Transcript: Biotechnology Sara Magnusson Ellen Johansson Interview with Magnus Carlquist The department of technical microbiology “The use of microorganisms in a technical context where the microorganisms are used to solve a problem. The subject also includes understanding of how microorganisms live and act as they are part of a technical process.” - Magnus Carlqvist Introduction Introduction Background Chemical technology, LTH Class of '99 Production Master's degree TMB Magnus' background Cells and enzymes TMB The researchers at TMB Production development Analytical techniques Food safety Developing genetic process strategies Microbial cell; Yeast Genetic strategies Codon optimization Physilogical fitness Phenotypic stability Projects that Magnus is involved in Magnus' Projects Hopes for his research Contribute to new and better processes Result that can be applied within the industry Magnus' hopes with his research Conclusion Conclusion Thank you Thank you
Transcript: Difference-gel electrophoresis is.... Confirmation of protein regulation by Western blotting For this study, we used a 2D-DIGE approach to identify proteins associated in natural resistance mechanisms to sulfadiazine (Supplemental data 2). Protein abundance was compared between sulfadiazine sensitive and resistant strains from T. gondii with same genotype. Introduction Identification of differentially expressed proteins in sulfadiazine resistant and sensitive strains of Toxoplasma gondii using difference-gel electrophoresis (DIGE) Discussion and Conclusion. Seven strains of T. gondii tachyzoites were used in this study: RH and ENT (Type I, sensitive strain), TgA 103001 (Type I, resistant strain), ME-49 and PRU (Type II, sensitive strain), TgH 32006 (Type II, resistant strain) and TgH 32045 (defined as Type II variant, resistant strain). Identification of differentially expressed proteins. Sydney Smith In conclusion, we have identified 31 proteins which are differentially modulated between sulfadiazine resistant and sensitive strains of T. gondii according to their genotype. These proteins were predicted to be involved in several different mechanisms such as carbohydrate metabolism, host cell interaction and protein translation. Although none of them allow us to identify directly resistance mechanisms to sulfadiazine at this stage, several of these proteins represent encouraging potential targets to be followed-up. We confirmed by Western blotting proteins regulation of several proteins identified in DIGE: ENO2, IMC1, ROP2, MIC2 and GRA7 in the different strains studied. We also analyzed these proteins regulation in two others sensitive strains of genotype I (ENT) and genotype II (PRU) Ajioka, J.W., Soldati, D., 2007. Toxoplasma Molecular and Cellular Biology. Horizon Biosciences, Norfolk. Ajzenberg, D., Bañuls, A.L., Su, C., Dumètre, A., Demar, M., Carme, B., Dardé, M.L., 2004. Genetic diversity, clonality and sexuality in Toxoplasma gondii. Int. J. Parasitol. 34 (10), 1185–1196. Ajzenberg, D., Collinet, F., Mercier, A., Vignoles, P., Dardé, M.L., 2010. Genotyping of Toxoplasma gondii isolates with 15 microsatellite markers in a single multiplex PCR assay. J. Clin. Microbiol. 48 (12), 4641–4645. Alban, A., David, S.O., Bjorkesten, L., Andersson, C., Sloge, E., Lewis, S., Currie, I., 2003. A novel experimental design for comparative two-dimensional gel analysis: two-dimensional difference gel electrophoresis incorporating a pooled internal standard. Proteomics 3, 36–44. Andrade, H.M., Murta, S.M., Chapeaurouge, A., Perales, J., Nirdé, P., Romanha, A.J., 2008. Proteomic analysis of Trypanosoma cruzi resistance to Benznidazole. J. Proteome Res. 7 (6), 2357–2367. Baatz, H., Mirshahi, A., Puchta, J., Gumbel, H., Hattenbach, L.O., 2006. Reactivation of Toxoplasma retinochoroiditis under atovaquone therapy in an immunocompetent patient. Ocul. Immunol. Inflamm. 14, 185–187. Bohne, W., Gross, U., Ferguson, D.J., Heesemann, J., 1995. Cloning and characterization of a bradyzoite-specifically expressed gene (hsp30/bag1) of Toxoplasma gondii, related to genes encoding small heat-shock proteins of plants. Mol. Microbiol. 