Over-expression and characterization of the recombinant small heat shock protein from Pyrococcus furiosus

The gene encoding a small heat shock protein (sHSP) from Pyrococcus furiosus was redesigned and chemically synthesized by using bacteria-preferred codons. The gene product was over-expressed in Escherichia coli BL21(DE)₃ and purified to homogeneity. In the presence of this protein, the activities of Taq DNA polymerase, DNA restriction endonuclease HindIII and lysozyme were protected at elevated temperature, and also, thermal aggregation of lysozyme was prevented by this purified recombinant sHSP.Huayou Chen, Zhongmei Chu, Contributed equally to this work     

Structural and functional analysis of the coupling subunit F in solution and topological arrangement of the stalk domains of the methanogenic A1AO ATP synthase

The first low-resolution shape of subunit F of the A₁A_O ATP synthase from the archaeon Methanosarcina mazei Gö1 in solution was determined by small angle X-ray scattering. Independent to the concentration used, the protein is monomeric and has an elongated shape, divided in a main globular part with a length of about 4.5 nm, and a hook-like domain of about 3.0 nm in length. The subunit-subunit interaction of subunit F inside the A₁A_O ATP synthase in the presence of 1-ethyl-3-(dimethylaminopropyl)-carbodiimide EDC was studied as a function of nucleotide binding, demonstrating movements of subunits F relative to the nucleotide-binding subunit B. Furthermore, in the intact A₁A_O complex, crosslinking of subunits D-E, A-H and A-B-D was obtained and the peptides, involved, were analyzed by MALDI-TOF mass spectrometry. Based on these data the surface of contact of B-F could be mapped in the high-resolution structure of subunit B of the A₁A_O ATP synthase.     

SK3 Trafficking in Hippocampal Cells: The Role of Different Molecular Domains

The regulative steps that control trafficking of ion channels are fundamental determinants of their qualitative and quantitative expression on the cell membrane. In this work the trafficking of the small conductance calcium-activated potassium channel, SK3 was studied in neurons in order to identify relevant molecular domains involved in this process. Hippocampal cell cultures were transfected with fusion proteins of green fluorescent protein (GFP) and different SK3 subunit truncations. The differential distribution of the mutants was analyzed by confocal microscopy and compared to the localization of the control fusion protein with full length SK3. The transport of chimeric proteins was quantified from fluorescence images by developing a morphometric analytical method. We found that the full length SK3 was distributed in cell body, axon and dendrites, whereas the deleted forms GFPΔ578–736 (deletion of the entire C-terminal domain), GFPΔCaMBD (deletion of the calmodulin-binding site) and GFPΔN (deletion of the N-terminal domain) were not transported into cell processes but accumulated in the cell body. The GFPΔ640–736 (deletion of the distal C-terminal domain) showed a distribution similar to control. The quantification and statistical analysis confirmed the differences in distribution across the three groups. In conclusion, the current work provides evidence for a fundamental role of the N-terminal domain and the calmodulin binding domain in SK3 trafficking in neurons.     

Induction of CML28-specific cytotoxic T cell responses using co-transfected dendritic cells with CML28 DNA vaccine and SOCS1 small interfering RNA expression vector

CML28 is an attractive target for antigen-specific immunotherapy. SOCS1 represents an inhibitory control mechanism for DC antigen presentation and the magnitude of adaptive immunity. In this study, we evaluated the potential for inducing CML28-specific cytotoxic T lymphocytes (CTL) responses by dendritic cells (DCs)-based vaccination. We constructed a CML28 DNA vaccine and a SOCS1 siRNA vector and then cotransfect monocyte-derived DCs. Flow cytometry analysis showed gene silencing of SOCS1 resulted in higher expressions of costimulative moleculars in DCs. Mixed lymphocyte reaction (MLR) indicated downregulation of SOCS1 stronger capability to stimulate proliferation of responder cell in DCs. The CTL assay revealed transfected DCs effectively induced autologous CML28-specific CTL responses and the lytic activities induced by SOCS1-silenced DCs were significantly higher compared with those induced by SOCS1-expressing DCs. These results in our study indicates gene silencing of SOCS1 remarkably enhanced the cytotoxicity efficiency of CML28 DNA vaccine in DCs.     

Semiautomated computer-assisted image analysis to quantify 3,3'-diaminobenzidine tetrahydrochloride-immunostained small tissues

This work aimed to develop a technique to measure stained areas in images from sample tissue sections, namely when the structure of interest does not fill the entire image field of the microscope. We propose a semiautomated computer-assisted image analysis (SACAIA) method in which brightfield color images of 3,3'-diaminobenzidene tetrahydrochloride (DAB)-stained antigens are converted to their blue component and boundaries are delineated to extract the object of interest. The number of pixels of a defined color (elicited by DAB) is counted and used to measure the stained area relative to the total area of the tissue under study. The percentages of area stained with adenosine A(1) receptor were 40.76+/-2.08 and 42.44+/-2.26% for manual analysis and SACAIA, respectively (P=0.582). A strong linear correlation of A(1) receptor quantification was found (r=0.98, P<0.001, and 95% CI=0.97 to 0.99 for manual method; r=0.99, P<0.001, and 95% CI=0.98 to 0.99 for SACAIA method). The extent to which misclassification affected staining quantification was evaluated by Bland-Altman analysis, indicating that this method can be applied accurately to quantify the immunohistochemical staining area (occupied by a specific antigen) in small sample tissues that do not fill the entire image field of the microscope.     

