abstract: Biophysical techniques have been increasingly applied toward answering biological questions with more precision. Here, three different biological systems were studied with the goal of understanding their dynamic differences, either conformational dynamics within the system or oligomerization dynamics between monomers. With Cy3 on the 5' end of DNA, the effects of changing the terminal base pair were explored using temperature-dependent quantum yields. It was discovered, in combination with simulations, that a terminal thymine base has the weakest stacking interactions with the Cy3 dye compared to the other three bases. With ME1 heterodimers, the goal was to see if engineering a salt bridge at the dimerization interface could allow for control over dimerization in a pH-dependent manner. This was performed experimentally by measuring FRET between monomers containing either a Dap or an Asp mutation and comparing FRET efficiency at different pHs. It was demonstrated that the heterodimeric salt bridge would only form in a pH range near neutrality. Finally, with DNA processivity clamps, one aim was to compare the equilibrium dissociation constants, kinetic rate constants, and lifetimes of the closed rings for beta clamp and PCNA. This was done using a variety of biophysical techniques but with three as the main focus: fluorescence correlation spectroscopy, single-molecule experiments, and time-correlated single photon counting measurements. The stability of beta clamp was found to be three orders of magnitude higher when measuring solution stability but only one order of magnitude higher when measuring intrinsic stability, which is a result of salt bridge interactions in the interface of beta clamp. Ongoing work built upon the findings from this project by attempting to disrupt interface stability of different beta clamp mutants by adding salt or changing the pH of the solution. Lingering questions about the dynamics of different areas of the clamps has led to another project for which we have developed a control to demystify some unexpected similarities between beta clamp mutants. With that project, we show that single-labeled and double-labeled samples have similar autocorrelation decays in florescence correlation spectroscopy, allowing us to rule out the dyes themselves as causing fluctuations in the 10-100 microsecond timescale. / Dissertation/Thesis / Doctoral Dissertation Chemistry 2015

A espectroscopia de correlação de fluorescência (FCS) é uma das diferentes técnicas de análise por imagens de alta resolução espacial e temporal de biomoléculas em concentrações extremamente baixas. Ela se tornou uma técnica extremamente poderosa e sensível em áreas como bioquímica e biofísica. Como uma técnica bem estabelecida, ela é utilizada para medir concentrações locais de biomoléculas, através da marcação com moléculas fluorescentes. Coeficientes de difusão e constantes cinéticas também podem ser medidos através de FCS assim como detecção de molécula única. Ela também pode dar informação precisa sobre interações de antígeno-anticorpo, ácidos nucleicos e proteínas. Através de uma combinação de marcadores de alto rendimento quântico, fontes de luz estável (lasers), detecção ultrassensível e microscopia confocal, é possível realizar medidas de FCS em volumes de fentolitros (fL) e em concentrações de nanomolar (nM) em soluções aquosas ou em células vivas. Em contraste com outras técnicas de fluorescência, a sensibilidade da FCS aumenta com a diminuição da concentração do fluoróforo marcador, porque o parâmetro de interesse não é a intensidade de emissão de fluorescência, mas sim as flutuações espontâneas da fluorescência. Durante o tempo em que a partícula ou molécula atravessa o volume de medida pode ocorrer mudanças conformacionais e reações químicas e fotofísicas que alteram as características de emissão do fluoróforo e causam flutuações no sinal detectado. Estas flutuações são então monitoradas e transformadas em uma curva de autocorrelação, por intermédio de um software comercial que emprega um modelo físico apropriado para FCS. Em nosso estudo, utilizamos um marcador comercial (ALEXA 488®) para marcar proteínas. Primeiramente utilizamos a técnica de FCS para medir concentrações extremamente baixas de marcadores fluorescentes. Também realizamos um experimento testando a influência da viscosidade do meio na difusão livre do fluoróforo, assim como as melhores condições em que temos um melhor sinal de FCS. Por fim, estudamos a difusão de proteínas marcadas (PUC II e IV) em meio aquoso (PBS) e no interior de células. / Fluorescence correlation spectroscopy (FCS) is one of the many different modes of high-resolution spatial and temporal analysis of extremely low concentrated biomolecules. It has become a powerful and sensitive tool in fields like biochemistry and biophysics. As a well established technique, it is used to measure local concentrations of fluorescently labeled biomolecules, diffusion coefficients, kinetic constants and single molecule studies. Through a combination of high quantum yield fluorescent dyes, stable light sources (lasers), ultrasensitive detection and confocal microscopy is possible to perform FCS measurements in femtoliters volumes and nanomolar concentrations in aquous solution or in live cells. Unlike with other fluorescence technics, its sensibility increases with the decrease of dye concentrarion, because the main factor is not the emission intensity itself. Instead this, spontaneous statistical fluctuation of fluorescence becomes the main factor in FCS analisys. During the time that the conjugated-dye cross the volume detection can occur conformational changes, chemical reaction and photophysical processes that can change the emission properties of the dye and, then, change the detected sinal. This fluctuations are tracked and changed into a autocorrelation curve, by a specific software, appropriate to perform FCS analisys. In our study, we use comercial dye (Alexa 488) to label proteins. Firstly, we applied FCS to measure extremally diluted concentrations of dyes (~1 nM). We have performed experiments testing the influence of the viscosity medium in the free difusion of the dyes and the optical apparatus and conditions that result in the best FCS signal. We also have studied protein diffusion (PUC II e IV) in aquous medium (PBS) and toward the inner of the cells.