16 (6), 1221–1230. Methods and Materials Toxoplasma gondii, the causative agent of toxoplasmosis, is an obligate intracellular protozoan parasite that infects more than one-third of the world’s human population. The population structure of T. gondii consists of three main clonal lineages (Types I, II and III) correlated with virulence expression in mice. Recently, a study reveal a biphasic pattern consisting of regions in the Northern Hemisphere where a few, highly clonal and abundant lineages predominate; elsewhere, and especially in portions of South America are characterized by a diverse assemblage of less common genotypes that show greater evidence of recombination. Results. What is Toxoplasma gondii? a. protozoan parasite b. bed bug c. a protein a. 2G DIGE b. DIGE c. analyzed gel In total, 31 proteins, including four hypothetical proteins, were identified from the three experiments, 44% were overexpressed in resistant strains and 56% were over-expressed in sensitive strains. Interestingly, GRA7 was identified in two gel spots and showed contradictory expression changes in these gel spots: one appearing more abundant in TgH 32045 and the other one in ME-49 There was a variety of methods used; cell structure, Preparation of tachyzoites, DIGE, Sypro Ruby staining, Image analysis and statistics, In-gel tryptic digestion and Western blot analysis Quiz Time!!!! References. How many different strains of T. gondii tachyzoites were used in this study? a. 31 b. 7 c. 1,000,000 There is increasing evidence for the emergence of strains of T. gondii that are resistant to treatment with sulfonamide and/or pyrimethamine-based compounds. In collaboration with Meneceur et al. (2008), we have recently isolated three strains of T. gondii resistant to sulfadiazine. As there is no apparent correlation with strain
Transcript: Food Packaging Sustainable Introduction Introduction Is our current food packaging plan sustainable? Why does it matter? Food Packaging 25% of household waste 70% of which is food-related total 17.5% of waste Landfill waste is a large greenhouse emissioner Rise of plastics in the Plastic Age 300 million tons produced per year plastic harms and poisons wildlife releases harmful chemicals to environment and humans How do we plan to reduce food packaging waste? Analysis of Food Packaging 1. 2. 3. 4. origin and accessibility of packaging material approximate cost to produce and transport recyclability or biodegradability effectiveness of preserving packaged content Controls Controls Glass GLASS 1. 2. 3. 4. mixture of sand and other mineral contents 100% recyclable content airtight storage that can maintain stored food quality ~3000 degrees Fahrenheit Plastic THERMOPLASTICS 1. 2. 3. 4. petroleum gases (like ethylene) or other synthetic materials ~25% of plastic is recycled can maintain stored food quality ~400 degrees Fahrenheit Potential Materials Potential Materials PHA PHA 1. 2. 3. 4. plastic made from renewable biomasses decomposes in 2 months maintains stored food quality ~200 degrees Fahrenheit GELATIN FILMS GELATIN FILMS 1. 2. 3. 4. made from hydrolysis of collagen in animal proteins consumed; end life unknown antioxidants and microbials to prevent food spoilage ~100 degrees Fahrenheit Barriers / Issues Barriers / Issues 1. 2. 3. primary, secondary, tertiary levels of packaging no more disposable packaging? efficiency of waste sorting Conclusion Conclusion Overall Results THERMOPLASTIC Results GLASS PHA GELATIN FILMS most costly to produce 100% recyclable content cheaper than glass to produce least reusable content potential to be more cost-saving cheaper but also requires additives biodegradable content in multiple environments made from renewable biomasses cheapest to produce potentially consumable and nutritious unknown end life if biodegraded fragile and heavier to transport Sources Bugnicourt, E., Cinelli, P., Lazzeri, A., & Alvarez, V. (2014). Polyhydroxyalkanoate (PHA): Review of synthesis, characteristics, processing and potential applications in packaging. Express Polymer Letters, 8(11), 791-808. doi:10.3144/expresspolymlett.2014.82 Etxabide, A., Uranga, J., Guerrero, P., & de la Caba, K. (2017). Development of active gelatin films by means of valorisation of food processing waste: A review. Food Hydrocolloids, 68, 192-198. doi:10.1016/j.foodhyd.2016.08.021 Ingarao, G., Licata, S., Sciortino, M., Planeta, D., Di Lorenzo, R., & Fratini, L. (2017). Life cycle energy and CO2 emissions analysis of food