{"id":738,"date":"2020-05-04T14:30:57","date_gmt":"2020-05-04T13:30:57","guid":{"rendered":"https:\/\/blogs.ncl.ac.uk\/bns\/?p=738"},"modified":"2022-03-21T20:40:01","modified_gmt":"2022-03-21T20:40:01","slug":"my-final-year-project","status":"publish","type":"post","link":"https:\/\/blogs.ncl.ac.uk\/bns\/my-final-year-project\/","title":{"rendered":"My Final Year Project"},"content":{"rendered":"\n<h3 class=\"wp-block-heading\"><span style=\"font-family:Arial\">By Liza Petrova, BSc (Hons) Biomedical Sciences<\/span><\/h3>\n\n\n\n<p><span style=\"font-family:Arial\"> Hi everyone! In January I began working on my final year project. In this blog post we will peek into a real neuroscience laboratory, check out the quirky equipment inside and I will share some details about experiments I do every day. <\/span> <\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><span style=\"font-family:Arial\">A bit of background<\/span><\/h3>\n\n\n\n<p><span style=\"font-family:Arial\">My project is about alpha-synucleinopathies, which are conditions where a protein called alpha synuclein (ASYN) is mutated and forms toxic \u201cclumps\u201d in the brain. Examples of alpha-synucleinopathies are Parkinson\u2019s disease and dementia with Lewy bodies. <\/span><\/p>\n\n\n\n<div class=\"wp-block-image\"><figure class=\"aligncenter\"><img decoding=\"async\" src=\"https:\/\/blogs.ncl.ac.uk\/bns\/files\/2020\/03\/Parkinsons-disease.png\" alt=\"Image of hand shaking whilst holding a glass.\" class=\"wp-image-741\" \/><figcaption> Parkinson\u2019s disease. Photo by Alessandro Grandini on Adobe Stock <\/figcaption><\/figure><\/div>\n\n\n\n<!--more-->\n\n\n\n<p><span style=\"font-family:Arial\">With my project colleague Dan Whitaker, we are looking into the brain of mice \u2013 both normal and mutant, producing human mutant ASYN \u2013 to compare the changes in some of the cell populations. I\u2019m focusing on the specific brain cells, microglia and astrocytes. I am investigating if these cells express ASYN, change their appearance, vary in number, and how they are distributed. <\/span><\/p>\n\n\n\n<p><\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><span style=\"font-family:Arial\">Why are there paintbrushes in the lab?<\/span><\/h3>\n\n\n\n<p><span style=\"font-family:Arial\">Every morning I find my way through the maze of corridors of the <a href=\"https:\/\/www.ncl.ac.uk\/medical-sciences\/research\/research-themes\/neuroscience\/\">Neuroscience department<\/a> to the lab. It\u2019s a small room, full of tables and shelves that are loaded with containers, beakers, flasks, pipettes and other laboratory reagents\/equipment. <\/span><\/p>\n\n\n\n<div class=\"wp-block-image\"><figure class=\"alignleft is-resized\"><img loading=\"lazy\" decoding=\"async\" src=\"https:\/\/blogs.ncl.ac.uk\/bns\/files\/2020\/03\/Picture_of_lab-e1583958650996-227x300.jpg\" alt=\"An image of a small cluttered room filled with lab equipment, bottles and chemicals.\" class=\"wp-image-742\" width=\"227\" height=\"300\" \/><figcaption>One of the small research labs where I did my neuroscience work<\/figcaption><\/figure><\/div>\n\n\n\n<p><span style=\"font-family:Arial\">There is even a fridge and a microwave \u2013 but don\u2019t put your lunch in! The fridge is stuffed with various heat-sensitive chemicals, solutions, and \u2013 yikes! \u2013 bits and pieces of animal brain and spinal cord tissue. The microwave is used to heat these samples up, essential for some experiments. Another surprising discovery for me was that the lab is full of\u2026 paintbrushes. But why? Well, because these brushes are used to transfer the brain samples (I will come back to this topic later). <\/span><\/p>\n\n\n\n\n\n<h3 class=\"wp-block-heading\"><span style=\"font-family:Arial\">What brain are we slicing today?<\/span><\/h3>\n\n\n\n<p><span style=\"font-family:Arial\">We store our brain samples in the fridge and when needed, we cut them into sections using a microtome. The brain is frozen and fixed on a mobile stage which is then pushed towards an incredibly sharp blade that produces thin and flaky sections. Freezing of the sample is essential otherwise it\u2019s easy to damage the soft brain tissue. A potential issue is that the cells may rupture after the brain has been frozen and thawed. To prevent this, the brain must be placed into a special solution overnight \u2013 that\u2019s why it\u2019s important to decide in advance which brain to section &#8211; from an old or young mouse? Mutant or normal?