Master of Science / Department of Kinesiology / Thomas J. Barstow / Limb blood flow increases linearly with exercise intensity; however, invasive measurements of microvascular muscle blood flow during incremental exercise have demonstrated submaximal plateaus. Diffuse correlation spectroscopy (DCS) noninvasively quantifies relative changes in microvascular blood flow at rest via a blood flow index (BFI). The purpose of this study was to quantify relative changes in tissue blood flow during exercise using DCS, compare the BFI of the flexor digitorum superficialis (BFI[subscript]FDS) muscle to brachial artery blood flow (Q̇[subscript]BA) measured via Doppler ultrasound, and employ near infrared spectroscopy (NIRS) alongside DCS to simultaneously measure perfusive and diffusive oxygen transport within a single volume of exercising skeletal muscle tissue. We hypothesized Q̇[subscript]BA would increase with increasing exercise intensity until task failure, BFI[subscript]FDS would plateau at a submaximal work rate, and muscle oxygenation characteristics (total-[heme], deoxy-[heme], and % saturation) measured with NIRS would demonstrate a plateau at a similar work rate as BFI[subscript]FDS. Sixteen subjects (23.3 ± 3.9 yrs; 170.8 ± 1.9 cm; 72.8 ± 3.4 kg) participated in this study. Peak power (P[subscript]peak) was determined for each subject (6.2 ± 1.4W) via an incremental handgrip exercise test to task failure. Measurements of Q̇[subscript]BA, BFI[subscript]FDS, total-[heme], deoxy-[heme], and % saturation were made during each stage of the incremental exercise test. Q̇[subscript]BA increased with exercise intensity until the final work rate transition (p < 0.05). No increases in BFI[subscript]FDS or muscle oxygenation characteristics were observed at exercise intensities greater than 51.5 ± 22.9% of P[subscript]peak and were measured simultaneously in a single volume of exercising skeletal muscle tissue. Differences in muscle recruitment amongst muscles of the whole limb may explain the discrepancies observed in Q̇[subscript]BA and BFI[subscript]FDS responses during incremental exercise and should be further investigated.

No description available.

Cell penetrating peptides have been the focus of drug delivery research for 15 years due to their apparent ability to deliver cargoes inside cells more readily than many other carriers. Using two of the most commonly studied peptides (tat47-57 and R9), the present study differs from previous work by deliberately choosing to observe uptake with lower peptide concentrations closer to potential therapeutic doses, and by implementing raster image correlation spectroscopy (RICS) on a commercial microscope to quantify uptake in parallel to other techniques such as fluorescence correlation spectroscopy (FCS), confocal microscopy, and mass spectroscopy.An initial study using mass spectrometry and ExPASy (Expert Protein Analysis System) revealed that the peptides are stable for at least one hour in PBS. Based on this initial information and other experimental conditions, the study took two main directions with regards to the peptide: the membrane interaction and accumulation in the cell.The peptides interaction with the cell membrane revealed that neither tat-TAMRA nor R9-TAMRA disrupts the membrane of cells: incorporation of FM2-10 in the membrane was not modified in K562 cells whilst it was in presence of the control lytic peptides GALA and mellitin. Based on this information confocal microscopy was utilised to assess the localisation on the cell membrane. Peptide binding to the membrane appeared to be heterogeneous in distribution at 1µM bulk concentration.Accumulation in cells of the peptides was observed incubated at 37°C, confocal microscopy showed punctuated distribution with intracellular aggregations of fluorescence measuring between 2.5-3.5µm in diameter. Co-staining with a nuclear dye revealed these aggregations to be focused around the nucleus of the cell. Initial FCS experiments indicated a concentration dependent accumulation of the peptide in the cells and a decrease of the intracellular diffusion coefficients at high concentration possibly corresponding with molecular crowding. Interestingly the anomalous diffusion model did not statistically improve the results.RICS was implemented to study the kinetics of entry of TAMRA labelled cell penetrating peptides in both Caco-2 and HeLa cells lines at concentrations between 500nM and 2µM. Concentrations above 1µM exhibited higher final intracellular concentrations, yet the measured diffusion coefficients were similarly independent of extracellular concentration. Both peptides appeared to enter the cell quickly with a fast initial uptake over the first 10 minutes, reaching a concentration maxima after 30 minutes.Overall, the study reveals that many published studies may be incorrect as they may only be reporting the presence of a fluorescent dye inside the cell not the peptide. The fast binding of the peptide to the membrane is likely to cause false positive results when traditionally studying internalisation kinetics such as using flow cytometry and confocal microscopy. Correlation spectroscopy techniques such as FCS, provide useful information on internalisation of the peptides, but the single spot measurement is limited when providing information on the entire cell. RICS is a progression of correlation spectroscopy and provides a more representative picture of the cell.

