Notes in Molecular Capstone Exam 2

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Published	12/01/2023	What does BLAST stand for?
Published	12/01/2023	BLAST uses {{c1::heuristics}} to verify and extend the match in the database. A {{c1::heuristic}} is {{c2::a rule or method}} that serve as a short cu…
Published	12/01/2023	BLAST finds regions of local {{c1::similarity}} between sequences.
Published	12/01/2023	BLAST is based on sequence similarity, not {{c1::homology}}.
Published	12/01/2023	DNA barcoding examined the {{c1::COI}} gene. THis gene encodes for a mitochondrial protein that is present in all mammals.
Published	12/01/2023	{{c1::Pain}} is one of the 5 vital signs. The other four are {{c2::blood pressure}}, {{c2::temperature}}, {{c2::heart rate}}, and {{c2::respiration ra…
Published	12/01/2023	NSAIDs are used for {{c1::minor}} pain and have a {{c1::ceiling effect }}.
Published	12/01/2023	Effects of {{c1::Opioid Use}}: AnalgesiaConstipationEuphoriaetc
Published	12/01/2023	{{c1::Receptor downregulation}}: when receptors leave the surface of the cell and get absorbed into the cell, causing them to no longer work.
Published	12/01/2023	{{c1::Iatrogenic}}: harm caused by the healthcare system
Published	12/01/2023	Opioid Risk Tool: determines how likely a patient is to develop substance use disorder
Published	12/01/2023	{{c1::ANKK1}} Gene is responsible for dopamine synthesis. This gene contains the SNP that we determined from gel electrophoresis CC, CT, TT.
Published	12/01/2023	{{c1::TT}} genotype: 532 bp{{c1::CC}} genotype: 284 and 248 bp
Published	12/01/2023	Genotype frequency: {{c1::# of participants with target genotype/ total number of participants}}
Published	12/01/2023	{{c1::Cytochrome P450}} enzyme metabolizes drugs
Published	12/01/2023	{{c1::Hayflick}} limit: limited life span
Published	12/01/2023	A BLAST bit score is based on: {{c1::The alignment of the sequence to a sequence in the database}}{{c2::The length of the sequence}}{{c1::The len…
Published	12/01/2023	The E-value in BLAST is the expected amount of random sequences that have equivalent sequence alignment. In other words, it is a measure of {{c1::how …
Published	12/01/2023	{{c1::Shorter}} sequences have higher {{c2::e-values}} because the probability of finding that sequence is higher.
Published	12/01/2023	Sequence similarity is {{c1::how similar the sequences are to each other}}
Published	12/01/2023	Sequence homology reflects {{c1::species have a common ancestor}}.
Published	12/01/2023	For highly similar sequences, we will have a {{c1::high}} bit score and a {{c1::low}} e-value
Published	12/01/2023	During DNA barcoding, the {{c1::COI}} gene was observed because {{c2::it is in mitochondria}} and {{c2::it is essential for life in mammals}}.
Published	12/01/2023	Interspecies variation during DNA barcoding is the genetic differences seen between 2 or more species. For our purposes, this should be {{c1::hig…
Published	12/01/2023	{{c2::Intraspecies}} variation in DNA barcoding is the genetic differences within a species. For our purposes, this should be {{c1::low}}.
Published	12/01/2023	We used COI primers as well as {{c1::an M13 tail}}, so that sequencing could be easier.
Published	12/01/2023	DNA Barcoding can be useful in: Counterfeit goods detectionIllegal logging{{c1::Misleading supplements}}{{c1::Species identification}}Endangered …
Published	12/01/2023	{{c2::Opioids}} have {{c1::no limit}} to their analgesic effect
Published	12/01/2023	Effects of Opioid use: {{c1::Analgesia}}{{c1::Constipation}}{{c2::Euphoria}}{{c2::CNS}} depression{{c2::Respiratory}} depression{{c3::Miosis}}Dep…
Published	12/01/2023	Opioid mechanism: {{c1::Opioids stimulate the Ventral Tegmental Area in the brain which is the reward center of the brain to release dopamine}}.&…
Published	12/01/2023	{{c1::After prolongued use of opioids}}, receptor downregulation occurs.
