Calpain cleaved-55kDa N-terminal huntingtin delocalizes from neurons to astrocytes after ischemic injury

The huntingtin (htt) mutation causes a polyglutamine expansion in the N-terminal region of protein. Mutant N-htt proteolytic fragments aggregate and cause cell death in Huntington's disease (HD). The normal huntingtin also can be cleaved by calpain and produce N-terminal htt fragments following ischemic injury, but the fate of cleaved fragment in dead neurons in the brain are unclear. To determine the localization of huntingtin following proteolysis, we examined htt expression after transient ischemic injury. Huntingtin immunoreactivity in mixed cultures of neuronal and astrocytes-derived clonal cells showed alteration of immunoreactivity from neurons into astrocytes. In the brain, both focal and global ischemia induced reactive astrocytes that were co-immunoreactive for huntingtin with elevated GFAP expression. The immunoreactive huntingtin was 55kDa calpain-cleaved N-terminal fragment, which appeared initially in the process, and extended into the cytoplasm of astrocytes. The results showed, after ischemic injury, huntingtin accumulated in astrocytes indicating that astrocytes may play a role in uptake of cleaved N-htt fragments.

Efficacy of autologous serum in human adipose-derived stem cells; cell markers, growth factors and differentiation

Human adipose-derived stem cells (hASCs) are a feasible source of stem cells for use in clinical applications. hASCs are typically cultured in medium containing fetal bovine serum (FBS); however, use of FBS is not recommended due to issues of clinical safety with regard to infections or immune response. Replacement of FBS with autologous human serum (autoHS) can eliminate these problems; however, their maintainability as potent ASCs in autoHS needs to be confirmed. Thus, we conducted an investigation of characterizations and functions of hASCs grown in medium containing autoHS compared to FBS. Cell counting and the WST-8 assay were used in assessment of the proliferation rate. In hASC cultured with culture medium plus autoHS or FBS, cell phenotypes were characterized by flow cytometry (CD13, CD29, CD31, CD34, and CD44) and expression of BDNF, HGF, IGF, LIF, NGF, and VEGF was determined by RT—PCR. Adipogenic differentiation was confirmed by oil red O stain. hASC showed greater expansion in AutoHS than in FBS. Cell surface markers of hASCs grown in autoHS (autoHS-hASCs) were similar to markers of those grown in FBS (FBS-hASCs). AutoHS-hASCs also expressed multiple growth factors as well as FBS-hASCs. In addition, autoHS was effective in growth of hASCs as well as FBS and autoHS-hASCs retained their ability for adipogenic differentiation. In summary, autoHS-hASCs have multiple growth factor expressions with the same cell surface markers as FBS—hASCs in vitro. Our results suggest that autoHS can provide sufficient ex vivo expansion of hASCs.

CHARMM: the biomolecular simulation program

CHARMM (Chemistry at HARvard Molecular Mechanics) is a highly versatile and widely used molecular simulation program. It has been developed over the last three decades with a primary focus on molecules of biological interest, including proteins, peptides, lipids, nucleic acids, carbohydrates, and small molecule ligands, as they occur in solution, crystals, and membrane environments. For the study of such systems, the program provides a large suite of computational tools that include numerous conformational and path sampling methods, free energy estimators, molecular minimization, dynamics, and analysis techniques, and model-building capabilities. The CHARMM program is applicable to problems involving a much broader class of many-particle systems. Calculations with CHARMM can be performed using a number of different energy functions and models, from mixed quantum mechanical-molecular mechanical force fields, to all-atom classical potential energy functions with explicit solvent and various boundary conditions, to implicit solvent and membrane models. The program has been ported to numerous platforms in both serial and parallel architectures. This article provides an overview of the program as it exists today with an emphasis on developments since the publication of the original CHARMM article in 1983.

Optimized atomic radii for protein continuum electrostatics solvation forces

Recently, we presented a Green's function approach for the calculation of analytic continuum electrostatic solvation forces based on numerical solutions of the finite-difference Poisson-Botzmann (FDPB) equation [Im et al., Comp. Phys. Comm. 111 (1998) 59]. In this treatment the analytic forces were explicitly defined as the first derivative of the FDPB continuum electrostatic free energy with respect to the coordinates of the solute atoms. A smooth intermediate region for the solute-solvent dielectric boundary needed to be introduced to avoid abrupt discontinuous variations in the solvation free energy and forces as a function of the atomic positions. In the present paper we extend the set of optimized radii, which was previously parametrized from molecular dynamics free energy simulations of the 20 standard amino acids with explicit solvent molecules [Nina et al., J. Phys. Chem. 101 (1997) 5239], to yield accurate solvation free energy by taking the influence of the smoothed dielectric region into account.

A Grand Canonical Monte Carlo-Brownian dynamics algorithm for simulating ion channels

A computational algorithm based on Grand Canonical Monte Carlo (GCMC) and Brownian Dynamics (BD) is described to simulate the movement of ions in membrane channels. The proposed algorithm, GCMC/BD, allows the simulation of ion channels with a realistic implementation of boundary conditions of concentration and transmembrane potential. The method is consistent with a statistical mechanical formulation of the equilibrium properties of ion channels (; Biophys. J. 77:139-153). The GCMC/BD algorithm is illustrated with simulations of simple test systems and of the OmpF porin of Escherichia coli. The approach provides a framework for simulating ion permeation in the context of detailed microscopic models.