abstract: The cell is a dense environment composes of proteins, nucleic acids, as well as other small molecules, which are constantly bombarding each other and interacting. These interactions and the diffusive motions are driven by internal thermal fluctuations. Upon collision, molecules can interact and form complexes. It is of interest to learn kinetic parameters such as reaction rates of one molecule converting to different species or two molecules colliding and form a new species as well as to learn diffusion coefficients. Several experimental measurements can probe diffusion coefficients at the single-molecule and bulk level. The target of this thesis is on single-molecule methods, which can assess diffusion coefficients at the individual molecular level. For instance, super resolution methods like stochastic optical reconstruction microscopy (STORM) and photo activated localization microscopy (PALM), have a high spatial resolution with the cost of lower temporal resolution. Also, there is a different group of methods, such as MINFLUX, multi-detector tracking, which can track a single molecule with high spatio-temporal resolution. The problem with these methods is that they are only applicable to very diluted samples since they need to ensure existence of a single molecule in the region of interest (ROI). In this thesis, the goal is to have the best of both worlds by achieving high spatio-temporal resolutions without being limited to a few molecules. To do so, one needs to refocus on fluorescence correlation spectroscopy (FCS) as a method that applies to both in vivo and in vitro systems with a high temporal resolution and relies on multiple molecules traversing a confocal volume for an extended period of time. The difficulty here is that the interpretation of the signal leads to different estimates for the kinetic parameters such as diffusion coefficients based on a different number of molecules we consider in the model. It is for this reason that the focus of this thesis is now on using Bayesian nonparametrics (BNPs) as a way to solve this model selection problem and extract kinetic parameters such as diffusion coefficients at the single-molecule level from a few photons, and thus with the highest temporal resolution as possible. / Dissertation/Thesis / Source code related to chapter 3 / Source code related to chapter 4 / Doctoral Dissertation Physics 2020

This diploma thesis deals with the use of fluorescence correlation spectroscopy technique for microrheological characterization of hydrogel in a system of hyaluronate-cetyltrimethylammonium bromide. Fluorescently labelled particles were used for microrheological FCS analysis. To optimize the method the most appropriate size of particles was chosen on the basis of Newtonian glycerol solutions analysis. Among other things, the discussion was focused on the influence of refractive index change of analysed solutions on analysis results. After hyaluronate solutions analysis it was possible to assess the biopolymer concentration and molecular weight impact on the FCS microrheology results, which could then be compared with analysis results of model hydrogels of hyaluronate and CTAB. Finally, usability and limitations of FCS microrheology have been discussed.

