Single-molecule spectromicroscopy: a route towards sub-wavelength refractometry

2015 ◽  
Vol 184 ◽  
pp. 263-274 ◽  
Author(s):  
T. A. Anikushina ◽  
M. G. Gladush ◽  
A. A. Gorshelev ◽  
A. V. Naumov
Keyword(s):  
Refractive Index ◽  
Single Molecule ◽  
Low Temperatures ◽  
Radiative Lifetime ◽  
Spatially Resolved ◽  
Local Fluctuations ◽  
Novel Approach ◽  
Spectral Linewidth ◽  
Spatial Fluctuations ◽  
Sub Wavelength

We suggest a novel approach for spatially resolved probing of local fluctuations of the refractive index n in solids by means of single-molecule (SM) spectroscopy. It is based on the dependence T1(n) of the effective radiative lifetime T1 of dye centres in solids on n due to the local-field effects. Detection of SM zero-phonon lines at low temperatures gives the values of the SM natural spectral linewidth (which is inversely proportional to T1) and makes it possible to reveal the distribution of the local n values in solids. Here we demonstrate this possibility on the example of amorphous polyethylene and polycrystalline naphthalene doped with terrylene. In particular, we show that the obtained distributions of lifetime limited spectral linewidths of terrylene molecules embedded into these matrices are due to the spatial fluctuations of the refractive index local values.

scholarly journals Automated analysis of filopodial length and spatially resolved protein concentration via adaptive shape tracking

2016 ◽  
Vol 27 (22) ◽  
pp. 3616-3626 ◽  
Author(s):  
Tanumoy Saha ◽  
Isabel Rathmann ◽  
Abhiyan Viplav ◽  
Sadhana Panzade ◽  
Isabell Begemann ◽  
...  
Keyword(s):  
Protein Concentration ◽  
Growth Dynamics ◽  
Automated Analysis ◽  
Cell Types ◽  
Control Mechanisms ◽  
Spatially Resolved ◽  
Novel Approach ◽  
Associated Proteins

Filopodia are dynamic, actin-rich structures that transiently form on a variety of cell types. To understand the underlying control mechanisms requires precise monitoring of localization and concentration of individual regulatory and structural proteins as filopodia elongate and subsequently retract. Although several methods exist that analyze changes in filopodial shape, a software solution to reliably correlate growth dynamics with spatially resolved protein concentration along the filopodium independent of bending, lateral shift, or tilting is missing. Here we introduce a novel approach based on the convex-hull algorithm for parallel analysis of growth dynamics and relative spatiotemporal protein concentration along flexible filopodial protrusions. Detailed in silico tests using various geometries confirm that our technique accurately tracks growth dynamics and relative protein concentration along the filopodial length for a broad range of signal distributions. To validate our technique in living cells, we measure filopodial dynamics and quantify spatiotemporal localization of filopodia-associated proteins during the filopodial extension–retraction cycle in a variety of cell types in vitro and in vivo. Together these results show that the technique is suitable for simultaneous analysis of growth dynamics and spatiotemporal protein enrichment along filopodia. To allow readily application by other laboratories, we share source code and instructions for software handling.

scholarly journals Spatially resolved transcriptomics reveals unique gene signatures associated with human temporal cortical architecture and Alzheimer's pathology

2021 ◽  
Author(s):  
Shuo Chen ◽  
Yuzhou Chang ◽  
Liangping Li ◽  
Diana Acosta ◽  
Cody Morrison ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Molecule ◽  
Brain Region ◽  
Expression Patterns ◽  
Middle Temporal Gyrus ◽  
Marker Genes ◽  
Gene Signatures ◽  
Unique Gene ◽  
Spatially Resolved ◽  
And Gender

Alzheimer's disease (AD) is pathologically characterized by amyloid beta (Aβ) plaques, neurofibrillary tangles (tau aggregates), and alterations in microglia, astrocytes and oligodendrocytes. The mesial temporal lobe is a vulnerable brain region in early AD; however, little is known about the transcriptome-scale gene expression in this region and its relation to AD pathology. Here we use the 10x Genomics Visium platform in combination with co-immunofluorescence staining of AD-associated pathological markers to define the spatial topography of gene expression in the middle temporal gyrus (MTG) from both early AD and age- and gender-matched control cases. We identify unique marker genes for six cortical layers and the adjacent white matter as well as gene expression patterns and alterations that showcase unique gene signatures and pathways associated with a range of AD pathology. Also, gene co-expression analyses of differentially expressed genes (DEGs) between AD and controls reveal four unique gene modules, which significantly change their co-expression patterns in the presence of variations of AD pathology. Furthermore, we validate the changes of key representative DEGs that are associated with AD pathology in neurons, microglia, astrocytes and oligodendrocytes using single-molecule fluorescent in situ hybridization. In summary, we provide a rich resource for the spatial transcriptomic profile of the human MTG, which will contribute to our understanding of the complex architecture and AD pathology of this vulnerable brain region.

scholarly journals The Milky Way Cepheid Leavitt law based on Gaia DR2 parallaxes of companion stars and host open cluster populations

2020 ◽  
Vol 643 ◽  
pp. A115 ◽  
Author(s):  
Louise Breuval ◽  
Pierre Kervella ◽  
Richard I. Anderson ◽  
Adam G. Riess ◽  
Frédéric Arenou ◽  
...  
Keyword(s):  
Milky Way ◽  
Open Cluster ◽  
Hubble Constant ◽  
Zero Point ◽  
Spatially Resolved ◽  
Trigonometric Parallax ◽  
Novel Approach ◽  
Classical Cepheids ◽  
Average Cluster ◽  
Gaia Dr2

