Homework

Weekly homework submissions:

  • Week 1 HW: Principles and Practices

    1. First, describe a biological engineering application or tool you want to develop and why. This could be inspired by an idea for your HTGAA class project and/or something for which you are already doing in your research, or something you are just curious about. My idea: • The use of biotechnology to make pills or capsules , that reduce the glucose spike after a meal rich in carbohydrates . • My idea came from some podcasts which have as principal subject the book “Glucose revolution” by Jessie Inchauspe and also from her videos . • -I think that if the pills contains mulberry leaf extract , acetic acid , eriocitrin, the result be long term and will came faster. • The pills should be useful for everyone , diabetics , nondiabetics, prediabetics • The addition of mulberry leaf extract to sucrose resulted in a significantly lower glycemic response and insulinemic response compared to a matched placebo (sucrose alone). The change in blood glucose measurements were significantly lower at 15 min (p < 0.001), 30 min (p < 0.001), 45 min (p = 0.008), and 120 min (p < 0.001) and plasma insulin measurements were significantly lower at 15 min (p < 0.001), 30 min (p < 0.001), 45 min (p < 0.001), 60 min (p = 0.001) and 120 min (p < 0.001). The glucose iAUC (- 42%, p = 0.001), insulin iAUC (- 40%, p < 0.001), peak glucose (- 40.0%, p < 0.001) and peak insulin (- 41%, p < 0.001) from baseline were significantly lower for white mulberry leaf extract compared with the placebo. White mulberry leaf extract was well tolerated and there were no reported adverse events. • This study evaluated the potential effectiveness of different doses of Eriomin® on hyperglycemia and insulin resistance associated with other metabolic biomarkers in prediabetic individuals. Prediabetes patients (n = 103, 49 ± 10 years) were randomly divided into four parallel groups: (a) Placebo; (b) Eriomin 200 mg; (c) Eriomin 400 mg; and (d) Eriomin 800 mg. Assessment of biochemical, metabolic, inflammatory, hepatic, renal, anthropometric markers, blood pressure, and dietary parameters were performed during 12 weeks of intervention. Treatment with all doses of Eriomin (200, 400, and 800 mg) had similar effects and altered significantly the following variables: blood glucose (-5%), insulin resistance (-7%), glucose intolerance (-7%), glycated hemoglobin (-2%), glucagon (-6.5%), C-peptide (-5%), hsCRP (-12%), interleukin-6 (-13%), TNFα (-11%), lipid peroxidation (-17%), systolic blood pressure (-8%), GLP-1 (+15%), adiponectin (+19%), and antioxidant capacity (+6%). Eriomin or placebo did not influence the anthropometric and dietary variables. Short-term intervention with Eriomin, at doses of 200, 400, or 800 mg/day, benefited glycemic control, reduced systemic inflammation and oxidative stress, and reversed the prediabetic condition in 24% of the evaluated patients. these studies were taken from : https://pubmed.ncbi.nlm.nih.gov/36644880/ https://pubmed.ncbi.nlm.nih.gov/33858439/ https://pubmed.ncbi.nlm.nih.gov/31183921/ 2. Next, describe one or more governance/policy goals related to ensuring that this application or tool contributes to an “ethical” future, like ensuring non-malfeasance (preventing harm). Break big goals down into two or more specific sub-goals. Below is one example framework (developed in the context of synthetic genomics) you can choose to use or adapt, or you can develop your own. The example was developed to consider policy goals of ensuring safety and security, alongside other goals, like promoting constructive uses, but you could propose other goals for example, those relating to equity or autonomy. Main objective: -Ensuring the responsible and rigorous use of nutrition engineering technologies; 2.1 Patient safety: Testing carefully and prevention of the extracts side effects; 2.2 Equity of access: Preventing inequitable access to the pills , where only small groups of population can use them. the benefits have to be accessible for everyone , both in terms of cost and the information about them, which can convince they to buy them to improve them lifestyle and in order to enjoy carbohydrate -rich meals.

  • Week 2-DNA Read, Write, & Edit

    title: ‘Week 2’ weight: 10 Part 1: Benchling & In-silico Gel Art Create a pattern/image in the style of Paul Vanouse’s Latent Figure Protocol artworks. You might find Ronan’s website a helpful tool for quickly iterating on designs! Part 2: Gel Art - Restriction Digests and Gel Electrophoresis

  • Week 3 HW: Opentrons art

    1 Generate an artistic design using the GUI at opentrons-art.rcdonovan.com. I searched some images and when I found what I wanted I made a screenshot of it and I put it in openntrons. Find and describe a published paper that utilizes the Opentrons or an automation tool to achieve novel biological applications.

  • Week 4 HW: Protein Design Part I

    A Answer any NINE of the following questions from Shuguang Zhang: (i.e. you can select two to skip)

  1. How many molecules of amino acids do you take with a piece of 500 grams of meat? (on average an amino acid is ~100 Daltons) A Dalton is equal to 1/12 atom of carbon, so aprox. 1.66x10-27kg. I will chose beef , because the type isn’t specified . 100g of beef has aporx. 25g protein, so 500g has 125g protein. 1g=6.022x1023 atomic mass units =>125g=7,5275 x 10^25 Dalton

  • Week 5— Protein Design Part II

    A P00441 is the unique identifier for Human Superoxide Dismutase 1. This is the original squence: MATKAVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ This is the mutation squence: utant Sequence (Target): MATKVVCVLKGDGPVQGIINFEQKESNGPVKVWGSIKGLTEGLHGFHVHEFGDNTAGCTSAGPHFNPLSRKHGGPKDEERHVGDLGNVTADKDGVADVSIEDSVISLSGDHCIIGRTLVVHEKADDLGKGGNEESTKTGNAGSRLACGVIGIAQ

  • Week 6 HW: Genetic Circuits Part I: Assembly Technologies

    What are some components in the Phusion High-Fidelity PCR Master Mix and what is their purpose? The components in the Phusion High-Fidelity PCR Master Mix are Phusion DNA Polymerase, deoxynucleodites, reaction buffer. -Phusion DNA Polymerase-copies the DNA -Reaction buffer-maintains optimal biochemical proprieties What are some factors that determine primer annealing temperature during PCR? -specific annealing enzyme use and their optimal catalysing activity temperature; There are two methods from this class that create linear fragments of DNA: PCR, and restriction enzyme digests. Compare and contrast these two methods, both in terms of protocol as well as when one may be preferable to use over the other.