Proceedings of the SMBE Tri-National Young Investigators' Workshop 2005. Coalescent-based estimation of population parameters when the number of demes changes over time

We expand a coalescent-based method that uses serially sampled genetic data from a subdivided population to incorporate changes to the number of demes and patterns of colonization. Often, when estimating population parameters or other parameters of interest from genetic data, the demographic structure and parameters are not constant over evolutionary time. In this paper, we develop a Bayesian Markov chain Monte Carlo method that allows for step changes in mutation, migration, and population sizes, as well as changing numbers of demes, where the times of these changes are also estimated. We show that in parameter ranges of interest, reliable estimates can often be obtained, including the historical times of parameter changes. However, posterior densities of migration rates can be quite diffuse and estimators somewhat biased, as reported by other authors.     

Stand structure and woody species diversity in relation to stand stratification in a subtropical evergreen broadleaf forest, Okinawa Island

Stand structure and woody species diversity in a subtropical evergreen broadleaf forest grown in a silicate habitat, Okinawa Island, have been investigated on the basis of stand stratification. The forest stand consisted of four layers. The floristic composition of the top and the lower three layers was only slightly similar, although approximately one-third of the species were common to them. Mean tree weight decreased from the top toward the bottom layer whereas tree density increased from the top downward. This trend resembled the mean weight–density trajectory of self-thinning plant populations. The relationship between mean tree height and tree density for the upper two layers supported Yamakuras quasi –1/2 power law of tree height. The values of the Shannon–Wiener index, H, and the equitability index, J, tended to increase from the top layer downward except for the bottom layer. The values of H and J were, respectively, 4.83 bit and 0.82 for trees taller than 0.10 m. The lower layers contained many species of smaller height. High species diversity of the forest depended on small trees in the lower layers. Conservation of small trees in the lower layers, especially the bottom layer, is indispensable for sound maintenance of Okinawan evergreen broadleaf forests.     

Dynamics of RhoA and ROKα translocation in single living cells

The RhoA-binding kinase (ROK) is one of the target kinases of RhoA and is known to play a critical role in regulating cytoskeletal rearrangement in cells. ROK translocates to the plasma membrane fraction; however, the mechanism of the translocation of ROK still remains obscure. To clarify the molecular mechanisms of the translocation of ROK, we co-transfected MDCK cells wity cyan fluorescent protein-tagged RhoA and yellow fluorescent protein-tagged ROKα, or their variants, and monitored the localization and translocation of the two different fluorescent tagged-molecules in single living cells during epithelial growth factor (EGF) stimulation. Both RhoA (wild-type) and ROKα (wild-type) translocated to ruffling membrane with EGF stimulation in several minutes. A ROKα mutant, in which Rho-binding ability is disrupted, is unable to translocate to the membrane with RhoA. However, RhoA mutant Q63L/C190R, an active form lacking membrane localization activity, abolished the translocation of wild-type ROKα, suggesting that the translocation of RhoA is critical for ROK translocation to the membrane. Another mutant lacking the pleckstrin homology domain failed in translocation as well. On the other hand, it was surprising that the kinase dead mutant succeeded in translocation to the membrane after EGF stimulation. Based on these results, we propose the following ROKα translocation mechanism. ROKα binds to RhoA in cytosol and translocates to the membrane based on the membrane-targeting ability of active RhoA. After ROKα associates with the membrane, the pleckstrin homology domain provides the stability of ROKα on the membrane. The activation of enzymatic activity or adenosine triphosphate binding, however, is not directly related to the translocation mechanism, although we found that the membrane association is critical for the activation of the kinase activity.     

A role for Wnt/planar cell polarity signaling during lens fiber cell differentiation?

Wnt signaling through frizzled (Fz) receptors plays key roles in just about every developmental system that has been studied. Several Wnt-Fz signaling pathways have been identified including the Wnt/planar cell polarity (PCP) pathway. PCP signaling is crucial for many developmental processes that require major cytoskeletal rearrangements. Downstream of Fz, PCP signaling is thought to involve the GTPases, Rho, Rac and Cdc42 and regulation of the JNK cascade. Here we report on the localization of these GTPases and JNK in the lens and assess their involvement in the cytoskeletal reorganisation that is a key element of FGF-induced lens fiber cell differentiation.