Does Hypericum perforatum L. extract show any specificity as photosensitizer for HL-60 leukemic cells and cord blood hemopoietic progenitors during photodynamic therapy?

Autologous bone marrow transplantation is a therapeutic modality that increases the survival rates for children with malignancies with poor prognosis but relapse rates are high and attributed partially to the existence of residual malignant cells. Photodynamic treatment (PDT) has been developed among purging strategies. We investigated the effect of the methanolic extract (ME) and its polar methanolic fraction (PMF) of Hypericum perforatum L., as a new photosensitizer for the leukemic cell line HL-60 and cord blood (CB) hemopoietic progenitors as well as the subcellular localization of the photosensitizer.

Methods

ME and PMF were prepared after extraction of the dry herb with methanol (ME), followed by liquid–liquid extraction with petroleum ether (PMF). Cells were incubated with the extracts before irradiation with Nd-Yvo Laser. Various concentrations of PMF or ME as well as irradiation doses were tested. Following irradiation, cell viability was determined by trypan blue in continuous liquid cultures for HL-60 cells and in clonogenic assays for CB cells. The subcellular localization of the photosensitizer was determined by confocal microscopy.

Results

Laser photoirradiation in the presence of both PMF and ME induces the killing of HL-60 cells. This effect is dose dependent. No CFU-GM and BFU-E growth was observed from CB mononuclear cells under the tested experimental conditions. Confocal microscopy revealed that the extracts localize mainly in the cytoplasm of the cells.

Conclusions

PDT with both PMF and ME induces the killing of HL-60 leukemic cells and the optimal conditions of treatment were determined. This effect of PDT/PMF was also exerted on CB progenitor cells indicative of the non-selective uptake of the photosensitizer by malignant cells. Though this suggests that PDT/PMF cannot be helpful in autologous bone marrow purging, these novel extracts can however be beneficial in the PDT treatment of tumors given their photostability, low toxicity and low cost.     

The low level laser therapy effect on the remodeling of bone extracellular matrix

The low level laser therapy (LLLT) has been used as an option to accelerate the regeneration of bone tissue. In this study, both femurs of male Wistar rats (30 animals) were injured with a drill and the effect of LLLT using a laser diode (100 mW at 660 nm) in the bone matrix on the left paw measured. LLLT effect on the healing bone tissue matrix was evaluated by a combination of immunohistochemical histomorphometry, confocal immunofluorescence microscopy and isolation and characterization of glycosaminoglycans. Histomorphometric analysis showed that LLLT increased bone matrix and showing more organized. Alcian Blue and PAS staining seems to suggest differential glycosaminoglycans and glycoproteins. The data showed increased expression of chondroitin sulfate and hyaluronic acid, after reduction as the LLLT and mature bone, resembling the expression of osteonectin and biglycan. The difference in expression of siblings (DMP‐1, OPN and BSP) is in accordance with the repair accelerated bone formation after the application of LLLT as compared with control. The expression of osteonectin and osteocalcin supports their role in bone mineralization protein, indicating that LLLT accelerates this process. The overall data show that LLLT bone changes dynamic array, shortening the time period involved in the bone repair.     

The pharmacological effects of morroniside and loganin isolated from Liuweidihuang Wan, on MC3T3-E1 cells

Liuweidihuang wan (LW), initially a well-known formula for curing "wu chi wu ruan", is commonly used nowadays for clinical treatment of postmenopausal osteoporosis (PO), but the identity of the effective substance(s) remains unclear. The present study was designed to evaluate the effects of morroniside and loganin isolated from LW on the proliferation, differentiation and apoptosis of MC3T3-E1 cells, as well as the possible mechanism of action. Morroniside and loganin had no effects on the proliferation of MC3T3-E1 cells, but both susbtances could improve the activity of alkaline phosphatase (ALP), and increase the contents of collagen type I and osteocalcin. Simultaneously, the mRNA expression of caspase-3, capase-9, RANKL was down-regulated and that of bcl-2 was up-regulated, which partially explains the anti-osteoporosis mechanism in MC3T3-E1 cells. In conclusion, morroniside and loganin may directly promote the differentiation and inhibit the apoptosis of MC3T3-E1 cells, and accordingly indirectly reduce bone resorption, which makes them promising natural drugs leads for treating PO in the near future.     