Aims. Classical Cepheids provide the foundation for the empirical extragalactic distance ladder. Milky Way Cepheids are the only stars in this class accessible to trigonometric parallax measurements. However, the parallaxes of Cepheids from the second Gaia data release (GDR2) are affected by systematics because of the absence of chromaticity correction, and occasionally by saturation. Methods. As a proxy for the parallaxes of 36 Galactic Cepheids, we adopt either the GDR2 parallaxes of their spatially resolved companions or the GDR2 parallax of their host open cluster. This novel approach allows us to bypass the systematics on the GDR2 Cepheids parallaxes that is induced by saturation and variability. We adopt a GDR2 parallax zero-point (ZP) of −0.046 mas with an uncertainty of 0.015 mas that covers most of the recent estimates. Results. We present new Galactic calibrations of the Leavitt law in the V, J, H, KS, and Wesenheit WH bands. We compare our results with previous calibrations based on non-Gaia measurements and compute a revised value for the Hubble constant anchored to Milky Way Cepheids. Conclusions. From an initial Hubble constant of 76.18 ± 2.37 km s−1 Mpc−1 based on parallax measurements without Gaia, we derive a revised value by adopting companion and average cluster parallaxes in place of direct Cepheid parallaxes, and we find H0 = 72.8 ± 1.9 (statistical + systematics) ±1.9 (ZP) km s−1 Mpc−1 when all Cepheids are considered and H0 = 73.0 ± 1.9 (statistical + systematics) ±1.9 (ZP) km s−1 Mpc−1 for fundamental mode pulsators only.

scholarly journals Spatially Resolved Cross-Linking Characterization by Imaging Low-Coherence Interferometry

Sensors ◽  
2019 ◽  
Vol 19 (5) ◽  
pp. 1152 ◽  
Author(s):  
Christopher Taudt ◽  
Bryan Nelsen ◽  
Elisabeth Rossegger ◽  
Sandra Schlögl ◽  
Edmund Koch ◽  
...  
Keyword(s):  
Refractive Index ◽  
Optical Thickness ◽  
Information Acquisition ◽  
Cross Linking ◽  
Imaging Spectrometer ◽  
Low Coherence ◽  
Spatially Resolved ◽  
Low Coherence Interferometry ◽  
Error Estimations ◽  
Phase Data

A method to characterize cross-linking differences in polymers such as waveguide polymers has been developed. The method is based on the scan-free information acquisition utilizing a low-coherence interferometer in conjunction with an imaging spectrometer. By the introduction of a novel analyzing algorithm, the recorded spectral-phase data was interpreted as wavelength-dependent optical thickness which is matchable with the refractive index and therefore with the degree of cross-linking. In the course of this work, the method was described in its hardware and algorithmic implementation as well as in its accuracy. Comparative measurements and error estimations showed an accuracy in the range of 10−6 in terms of the refractive index. Finally, photo-lithographically produced samples with laterally defined cross-linking differences have been characterized. It could be shown, that differences in the optical thickness of ±1.5 μm are distinguishable.

scholarly journals Stretching single titin molecules from failing human hearts reveals titin’s role in blunting cardiac kinetic reserve

2019 ◽  
Vol 116 (1) ◽  
pp. 127-137
Author(s):  
Mei-Pian Chen ◽  
Salome A Kiduko ◽  
Nancy S Saad ◽  
Benjamin D Canan ◽  
Ahmet Kilic ◽  
...  
Keyword(s):  
Heart Rate ◽  
Single Molecule ◽  
Left Ventricular ◽  
Passive Tension ◽  
Frequency Dependent ◽  
Heart Rates ◽  
Human Cardiomyocytes ◽  
Sarcomeric Protein ◽  
Novel Approach ◽  
Speed Up

Abstract Aims Heart failure (HF) patients commonly experience symptoms primarily during elevated heart rates, as a result of physical activities or stress. A main determinant of diastolic passive tension, the elastic sarcomeric protein titin, has been shown to be associated with HF, with unresolved involvement regarding its role at different heart rates. To determine whether titin is playing a role in the heart rate (frequency-) dependent acceleration of relaxation (FDAR). W, we studied the FDAR responses in live human left ventricular cardiomyocytes and the corresponding titin-based passive tension (TPT) from failing and non-failing human hearts. Methods and results Using atomic force, we developed a novel single-molecule force spectroscopy approach to detect TPT based on the frequency-modulated cardiac cycle. Mean TPT reduced upon an increased heart rate in non-failing human hearts, while this reduction was significantly blunted in failing human hearts. These mechanical changes in the titin distal Ig domain significantly correlated with the frequency-dependent relaxation kinetics of human cardiomyocytes obtained from the corresponding hearts. Furthermore, the data suggested that the higher the TPT, the faster the cardiomyocytes relaxed, but the lower the potential of myocytes to speed up relaxation at a higher heart rate. Such poorer FDAR response was also associated with a lesser reduction or a bigger increase in TPT upon elevated heart rate. Conclusions Our study established a novel approach in detecting dynamic heart rate relevant tension changes physiologically on native titin domains. Using this approach, the data suggested that the regulation of kinetic reserve in cardiac relaxation and its pathological changes were associated with the intensity and dynamic changes of passive tension by titin.

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