DNA probes on beads arrayed in a capillary, ‘Bead-array’, exhibited high hybridization performance

A DNA analysis platform called ‘Bead-array’ is presented and its features when used in hybridization detection are shown. In ‘Bead-array’, beads of 100-µm diameter are lined in a determined order in a capillary. Each bead is conjugated with DNA probes, and can be identified by its order in the capillary. This probe array is easily produced by just arraying beads conjugated with probes into the capillary in a fixed order. The hybridization is also easily completed by introducing samples (1–300 µl) into the capillary with reciprocal flow. For hybridization detection, as little as 1 amol of fluorescent-labeled oligo DNA was detected. The hybridization reaction was completed in 1 min irrespective of the amount of target DNA. When the number of target molecules was smaller than that of probe molecules on the bead, 10 fmol, almost all targets were captured on the bead. ‘Bead-array’ enables reliable and reproducible measurement of the target quantity. This rapid and sensitive platform seems very promising for various genetic testing tasks.     

Protein Adsorption at Polymer-grafted Surfaces: Comparison between a Mixture of Saliva Proteins and some Well-defined Model Proteins

Grafting a dense layer of soluble polymers onto a surface is a well-established method for controlling protein adsorption. In the present study, polyethylene oxide (PEO) layers of three different grafting densities were prepared, i.e. 10?–?15 nm², 5.5 nm² and 4 nm² per polymer chain, respectively. The adsorption of different proteins on the PEO grafted surfaces was measured in real time by reflectometry. Furthermore, the change of the zeta-potential of such surfaces resulting from adsorption of the proteins was determined using the streaming potential method. Both the protein adsorption and the zeta-potential were monitored for 1?h after exposure of the protein solution to the surface. The adsorption pattern for a mixture of saliva proteins was compared to those observed for a number of well-defined model-proteins (lysozyme, human serum albumin, β-lactoglobulin and ovalbumin). The results of the adsorption kinetics and streaming potential measurements indicate that the effect of the PEO layer on protein adsorption primarily depends on the size and the charge of the protein molecules. The saliva proteins are strongly blocked for adsorption, whereas the change in the zeta-potential is larger than for the other proteins (except lysozyme). It is concluded that positively charged protein molecules, having dimensions larger than those of lysozyme, are involved in the initial stage of adsorption from saliva onto a negatively charged surface.     

A unique ATP hydrolysis mechanism of single-headed processive myosin, myosin IX

Recent studies have revealed that myosin IX is a single-headed processive myosin, yet it is unclear how myosin IX can achieve the processive movement. Here we studied the mechanism of ATP hydrolysis cycle of actomyosin IXb. We found that myosin IXb has a rate-limiting ATP hydrolysis step unlike other known myosins, thus populating the prehydrolysis intermediate (M.ATP). M.ATP has a high affinity for actin, and, unlike other myosins, the dissociation of M.ATP from actin was extremely slow, thus preventing myosin from dissociating away from actin. The ADP dissociation step was 10-fold faster than the overall ATP hydrolysis cycle rate and thus not rate-limiting. We propose the following model for single-headed processive myosin. Upon the formation of the M.ATP intermediate, the tight binding of actomyosin IX at the interface is weakened. However, the head is kept in close proximity to actin due to the tethering role of loop 2/large unique insertion of myosin IX. There is enough freedom for the myosin head to find the next location of the binding site along with the actin filament before complete dissociation from the filament. After ATP hydrolysis, Pi is quickly released to form a strong actin binding form, and a power stroke takes place.     