Das Wasser der Elbe auf der Höhe von Dresden enthält anorganische Kolloidpartikel, deren Partikelgrößenverteilung nahezu den gesamten kolloidalen Definitionsbereich (1 nm bis 1 µm) überstreicht und die vor allem aus sekundär ausgeschiedener amorpher Kieselsäure sowie aus Oxyhydroxiden des Fe, Al und Mn bestehen. Als wichtigstes Schwermetall führen sie Zn. Ihre Konzentration liegt unter 5×10-1 mg/l, um etwa Faktor 30 unter der Konzentration der Schwebstoffe des Elbwassers (Partikel >1 µm). Wegen ihrer hohen spezifischen Oberfläche sind die Kolloidpartikel als potentielle Träger für Schadstoffe trotz dieser geringeren Massekonzentration nicht gegenüber den Schwebstoffen zu vernachlässigen. Die in der Elbe gemessene Partikelgrößenverteilung ähnelt derjenigen, die zu einem früheren Zeitpunkt im Rhein gefunden worden war. Auch die chemische Zusammensetzung der Kolloidpartikel in der Elbe ist der der Partikel des Rheins ähnlich. Die Konzentration der Kolloidpartikel in der Elbe war aber um Faktor 5 bis 10 höher als im Rhein. Grund für letzteres ist wahrscheinlich der höhere Gehalt des Elbwassers an gelöstem Kohlenstoff (DOC). Im "Bulk" eines Flusses sind kolloidgetragene Schadstoffe - anders als schwebstoffgetragene - vermutlich fast genauso mobil wie echt gelöste. Unterschiede zwischen den Transportgeschwindigkeiten der kolloidgetragenen und der echt gelösten Spurenstoffe treten in bestimmten Situationen auf, in denen das Wasser den "Bulk" eines Flusses verlässt (Sickerbereich unter dem Fluss, Ästuar). Es werden Schlussfolgerungen über die Rolle von Kolloidpartikeln im Ökosystem eines Flusses gezogen und noch bestehende Forschungsdesiderate benannt.

In this dissertation research, two fundamental studies involving gas chromatography mass spectrometry of n-butylbenzene and pyrolysis products are presented. In the first study, fragmentation pathways of n-butylbenzene in quadrupole ion trap have been investigated. At low energy, product ion corresponding to m/z 92 and m/z 91 are formed via competitive parallel dissociation. Studies have also shown that at higher energy m/z 92 has sufficient internal energy to undergo further fragmentation yielding m/z 91 via consecutive dissociation. Thus in order to discern the fragmentation pathways of n-butylbenzene, the technique of two-dimensional correlation spectroscopy (2DCOS) was applied to the mass spectral data. Application of 2DCOS resulted in two 2D correlation spectra namely synchronous and asynchronous. A third spectra known as coherence spectra was obtained from the ration of asynchronous to synchronous correlation intensities. For the elucidation of n-butylbenzene fragmentation pathways, all the three spectra were utilized in this study. The second study in this dissertation involves investigation of pyrolysis products to aid in fire debris analysis. One of the major concerns in fire debris analysis is that pyrolysis products can mask the patterns of compounds of interest and make the chromatographic results interpretation extremely difficult. One of the approaches for investigating the formation of pyrolysis products is to subject the commonly found building materials to controlled heating in laboratory. In this study, new heating methodologies for controlled heating of substrates involving furnace, paint-cans and flat steel pans have been developed. The substrates used for investigating pyrolysis products were polystyrene, polyvinylchloride, polybutadiene, yellow-pine, nylon carpet and padding. Experiments were also performed to investigate the influence of hydrocarbons on the formation of pyrolysis.

Cerebral hemodynamics monitoring is vital in the neuroscience intensive care unit to assess brain health. Diffuse optical methods using near-infrared light, e.g., near-infrared spectroscopy (NIRS) and diffuse correlation spectroscopy (DCS), allow for non-invasive prolonged monitoring of cerebral hemoglobin oxygenation and blood flow. For patients suffering from cerebral fluid or tissue volume buildup, intracranial pressure (ICP) is monitored invasively as its elevation compromises cerebral perfusion. The critical closing pressure (CrCP) is a transcranial doppler (TCD) derived non-invasive parameter that correlates with ICP; however, its use is limited due to discomfort during extended TCD measurement. I expanded on Sutin’s preliminary study using DCS to estimate CrCP and found high correlations between DCS obtained CrCP against TCD (R2: 0.77-0.83) in stroke patients. The use of DCS to monitor CrCP is advantageous because its sensors are comfortable to wear and easy to use continuously without the need of a specialized operator. However, the low DCS signal-to-noise ratio (SNR) limits the depth sensitivity and temporal resolution of CrCP measures. Following these encouraging results, I built a low-cost wireless cerebral oximeter based on multi-distance continuous wave NIRS called FlexNIRS, which exhibits high SNR (NEP < 70 fw/Hz0.5) and high sampling rate (266 Hz). This device not only quantifies cerebral oxygenation but resolves the pulsatile blood volume signal at large source-detector separations (33 mm). Using the relationship between blood flow and volume, I augmented pulsatile DCS blood flow measurements with FlexNIRS pulsatile signals. I experimentally demonstrated the high fidelity (R2: 0.98) and > 50-fold SNR improvement of the method, resulting in a one order of magnitude increase in the temporal resolution of CrCP estimates. / 2024-06-12T00:00:00Z