Doctor of Philosophy

dissertationKnowledge of physical and chemical properties such as size, diffusivity, concentration and stability of an analyte in a sample is critical in science and engineering. When working in a small size range (0.1-100 nm), which includes short-chain molecules (e.g., ethanol) and nanoparticles, the number of methods that can be used for their characterization becomes sparse and each one has its limitation such as accuracy, resolution, cost of instrumentation and time needed for sample preparation and analysis which introduces more complexity to the problem being solved. This became the motivation and focus of the presented work. The goal of the conducted research was to explore the available methods as well as develop new methods that can be used for characterization of different analytes. The first half of the dissertation introduces the use of interfacial tension for estimating stability of nanobubbles that can be applied as contrast agents for ultrasound imaging or as vehicles for drug delivery. Use of interfacial tension is then shown to be applicable in a new setup and conditions to determine the diffusion coefficient and concentration of an analyte in any given location. Adsorption of perfluorocarbon vapor to the water surface is then explored. The second half of the dissertation focuses on characterization of endogenous nanovesicles called exosomes. This section continues the first section by presenting a novel finding of surface activity of exosomes which provides a potential mechanism of their adsorption to the cell membrane as well as application of dynamic interfacial tension for measuring exosome concentration in a sample. This section continues by comparing techniques that were previously used by others to determine size and shape of exosomes but were not compared to each other either due to unavailability of instrumentation or focus of the study being unrelated to size and shape. This study not only allowed examining the advantages and disadvantages of each technique but also lead to new findings about the biophysical properties of exosomes. This section ends with an application of quartz crystal microbalance method for measuring average mass and concentration of exosomes in a sample

Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches

Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year-on-year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non-vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its 'Minimal Information for Studies of Extracellular Vesicles', which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly

Identification and Analysis of Exosomes by Surface-Enhanced Raman Spectroscopy

The concept of liquid biopsy has emerged as a novel approach for cancer screening, which is based on the analysis of circulating cancer biomarkers in body fluids. Among the various circulating cancer biomarkers, including Food and Drug Administration (FDA)-approved circulating tumor cells (CTC) and circulating tumor DNA (ctDNA), exosomes have attracted tremendous attention due to their ability to diagnose cancer in its early stages with high efficiency. Recently, surface-enhanced Raman spectroscopy (SERS) has been applied for the detection of cancer exosomes due to its high sensitivity, specificity, and multiplexing capability. In this article, we review recent progress in the development of SERS-based technologies for in vitro identification of circulating cancer exosomes. The accent is made on the detection strategies and interpretation of the SERS data. The problems of detecting cancer-derived exosomes from patient samples and future perspectives of SERS-based diagnostics are also discussed

Variable speed electric drive of centrifugal pump in oil lifting plants

Актуальность работы обусловлена необходимостью снижения аварийности частотно-регулируемых асинхронных электроприводов центробежных насосных установок добычи нефти вследствие перегрева асинхронных двигателей. Цель: исследовать частотно-регулируемые электроприводы центробежных насосных установок добычи нефти, работающих при скорости выше номинальной. Методы исследования основаны на использовании теории автоматического управления и имитационного моделирования в программной среде MatLab-Simulink. Результаты. Составлена схема имитационного моделирования скалярного частотно-регулируемого асинхронного электропривода центробежных насосных установок добычи нефти, учитывающая основные особенности реального электропривода. Расcчитаны механические характеристики электропривода насосной установки. Определены возможные диапазоны регулирования скорости электропривода насосной установки исходя из допустимых потерь мощности в установившихся и переходных режимах. Выводы. Несмотря на то, что статическая механическая характеристика электропривода с частотой напряжения преобразователя 30 Гц является минимально возможной для добычи нефти с помощью погружных насосов, диапазон регулирования скорости в асинхронном электроприводе погружного насоса необходимо расширить до D=1:10 для плавного пуска электропривода. Установлено, что для уменьшения ударных моментов при пуске асинхронного частотно регулируемого электропривода темп роста частоты на выходе задатчика интенсивности должен составлять несколько десятков секунд даже при пуске на минимальную рабочую скорость электропривода. Неизбежное завышение по мощности асинхронного двигателя для погружного центробежного насоса при его выборе как ближайшего большего из ряда номинальных значений позволяет электроприводу насоса с частотным регулированием скорости работать без перегрева на статических характеристиках выше номинальной. Установлено, что в частотно-регулируемом асинхронном электроприводе центробежного насоса возможное повышение скорости на 10-12 % от номинальной позволяет увеличить объем добычи нефти без замены оборудования.Relevance of the work is caused by the need to create reliable frequency-controlled variable speed asynchronous induction motor drives of centrifugal pumping units for oil lifting. The main aim of the research is to study the frequency-controlled electric drives of centrifugal pumping units for oil lifting that operate at a speed higher than the nominal (rated) one. Methods of the research are based on the use of the automatic control theory and simulation in the MatLab - Simulink software environment. Results. The authors have made up the block scheme for simulation of a scalar frequency-controlled asynchronous induction motor drive of centrifugal pumping units for oil lifting. The scheme takes into account the main features of the real electric drive. The authors calculated mechanical characteristics of the electric drive of the pumping unit and determined the accessible ranges for controlling the speed of the electric drive of the pump unit based on the allowable power losses in steady-state and transient modes. Findings. Despite the fact that the static mechanical characteristic of an electric drive with ac converter frequency of 30 Hz is the minimum possible for oil lifting using submersible pumps, the range of speed control in an asynchronous induction motor drive of a submersible pump must be expanded to D=1:10 for a soft starting of the electric drive. It was found that in order to reduce high torque when starting an asynchronous frequency-controlled induction motor drive the frequency ramp-up rate at the output of the ramp generator should be several tens of seconds even for starting at the minimum operating speed of the electric drive. It was established that the inevitable power overrating of the induction motor for a submersible centrifugal pump, when it is selected as the closest higher one from a series of nominal values, allows the electric drive of the pump with frequency speed control to work without overheating on static characteristics above the nominal (rated) one. It was found that in frequency-controlled asynchronous induction motor drives the increase in the pump electric drive speed as a rule does not exceed 10-12 % of the nominal (rated) one, which allows increasing oil lifting output without upgrading the electric drive equipment

