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Biochem Presentation

Transcript: Hayley Kim and Jamie Woych Treatment of HIV/AIDS by Inhibition of HIV-1 RT What is HIV? What is HIV 1-Reverse Transcriptase? Specific Antiretroviral Drugs Broad Spectrum Antiretroviral Drugs Current and Future research Overview Overview Human Immunodeficiency Virus, or HIV, attacks the body’s immune system, specifically the CD4 cells (T cells). HIV results in a higher susceptibility to attack on the immune system by disease and cancer This virus also leads to AIDS, a debilitating and deadly disease of the human immune system. HIV/AIDS is affecting over 1.2 million people in America What is HIV? HIV HIV-1 RT HIV-1 Reverse Transcriptase is an enzyme encoded for within the Human Immunodeficiency Virus (HIV) genome Function is transcribing double stranded DNA from the ss viral RNA template. HIV-1 RT is currently being studied as a target for HIV treatment HIV-1 RT also transcribes mistakes every 1 in 2000 base pairs HIV 1-RT HIV-1 RT has two active sites: polymerase active site, and RNase H active site. The polymerase active site acts in the polymerization of DNA strands The RNase H active site works to cleave RNA strands from RNA/DNA hybrids created during the replication process. Active Sites of HIV-1 Reverse Trascriptase Specific Antiretroviral Drugs Specific Drugs Antiretroviral drugs are subdivided into two categories: nucleoside reverse transcriptase inhibitors (NRTIs) and non-nucleoside reverse transcriptase inhibitor (NNRTIs) NRTIs Nucleoside reverse transriptase inhibitors (NRTIs) NRTIs are inhibitors that terminate the polymerization of the viral DNA strand. They can act as substrates that competitively inhibit the replication process. NRTIs have structural similarity to nucleosides, and can imitate a dNTP during the replication process and stop elongation. Azidothymidine (AZT) is a NRTI drugs that utilizes their structural similarity with thymine to halt DNA replication Thymidine analogues such as azidothymidine (AZT Structural Similarity NNRTIs NNRTIs have varying chemical structures, and act as noncompetitive inhibitors to the replication process. NNRTIs bind more specifically, targeting hydrophobic pockets that are close in proximity to the polymerase active site This higher specificity can suppress HIV replication even at lower concentrations Nevirapine is an NNRTI used that allosterically binds to this pocket and incites a conformational change in the enzyme, blocking the binding of the RNA template strand. Non-nucleoside reverse transcriptase inhibitor (NNRTIs) Nevirapine is an NNRTI used that allosterically binds to the hydrophobic pocket. The binding of NNRTIs Highly active antiretroviral therapy The use of a combination of NRTIs and NNRTIs has proven to be much more effective for the repression of viral replication. Highly active antiretroviral therapy or (HAART) is the use of multiple drugs with more than one target site for peak efficiency of treatment. Different sets of drugs are delivered to the patient in a rotating fashion to combat drug resistant strains Yet it still caused a drastic increase in multiple drug resistant strains of HIV This is due to its heightened ability for mutation These NRTI and NNRTI resistant mutations have created a demand for alternative antiretroviral drug treatments Highly active antiretroviral therapy Broad Drugs Broad Spectrum Drugs decrease in specificity of drug binding allows for a broader range of target domains, with limited resistance Broad spectrum drugs are able to inhibit many variants of the viral structure KM-1 Highly efficient on a wide range of enzyme conformations KM-1 inhibits replication similarly to NNRTIs by lowering HIV-1 RT’s affinity for the dNTP substrates This compound does not bind the hydrophobic pocket but rather inhibits RT by lowering the affinity of the enzyme toward the nucleic acid substrate KM-1 NAPETA N-{2-[4-(aminosulfonyl)phenyl]ethyl}-2-(2-thienyl)acetamide (NAPETA) Low specificity of binding results in a lower risk of resistance to the drug. The functions of NAPETA include: interfering with the formation of the Reverse Trascriptase DNA complex. decreases enzyme affinity, and acts as a DNA Polymerase inhibitor, wholly repressing polymerase activity of the virus. NAPETA Current Research These drugs target both HIV-1 RT and Integrase (IN) enzymes in the virion, and are engineered by rational design based on the targets. Integrase (IN) enables the viral genetic material to be integrated into the DNA of the infected cell. Current research has focused on the individual enzyme targets, but future shifts will focus on studying the maturation process of the enzymes The folding patterns of HIV-1 RT is presently known, and through rational design, inhibition of this pathway may be targeted to prevent these enzymes from assuming structurally functional forms. Current Research Dual Inhibitory Drugs Conclusion What is HIV? What is HIV 1-Reverse Transcriptase? Specific & Broad Spectrum Antiretroviral Drugs Future research possibilities