Ribonuclease protection assay on microchip electrophoresis

We describe the potential of microchip electrophoresis with a Hitachi SV1210, which can be used to evaluate the integrity of total RNA, for the analysis of mRNA expression. The ribonuclease (RNase) protection assay was performed by using microchip electrophoresis with cyanine 5 (Cy5) labeled 248-base antisense RNA probe (riboprobe) encoding adipose-type fatty acid binding protein (A-FABP) as the riboprobe. The fluorescence intensity corresponding to the protected RNA fragment increased in a dose-dependent manner with respect to the complementary strand RNA. Results were obtained in 120 s, and the same amount of Cy5-labeled antisense riboprobe as used in the conventional method can be used. Furthermore, 8 times more sensitive detection of mRNA by microchip electrophoresis could be obtained. An obvious increase in the mRNA expression of A-FABP, which is known as a differentiation marker of adipocytes, occurred during the adipocyte differentiation of 3T3-L1 cells. These results clearly indicate the potential of microchip electrophoresis for the analysis of mRNA expression in cells.     

A comparison of methods to compute the potential of mean force.

Most processes occurring in a system are determined by the relative free energy between two or more states because the free energy is a measure of the probability of finding the system in a given state. When the two states of interest are connected by a pathway, usually called reaction coordinate, along which the free-energy profile is determined, this profile or potential of mean force (PMF) will also yield the relative free energy of the two states. Twelve different methods to compute a PMF are reviewed and compared, with regard to their precision, for a system consisting of a pair of methane molecules in aqueous solution. We analyze all combinations of the type of sampling (unbiased, umbrella-biased or constraint-biased), how to compute free energies (from density of states or force averaging) and the type of coordinate system (internal or Cartesian) used for the PMF degree of freedom. The method of choice is constraint-bias simulation combined with force averaging for either an internal or a Cartesian PMF degree of freedom.     

中国小型猪骨髓间充质干细胞的蛋白质组研究

报道了骨髓间充质干细胞(MSCs)的蛋白质组表达研究。从体外培养的MSCs提取细胞蛋白,经二维电泳分离后用银染方法可检出蛋白点约1600个,选取48个蛋白点进行胶内酶解及质谱分析,经数据库检索成功鉴定了37个蛋白,并对蛋白功能进行初步分析。本实验数据为进一步分析MSCs增殖、分化或凋亡的分子机理提供相关信息。     

CO_2在三聚氰胺酚醛纤维上的吸附分离

以三聚氰胺、间苯三酚和甲醛为原料,通过水热缩聚反应合成了三聚氰胺酚醛纤维(PMF),考察了温度对PMF合成的影响。以扫描电子显微镜(SEM)、透射电子显微镜(TEM)、N_2吸脱附和傅里叶变换红外(FT-IR)光谱等表征了PMF的形貌和结构,并采用体积法测定不同温度下CO_2和N_2在PMF上的单组分吸附平衡等温线。结果表明,在393 K下合成的PMF具有较大的比表面积(64 m2/g)和较高的CO_2吸附量(1.83 mmol/g,298 K、118 k Pa)。穿透柱实验表明,在298 K、200-600 k Pa,CO_2-N_2混合气在PMF上均可实现有效分离。将PMF在873 K下,N_2、H2及水蒸气等多种气氛中进行后处理,其比表面积和微孔孔容均显著增加,其中,在15%H_2O气氛中处理后,样品CO_2吸附量提高至2.83 mmol/g(298 K、118 k Pa)。     

The multiscale coarse-graining method. VII. Free energy decomposition of coarse-grained effective potentials