Proteomic analysis of hepatitis C virus (HCV) core protein transfection and host regulator PA28γ knockout in HCV pathogenesis: a network-based study

Hepatitis C virus (HCV) causes chronic liver disease worldwide. HCV Core protein (Core) forms the viral capsid and is crucial for HCV pathogenesis and HCV-induced hepatocellular carcinoma, through its interaction with the host factor proteasome activator PA28γ. Here, using BD-PowerBlot high-throughput Western array, we attempt to further investigate HCV pathogenesis by comparing the protein levels in liver samples from Core-transgenic mice with or without the knockout of PA28γ expression (abbreviated PA28γ(-/-)CoreTG and CoreTG, respectively) against the wild-type (WT). The differentially expressed proteins integrated into the human interactome were shown to participate in compact and well-connected cellular networks. Functional analysis of the interaction networks using a newly developed data warehouse system highlighted cellular pathways associated with vesicular transport, immune system, cellular adhesion, and cell growth and death among others that were prominently influenced by Core and PA28γ in HCV infection. Follow-up assays with in vitro HCV cell culture systems validated VTI1A, a vesicular transport associated factor, which was upregulated in CoreTG but not in PA28γ(-/-)CoreTG, as a novel regulator of HCV release but not replication. Our analysis provided novel insights into the Core-PA28γ interplay in HCV pathogenesis and identified potential targets for better anti-HCV therapy and potentially novel biomarkers of HCV infection.     

