechanism which explains an excess peak in spectra of molecular fluids. Using molecular dynamics simulation on up to 4096 particles and on solving the molecular mode coupling equation we investigate dynamic properties of the peak and prove its orientational origin.

Ring closing metathesis mediated synthesis of 4a-aryloxodecahydroisoquinolines, intermediates in the preparation of novel opiates

[reaction: see text]. The concise syntheses of the 4a-aryldecahydroisoquinolines 1 and 2 through a uniform strategy starting from N-methyl-3-allyl-4-piperidinone are reported in this Letter. Key transformations include a ring closing metathesis reaction to prepare a trans-octahydroisoquinoline common intermediate and a regiocontrolled hydroboration-oxidation sequence.

Myocyte enhancer factor 2A and 2D undergo phosphorylation and caspase-mediated degradation during apoptosis of rat cerebellar granule neurons

Myocyte enhancer factor 2 (MEF2) proteins are important regulators of gene expression during the development of skeletal, cardiac, and smooth muscle. MEF2 proteins are also present in brain and recently have been implicated in neuronal survival and differentiation. In this study we examined the cellular mechanisms regulating the activity of MEF2s during apoptosis of cultured cerebellar granule neurons, an established in vitro model for studying depolarization-dependent neuronal survival. All four MEF2 isoforms (A, B, C, and D) were detected by immunoblot analysis in cerebellar granule neurons. Endogenous MEF2A and MEF2D, but not MEF2B or MEF2C, were phosphorylated with the induction of apoptosis. The putative sites that were phosphorylated during apoptosis are functionally distinct from those previously reported to enhance MEF2 transcription. The increased phosphorylation of MEF2A and MEF2D was followed by decreased DNA binding, reduced transcriptional activity, and caspase-dependent cleavage to fragments containing N-terminal DNA binding domains and C-terminal transactivation domains. Expression of the highly homologous N terminus of MEF2A (1-131 amino acids) antagonized the transcriptional activity and prosurvival effects of a constitutively active mutant of MEF2D (MEF2D-VP16). We conclude that MEF2A and MEF2D are prosurvival factors with high transcriptional activity in postmitotic cerebellar granule neurons. When these neurons are induced to undergo apoptosis by lowering extracellular potassium, MEF2A and MEF2D are phosphorylated, followed by decreased DNA binding and cleavage by a caspase-sensitive pathway to N-terminal fragments lacking the transactivation domains. The degradation of MEF2D and MEF2A and the generation of MEF2 fragments that have the potential to act as dominant-inactive transcription factors lead to apoptotic cell death.

Genetic evidence that the alpha5 helix of the receiver domain of PhoB is involved in interdomain interactions

Two-component signaling proteins are involved in transducing environmental stimuli into intracellular signals. Information is transmitted through a phosphorylation cascade that consists of a histidine protein kinase and a response regulator protein. Generally, response regulators are made up of a receiver domain and an output domain. Phosphorylation of the receiver domain modulates the activity of the output domain. The mechanisms by which receiver domains control the activities of their respective output domains are unknown. To address this question for the PhoB protein from Escherichia coli, we have employed two separate genetic approaches, deletion analysis and domain swapping. In-frame deletions were generated within the phoB gene, and the phenotypes of the mutants were analyzed. The output domain, by itself, retained significant ability to activate transcription of the phoA gene. However, another deletion mutant that contained the C-terminal alpha-helix of the receiver domain (alpha5) in addition to the entire output domain was unable to activate transcription of phoA. This result suggests that the alpha5 helix of the receiver domain interacts with and inhibits the output domain. We also constructed two chimeric proteins that join various parts of the chemotaxis response regulator, CheY, to PhoB. A chimera that joins the N-terminal approximately 85% of CheY's receiver domain to the beta5-alpha5 loop of PhoB's receiver domain displayed phosphorylation-dependent activity. The results from both sets of experiments suggest that the regulation of PhoB involves the phosphorylation-mediated modulation of inhibitory contacts between the alpha5 helix of its unphosphorylated receiver domain and its output domain.

Molecular-dynamics study of the nematic-isotropic interface

We present large-scale molecular-dynamics simulations of a nematic-isotropic interface in a system of repulsive ellipsoidal molecules, focusing in particular on the capillary-wave fluctuations of the interfacial position. The interface anchors the nematic phase in a planar way, i.e., the director aligns parallel to the interface. Capillary waves in the direction parallel and perpendicular to the director are considered separately. We find that the spectrum is anisotropic, the amplitudes of capillary waves being larger in the direction perpendicular to the director. In the long-wavelength limit, however, the spectrum becomes isotropic and compares well with the predictions of a simple capillary-wave theory.