Biochem Presentation

Transcript: Worldwide growing demand for natural products Currently very little of produced vanillin is by natural means Biovanillin is considered natural Idea 3 eat more ice cream Biovanillin as an Alternative Adsorbent Resins What do these have in common? poop pooop poooop Presentation Contents XAD-2 poop pooop poooop DM11 Reactor Conditions -the dominant flavouring component of natural vanilla extract Vanillin is toxic to microorganisms Vanillin product gets reduced to less toxic compounds Solution then, is to reduce toxicity and prevent further transformation The Main Problem With Biovanillin Production What is vanillin? Solution

Biochem Presentation

Transcript: B-actin B-tublin Glyceraldehyde-3-phosphate dehydrogenase (i) B-tubulin: forward primer 5'-CTGTTCGCTCAGGTCCTTTTG-3' and reverse primer 3'-CCTCCTTCCGTACCACATCCA-5' (ii) B-actin: forward primer 5'AGGCATCCTCACCCTGAAGT-3' and reverse primer 3'-AGGGATAGCACAGCCTGGAT-5' (iii) GAPDH: forward primer 5'-CATGAGAAGTATGACAACAGCCT-3' and reverse primer 3'-AGTCCTTCCACGATACCAAAGT-5' Extracted total RNA from different leukocytes using RNeasy kit. Dissolved RNA pellets in DEPC- treated water and stored at -20°C until needed 200 ng RNA mixed with 1μl dNTP and 5μl oligo dT for 5 minutes at 65°C Mixed with 4μl of 5X buffer, 2μl 0.1 M DTT (dithiothreitol), and 1μl of RNaseOUT = total volume of 20μl before reverse transcription (RT) for 60 minutes at 42°C using reverse transcriptase Lower b-actin expression in CBMCs was due mainly to monocytes Conclusion Products were subjected to PCR amplification using specific primers and SYBR Green quantification to amplify three different transcripts as follows Activated by heating for 10 minutes at 95°C, then 60 seconds at 60°C, and for 15 seconds at 95°C for 40 cycles in PCR mix containing 2μl of cDNA template, 1X quantitative PCR mastermix 100 nM of each primer, 1μl of SYBR Green = total volume of 30μl. All reactions performed in an ABI PRISM 7500 Sequence Detection System Only GAPDH was expressed at a consistently stable level B-actin was expressed at much lower levels in MNCs from children less than 3 years old B-tubulin exhibited large individual differences across the age groups Glyceraldehyde-3-phosphate dehydrogenase is a reliable internal control in Western blot analysis of leukocyte subpopulations from children Expression of b-actin protein in MNCs was age dependent Compared expression levels of b-actin, b-tubulin, and GADPH in both PBMCs and CBMCs Found that only GADPH was expressed at equal amounts in both Serial dilution to determine if GAPDH remained constant Both cell types incubated with anti-GAPDH exhibited similar signal intensities, which were gradually increased ββ Collected in heparinized tubes (10 U/ml) by cordocentesis PMBCs (peripheral blood mononuclear cells & CMBCs (umbilical