Multi-color fluorescent DNA analysis in an optofluidic chip

Modulation-frequency-encoded fluorescence excitation enables the identification of end-labeled DNA samples of different genetic origin during their electrophoretic separation, opening perspectives for intrinsic size calibration, malign / healthy sample comparison, and exploitation of multiplex ligation-dependent probe amplification

Delay-dependent amplification of a probe pulse via stimulated Rayleigh scattering

Stimulated Rayleigh scattering of pump and probe light pulses of close carrier frequencies is considered. A nonzero time delay between the two pulses is shown to give rise to amplification of the delayed (probe) pulse accompanied by attenuation of the pump, both on resonance and off resonance. In either case, phase-matching effects are shown to provide a sufficiently large gain, which can exceed significantly direct one-photon-absorption losses

Multiplex ligation-dependent probe amplification (MLPA) analysis is an effective tool for the detection of novel intragenic PLA2G6 mutations: Implications for molecular diagnosis

Phospholipase associated neurodegeneration (PLAN) comprises a heterogeneous group of autosomal recessive neurological disorders caused by mutations in the PLA2G6 gene. Direct gene sequencing detects 85% mutations in infantile neuroaxonal dystrophy. We report the novel use of multiplex ligation-dependent probe amplification (MLPA) analysis to detect novel PLA2G6 duplications and deletions. The identification of such copy number variants (CNVs) expands the PLAN mutation spectrum and may account for up to 12.5% of PLA2G6 mutations. MLPA should thus be employed to detect CNVs of PLA2G6 in patients who show clinical features of PLAN but in whom both disease-causing mutations cannot be identified on routine sequencin

Unambiguous determination of spin dephasing times in ZnO

Time-resolved magneto-optics is a well-established optical pump probe technique to generate and to probe spin coherence in semiconductors. By this method, spin dephasing times T_2^* can easily be determined if their values are comparable to the available pump-probe-delays. If T_2^* exceeds the laser repetition time, however, resonant spin amplification (RSA) can equally be used to extract T_2^*. We demonstrate that in ZnO these techniques have several tripping hazards resulting in deceptive values for T_2^* and show how to avoid them. We show that the temperature dependence of the amplitude ratio of two separate spin species can easily be misinterpreted as a strongly temperature dependent T_2^* of a single spin ensemble, while the two spin species have T_2^* values which are nearly independent of temperature. Additionally, consecutive pump pulses can significantly diminish the spin polarization, which remains from previous pump pulses. While this barely affects T_2^* values extracted from delay line scans, it results in seemingly shorter T_2^* values in RSA.Comment: 11 pages, 10 figure

Cluster analysis of multiplex ligation-dependent probe amplification data in choroidal melanoma.

PurposeTo determine underlying correlations in multiplex ligation-dependent probe amplification (MLPA) data and their significance regarding survival following treatment of choroidal melanoma (CM).MethodsMLPA data were available for 31 loci across four chromosomes (1p, 3, 6, and 8) in tumor material obtained from 602 patients with CM treated at the Liverpool Ocular Oncology Center (LOOC) between 1993 and 2012. Data representing chromosomes 3 and 8q were analyzed in depth since their association with CM patient survival is well-known. Unsupervised k-means cluster analysis was performed to detect latent structure in the data set. Principal component analysis (PCA) was also performed to determine the intrinsic dimensionality of the data. Survival analyses of the identified clusters were performed using Kaplan-Meier (KM) and log-rank statistical tests. Correlation with largest basal tumor diameter (LTD) was investigated.ResultsChromosome 3: A two-cluster (bimodal) solution was found in chromosome 3, characterized by centroids at unilaterally normal probe values and unilateral deletion. There was a large, significant difference in the survival characteristics of the two clusters (log-rank, p<0.001; 5-year survival: 80% versus 40%). Both clusters had a broad distribution in LTD, although larger tumors were characteristically in the poorer outcome group (Mann-Whitney, p<0.001). Threshold values of 0.85 for deletion and 1.15 for gain optimized the classification of the clusters. PCA showed that the first principal component (PC1) contained more than 80% of the data set variance and all of the bimodality, with uniform coefficients (0.28±0.03). Chromosome 8q: No clusters were found in chromosome 8q. Using a conventional threshold-based definition of 8q gain, and in conjunction with the chromosome 3 clusters, three prognostic groups were identified: chromosomes 3 and 8q both normal, either chromosome 3 or 8q abnormal, and both chromosomes 3 and 8q abnormal. KM analysis showed 5-year survival figures of approximately 97%, 80%, and 30% for these prognostic groups, respectively (log-rank, p<0.001). All MLPA probes within both chromosomes were significantly correlated with each other (Spearman, p<0.001).ConclusionsWithin chromosome 3, the strong correlation between the MLPA variables and the uniform coefficients from the PCA indicates a lack of evidence for a signature gene that might account for the bimodality we observed. We hypothesize that the two clusters we found correspond to binary underlying states of complete monosomy or disomy 3 and that these states are sampled by the complete ensemble of probes. Consequently, we would expect a similar pattern to emerge in higher-resolution MLPA data sets. LTD may be a significant confounding factor. Considering chromosome 8q, we found that chromosome 3 cluster membership and 8q gain as traditionally defined have an indistinguishable impact on patient outcome

Multiplex quantitative analysis of microRNA expression via exponential isothermal amplification and conformation-sensitive DNA separation

Expression profiling of multiple microRNAs (miRNAs) generally provides valuable information for understanding various biological processes. Thus, it is necessary to develop a sensitive and accurate miRNA assay suitable for multiplexing. Isothermal exponential amplification reaction (EXPAR) has received significant interest as an miRNA analysis method because of high amplification efficiency. However, EXPAR cannot be used for a broader range of applications owing to limitations such as complexity of probe design and lack of proper detection method for multiplex analysis. Here, we developed a sensitive and accurate multiplex miRNA profiling method using modified isothermal EXPAR combined with high-resolution capillary electrophoresis-based single-strand conformation polymorphism (CE-SSCP). To increase target miRNA specificity, a stem-loop probe was introduced instead of a linear probe in isothermal EXPAR to allow specific amplification of multiple miRNAs with minimal background signals. CE-SSCP, a conformation-dependent separation method, was used for detection. Since CE-SSCP eliminates the need for probes to have different lengths, easier designing of probes with uniform amplification efficiency was possible. Eight small RNAs comprising six miRNAs involved in Caenorhabditis elegans development and two controls were analyzed. The expression patterns obtained using our method were concordant with those reported in previous studies, thereby supporting the proposed method's robustness and utility.113sciescopu

Parametric amplification of optical phonons

Amplification of light through stimulated emission or nonlinear optical interactions has had a transformative impact on modern science and technology. The amplification of other bosonic excitations, like phonons in solids, is likely to open up new remarkable physical phenomena. Here, we report on an experimental demonstration of optical phonon amplification. A coherent mid-infrared optical field is used to drive large amplitude oscillations of the Si-C stretching mode in silicon carbide. Upon nonlinear phonon excitation, a second probe pulse experiences parametric optical gain at all wavelengths throughout the reststrahlen band, which reflects the amplification of optical-phonon fluctuations. Starting from first principle calculations, we show that the high-frequency dielectric permittivity and the phonon oscillator strength depend quadratically on the lattice coordinate. In the experimental conditions explored here, these oscillate then at twice the frequency of the optical field and provide a parametric drive for lattice fluctuations. Parametric gain in phononic four wave mixing is a generic mechanism that can be extended to all polar modes of solids, as a new means to control the kinetics of phase transitions, to amplify many body interactions or to control phonon-polariton waves