Computer simulation of topological defects around a colloidal particle or droplet dispersed in a nematic host

We use molecular dynamics to study the ordering of a nematic liquid crystal around a spherical particle or droplet. Homeotropic boundary conditions and strong anchoring create a hedgehog (radial point defect) director configuration on the particle surface and in its vicinity; this topological defect is canceled by nearby defect structures in the surrounding liquid crystal, so as to give a uniform director field at large distances. We observe three defect structures for different particle sizes: a quadrupolar one with a ring defect surrounding the particle in the equatorial plane; a dipolar one with a satellite defect at the north or south pole; and a transitional, nonequatorial, ring defect. These observations are broadly consistent with the predictions of the simplest elastic theory. By studying density and order-parameter maps, we are able to examine behavior near the particle surface, and in the disclination core region, where the elastic theory is inapplicable. Despite the relatively small scale of the inhomogeneities in our systems, the simple theory gives reasonably accurate predictions of the variation of defect position with particle size.

Myocyte enhancer factors-2B and -2C are required for adhesion related kinase repression of neuronal gonadotropin releasing hormone gene expression

Synthesis of the hypothalamic peptide, gonadotropin releasing hormone (GnRH), is paramount for reproductive function. GnRH neurons originate in the olfactory region and migrate into the forebrain during development. We recently implicated adhesion related kinase (Ark) in GnRH neuron development based on its differential expression in two GnRH producing cell lines, GT1-7 and Gn10. The Ark membrane receptor encodes an extracellular domain resembling cell adhesion molecules and an intracellular tyrosine kinase. Ark is expressed in Gn10 cells derived from migrating GnRH neurons but not GT1-7 cells of the post-migratory phenotype. Here, we show that Ark and GnRH transcripts are colocalized in the cribriform plate at midgestation, suggesting that Ark is expressed in migrating GnRH neurons in vivo. Furthermore, we have identified the GnRH gene as a downstream target of Ark signaling. Ark inhibits GnRH gene expression in GnRH neuronal cells via the coordinated binding of myocyte enhancer factor-2B and -2C (MEF-2B and -2C) and a putative homeoprotein within the proximal rat GnRH promoter. Given that MEF-2 proteins are widely expressed in the brain, these studies provide further evidence for MEF-2 action during neuronal development. Moreover, our studies elucidate a potential role for Ark in regulating GnRH gene expression during GnRH neuronal migration.

Liquid crystal director fluctuations and surface anchoring by molecular simulation

We propose a simple and reliable method to measure the liquid crystal surface anchoring strength by molecular simulation. The method is based on the measurement of the long-range fluctuation modes of the director in confined geometry. As an example, molecular simulations of a liquid crystal in slab geometry between parallel walls with homeotropic anchoring have been carried out using the Monte Carlo technique. By studying different slab thicknesses, we are able to calculate separately the position of the elastic boundary condition and the extrapolation length.

Isotropic-nematic interface of soft spherocylinders

The isotropic-nematic interface of a simple model of liquid-crystal molecules has been investigated using computer simulation, and by numerical minimization of the Onsager free-energy functional. The molecules are represented by long spherocylindrical particles interacting via the Kihara potential. The agreement between simulation and theory is excellent, apart from the bulk coexistence densities which are over estimated by the theory. Planar alignment of the molecules at the interface is preferred in all cases. The number density profile is found to vary monotonically, both in simulation and in theory. Biaxiality of the molecular orientational distribution near the interface is demonstrated.

Design, synthesis and biological evaluation of 3-amino-3-phenylpropionamide derivatives as novel mu opioid receptor ligands

3-Amino-3-phenylpropionamide derivatives were produced as small molecule mimics of the cyclic octapeptide octreotide from readily available imine 1. The compounds exhibit high affinity for the mu opioid receptor.

Molecular simulation and theory of a liquid crystalline disclination core

Molecular simulations of a nematic liquid crystal confined in cylinder geometry with homeotropic anchoring have been carried out. The core structure of a disclination line defect of strength +1 has been examined, and comparison made with various theoretical treatments, which are presented in a unified way. It is found that excellent fits to the cylindrically symmetrized order tensor profiles may be obtained with appropriate parameter choices; notwithstanding this, on the time scales of the simulation, the cylindrical symmetry of the core is broken and two defects of strength +1 / 2 may be resolved.