packaging: an insight into the methodology from an Italian perspective. International Journal of Sustainable Engineering, 10(1), 31-43. doi:10.1080/19397038.2016.1233296 Manzardo, A., Loss, A., Mazzi, A., & Scipioni, A. (2015). Organization Life-Cycle Assessment(OLCA): Methodological Issues and Case Studies in the Beverage-Packaging Sector. In S.S. Muthu (Ed.), Environmental Footprints of Packaging (pp. 47-73). Singapore: Springer Singapore. doi:10.1007/978-981-287-913-4_3 Risch, S. (2009). Food Packaging History and Innovations. Journal of Agricultural and Food Chemistry, 57, 8089-8092. doi:10.1021/jf900040r US Department of Energy. (2015). Barriers to Industrial Energy Efficiency. Washington, DC: United States Department of Energy. Sources
Transcript: BioTech Presentation -CRISPR- Michelle Seymore, Sofia Bufano, Genavieve Goss CRISPR Introduction Overview of CRISPR CRISPR is a natural process that frequently occurs in nature, especially in Bacteria. Today thanks to research, CRISPR is a way to cut and rewrite the code of life. In 2012 scientists figured out a way to use CRISPR not just to fight viral DNA but they discovered a way to apply this knowledge to any kind of DNA. Who discovered CRISPR: CRISPR was discovered by two women, Jennifer Doudna and Emmanuelle Charpentier and they received a Nobel Prize in Chemistry in 2020. In 2011 their research started when Dr. Charpentier was studying TracrRNA and traced it back to a bacteria’s immune system, the CRISPR/Cas that targets viruses DNA. Dr.Charpentier and Dr. Doudna worked together and they were able to recreate the same procedure on a test tube. What does that mean? CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats), can be defined by “a segment of DNA containing short repetitions of base sequences, involved in the defense mechanisms of prokaryotic organisms to viruses.” This DNA sequence is used to edit the base pairs of proteins in humans. Cas9 is a protein used in CRISPR to influence a change in the DNA sequence by cutting the DNA. TracrRNA, or Trans-activating CRISPR RNA, is a type of RNA that aids in the CRISPR mutation process. In this process, TracrRNA base pairs with crRNA (CRISPR RNA) and forms a functional guide RNA (gRNA). Cas9 protein uses this RNA as a handle, while the crRNA sequence directs the complex to a matching viral sequence. Important Terms CRISPR Process Visual Explanation Genetic Process of CRISPR Prokaryotic Vs. Eukaryotic Prokaryotic Vs. Eukaryotic Although CRISPR can occur naturally, enginers are learning how to tailor Eurkaryotic genes. The CRISPR process occurs differently in Prokaryotic and Eukaryotic cells. Eukaryotic Eurkaryotic Process : 2 The CRISPR RNA molecule binds to an endonuclease called Cas9. Cas9 cuts both strands of the DNA within the target sequence. 3 TracrRNA creates a guide for crRNA to follow. crRNA follows the TracrRNA guide and base pairs to the DNA strand. 4 1 Prokaryotic 2 Prokaryotes Segments of DNA (CRISPR) get cut by Cas 3 The viral DNA is inserted in the sequence CRISPR RNA is made CRISPR RNA targets virus that comes in 4 1 CRISPR in Bacteria Diagram CRISPR's Contributions to Science and Nature CRISPR in Society CRISPR is a known advance in the process of genome editing, the change of a DNA sequence. CRISPR specifically uses the CRISPR enzyme (Cas-9 protein and guide RNA) to cut a part of a DNA sequence and a different sequence can be added in place of it. The advance of gene editing with CRISPR has many effects on nature and society. Changing a DNA sequence can cure genetic diseases, and has the possibility to cure the following: Cancers Blood disorder Blindness Aids Cystic fibrosis Muscular dystrophy Huntington’s disease How It Affects Science, Society, and Nature How It Affects Science, Society, and Nature CRIPSR contributes to science by advancing genome editing, which can then advance the health of people who have their DNA edited. CRISPR can affect nature entirely by causing offspring of animals with certain expressed genes to not carry their original genes anymore. Many controversial topics have been touched because of CRISPR because of moral dilemmas on changing natural occurrence of genes. Example of curing a blood disorder using genome editing Victoria Gray Victoria Gray, from Forest, Mississippi, was affected by sickle