Involvement of Ceramide in the Propagation of Japanese Encephalitis Virus

Japanese encephalitis virus (JEV) is a mosquito-borne RNA virus and one of the most important flaviviruses in the medical and veterinary fields. Although cholesterol has been shown to participate in both the entry and replication steps of JEV, the mechanisms of infection, including the cellular receptors of JEV, remain largely unknown. To clarify the infection mechanisms of JEV, we generated pseudotype (JEVpv) and recombinant (JEVrv) vesicular stomatitis viruses bearing the JEV envelope protein. Both JEVpv and JEVrv exhibited high infectivity for the target cells, and JEVrv was able to propagate and form foci as did authentic JEV. Anti-JEV envelope antibodies neutralized infection of the viruses. Treatment of cells with inhibitors for vacuolar ATPase and clathrin-mediated endocytosis reduced the infectivity of JEVpv, suggesting that JEVpv enters cells via pH- and clathrin-dependent endocytic pathways. Although treatment of the particles of JEVpv, JEVrv, and JEV with cholesterol drastically reduced the infectivity as previously reported, depletion of cholesterol from the particles by treatment with methyl β-cyclodextrin enhanced infectivity. Furthermore, treatment of cells with sphingomyelinase (SMase), which hydrolyzes membrane-bound sphingomyelin to ceramide, drastically enhanced infection with JEVpv and propagation of JEVrv, and these enhancements were inhibited by treatment with an SMase inhibitor or C₆-ceramide. These results suggest that ceramide plays crucial roles in not only entry but also egress processes of JEV, and they should assist in the clarification of JEV propagation and the development of novel therapeutics against diseases caused by infection with flaviviruses.Japanese encephalitis virus (JEV) is a small, enveloped virus belonging to the family Flaviviridae and the genus Flavivirus, which also includes Dengue virus (DENV), West Nile virus (WNV), Yellow fever virus, and Tick-borne encephalitis virus (11). JEV is the most common agent of viral encephalitis, causing approximately 50,000 cases annually, of which 15,000 will die, and up to 50% of survivors are left with severe residual neurological complications. JEV has a single-stranded positive-sense RNA genome of approximately 11 kb, encoding a single large polyprotein, which is cleaved by the host- and virus-encoded proteases into three structural proteins, capsid (C), premembrane (PrM), and envelope (E), and seven nonstructural proteins. The structural proteins are components of viral particles, and the E protein is suggested to interact with a cell surface receptor molecule(s). Although a number of cellular components, including heat shock cognate protein 70 (33), glycosaminoglycans, such as heparin or heparan sulfate (21, 41), and laminin (3), have been shown to participate in JEV infection, the precise mechanisms by which these receptor candidates participate in JEV infection remain largely unclear.In addition to the many studies identifying and characterizing receptor molecules in numerous viruses, data suggesting the involvement of membrane lipids, such as sphingolipids and cholesterol, in viral infection have also been accumulating. Lipid rafts consisting of sphingolipids and cholesterol and distributing to the outer leaflet of the cell membrane have been shown to be involved in the infection of not only many viruses but also several bacteria and parasites (24), in addition to playing roles in various functions such as lipid sorting, protein trafficking (26, 47), cell polarity, and signal transduction (38). With respect to cholesterol itself, various aspects of the life cycle of flaviviruses have been shown to involve this lipid, including the entry of DENV (34), hepatitis C virus (HCV) (16), and WNV (27), the membrane fusion of tick-borne encephalitis virus (40), and the replication of HCV (14, 17), WNV (23), and DENV (35). Recently Lee et al. (20) showed that treatment with cholesterol efficiently impairs both the entry and replication steps of JEV and DENV-2 but enhances infection with the Sindbis virus (22).On the other hand, sphingolipids, including sphingomyelins and glycosphingolipids, are ubiquitous components of eukaryotic cell membrane structures, providing integrity to cellular membranes. Ceramide is one of the intermediates of sphingolipids and plays roles in cell differentiation, regulation of apoptosis and protein secretion, induction of cellular senescence, and other processes (2). Ceramide is generated from the hydrolysis of sphingomyelin by sphingomyelinase (SMase) or from catalysis by serine-palmitoyl-coenzyme A (CoA) transferase and ceramide synthase. Ceramide spontaneously self-associates to form ceramide-enriched microdomains and then to form larger ceramide-enriched membrane platforms which serve as the spatial and temporal organization for cellular signalosomes and for regulation of protein functions (2). The ceramide-enriched platforms have also been used by many pathogens to facilitate entry and infection (2). The acid SMase is activated not only by multiple stimuli, including receptor molecules, gamma irradiation, and some chemicals, but also by infection with some bacteria or viruses (36). Rhinovirus activates the SMase for generation of ceramide and forms ceramide-enriched membrane platforms that serve in the infection of target cells (10). Sindbis virus also activates the SMase and induces apoptosis through a continuous release of ceramide (15). In contrast to these viruses, ceramide inhibits infection with HIV (7) and HCV (48). Ceramide enrichment of the plasma membrane reduces expression of HCV receptor molecules through an ATP-independent internalization and impairs entry of HCV.Pseudotype and recombinant viruses based on the vesicular stomatitis virus (VSV) bearing foreign viral envelope proteins have been shown to be powerful tools for the investigation of viral entry and the development of vaccines. These systems have been used to study infection with viruses that do not propagate readily (31, 43) or that are difficult to handle due to their high-level pathogenicity for humans (42). In addition, the systems allow us to focus on the investigation of entry mechanisms of particular viral envelope proteins by using control viruses harboring an appropriate protein on identical particles.In the present study, we generated pseudotype (JEVpv) and recombinant (JEVrv) VSVs bearing the JEV envelope protein in human cell lines and determined the involvement of sphingolipids, especially ceramide, and cholesterol in infection of human cell lines with JEV. Both JEVpv and JEVrv exhibited infection of target cells via pH- and clathrin-dependent endocytosis. Treatment of cells with cholesterol impaired infection with JEVpv and JEVrv, as previously found in JEV infection (20). In contrast, treatment of cells with SMase drastically enhanced infection with both JEVpv and JEVrv and the production of infectious JEVrv particles. These results indicate that ceramide plays crucial roles in the entry and egress of JEV.     

Hepatoprotective effect of sesquiterpenes in turmeric

Hepatoprotective effect of turmeric together with its sesquiterpenes and curcuminoids fractions were examined on D-galactosamine induced liver injury in rats. All the diets individually contained the turmeric extract, the curcuminoids fraction, and the sesquiterpenes fraction suppressed the increase of LDH, ALT, and AST levels caused by D-GalN treatment. Since few anti-oxidative activities are expected in the sesquiterpenes fraction, it is presumed that hepatoprotective mechanism of sesquiterpenes in turmeric is different from that of curuminoids.     