The potential of mean force (PMF) with respect to coarse-grained (CG) coordinates is often calculated in order to study the molecular interactions in atomistic molecular dynamics (MD) simulations. The multiscale coarse-graining (MS-CG) approach enables the computation of the many-body PMF of an atomistic system in terms of the CG coordinates, which can be used to parameterize CG models based on all-atom configurations. We demonstrate here that the MS-CG method can also be used to analyze the CG interactions from atomistic MD trajectories via PMF calculations. In addition, MS-CG calculations at different temperatures are performed to decompose the PMF values into energetic and entropic contributions as a function of the CG coordinates, which provides more thermodynamic information regarding the atomistic system. Two numerical examples, liquid methanol and a dimyristoylphosphatidylcholine lipid bilayer, are presented. The results show that MS-CG can be used as an analysis tool, comparable to various free energy computation methods. The differences between the MS-CG approach and other PMF calculation methods, as well as the characteristics and advantages of MS-CG, are also discussed.     

Temperature dependence of NMR order parameters and protein dynamics

The helical subdomain, HP36, of the F-actin-binding headpiece domain of chicken villin, is the smallest naturally occurring polypeptide that folds to a thermostable compact structure. Unconstrained molecular dynamics simulations and constrained molecular dynamics simulations using umbrella sampling are used to study the temperature dependence of internal motions of the backbone amide moieties of HP36. The potential of mean force (PMF) for the N-H bond vector, determined from the constrained simulations, is found to be temperature dependent. A simple analytical expression is derived that describes the temperature dependence of the PMF. The parameters of this model are obtained from the PMF, from the unconstrained molecular dynamics simulations, or from experimental values of the generalized order parameter. The results provide a linkage between experimental and theoretical measures of the temperature dependence of protein motions.     

Homogeneous organic/inorganic hybrid scaffolds with high osteoinductive activity for bone tissue engineering

Composite scaffolds of polymers/β-tricalcium phosphate (TCP) have been widely used for bone regeneration due to the combination of osteoinductivity of TCP and mechanical properties of the polymers. However, the difference in surface properties of the two material causes composite has poor uniformity and weak two-phase interaction, resulting in poor TCP release and weak new bone-forming ability. In this research, a TCP sol was developed to replace traditional TCP nanoparticles for the preparation of homogeneous polycaprolactone (PCL)/TCP sol nanofibrous scaffolds. It was found that compared with TCP nanoparticles, TCP sol homogeneously distributed in PCL nanofibers, and greatly improved the hydrophilicity, biodegradability, and mechanical properties of the scaffolds. It is also confirmed that loading TCP sol promoted the formation of bone-like apatite on the surface of the scaffolds. Biological experiments showed that all scaffolds supported rat bone marrow mesenchymal stem cells (rBMSCs) proliferation, especially scaffolds loaded with TCP sol. The increase in alkaline phosphatase activity and collagen production, enhanced calcium deposition, and up-regulation of osteocalcin expression demonstrated that the loading TCP sol expanded an advantage of scaffolds in promoting rBMSCs osteogenic differentiation, suggesting it dramatically improved the osteoinductive activity of PCL/TCP hybrid system and had a great potential application in bone regeneration.     

Potential of mean force of hydrophobic association: dependence on solute size

The potentials of mean force (PMFs) were determined for systems involving formation of nonpolar dimers composed of methane, ethane, propane, isobutane, and neopentane, respectively, in water, using the TIP3P water model, and in vacuo. A series of umbrella-sampling molecular dynamics simulations with the AMBER force field was carried out for each pair in either water or in vacuo. The PMFs were calculated by using the weighted histogram analysis method (WHAM). The shape of the PMFs for dimers of all five nonpolar molecules is characteristic of hydrophobic interactions with contact and solvent-separated minima and desolvation maxima. The positions of all these minima and maxima change with the size of the nonpolar molecule, that is, for larger molecules they shift toward larger distances. The PMF of the neopentane dimer is similar to those of other small nonpolar molecules studied in this work, and hence the neopentane dimer is too small to be treated as a nanoscale hydrophobic object. The solvent contribution to the PMF was also computed by subtracting the PMF determined in vacuo from the PMF in explicit solvent. The molecular surface area model correctly describes the solvent contribution to the PMF together with the changes of the height and positions of the desolvation barrier for all dimers investigated. The water molecules in the first solvation sphere of the dimer are more ordered compared to bulk water, with their dipole moments pointing away from the surface of the dimer. The average number of hydrogen bonds per water molecule in this first hydration shell is smaller compared to that in bulk water, which can be explained by coordination of water molecules to the hydrocarbon surface. In the second hydration shell, the average number of hydrogen bonds is greater compared to bulk water, which can be explained by increased ordering of water from the first hydration shell; the net effect is more efficient hydrogen bonding between the water molecules in the first and second hydration shells.     