cell disease; a disease that causes bone marrow to produce a defective protein that makes blood cells sickle-shaped. In 2019, she received treatment using CRISPR at the Sarah Cannon Research Institute in Nashville, Tennessee. Using CRISPR, scientists create fetal hemoglobin with the patient's bone marrow. They then undergo chemotherapy as a part of a bone marrow transplant, and that wipes out cells with the existing defect. They receive billions of their own new cells. Victoria Gray Carlene Knight Carlene Knight is a CRISPR patient that was born with a rare genetic eye disease. She was one out of seven people with a rare genetic eye disease to volunteer to use CRISPR to edit their DNA. When using CRISPR for these patients, it was injected directly into the cells of the patient's bodies. For Carlene, the genes in her retina were edited. Knight has said that CRISPR has given her the ability to see much brighter and more vivid colors and images. Before CRISPR, she couldn't move around her workplace, even with a cane. Carlene Knight CRISPR Research CRISPR research is currently being used to cure illnesses such as common blood disorders and cancer. This research is proving effective in this respect. CRISPR Research CRISPR in Blood disorders CRISPR is a relatively new technology that is constantly being tested to see how this method can be used to cure diseases. In 2019 this method was tested with sickle cells and
Transcript: Conclusion Assumptions After much research, I found that the brain works through a series of synaptic transmissions between neurons and by using information encoded by past transmissions across synapses. Who you are and how your brain functions depends on the patterns of interconnectivity between neurons in your brain. The part of your brain that affects memory is the hippocampus. The hippocampus is the part of your brain that plays a vital role in memory, acting as a gatekeeper and deciding whether or not to accept information and pass it on to your long-term memory. Your memory is composed of information processed by the prefrontal lobe or the hippocampus. The pre-frontal lobe manages your short term memory while the hippocampus manages your long term memory.In order to memorize information, your eyes must see and process the images to your brain. In order to do so, Your retinas capture the image of this painting and route it, in the form of nerve impulses, to the visual zone of your brain, which reconstructs the overall image. These impulses are then routed to your hippocampus, which acts as the gatekeeper and decides whether or not to accept the information and pass it on to your long-term memory. If your hippocampus does not let this information in, you will probably forget the image of the painting within a minute. But if your hippocampus does accept this information, it will eventually be returned to the area it came from: the visual cortex. Subproblems Planning The Project The Question Keon Proctor Biotech Appl 2 Period 2B The Question posed was "Is your ability to memorize patterns and reaction time directly affected by seeing colors if I were to use two different games". After performing the experiment, the data was not sufficient enough to conclude whether your ability to memorize patterns and reaction time is directly affected by seeing colors. The analysis of Chapter Four's statistics shows the reaction time and level completed amongst each test subject. Although the data gathered can be used in coming to a conclusion, the experiment and data must be expanded in order to come to a true conclusion. A test that should be added in order to give more information is another color memory game that tests the subject’s ability to repeat the color pattern given. There should also be a test to test the subject’s ability to see a color using their peripheral vision in order to test which color is more appealing to each subject. The data given was not related to the question posed. The data needs to be extended while the experimental technique needs improvement. The data and experimental technique needs to relate memorizing patterns and reaction time to seeing colors. A new question posed after performing this experiment is “What directly affects memorizing patterns and reaction time”. Is your ability to memorize patterns and