12 research outputs found
Measurement of Photon Statistics with Live Photoreceptor Cells
We analyzed the electrophysiological response of an isolated rod
photoreceptor of Xenopus laevis under stimulation by coherent and
pseudo-thermal light sources. Using the suction electrode technique for single
cell recordings and a fiber optics setup for light delivery allowed
measurements of the major statistical characteristics of the rod response. The
results indicate differences in average responses of rod cells to coherent and
pseudo-thermal light of the same intensity and also differences in
signal-to-noise ratios and second order intensity correlation functions. These
findings should be relevant for interdisciplinary studies seeking applications
of quantum optics in biology.Comment: 6 pages, 7 figure
Correlation Measurement of Squeezed Light
We study the implementation of a correlation measurement technique for the
characterization of squeezed light which is nearly free of electronic noise.
With two different sources of squeezed light, we show that the sign of the
covariance coefficient, revealed from the time resolved correlation data, is
witnessing the presence of squeezing in the system. Furthermore, we estimate
the degree of squeezing using the correlation method and compare it to the
standard homodyne measurement scheme. We show that the role of electronic
detector noise is minimized using the correlation approach as opposed to
homodyning where it often becomes a crucial issue
Using genome-wide measurements for computational prediction of SH2āpeptide interactions
Peptide-recognition modules (PRMs) are used throughout biology to mediate proteināprotein interactions, and many PRMs are members of large protein domain families. Recent genome-wide measurements describe networks of peptideāPRM interactions. In these networks, very similar PRMs recognize distinct sets of peptides, raising the question of how peptide-recognition specificity is achieved using similar protein domains. The analysis of individual protein complex structures often gives answers that are not easily applicable to other members of the same PRM family. Bioinformatics-based approaches, one the other hand, may be difficult to interpret physically. Here we integrate structural information with a large, quantitative data set of SH2 domaināpeptide interactions to study the physical origin of domaināpeptide specificity. We develop an energy model, inspired by protein folding, based on interactions between the amino-acid positions in the domain and peptide. We use this model to successfully predict which SH2 domains and peptides interact and uncover the positions in each that are important for specificity. The energy model is general enough that it can be applied to other members of the SH2 family or to new peptides, and the cross-validation results suggest that these energy calculations will be useful for predicting binding interactions. It can also be adapted to study other PRM families, predict optimal peptides for a given SH2 domain, or study other biological interactions, e.g. proteināDNA interactions.National Institutes of Health. National Centers for Biomedical Computing (Informatics for Integrating Biology and the Bedside)National Institutes of Health (U.S.) (grant U54LM008748
A molecular signature in blood identifies early Parkinson's disease
BACKGROUND: The search for biomarkers in Parkinson's disease (PD) is crucial to identify the disease early and monitor the effectiveness of neuroprotective therapies. We aim to assess whether a gene signature could be detected in blood from early/mild PD patients that could support the diagnosis of early PD, focusing on genes found particularly altered in the substantia nigra of sporadic PD. RESULTS: The transcriptional expression of seven selected genes was examined in blood samples from 62 early stage PD patients and 64 healthy age-matched controls. Stepwise multivariate logistic regression analysis identified five genes as optimal predictors of PD: p19 S-phase kinase-associated protein 1A (odds ratio [OR] 0.73; 95% confidence interval [CI] 0.60-0.90), huntingtin interacting protein-2 (OR 1.32; CI 1.08-1.61), aldehyde dehydrogenase family 1 subfamily A1 (OR 0.86; 95% CI 0.75-0.99), 19āS proteasomal protein PSMC4 (OR 0.73; 95% CI 0.60-0.89) and heat shock 70-kDa protein 8 (OR 1.39; 95% CI 1.14-1.70). At a 0.5 cut-off the gene panel yielded a sensitivity and specificity in detecting PD of 90.3 and 89.1 respectively and the area under the receiving operating curve (ROC AUC) was 0.96. The performance of the five-gene classifier on the de novo PD individuals alone composing the early PD cohort (nā=ā38), resulted in a similar ROC with an AUC of 0.95, indicating the stability of the model and also, that patient medication had no significant effect on the predictive probability (PP) of the classifier for PD risk. The predictive ability of the model was validated in an independent cohort of 30 patients at advanced stage of PD, classifying correctly all cases as PD (100% sensitivity). Notably, the nominal average value of the PP for PD (0.95 (SDā=ā0.09)) in this cohort was higher than that of the early PD group (0.83 (SDā=ā0.22)), suggesting a potential for the model to assess disease severity. Lastly, the gene panel fully discriminated between PD and Alzheimer's disease (nā=ā29). CONCLUSIONS: The findings provide evidence on the ability of a five-gene panel to diagnose early/mild PD, with a possible diagnostic value for detection of asymptomatic PD before overt expression of the disorder