cord blood mononuclear cells) isolated by 4.5% dextran sedimentation Blood mixed at a 5:1 ratio of 4.5% (w/v) dextran in 10-ml tubes and stood upright undisturbed at room temperature for 30 minutes Gently layered leukocyte supernatant on top of Ficoll-Paque at a 2:1 ratio Introduction Cell Culture & Treatment Housekeeping genes of B-actin and b-tubulin exhibited consistent levels of mRNA expression in different leukocytes populations from new borns and adults mRNA's, not proteins encoded by housekeeping genes consistently expressed Post translational regulation responsible for low B-actin Neither B-actin nor B-tubulin was a reliable control GAPDH was a reliable control for protein assessment of samples for subjects of all ages GADPH was a more reliable internal loading control than b-actin and b-tubulin in Western blot analysis Leukocytes lysed in cold radioimmunoprecipitation assay (RIPA) lysis buffer containing protease inhibitors. Protein concentration determined using protein assay kit Aliquots of crude extracts (containing 10 μg protein) used in Western blot analysis. CD3-, CD14-, and CD19-positive T cells, monocytes, and B cells isolated from adult PBMCs and CBMCs using isolation kits Positive magnetic sorting using autoMACS Separator. Purified using flow cytometry Western Blotting •Hong-Ren Yu, Ho-Chang Kuo, Hsin-Chun Huang, Li-Tung Huang, You-Lin Tain, Chih-Cheng Chen, Chi-Di Liang, Jiunn-Ming Sheen, I-Chun Lin, Chi-Chiang Wu, Chia-Yu Ou, Kuender D. Yang. Glyceraldehyde-3-phosphate dehydrogenase is a reliable internal control in Western blot analysis of leukocyte subpopulations from children. Analytical Biochemistry. Volume 413, Issue 1, Pg 24-29. 1 June 2011. RT-PCR Aliquots of monocytes in RPMI-1640 medium containing 10% heat-inactivated fetal bovine serum were treated with actinomycin D, cycloheximide, or MG132, each prepared in a stock solution made in water or (DMSO) Cells harvested by centrifugation for total RNA or protein collection Western Blotting Housekeeping Proteins B-Actin B-Tubulin GAPDH Monocyte Neonate Centrifuged at 1500 rpm for 30 minutes to separate PMNs from MNCs Collect MNCs by pipetting cells directly from interface Transferred cells to new tube, washed, and suspended with phosphate-buffered saline Membrane blots blocked using TBST containing 5% nonfat dry milk before exposing to the primary antibodies Horseradish peroxidase-conjugated secondary antibodies for 2 hours Developed membranes using ECL Plus Kit and Kodak X-ray film exposure. Densitometric intensity measured and analyzed using an LAS-3000 and Multi Gauge version 3.0 Posttranslational regulation was responsible for low b-actin expression in neonatal monocytes Collection & Preparation Collection Materials & Methods Measured b-actin mRNA level and protein level in cord and adult blood monocytes Expression