<\/span><\/p>\n\n\n\n<figure class=\"wp-block-embed is-type-video is-provider-youtube wp-block-embed-youtube wp-embed-aspect-16-9 wp-has-aspect-ratio\"><div class=\"wp-block-embed__wrapper\">\n<iframe loading=\"lazy\" title=\"How to use a microtome\" width=\"525\" height=\"295\" src=\"\/\/www.youtube.com\/embed\/HTjqgJ4u5UY?feature=oembed\" frameborder=\"0\" allow=\"accelerometer; autoplay; clipboard-write; encrypted-media; gyroscope; picture-in-picture; web-share\" referrerpolicy=\"strict-origin-when-cross-origin\" allowfullscreen><\/iframe>\n<\/div><\/figure>\n\n\n\n<p>Check out this video to see how the microtome works!<\/p>\n\n\n\n<div class=\"wp-block-image\"><figure class=\"alignleft\"><img decoding=\"async\" src=\"https:\/\/blogs.ncl.ac.uk\/bns\/files\/2020\/03\/Sections_floating_in_microtitre_plate-142x300.jpg\" alt=\"A microtiter plate with brain sections in the wells\" class=\"wp-image-745\" \/><figcaption>A microtiter plate with brain sections in the wells<\/figcaption><\/figure><\/div>\n\n\n\n<div class=\"wp-block-image\"><figure class=\"alignright\"><img decoding=\"async\" src=\"https:\/\/blogs.ncl.ac.uk\/bns\/files\/2020\/03\/Check_sections_microscope-142x300.jpg\" alt=\"\" class=\"wp-image-744\" \/><figcaption>We often use this microscope to check if the sections are turning out good and if any adjustment is needed. <\/figcaption><\/figure><\/div>\n\n\n\n<p><\/p>\n\n\n\n<p>Once the section is made it\u2019s transferred into the microtiter plate and checked on a microscope. <\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><span style=\"font-family:Arial\">Finding the cells<\/span><\/h3>\n\n\n\n<p>Once we get our sections, we can proceed to our experiments. Time to pull the nitrile gloves on! <\/p>\n\n\n\n<p><span style=\"font-family:Arial\">I mainly use immunohistochemistry \u2013 a technique that involves use of antibodies &#8211; proteins, which are naturally produced in mammals that can recognize and bind a specific target. <\/span><\/p>\n\n\n\n<p><span style=\"font-family:Arial\">The primary antibodies that I use are made against ASYN, microglia and astrocytes; this means, that these antibodies attach to proteins on the respective cells. I usually do double labelling where I stain against ASYN alongside with either microglia or astrocytes. Antibodies are quite expensive \u2013 100 \u00b5l can easily cost over \u00a3200! \u2013 so I need to be sure to plan my experiments carefully.<\/span><\/p>\n\n\n\n<h3 class=\"wp-block-heading\"><span style=\"font-family:Arial\">They glow in the dark!<\/span><\/h3>\n\n\n\n<p><span style=\"font-family:Arial\">After the samples have been incubated in primary antibody solutions overnight, we wash off the excess antibodies. To visualise the primary antibodies, we bind with secondary antibodies that carry a fluorescent tag. This allows the binding signal to be amplified and easier to see. Basically, under the microscope, labelled cells and areas with ASYN glow in the dark!<\/span><\/p>\n\n\n\n<figure class=\"wp-block-image\"><img decoding=\"async\" src=\"https:\/\/blogs.ncl.ac.uk\/bns\/files\/2020\/03\/Immunohistochem_diagram.png\" alt=\"\" class=\"wp-image-746\" \/><figcaption> A diagram that illustrates the basics of immunohistochemistry. Primary antibodies are \u201cinvisible\u201d tags that mark the cells, secondary antibodies are the glow in the dark labels, that bind to the primary and let us see the cells and proteins of interest. <\/figcaption><\/figure>\n\n\n\n<p><\/p>\n\n\n\n<h1 class=\"wp-block-heading\"><span style=\"font-family:Arial\">Challenge your patience<\/span><\/h1>\n\n\n\n<p><span style=\"font-family:Arial\">Once the treatment with antibodies is complete, we need to transfer our samples onto the microscope slide for visualisation. Here comes the tricky part: how to pick up and unfold the the incredibly thin and fragile sections without damaging them?<\/span><\/p>\n\n\n\n<p><span style=\"font-family:Arial\">This requires a lot of patience as you can see from this <a href=\"https:\/\/www.youtube.com\/watch?v=X9VUSX9MBeE\">video <\/a>of me trying to unfold one of the sections. Perhaps, this part of preparing the slide is the most exhausting. <\/span> <\/p>\n\n\n\n<p><span style=\"font-family:Arial\">Imagine trying to lift a tiny piece of tissue paper with a paint brush out of a water-filled bottlecap and place it flat on a plate, without any fold-overs! The sections are easy to tear, I completely messed up my first few (but I improved!). Some people, like me, use painting brushes, while others prefer pipettes. <\/span><\/p>\n\n\n\n<figure class=\"wp-block-image\"><img decoding=\"async\" src=\"https:\/\/blogs.ncl.ac.uk\/bns\/files\/2020\/04\/Slide_with_flat_sections-e1588232546209-1024x495.jpg\" alt=\"A glass microscope slide with 4 brain sections in the process of drying, the two sections on the right are fresh and less dry.\" class=\"wp-image-750\" \/><figcaption>A glass microscope slide with 4 brain sections in the process of drying, the two sections on the right are fresh and less dry.  <\/figcaption><\/figure>\n\n\n\n<p><span style=\"font-family:Arial\">The samples must be completely dry before being\n\u201cmounted\u201d &#8211; covered with a glass slip. Mounting is also a challenge: placing a\nvery thin glass rectangle right over the sections and securing it in place\nwithout any bubbles hiding underneath \u2013 these can cover the areas of interest\nand ruin the image!<\/span> <\/p>\n\n\n\n<p><span style=\"font-family:Arial\">Finally, after all the staining, washing, drying and mounting, the slide is ready for viewing under a microscope!<\/span> <\/p>\n\n\n\n<p><span style=\"font-family:Arial\">When the samples were illuminated with light of different wavelengths ASYN appeared red, while the cells appeared green. I took multiwavelength images, where both red and green staining were combined.<\/span><\/p>\n\n\n\n<figure class=\"wp-block-image\"><img decoding=\"async\" src=\"https:\/\/blogs.ncl.ac.uk\/bns\/files\/2020\/05\/IMAGE_GFAP-1024x283.jpg\" alt=\"Three images of astrocyte cells under the microscope. Using different wavelengths of light ASYN appeared red, while cells (atsrocytes in this case) appeared green. The final image is combined of the previous two to provide a quantifiable image.\" class=\"wp-image-771\" \/><figcaption><em>One of my samples viewed under the microscope and illuminated with light of different wavelengths: ASYN appeared red, while cells (atsrocytes in this case) appeared green. Combining these two images produces an image that can be analysed and quantified.<\/em> <\/figcaption><\/figure>\n\n\n\n<p><p><span style=\"font-family:Arial\">Qualitative observations and image quantification showed some remarkable changes in both astrocytes and microglia. However, neither of these cell types were found to take up ASYN. <\/span><\/p>\n\n\n\n<p><span style=\"font-family:Arial\">My overall experience of working in a lab was positive and enjoyable. After the first couple of days of adjusting to the new environment and experimenting, I was excited to see the outcome under the microscope and to observe the interesting patterns and trends in my samples. It isn&#8217;t easy, but it is very rewarding and you learn so much!<\/span><\/p>\n\n\n\n<p><span style=\"font-family:Arial\">Find out more about <a href=\"https:\/\/www.parkinsons.org.uk\/information-and-support\/what-parkinsons\">Parkinson&#8217;s disease<\/a> and about what else you can study on our <a href=\"https:\/\/www.ncl.ac.uk\/undergraduate\/degrees\/b940\/#courseoverview\">Biomedical Sciences Degree<\/a> here at Newcastle University.<\/span><\/p>\n","protected":false},"excerpt":{"rendered":"<p>By Liza Petrova, BSc (Hons) Biomedical Sciences Hi everyone! In January I began working on my final year project. In this blog post we will peek into a real neuroscience laboratory, check out the quirky equipment inside and I will share some details about experiments I do every day. A bit of background My project &hellip; <\/p>\n<p class=\"link-more\"><a href=\"https:\/\/blogs.ncl.ac.uk\/bns\/my-final-year-project\/\" class=\"more-link\">Continue reading<span class=\"screen-reader-text\"> &#8220;My Final Year Project&#8221;<\/span><\/a><\/p>\n","protected":false},"author":2915,"featured_media":0,"comment_status":"open","ping_status":"open","sticky":false,"template":"","format":"standard","meta":{"footnotes":""},"categories":[168,161],"tags":[122,131,144,130,143,18,145],"class_list":["post-738","post","type-post","status-publish","format-standard","hentry","category-all-posts","category-inside-the-lab","tag-biomedical-science","tag-final-year","tag-neuroscience","tag-numed","tag-research-project","tag-student-projects","tag-student-research"],"_links":{"self":[{"href":"https:\/\/blogs.ncl.ac.uk\/bns\/wp-json\/wp\/v2\/posts\/738","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/blogs.ncl.ac.uk\/bns\/wp-json\/wp\/v2\/posts"}],"about":[{"href":"https:\/\/blogs.ncl.ac.uk\/bns\/wp-json\/wp\/v2\/types\/post"}],"author":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/bns\/wp-json\/wp\/v2\/users\/2915"}],"replies":[{"embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/bns\/wp-json\/wp\/v2\/comments?post=738"}],"version-history":[{"count":27,"href":"https:\/\/blogs.ncl.ac.uk\/bns\/wp-json\/wp\/v2\/posts\/738\/revisions"}],"predecessor-version":[{"id":1424,"href":"https:\/\/blogs.ncl.ac.uk\/bns\/wp-json\/wp\/v2\/posts\/738\/revisions\/1424"}],"wp:attachment":[{"href":"https:\/\/blogs.ncl.ac.uk\/bns\/wp-json\/wp\/v2\/media?parent=738"}],"wp:term":[{"taxonomy":"category","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/bns\/wp-json\/wp\/v2\/categories?post=738"},{"taxonomy":"post_tag","embeddable":true,"href":"https:\/\/blogs.ncl.ac.uk\/bns\/wp-json\/wp\/v2\/tags?post=738"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}