Synthesis of DnaK and GroEL in Escherichia coli cells exposed to different magnetic field signals

The effects of extremely low frequency magnetic field (ELF-MF)(1 mT, 50 Hz) on the heat shock protein (HSP) synthesis in Escherichia coli were investigated. Two magnetic field signals were studied: sinusoidal (SMF) and pulsed square wave (PMF). It was found that bacteria exposed to SMF showed a significantly higher level of DnaK and GroEL proteins as compared to sham-exposed bacteria as revealed by Western blot, whereas a lower level was observed after PMF exposure. Similar results were obtained when bacterial cells were exposed to heat shock (HS) after ELF-MF exposure: again SMF and PMF resulted in an increase and in a reduction of HSP amount in comparison with sham control, respectively. In conclusion, the MF influences the synthesis of HSPs in E. coli in a way that critically depends on the signal characteristics.     

Retrospective docking study of PDE4B ligands and an analysis of the behavior of selected scoring functions

Scoring forms a major obstacle to the success of any docking study. In general, fast scoring functions perform poorly when used to determine the relative affinity of ligands for their receptors. In this study, the objective was not to rank compounds with confidence but simply to identify a scoring method which could provide a 4-fold hit enrichment in a screening sample over random selection. To this end, LigandFit, a fast shape matching docking algorithm, was used to dock a variety of known inhibitors of type 4 phosphodiesterase (PDE4B) into its binding site determined crystallographically for a series of pyrazolopyridine inhibitors. The success of identifying good poses with this technique was explored through RMSD comparisons with 19 known inhibitors for which crystallographic structures were available. The effectiveness of five scoring functions (PMF, JAIN, PLP2, LigScore2, and DockScore) was then evaluated through consideration of the success in enriching the top ranked fractions of nine artificial databases, constructed by seeding 1980 inactive ligands (pIC50 < 5) with 20 randomly selected inhibitors (pIC50 > 6.5). PMF and JAIN showed high average enrichment factors (greater than 4 times) in the top 5-10% of the ranked databases. Rank-based consensus scoring was then investigated, and the rational combination of 3 scoring functions resulted in more robust scoring schemes with (cScore)-DPmJ (consensus score of DockScore, PMF, and JAIN) and (cScore)-PPmJ (PLP2, PMF, and JAIN) yielding particularly good results. These cScores are believed to be of greater general application. Finally, the analysis of the behavior of the scoring functions across different chemotypes uncovered the inherent bias of the docking and scoring toward compounds in the same structural family as that employed for the crystal structure, suggesting the need to use multiple versions of the binding site for more successful virtual screening strategies.     

Calculation of the absolute thermodynamic properties of association of host-guest systems from the intermolecular potential of mean force

The authors report calculations of the intermolecular potential of mean force (PMF) in the case of the host-guest interaction. The host-guest system is defined by a water soluble calixarene and a cation. With an organic cation such as the tetramethylammonium cation, the calixarene forms an insertion complex, whereas with the Lanthane cation, the supramolecular assembly is an outer-sphere complex. The authors apply a modified free energy perturbation method and the force constraint technique to establish the PMF profiles as a function of the separation distance between the host and guest. They use the PMF profile for the calculation of the absolute thermodynamic properties of association that they compare to the experimental values previously determined. They finish by giving some structural features of the insertion and outer-sphere complexes at the Gibbs free energy minimum.     