Behavior pattern (innate action) of individuals in fish schools generating efficient collective evasion from predation

The schooling of fishes is one typical animal social behavior. One primary function of fish school is to protect members when attacked by predators. One main way that the school reduces the predator's chance of making a successful kill is to confuse the predator as it makes its strike. This may be accomplished by collective evasion behaviors organized through integration of motions of individual fish made based on their innate actions (behavior patterns). In order to investigate what kind of behavior pattern of individuals can generate the efficient collective evasion of a school, we present a model of evasion behavior pattern which consists of three component behavior patterns, schooling, cooperative escape, and selfish escape behavior patterns and the rule for choice of one among them with proper timing. Each fish determines its movement direction taking into account simultaneously three kinds of elemental motions, mimicking its neighbors, avoiding collisions with its nearest neighbors, and escaping from an approaching predator. The weights of three elemental motions are changed depending on which component behavior pattern the fish carries out. The values of the weights for three component behavior patterns can be definitively determined under the condition that the collective evasion of the school becomes the most efficient, that is, the probability that any member is eaten by the predator becomes minimum.     

The significance of duration of salt loading on cardiovascular response and urinary excretion of catecholamine in rats

To analyze the conflicting data on the relationship between sodium intake and catecholamine release, the effect of the duration of high sodium loading on cardiovascular response and catecholamine release was examined in conscious rats. Urinary excretions of norepinephrine (NE), and dopamine (DA) were measured frequently over a 4 week period. Male Wistar rats at 4 weeks of age were given a diet containing either basal (0.3%) or high (3.1%) sodium content. Systolic blood pressure was measured weekly by the tail cuff method. Twenty-four hour urine collections were made for analysis of catecholamines in metabolic cages every other day during the initial 2 weeks and once a week in the following 2 weeks of salt loading. High sodium intake resulted in a rise in blood pressure and a reduction in heart rate. Bradycardia was significant during the initial 2 weeks and not significant during the following 2 weeks after the initiation of salt loading. Urinary excretion of NE did not change during the initial 2 weeks of salt loading but increased significantly following the 2 week period after salt loading. Urinary excretion of DA increased diphasically, showing the first peak at 1 week after salt loading and the second peak at 4 weeks after the initiation of salt loading. These results suggest that the heart rate and urinary excretion of catecholamine are influenced by the duration of salt loading. When we estimate the effect of salt loading on cardiovascular response and urinary excretion of catecholamine, we should draw attention to the importance of the duration of salt loading, because this duration of time further elicites delayed response in the sympathetic nervous system.     

A model for self-sustained potential oscillation of lipid bilayer membranes induced by the gel-liquid crystal phase transitions.

To clarify the mechanism of self-sustained oscillation of the electric potential between the two solutions divided by a lipid bilayer membrane, a microscopic model of the membrane system is presented. It is assumed, on the basis of the observed results (Yoshikawa, K., T. Omachi, T. Ishii, Y. Kuroda, and K. liyama. 1985. Biochem. Biophys. Res. Commun. 133:740-744; Ishii, T., Y. Kuroda, T. Omochi, and K. Yoshikawa. 1986. Langmuir. 2:319-321; Toko, K., N. Nagashima, S. liyama, K. Yamafuji, and T. Kunitake. Chem. Lett. 1986:1375-1378), that the gel-liquid crystal phase transition of the membrane drives the potential oscillation. It is studied, by using the model, how and under what condition the repetitive phase transition may occur and induce the potential oscillation. The transitions are driven by the repetitive adsorption and desorption of proton by the membrane surface, actions that are induced the periodic reversal of the direction of protonic current. The essential conditions for the periodic reversal are (a) at least one kind of cations such as Na+ or K+ are included in the system except for proton, and the variation of their permeability across the membrane due to the phase transition is noticeably larger than that of proton permeability; and (b) the phase transition has a hysteresis. When these conditions are fulfilled, the self-sustained potential oscillation may be brought about by adjusting temperature, pH, and the cation concentration in the solutions on both sides of the membrane. Application of electric current across the membrane also induces or modifies the potential oscillation. Periodic, quasiperiodic, and chaotic oscillations appear especially, depending on the value of frequency of the applied alternating current.