your reaction time directly affected by seeing colors if I were to use two different color games? The Tools of Research I am assuming that everyone has 20/20 vision and can see colors normally. The outcome of the experiment is based on a person's memory and how they see colors Abstract When it comes to colors, your eyes perceive color by responding to three different kinds of vibration and stimulating the three responses in varying degrees of strength. The three different kinds of vibrations are three different wavelengths chosen from the red, green, and blue bands of the spectrum. Once your eyes sends the information to the brain, it is the brain’s job to process it which is done through saccades; a rapid movement of both eyes yoked together. The brain aims to reach a particular spot; once the eyeball is launched, no visual control is exerted until the eye comes to rest again. You read by skipping with a series of small saccades across the text. The intervals between saccades are brief, as short as 120-130 msec. This corresponds to the minimum time needed to process visual information during the fixation periods. Your eyesight and eye muscle can also come into play when it comes to perceiving colors. Evidently, even though the eye needs different brightness ratios, distributed over various parts of the image, to perceive colors, the ratios that the eye is interested in are not simple arithmetic ones. When it comes to your eye muscle, six eye muscles are responsible for rotating the eyeball in several distinct patterns. If eye movements are prevented (for instance, by artificially stabilizing an image at the same retinal location), vision rapidly fades. LeDoux, Joseph. "The Big One." Synpatic Self: How Our Brains Become Who We Are. New York: Penguin Group, 2003. 2. Print. Rodieck, R. W. The First Steps in Seeing. Sunderland: Sinauer Associates, n.d. Print. Dubuc, Bruno. "THE BRAIN FROM TOP TO BOTTOM." THE BRAIN FROM TOP TO BOTTOM. Land, Edwin H. "The Old Theory." Experiments In Color Vision. N.p.: n.p., 1959. 286-98. Print. The question I posed was "Is your ability to memorize
Transcript: Jeffreys Big Discovery Jeffreys put together all of the research he had and figured out a way to put the information together The information included a group of messy genetic material that didnt give a clear conclusion https://web.mit.edu/iment/iou/jeffreys.html http://genome.welcome.ac.uk/doc.wtd020877.html http://www.thebrightesthub.com Jeffreys observations led to the last step of his research projects This project was created to look deeper and closely into the different inherited types of genes After coming up with a complicated plan on how to do his research, Jeffreys noticed a new type of DNA formation Jeffreys Shocking Dicovery Jeffreys Research In England Jeffreys learned how to detect single copies if human genes Makes the first observations of introns (non-coding sections of DNA that split up genes) Citations Sir Alec Jeffreys Jeffreys Conclusion Research In Leicester Famous British geneticist Went to Leicester,England to work on his own research in 1997 DNA Fingerprinting Jeffreys' research lead to another discovery. He found out that RFLP's (Restriction Fragment Length Polymorphism), which are segments of DNA that make changes he generic group, were proof of variation in inherited DNA levels After discovering what the RFLP's do, he then pointed out that some DNA segements couldnt inform you about the different types of inherited genes Sir Alec Jeffreys began to see patterns in the genetic formation, he noticed that the DNA this group contained, was the information of a single individual Jeffreys made a conclusion on September 1984, that the projects had led to the discovery of the very first DNA fingerprints ever created