Gene transfection using biodegradable nanospheres: results in tissue culture and a rat osteotomy model

In this paper, we have investigated sustained release biodegradable nanospheres for the delivery of plasmid DNA. The nanospheres were formulated using a proprietary co-polymer emulsion technique to encapsulate plasmid DNA. Gene transfection with nanospheres containing reporter genes (human placental alkaline phosphatase (AP) or Luciferase) was demonstrated in tissue culture (293T and COS-7 cells), and also in vivo in a nonunion femoral fracture (osteotomy) rat model. The bone gap was filled with nanospheres and gene expression in the implantation site was measured five weeks after the initial surgery. The nanospheres had a mean diameter of 230 nm, with a DNA loading of 0.7%w/w. These nanospheres demonstrated sustained release of the encapsulated DNA under in vitro physiologic conditions with an 82% cumulative DNA release over 17 days. The transfection efficiency of the nanospheres in tissue culture was two to five orders of magnitude greater than the gene expression with the same amount of plasmid DNA in solution. In the rat studies, the mean AP activity in the tissue retrieved from the osteotomy site in the experimental group was 291.8±52.5 cpm Versus 54.1±26.5 cpm (mean±S.E.M., P=0.03) in the sham control group. In conclusion, plasmid DNA nanospheres could be used as an effective nonviral method of gene delivery. In the future, nanospheres containing therapeutic genes, such as those encoding parathyroid hormone peptide, 1–34 amino acids (PTH-34) or Bone Morphogenic Protein-4 (BMP-4), could be used for the healing of nonunion bone fracture sites.     

Determination of side‐chain‐rotamer and side‐chain and backbone virtual‐bond‐stretching potentials of mean force from AM1 energy surfaces of terminally‐blocked amino‐acid residues,for coarse‐grained simulations of protein structure and folding. I. The method

In this and the accompanying article, we report the development of new physics‐based side‐chain‐rotamer and virtual‐bond‐deformation potentials which now replace the respective statistical potentials used so far in our physics‐based united‐reside UNRES force field for large‐scale simulations of protein structure and dynamics. In this article, we describe the methodology for determining the corresponding potentials of mean force (PMF's) from the energy surfaces of terminally‐blocked amino‐acid residues calculated with the AM1 quantum‐mechanical semiempirical method. The approach is based on minimization of the AM1 energy for fixed values of the angles λ for rotation of the peptide groups about the C^α ··· C^α virtual bonds, and for fixed values of the side‐chain dihedral angles χ, which formed a multidimensional grid. A harmonic‐approximation approach was developed to extrapolate from the energy at a given grid point to other points of the conformational space to compute the respective contributions to the PMF. To test the applicability of the harmonic approximation, the rotamer PMF's of alanine and valine obtained with this approach have been compared with those obtained by using a Metropolis Monte Carlo method. The PMF surfaces computed with the harmonic approximation are more rugged and have more pronounced minima than the MC‐calculated surfaces but the harmonic‐approximation‐and MC‐calculated PMF values are linearly correlated. The potentials derived with the harmonic approximation are, therefore, appropriate for UNRES for which the weights (scaling factors) of the energy terms are determined by force‐field optimization for foldability. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Traveling Time of a translating ribosome along messenger RNA monitored directly on a quartz crystal microbalance

During translation, the biosynthesis of polypeptides is dynamically regulated. The translation rate along messenger RNA (mRNA), which is dependent on the codon, structure, and sequence, is not always constant. However, methods for measuring the duration required for polypeptide elongation on an mRNA of interest have not been developed. In this work, we used a quartz crystal microbalance (QCM) technique to monitor mRNA translation in an Escherichia coli cell-free translation system in real time. This method permitted us to evaluate the translation of proteins of interest fused upstream of a streptavidin-binding peptide (SBP) fusion protein. The translation of mRNA encoding the SBP fusion protein alone was observed as a mass increase on a streptavidin-modified QCM plate. Addition of the protein of interest resulted in a delay in the mass change corresponding to the traveling time of the ribosome along the coding region of the protein of interest. With this technique, the lengths of coding sequences, codon usages, influences of unique sequences, and various protein-coding sequences were evaluated. The results showed that the traveling time of the translating ribosome depends on the length of the coding region translated but is also affected by the sequence itself. Differences in the time lags for various proteins imply that mRNA coding sequences may regulate gene expression.