Growth arrest-specific gene 6 (Gas6)/adhesion related kinase (Ark) signaling promotes gonadotropin-releasing hormone neuronal survival via extracellular signal-regulated kinase (ERK) and Akt

We identified Ark, the mouse homolog of the receptor tyrosine kinase Axl (Ufo, Tyro7), in a screen for novel factors involved in GnRH neuronal migration by using differential-display PCR on cell lines derived at two windows during GnRH neuronal development. Ark is expressed in Gn10 GnRH cells, developed from a tumor in the olfactory area when GnRH neurons are migrating, but not in GT1-7 cells, derived from a tumor in the forebrain when GnRH neurons are postmigratory. Since Ark (Ax1) signaling protects from programmed cell death in fibroblasts, we hypothesized that it may play an antiapoptotic role in GnRH neurons. Gn10 (Ark positive) GnRH cells were more resistant to serum withdrawal-induced apoptosis than GT1-7 (Ark negative) cells, and this effect was augmented with the addition of Gas6, the Ark (Ax1) ligand. Gas6/Ark stimulated the extracellular signal-regulated kinase, ERK, and the serine-threonine kinase, Akt, a downstream component of the phosphoinositide 3-kinase (PI3-K) pathway. To determine whether ERK or Akt activation is required for the antiapoptotic effects of Gas6/Ark in GnRH neurons, cells were serum starved in the absence or presence of Gas6, with or without inhibitors of ERK and PI3-K signaling cascades. Gas6 rescued Gn10 cells from apoptosis, and this effect was blocked by coincubation of the cells with the mitogen-activated protein/ERK kinase (MEK) inhibitor, PD98059, or wortmannin (but not rapamycin). These data support an important role for Gas6/Ark signaling via the ERK and PI3-K (via Akt) pathways in the protection of GnRH neurons from programmed cell death across neuronal migration.

Granzymes D, E, F, and G are regulated through pregnancy and by IL-2 and IL-15 in granulated metrial gland cells

Granulated metrial gland (GMG) cells are NK cells that proliferate and differentiate within the murine uterus during pregnancy. They have been predicted to play important roles in nurturing the embryo, normal placentation, and uterine tissue remodeling. GMG cell differentiation is manifested by the accumulation of the cytolytic mediators, perforin, granzyme A, and granzyme B, within cytoplasmic granules. The signaling mechanisms required for GMG cell differentiation are largely unknown, although recent in vitro assays have implicated IL-15 in these events. In this report, we demonstrate that granzymes D, E, F, and G (granzymes D-G) are also expressed in GMG cells but at a later stage in pregnancy when compared with granzyme A expression. Whereas granzyme A is expressed in early to mid-gestation, the expression of granzymes D-G peak in mid- to late gestation. In addition, we show that the expression patterns of IL-2Rbeta and the IL-2Rgamma mRNAs overlap with that of granzyme D-G mRNAs in the pregnant uterus. Finally, we demonstrate that granzymes D-G are up-regulated by IL-2 and IL-15 in primary cultures containing GMG cells. Taken together, these results suggest that IL-2 and/or IL-15 may regulate GMG cell differentiation in vivo, and that granzymes D-G may have different functions than granzyme A during pregnancy.

Cholesterol in fingerstick capillary specimens can be equivalent to conventional venous measurements

Current interest in coronary heart disease and cholesterol has led to the development of a new generation of compact analysis systems designed for fingerstick whole blood measurement. Since reliable classification of patients based on national cut-points for serum cholesterol concentration requires accurate results, the question whether results from fingerstick capillary specimens are equivalent to those from conventional venous-derived serum specimens, the basis for the national cut-points, is germane. Earlier studies in the literature are contradictory, with fingerstick differences ranging from 9% low to 6% high. We developed guidelines for reliable fingerstick collection and, following these guidelines, achieved results that were comparable to results derived from concurrently collected venous serum specimens. Results measured either by an accurate, standardized enzymatic assay or by the AccuMeter, a new noninstrumented device, were in close agreement with serum results, ie, within 1% and 1.7%, respectively, suggesting that fingerstick measurements are appropriate for identifying individuals with elevated cholesterol levels and monitoring their treatment.

Inactivation of aminated horseradish peroxidase by interaction with S-Sepharose

Horseradish peroxidase which had been aminated by periodate oxidation and reductive amination was purified by cation-exchange chromatography on S-Sepharose. Instead of the expected single peak of aminated enzyme, two distinct peaks of protein were eluted from the column. Evaluation of the protein in each of the two distributions showed that peak number 1 had spectral properties and specific activity similar to those of native enzyme. Distribution number 2 had a threefold reduction in the extinction in the Soret region at 404 nm and was completely devoid of enzymatic activity. This inactivation was caused by a specific interaction between the aminated peroxidase and the S-Sepharose matrix, resulting in a displacement of the heme prosthetic group out of its native orientation. The inactivation of the aminated peroxidase was found to be dependent on time, pH, and the support matrix itself. These results indicate that the S-Sepharose and Mono-S resins are not interchangeable, despite the chemical similarities of the two resins.