Air-Filled Bubbles Stabilized by Gold Nanoparticle/Photodynamic Dye Hybrid Structures for Theranostics

Microbubbles have already reached clinical practice as ultrasound contrast agents for angiography. However, modification of the bubbles’ shell is needed to produce probes for ultrasound and multimodal (fluorescence/photoacoustic) imaging methods in combination with theranostics (diagnostics and therapeutics). In the present work, hybrid structures based on microbubbles with an air core and a shell composed of bovine serum albumin, albumin-coated gold nanoparticles, and clinically available photodynamic dyes (zinc phthalocyanine, indocyanine green) were shown to achieve multimodal imaging for potential applications in photodynamic therapy. Microbubbles with an average size of 1.5 ± 0.3 μm and concentration up to 1.2 × 109 microbubbles/mL were obtained and characterized. The introduction of the dye into the system reduced the solution’s surface tension, leading to an increase in the concentration and stability of bubbles. The combination of gold nanoparticles and photodynamic dyes’ influence on the fluorescent signal and probes’ stability is described. The potential use of the obtained probes in biomedical applications was evaluated using fluorescence tomography, raster-scanning optoacoustic microscopy and ultrasound response measurements using a medical ultrasound device at the frequency of 33 MHz. The results demonstrate the impact of microbubbles’ stabilization using gold nanoparticle/photodynamic dye hybrid structures to achieve probe applications in theranostics

CellProfiler 3.0: Next-generation image processing for biology

<div><p>CellProfiler has enabled the scientific research community to create flexible, modular image analysis pipelines since its release in 2005. Here, we describe CellProfiler 3.0, a new version of the software supporting both whole-volume and plane-wise analysis of three-dimensional (3D) image stacks, increasingly common in biomedical research. CellProfiler’s infrastructure is greatly improved, and we provide a protocol for cloud-based, large-scale image processing. New plugins enable running pretrained deep learning models on images. Designed by and for biologists, CellProfiler equips researchers with powerful computational tools via a well-documented user interface, empowering biologists in all fields to create quantitative, reproducible image analysis workflows.</p></div

Segmentation steps for the quantification of transcripts per cell within a 3D blastocyst.

<p>Images were captured of a mouse embryo blastocyst cell membrane stained with WGA and FISH for GAPDH transcripts. (A) Original 3D image of blastocyst cell membrane prior to analysis. (B) CellProfiler 3.0 image processing modules used for membrane image processing. Figure labels: RH (“RemoveHoles”), Close (“Closing”), Erode (“Erosion”), Mask (“MaskImage”), Math (“ImageMath”), EorS Features (“EnhanceOrSuppressFeatures”). (C) Nuclei after segmentation by CellProfiler, as viewed in Fiji. (D) Segmentation of cells after setting nuclei as seeds by CellProfiler, as viewed in Fiji. (E) Segmentation of GAPDH transcript foci using CellProfiler, as viewed in Fiji. (F) Examples of analysis that can be done by CellProfiler: (top) cell volume relative nucleus volume, (middle) GAPDH transcript quantity in each cell using CellProfiler’s “RelateObjects” module, (bottom) number of GAPDH transcripts in Z-plane (bin size = 2.5 μm). The underlying measurements may be downloaded as <a href="http://www.plosbiology.org/article/info:doi/10.1371/journal.pbio.2005970#pbio.2005970.s012" target="_blank">S1 File</a>. <i>Images were provided by Javier Frias Aldeguer and Nicolas Rivron from Hubrecht Institute</i>, <i>Netherlands</i>, <i>and are available from the Broad Bioimage Benchmark Collection (<a href="https://data.broadinstitute.org/bbbc/BBBC032/" target="_blank">https://data.broadinstitute.org/bbbc/BBBC032/</a></i>). 3D, three-dimensional; FISH, fluorescent in situ hybridization; GAPDH, glyceraldehyde 3-phosphate dehydrogenase; WGA, wheat germ agglutinin.</p