On Friday 8.12 (at 13-16 in YN121) we have a Nanoscience Master´s Seminar where the MSc students present their thesis work.
13:15-13:40: Abhishek Thakur
Paraffin Assisted Graphene Transfer
Abstract:
In this master’s thesis, we propose Paraffin support layer as an alternative to the well established and widely used PMMA for CVD grown Graphene transfer process. The motivation behind the project being to eliminate the two key drawbacks of PMMA transferred graphene i.e., leftover PMMA residue after layer removal, which contaminates and reduces the quality of the final film. And the cracks and wrinkles observed in the graphene post-transfer. In the works of Leong et. al. and Villa et. al., they demonstrate that paraffin helps mitigate these issues as it is easier to remove, thanks to its alkane properties and low melting point. Furthermore, paraffin also has a higher coefficient of thermal expansion which can be utilized to stretch the graphene during transfer to help get rid of wrinkles and its flexible nature helps keep the graphene intact.
In our work, we tried recreating those results by simulating similar transfer parameters to the best of our ability as well as trying some different iterations of our own. Our results show some promise in terms of obtaining cleaner and wrinkle free Graphene films, but keeping large areas of the films intact during transfer remains a challenge. Thus, further optimizations at several stages of the transfer process are required
Supervisors: Andreas Johansson
13:40-14:05: Henna Littunen
Interplay of Leukocytes and Micro-RNAs – Origin of Lynch Syndrome related micro-RNAs and their impact on cytokine expression
Abstract:
Leukocytes are immune cells that defend human body against pathogens and also cancer and are recognized to be present at least in clear majority of cancerous tissues. Micro-RNAs are small non-coding RNA molecules that regulate gene expression. In leukocytes, they regulate the gene expression of cytokines, which are active inflammation inducing molecules, implying that micro-RNAs could affect inflammation reaction. Evidence show similarity in expression patterns of circulating micro-RNAs between colorectal cancer patients and healthy carriers of Lynch syndrome, an inherited disease predisposing the carriers to multiple cancers already at young age. However, the origin of these Lynch micro-RNAs is still unclear and one option could be that they originate from leukocytes. This thesis explores the link between these Lynch micro-RNAs and leukocytes by examining if the micro-RNAs are found in different type of leukocytes and whether they have impact on cytokine expression in these cells. To implement this study, the first step was to optimize a method for studying whether the differentially expressed circulating micro-RNAs originated from leukocytes. Results revealed that all leukocytes expressed the micro-RNAs at least slightly, neutrophils seeming to be the most abundant source of studied Lynch micro-RNAs. Regarding the cytokine expression, the effect of one micro-RNA was tested but it did not show significant impact. However, the possible impact of other micro-RNAs should still be studied. Overall, the method optimization was successful and the method could be used to evaluate the expression of other micro-RNAs in leukocytes as well. Also, it could be utilized in collecting and comparing the number of different leukocytes and micro-RNAs of healthy individuals, healthy and cancer diagnosed Lynch syndrome carriers to find new biomarkers to predict the cancer risk.
Supervisors: Tiina Jokela and Andreas Johansson
14:05 - 14:30: Petja Kuhmonen
Development of a microfiltration system for blood plasma separation in cell-free DNA applications
Abstract: Blood contains many molecules and compounds for the study and monitoring of diseases and overall health. One potential biomarker found in blood, and specifically in plasma and serum, is cell-free DNA (cfDNA). This marker can be used for example, as an indicator in prenatal screening and oncological liquid biopsy. Both tests can be done non-invasively by drawing blood, which work as a substitute for invasive tests such as amniocentesis and tissue biopsy. Monitoring even just the levels of cfDNA with a quick and easy method can in future be a vital part in helping physicians and healthcare professionals when diagnosing and treating patients. The process of separating plasma from blood is still time consuming and requires skilled personnel. Here we focus on a novel filtration system for separating plasma from whole blood. The filtration system uses miniaturized hollow fibre filtration (HFF) technology driven by air pressure. This system is a part of an automated extraction and transfer cartridge for blood-based biomarkers and was developed using an agile prototyping model. A comprehensive analysis on the evolution of the filtration system was done using the data collected during the development cycle. The data includes optimization of driving pressure of the filtration system, mechanical parts such as valves and modules, material chemistry and manufacturing methods, separate methods such as priming the filter and wash cycles to increase yield of the product. The success and effect of the parameter changes were quantitively measured by the cfDNA yield. The results will be used to conclude on how the new iterations of the system compare to the previous iterations and to the reference method of a standard two-step-centrifugation. Critical factors and their evolution from a concept into a part of a commercially viable product will also be discussed. The laboratory work of this project is a part of the ongoing research and product development efforts at Biopsense Oy.
Supervisors: Prof. Marja Tiirola, FT Elina Ruuhilehto, FM Veli-Mikko Puupponen
BREAK 14:30 - 14:40
14:40 - 15:05: Aku Kaasinen
Ion Milling of Catalytic Copper Surface to shape CVD Grown Graphene
Abstract: In this master’s thesis I modified a copper surface deposited on Al2O3 with a Neon beam in order to see if CVD grown graphene would follow the milled surface topology. This work will ideally answer some fundamental questions about growing graphene on modified surfaces especially when it comes to the temperature at which surface features survive or don’t. Also I will go over the experimental flow and explain how further work will be done since unfortunately during my experimental work the sample got destroyed during an annealing test to see if its quality would be improved.
The motivation for this work is to determine if this modified graphene would be possible to make and what characteristics it would have due to its shape. These characteristics have multitudes of uses in sensors, electronic circuits, plasmonic structures, models for electronic environments and even as models for astrophysics i.e. black holes.
Supervisors: Andreas Johansson
15:05 - 15:40: Inka Huusko
Visualizing the effects of HSV-1 infection in the nucleus with ten-fold robust expansion microscopy
Expansion microscopy has been developed to access sub-diffraction resolution 3D data of cells and tissues, and to make it available for laboratories using a regular confocal microscope. Today, there are numerous different expansion microscopy methods with varying degrees of expansion and applicability. Ten-fold robust expansion microscopy (TREx), published in early 2022, has optimized a gel recipe that reaches 10-fold expansion of the sample while maintaining the integrity of the gel and keeping the protocol simple. It can also be used to expand both cell and tissue samples. Dense bodies are spherical protein dense structures that are caused by viral infection and do not have a known function in the infection. My thesis aimed to visualize these changes in the nucleus caused by Herpes Simplex type 1 virus (HSV-1) infection by testing the compatibility of antibodies labeling the viral capsids and nuclear proteins as well as NHS-stains that label the whole proteome of the cell. The results show that the distribution of capsids in the nucleus is random and proximity to dense bodies is coincidental which indicates that dense bodies do not have a connection to capsid assembly. The disassembly of the nucleolus caused by the infection was brightly visible with nucleolin and fibrillarin. The capsid proteins, VP5 and VP26, as well as nucleolin and fibrillarin localized in dense bodies. While the function of dense bodies is still unclear, TREx appears to be a promising tool for HSV-1 research.
Supervisors: Visa Ruokolainen and Sami Salminen