A noninstrumented quantitative test system and its application for determining cholesterol concentration in whole blood

A novel noninstrumented technology has been developed for quantifying analytes of clinical interest in biological fluids. Application of this technology is exemplified by the development of a quantitative cholesterol test with performance equivalent to state-of-the-art instrumented methods. The assay chemistry combines two separate processes located in different areas of a test strip: enzymatic action on serum cholesterol to produce hydrogen peroxide (5 x 10 mm enzyme reagent pad) and quantification of the hydrogen peroxide (5 x 70 mm measurement region). Color bands are formed in the measurement area through the use of a redox-coupled indicator system. The height of the color band on the strip is directly proportional to the sample cholesterol concentration. A one-step cassette contains all components necessary to run the test and includes blood filtration and automatic sample measurement, so that unmeasured finger-stick whole-blood specimens can be analyzed by the non-technically trained user. The test is complete in less than 15 min, is read visually like a thermometer, and gives results that are in excellent correlation with established instrumented methods.

A noninstrumented quantitative test system and its application for determining cholesterol concentration in whole blood

A novel noninstrumented technology has been developed for quantifying analytes of clinical interest in biological fluids. Application of this technology is exemplified by the development of a quantitative cholesterol test with performance equivalent to state-of-the-art instrumented methods. The assay chemistry combines two separate processes located in different areas of a test strip: enzymatic action on serum cholesterol to produce hydrogen peroxide (5 x 10 mm enzyme reagent pad) and quantification of the hydrogen peroxide (5 x 70 mm measurement region). Color bands are formed in the measurement area through the use of a redox-coupled indicator system. The height of the color band on the strip is directly proportional to the sample cholesterol concentration. A one-step cassette contains all components necessary to run the test and includes blood filtration and automatic sample measurement, so that unmeasured finger-stick whole-blood specimens can be analyzed by the non-technically trained user. The test is complete in less than 15 min, is read visually like a thermometer, and gives results that are in excellent correlation with established instrumented methods.

Computer simulation of liquid crystals

We review recent progress in the computer simulation of liquid crystals, with special emphasis on hard particle models. Surprisingly, the simplest molecular models, taking account only of molecular size and shape, are sufficient to generate a wide variety of liquid crystalline phases, closely analogous to those observed in real life. Thermodynamic stability of different phases is very sensitive to shape, and presumably will also be sensitive to further details of intermolecular interactions as they are incorporated into the model. Realistic atom-atom potential models of liquid crystals are available, but the associated simulations are quite expensive. Thus, while idealized models may be used to study quite general, fundamental properties of mesophases, the modelling of specific liquid crystal systems in a realistic way remains a great challenge. Progress continues to be made on both these fronts.

Kinetic parameters of metal-substituted leucine aminopeptidase from bovine lens

Leucine aminopeptidase (LAP) is a protease requiring two divalent metal cations per subunit for activity. Zn2+, Mg2+, and Co2+ metal-substituted forms of LAP have been prepared and investigated kinetically. Substitution of metal into the two binding sites independently resulted in the preparation of Zn2+Zn2+, Mg2+Zn2+, Co2+Co2+, Zn2+Co2+, Mg2+Co2+, and Co2+Zn2+ LAP derivatives that were characterized by atomic absorption spectrophotometry. Kinetic analysis of the metal-substituted enzymes indicated that site 1 (fast exchanging) metal substitution results in a Km decrease in the relative order Zn2+ greater than Mg2+ greater than Co2+. Similar comparisons for the site 2 metal (slow exchanging) involved only Zn2+ and Co2+, since only these metals have been shown to compete effectively for this site. Substitution of these two metals into site 2 revealed a Km decrease in the order Zn2+ greater than Co2+. It was suggested previously [e.g., Thompson, G. A., & Carpenter, F. H. (1976) J. Biol. Chem. 251, 1618-1624] that the fast-exchanging site 1 metal predominantly effects kcat while the slow-exchanging metal in site 2 exerts effects exclusively on Km. The present study, the first direct comparison of Km change resulting from metal substitution into both sites, clearly indicates that both metal sites exert significant effects on Km. In addition, the data suggest a more complex interaction between the two bound metals than previously suspected.