High-throughput single-molecule fluorescence spectroscopy using parallel detection

Solution-based single-molecule fluorescence spectroscopy is a powerful new experimental approach with applications in all fields of natural sciences. The basic concept of this technique is to excite and collect light from a very small volume (typically femtoliter) and work in a concentration regime resulting in rare burst-like events corresponding to the transit of a single-molecule. Those events are accumulated over time to achieve proper statistical accuracy. Therefore the advantage of extreme sensitivity is somewhat counterbalanced by a very long acquisition time. One way to speed up data acquisition is parallelization. Here we will discuss a general approach to address this issue, using a multispot excitation and detection geometry that can accommodate different types of novel highly-parallel detector arrays. We will illustrate the potential of this approach with fluorescence correlation spectroscopy (FCS) and single-molecule fluorescence measurements obtained with different novel multipixel single-photon counting detectors.

Single Nucleotide Polymorphism (SNP) in RASSF1 and Clinical Outcomes of Breast Cancer Patients Treated with Neoadjuvant Docetaxel/Doxorubicin Chemotherapy

PurposeThe tumor suppressor gene RASSF1 (Ras association domain family member 1) regulates cell cycle, progression, apoptosis, and microtubule stability, and is inactivated by promoter hypermethylation in breast cancer. We analyzed the SNPs in RASSF1 and their predictive and prognostic value in stage II or III breast cancer patients who received neoadjuvant docetaxel/doxorubicin chemotherapyMethodsA total of 139 stage II or III breast cancer patients who received neoadjuvant docetaxel/doxorubicin chemotherapy were enrolled in this study. The patients received three cycles of neoadjuvant chemotherapy followed by curative surgery, and received additional three cycles of docetaxel/doxorubicin chemotherapy as an adjuvant. Germline DNA from peripheral blood mononuclear cells was extracted. The genotypes were performed using Illumina GoldenGate® Assay. We analyzed 3 SNPs in RASSF1 genes: rs3213621 T>C in 3'UTR, rs2073499 G>A in intron, and rs2073498 C>A in exon 3 Ala133Ser.ResultsThe overall radiologic response rate (RR) for neoadjuvant chemotherapy was 79.8% and 10 patients (7.2%) achieved a pathologic complete remission (pCR). None of the SNPs were correlated with radiologic RR or pCR rate. SNP in intron of RASSF1 (rs2073499) was associated with relapse free survival (RFS). RFS was longer in GA/AA genotype than GG genotype (Hazard ratio [HR]=0.374, p=0.034) After adjusting age and hormone status, prognostic value of RASSF1 SNP remained significant (HR=0.393, p=0.050). Other two SNPs were not significantly associated with RFS.ConclusionsThe GA/AA genotype in SNP of RASSF1 (rs2073499) is associated with significantly longer RFS than the GG genotype. Further research is warranted to identify the biologic characteristics of RASSF1.

Citation Information: Cancer Res 2009;69(24 Suppl):Abstract nr 6061.

Expression of Ca2+ -activated K+ channels in human dermal fibroblasts and their roles in apoptosis

BACKGROUNDS/AIMS

Cell proliferation and apoptosis are responsible for maintaining normal tissue homeostasis, and K(+) currents play important roles in regulating the physiological balance between them. This function of Ca(2+)-activated K(+) (K(Ca)) channels has been demonstrated in many types of tissues, but not in dermal fibroblasts. We investigated the expression of K(Ca) channels and their effects on proliferation and apoptosis in human dermal fibroblasts.

METHODS

We used discoidin domain receptor 2 immunostaining to identify human dermal fibroblasts, and reverse transcription polymerase chain reaction, Western blot analysis and electrophysiological patch clamp recordings to evaluate the expression and characteristics of 3 members of the K(Ca) channel family, large-conductance K(Ca) (BK), intermediate-conductance K(Ca) (IK) and small-conductance K(Ca) channels. We also used the 3-(4,5-dimethyl-2-yl)-2,5-diphenyltetrazolium bromide assay, flow cytometry, Hoechst 33258 staining and Depsipher staining to investigate the effects of K(Ca) channels on cell proliferation and the mechanisms involved.

RESULTS AND CONCLUSIONS

All 3 members of the K(Ca) channel family were found in fibroblasts. 1,3-Dihydro-1-[2-hydroxy-5-(trifluoromethyl)phenyl]-5-(trifluoromethyl)-2H-benzimidazol-2-one (NS1619, a BK channel activator) or 1-ethyl-2-benzimidazolinone (EBIO, an IK channel activator) decreased the proliferation of fibroblasts and induced apoptotic changes by mitochondrial membrane potential disruption. However, a pan-caspase inhibitor (Z-VAD-fmk) failed to prevent the apoptotic changes. Our findings indicate that 3 types of functional K(Ca) channels are expressed in human dermal fibroblasts and are involved in apoptosis of the cells through the mitochondrial apoptotic pathway, but seemingly in a caspase-independent manner.

Optimizing Cubature for Efficient Integration of Subspace Deformations

We propose an efficient scheme for evaluating nonlinear subspace forces (and Jacobians) associated with subspace deformations. The core problem we address is efficient integration of the subspace force density over the 3D spatial domain. Similar to Gaussian quadrature schemes that efficiently integrate functions that lie in particular polynomial subspaces, we propose cubature schemes (multi-dimensional quadrature) optimized for efficient integration of force densities associated with particular subspace deformations, particular materials, and particular geometric domains. We support generic subspace deformation kinematics, and nonlinear hyperelastic materials. For an r-dimensional deformation subspace with O(r) cubature points, our method is able to evaluate subspace forces at O(r(2)) cost. We also describe composite cubature rules for runtime error estimation. Results are provided for various subspace deformation models, several hyperelastic materials (St.Venant-Kirchhoff, Mooney-Rivlin, Arruda-Boyce), and multimodal (graphics, haptics, sound) applications. We show dramatically better efficiency than traditional Monte Carlo integration. CR CATEGORIES: I.6.8 [Simulation and Modeling]: Types of Simulation-Animation, I.3.5 [Computer Graphics]: Computational Geometry and Object Modeling-Physically based modeling G.1.4 [Mathematics of Computing]: Numerical Analysis-Quadrature and Numerical Differentiation.