Biochem Presentation

Transcript: Future Research E. D. Steinberg et al. , 1998 A2780 (ECACC 93112519) Wavelengths tested don't penetrate far into tissue: Toxicity of Tetraplatinated Poryphrins in Cell Culture Platinum Based Pharmaceuticals Domcke, Silvia et al. "Evaluating Cell Lines As Tumour Models By Comparison Of Genomic Profiles". Nature Communications 4 (2013). Harvested from untreated patient Cisplatin Sensitive Ovarian Carcinoma Cells Viscosity Testing Produce extracellular structural proteins (eg collagen, elastic fibers HeLa Cells Paul Goodland, Kim Fields, and Peter Zhang, n. d. Naik et al. 2014 Control Porphyrins Cisplatin Resistant Ovarian Carcinoma Cells Conjugated, aromatic heterocycles Naturally occurring- heme, chlorophyll, cytochromes, vitamin B12 Four nitrogen in middle can coordinate to metals Absorb light > electron promoted > upon return to ground state, energy transferred to molecular oxygen, producing singlet oxygen Photocleavage Oldest human cell line Kelland, Lloyd. "The Resurgence Of Platinum-Based Cancer Chemotherapy". Nature Reviews Cancer 7.8 (2007): 573-584. Localization Guanosine Binding ROS can damage nucleic acids, and oxidize fats, proteins, and cofactors Photosensitizer activated by light Generates ROS, induce cell death Can precisely control when, where activated Promising cancer treatment Merged Combine photodynamic therapy and platinum Kelland, 2007 These compounds localized to the nucleus Characterization DIC Anu Naik, Riccardo Rubbiani, Gilles Gasser, and Bernhard Spingler http://www.phe-culturecollections.org.uk Normal human fetal lung cell line used Naik et al. 2014 Naik et al. 2014 2 Conclusions A2780cis (ECACC 93112517) EtBr Competition Assay DNA Binding ISTOCKPHOTO/THINKSTOCK Immortal Play role in tumor inflammation response via ECM remodeling Cell Culture Nedime Serakinci, Rikke Christensen and Umut Fahrioglu, 2011 Nedime Serakinci, Rikke Christensen, and Umut Fahrioglu. Transformation Of Mesenchymal Stem Cells. 1st ed. INTECH Open Access Publisher, 2011. Convert large molecules to gaseous ionic state for mass spec For all compounds tested, high concentration needed to kill cells in dark; low concentration needed to kill cells with light exposure 3 Cervical cancer Dolmans, Fukumura and Jain, 2003 Research Approach Dolmans, Dennis E.J.G.J., Dai Fukumura, and Rakesh K. Jain. "TIMELINE: Photodynamic Therapy For Cancer". Nature Reviews Cancer 3.5 (2003): 380-387. IR HNMR PtNMR ESI-MS Elemental analysis UV/Vis spectroscopy Same as in previous slide, but resistant to cisplatin Human Fibroblasts They bind to guanosine in DNA and DNA is damaged upon exposure to 420 nm light Mitotracker The tetraplatinated compounds synthesized were toxic cancer to cells upon exposure to light http://www.phe-culturecollections.org.uk References Angelo Frei, Wikimedia Common, 2013 Potentially not suitable as ovarian cancer model (Domcke et. al, 2013), probably fine for this research Provides ability to control temporal, spatial activation of drug + action of Pt based compounds Sternberg, Ethan D, David Dolphin, and Christian Brückner. "Porphyrin-Based Photosensitizers For Use In Photodynamic Therapy". Tetrahedron 54.17 (1998): 4151-4202. Naik et al. 2014 Visible-Light-Induced Annihilation of Tumor Cells with Platinum– Porphyrin Conjugates DAPI Elucidate mechanism of DNA cleavage Determine if results similar in vivo Determine if compounds always intercalate with DNA, or only upon light exposure- potential issues if intercalates in dark Mixed cell culture, determine if differential localization based on cell type 4 Naik et al. 2014 Photodynamic Therapy HeLa cells Human fibroblasts Cisplatin sensitive ovarian carcinoma cells Cisplatin resistant cells ovarian carcinoma cells Poryphrin Synthesis Compound Binding of compound 4 results in the formation of new downfield shifted peaks UV/Vis Absorbance Changes with addition of DNA to Compound 4 Naik, Anu et al. "Visible-Light-Induced Annihilation Of Tumor Cells With Platinum-Porphyrin Conjugates". Angewandte Chemie 126.27 (2014): 7058-7061. 1 https://www.atcc.org/products/all/CCL-171.aspx#characteristics