Transcript: Biotechnology Design Team 2007-2 5 3 1 What is Cancer? Cancer: uncontrollably dividing cells that form a tumor This is the most common way to remove tumors where surgeons manually remove the tumor along with some nearby tissue. The Issue: Re-operation 2 Cancer Surgery Surrounding Tissue Surrounding Tissue The surgeon cuts out some surrounding tissue to make sure all possible “hidden” cancer cells have been removed It's hard for surgeons to tell how much surrounding tissue is cancerous during surgery. Post-operative biopsy No left over cancer cells: no re-operation Left over cancer cells: needs re-operation Impacts of the Issue Although re-operation is very common, it is a problematic procedure with far-reaching impacts. Explanation of Impacts Considerations of Re-operation Risk of complications after surgery Psychological and emotional effects Financially Overburdening Increased mortality rate Delayed recovery and treatment Impacts of Re-operation Excessive bleeding, blood clots, or infections in other parts of body $31,000 Average American's salary $150,000 Average cost of cancer treatment May increase anxiety and inflict emotional trauma on patient and family This data was found in a study conducted by the BMJ Journal of Ethics. Mortality rates increase by 27% - 28% Increases the patient's recovery time and delays treatment Risks of no re-operation Risks of Not Re-operating Percent of accurate biopsies 57% 43% "False Negative" - biopsy shows no cancer, but there actually is Percent of Inaccurate biopsies - this means cancer is left undetected and advances to even more dangerous stages. 4 The Solution: iKnife Step 1 1 Electricity heats up the tip of the iKnife 2 Step 2 The hot blade causes cells in the tissue to explode, releasing particles in smoke 3 Step 3 Particles are sucked into a tube, heated, ionized 4 Step 4 The particles in the tube are then fed into a mass spectrometer (which is like an extremely accurate weighing scale) 5 Step 5 A detector on the mass spectrometer outputs this data, which lets surgeons distinguish between cancerous and non-cancerous tissues during the surgery. Overall accuracy of iKnife is Success of iKnife 97.8 % Real Life Scenario Real-Life Scenarios Ben Normal surgery More hidden cancerous tissue left Needed re-operation. Jake False negative Later found that cancer had spread More complicated re-operation was needed Clara Surgery with iKnife All cancerous tissue was removed No re-operation was required
Transcript: C Q&A Frontier Issues & UNFPA T - Benefits of Frontier Tech Overview - Biotech one example - Why should we care about frontier tech? Frontier Technology - CRISPR-Cas9 - In Vitro Fertilization - The combinative value The Technology: The Technology 1 - Revolutionized genetic therapy. - Gene manipulation i.e. "Designer Babies". - Curing previously incurable diseases. For us that means HIV. - Reduce total number of maternal deaths are attributed to HIV. CRISPR-Cas9 2 - Tech isn't cutting edge, its uses are. - Preimplantation Genetic Screening/Diagnosing (PGS/PGD). - Goodbye unwanted inherited traits! No more sickle cell, Huntington's, double X chromosones, hemophilia, etc...wait a minute. - 117 million women missing from Eastern Europe and Asia, with certain areas seeing up to 25% more male births than female. Any country with less regulation of sex selection pose serious threat for female population...or maybe not? In Vitro Fertilization 3 - Current CRISPR-Cas9 treatments cost ~$375,000. - Possible to apply CRISPR treatments via in vitro to reduce price. $20,000-40,000 The Synergy - Germline modification = exponential proliferation of resistant gene. - A couple generations later inoculated population. Business Model How This Fits Additional Benefits/Concerns Global Concerns - Global scale implications of this technology. Unregulated, ungoverned, ethically ambiguous. To name a few... - Pricing = unviable for low-income countries/persons. (SDG 10.3) - 10/90 gap. - Safety is a major concern. The Bad The Bad - Healthcare costs overall reduced. - Bring the research to them/promote economic growth. The Good The Good - Ethically, this tech lacks globally-accepted framework of control/regulation. - Conflicting views on restrictions. Varying restrictions government to government/institution to institution. - CEB has input: need for universal agenda. - At this stage moral complexity of tech is low. Difficult choices are down the road. Ethical Implications Ethical Implications Two major concerns: 1) "Too much potential harm. We should be denouncing this technology instead!" 2) "This is not what we do at UNFPA. We should be focusing on improving our approach to our mandate, not on things that have nothing to do with us." Causes For Concern Causes for Concern Questions? Questions?
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