Biochem Presentation

Transcript: Gene Therapy for lysosomal storage diseases What are LSD's? LSDs Lysosomal storage diseases are inherited metabolic diseases where the lysosomes no longer function and a buildup of toxins cannot be excreted from the cell. Examples of lysosmal storage diseases are Gaucher disease, Pompe disease, Wolman disease, infantile Batten disease, etc. Examples of different LSDs Figure 1.1 shows different types of lysosomal storage diseases and the enzyme associated with the disease that is difficient. In addition, the figure shows the age of onset and the type of symptom it will exhibit whether it is exhibited through the central nervous system or a systemic disease. Eample of mechanism Figure 1.2 shows lysosomal enzyme trafficking and cross correction. Cross correction is the mechanism in which normal neighboring cells lead to the correction of neighboring enzyme deficient cells. Most of the lysosomal enzymes are glycosylated in the ER and then bind with the mannose 6-phosphate receptor. However some of the lysosomal enzyme are secreted from the cell and can bind to the M6PR or ManR where endocytosis can be mediated. In vivo gene therapy vs ex vivo gene therapy Type of gene therapy For in vivo gene therapy, the vector used to deliver the genomic data is inserted directly to the cell. For ex vivo gene therapy, the cells are removed from the body to be treated and cultured outside of the body. They are then reinserted into the body once modified. 05 Viral vector gene therapy 04 03 What are viral vectors? Viral vector gene therapy is a type of gene therapy where viruses are modified to introduce specific DNA sequences or therapeutic substrates. The virus is modified by removing the genes encoding polymerase and structural proteins to render them unable to replicate so they only deliver the specific DNA sequence. 02 01 Types of Viral Vectors Types of viral vectors Retroviral: These vectors can deliver large packages of RNA ut these viruses integrate themselves into the genome of the host cell . Retroviruses are best used for replicating cells so the therapeutic DNA sequence isnt lost through cell division. Adenovial: Similar to AAVs but can deliver larger sequences of DNA. In addition, there is more risk because adenoviruses are more likely to cause an immune response leading to decreased effectiveness of the therapy. Adeno-associated viral: Known as AAVs and are used to deliver smaller DNA sequences. AAVs are nonintegrating meaning it will not insert itself into the cell's genome. The therapeutic gene will not be copied throughout cell division and will be lost over time. Considerations for gene therapy considerations & discussion The safety of viral vector use in a large concern for a majority. There are many risks when using the retroviral mediated gene therapy because studies reported incidenes of leukemia when treating X-linked SCID. The article then further questioned if instead vectors that express higher levels than normal of a pecific enzyme could be a different approach to treat these diseases WHy is this related to biochemistry How is this related to biochemistry? The metabolic process of lysosomes is vital to the biochemistry of our bodies and how we function. Without properly functioning lysosomes, toxins build up in the body and can have fatal results. Through treatmets these deficiencies can be corrected so normal enzymatic activity can take place. discussion Possible inquiries A further in depth study into each form of gene therapy would be beneficial since the article was an overview of many different types.

Biochem presentation

Transcript: Experimental Design Protocol: NAD+, FAD, Coenzyme Q and the Cytochromes are important electron acceptors in aerobic cellular respiration. Electron Acceptors DCIP can act as an electron acceptor, and changes colour when it is reduced. DCIP as an electron acceptor Oxidised (no electrons) Reduced (gain electrons) Biological Oxidation Reactions Lack of NAD+ will affect oxidation of pyruvate, lactate and malate. Hypotheses Adding NAD+ will allow all substrates to be oxidised. Malonate will only affect succinate oxidation. Controls No NAD+ No malonate NAD+ only Malonate only NAD+ and Malonate

BioChem presentation

Transcript: Phase Changes & States of Matter Intro 1 States of Matter This presentation will cover the four states of matter: Solids Liquids Gases Plasma Particle Behaviour: Solids States of Matter Solids are made up of particles that are very close together. (Strong forces of attraction hold the particles together.) The particles in solids vibrate in fixed positions. The shape and volume of solids do not change. Solids cannot be squashed and do not flow. Liquids Particle Behaviour: Liquids Liquids are made up of particles that are fairly close together. (Quite strong forces of attraction hold the particles together.) The particles in liquids are able to move past each other. Liquids have a fixed volumes but their shape can change to fit the container as they flow easily. Liquids cannot be easily compressed (squashed). Gases Particle Behaviour: Gases Gases are made up of particles that are well spread out. (There are only weak forces of attraction between the particles.) The particles in gases move about freely in all directions. The shape and the volume of gases can change as they flow very easily and spread out. Gases can be compressed (squashed) quite easily. Plasma Particle Behaviour: Plasma Plasma is an electrically charged gas: (Because of this they are affected by electrical and magnetic fields.) Plasma consists of particles of extremely high kinetic energy Electricity is used to ionize noble gases and create glowing signs which are essentially plasma. For example: Stars, nebulas, northern lights Phase Changes: A phase change is when matter changes from one state to another Intro 2 The phase changes include: Vaporization Melting Freezing Condensation Deposition Sublimation Occurence Phase Change Occurence Phase changes occur when sufficient energy and pressure is applied to a sytem. Increasing temperature gives atoms and molecules more kinetic energy, helping them break bonds and move further apart. Decreasing temperature slows down particles and makes it easier for them to gain rigid structures. Vaporization Vaporization is the process of converting liquid into gas by applying heat. Due to the increase in temperature the kinetic energy of the molecules builds up, causing the forces of attraction between the particles to break. When evaporation takes place, liquid particles gain energy from their surroundings in order to overcome the force of attraction between them, making the atoms spread apart. This means that the forces of attraction between the particles reduce. Phase Changes Melting Melting/Fusion Melting is the change from a solid to liquid when heat is applied. As heat is applied Kinetic energy increases, causing the molecules to speed up, and therefore breaking the forces of attraction. Eventually, the melting point of the substance is reached. Freezing Freezing/Solidification Freezing is when a liquid substance turns into a solid. This happens when the temperature is lowered below the freezing point. The kinetic energy decreases causing the molecules to slow down. Condensation Condensation Condensation is the process by which gas in the atmosphere is changed into a liquid. Condensation occurs when molecules lose heat causing them to lose energy, slowing them down. The molecules combine to form a liquid. Deposition Deposition Deposition is the change in which a gas is converted directly into a solid. This happens when there is a decrease in temperature, causing the kinetic energy to reduce. One good example of deposition is when carbon dioxide turns into dry ice. Sublimation Sublimation Sublimation is when a solid is converted directly into a gas. During this change the kinetic energy speeds up, causing the molecules to move further apart due to the increase in temperature. One example of sublimation is dry ice turning back into carbon dioxide. Cited Sources Sources Works Cited Britannica. www.google.com/url?q=https://www.britannica.com/science/plasma-state-of-matter&sa=D&source=editors&ust=1698130264034712&usg=AOvVaw29AYfMLiJdHnWD4qH3aHJp. Cambridge International. www.cambridgeinternational.org/programmes-and-qualifications/cambridge-international-as-and-a-level-chemistry-9701/published-resources/. Live Science. www.livescience.com/46506-states-of-matter.html. Nasa. www.nasa.gov/podcasts/curious-universe/plasma-plasma-everywhere/#:~:text=The%20night%20sky%20is%20full%20of%20planets%2C%20satellites%20and%20cosmic,of%20it%20is%20called%20plasma. Pearson Education. Pearson Education Ltd (2014) The particle theory. London: Pearson Education Ltd. UCAR. scied.ucar.edu/learning-zone/sun-space-weather/plasma#:~:text=Plasma%20is%20one%20of%20the,a%20gas%20and%20a%20plasma. Image Sources Image Sources Works Cited Chocolate Melted.

BioChem Presentation

Transcript: Regarding the physical principles behind hypochromism: Cantor, C.R., Schimmel, P.R. 1980, Biophysical Chemistry. Part II. pp 399-404. Modern Experimental Biochemistry. Boyer 90˚C Ice Sodium Perchlorate Chloroform/Isoamyl Alcohol Key term: Melting Temperature Intent pH=8 Wikipedia for chemical structures References 2 Purposes EDTA Low pH and Histones Why do we care? ABS=.4 90˚C Extraction and Characterization of E. coli DNA Purify DNA Consider how well documented success with this procedures is Sodium Dodecyl Sulfate (SDS) Heat Viscosity Increases Centrifuge at 10,000g Extract top Layer Slow Cool The Hyperchromic Effect Control-RT throughout Ice Bath A-260/A-280 Ratio changes with temperature Add Two Equivalents EtOH Spool DNA out on Glass Rod Centrifuge, Reextract 15 min Method Observe Hyper/Hypo Chromism ABS=.4 Consider from where impurities arise 15 min Detergent What Does the ratio tell us DNA isolation from other organisms? Straightforward and Logical Procedure Are there any steps that we could take to improve purity The absorbance of denatured DNA decreases More Pure DNA??? Heat and slow cool Does knowing this procedure matter? From whence do the the differential absorbances arise Lysozyme then incubate ABS=.6 To the UV-VIS Suspend Cells in Saline-EDTA The Grand Finale

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