Published	12/01/2023	Effects of {{c1::withdrawal}}: {{c2::Anxiety}}{{c2::Insomnia}}{{c3::Rhinorrhea}}{{c3::Diarrhea}}{{c4::Emesis}}{{c4::Mydriasis}}Piloerection{{c5::…
Published	12/01/2023	The ANKK1 gene, which we looked at in Opioid labs, encodes for {{c1::protein kinase K2}} which is involved in {{c1::dopamine synthesis}}. The ANK…
Published	12/01/2023	The ANKK1 gene is next to the {{c1::dopamine receptor}} gene and may influence its expression.
Published	12/01/2023	In the Opioid lab, we were trying to determine whether a particular {{c1::genotype}} or {{c1::allele}} puts you at higher risk for developing {{c2::a …
Published	12/01/2023	The {{c2::TT}} genotype {{c1::cannot be cut}} by the restriction enzyme
Published	12/01/2023	Allele frequency: {{c1::# of participants with the target allele (if allele C, include CC and CT participants) / 2 times the total number of participa…
Published	12/01/2023	{{c2::CYP 2D6}} metabolizes {{c1::codeine}} into {{c1::morphine}}.
Published	12/01/2023	{{c1::Personalized}} medicine is taking patients with {{c1::the same diagnosis}}, collecting samples from them, {{c2::isolating}} their DNA, sequencin…
Published	12/01/2023	The results from personalized medicine genome sequencing {{c1::only tell you your relative risk}}, not {{c1::your imminent future}}.
Published	12/01/2023	GWAS stands for {{c1::Genome Wide Association Studies}}. One example of a GWAS is {{c1::23&Me}}
Published	12/01/2023	{{c2::GWAS's}} take entire genomes to determine {{c1::which genes}} have an effect on {{c1::what we're researching (cancer, diseases, etc.)}}
Published	12/01/2023	GWAS's need {{c1::huge}} sample sizes to avoid {{c1::false positives}} and make statistically significant conclusions because the human geno…
Published	12/01/2023	GWAS's goal are to look for genes that come up a lot in case study groups to find {{c1::statistically significant}} hits.
Published	12/01/2023	Mammalian cell culture can be {{c1::primary}} or {{c1::immortalized}} cell lines.
Published	12/01/2023	A primary mammalian cell culture: Isolated {{c1::directly from a living organism}}{{c1::Normal}} cell behavior{{c2::Hayflick limit}}Ex: {{c2::Neu…
Published	12/01/2023	{{c2::Immortalized}} cell cultures:No {{c1::hayflick limit}} so, {{c1::cancer cells}}Example: {{c1::CHO K1 cells}}
Published	12/01/2023	A {{c2::hayflick limit}} just means {{c1::the cell has a limited lifespan}}
Published	12/01/2023	CHO K1 stands for {{c1::Chinese Hamster Ovary K1}}.
Published	12/01/2023	Mammalian cell culture is Very different from {{c1::bacterial culture}}Very useful for {{c1::pharmaceutical production}} ({{c2::insulin and monoc…
Published	12/01/2023	The media is warmed before added because {{c1::cells are sensitive and we try not to shock them}}
Published	12/01/2023	The {{c4::DMEM/F12}} media is made of: {{c1::Fetal Bovine Serum}} (don't know why this is really used but is essential){{c2::Proteins}}{{c2::Amin…
Published	12/01/2023	To prepare for cell culture, {{c1::the UV light is turned on 15 minutes before}}, {{c1::sterile gloves are donned by researchers}}, and {{c1::the safe…
Published	12/01/2023	The DMEM/F12 media must be warmed to {{c1::37C}}.
Published	12/01/2023	The {{c1::microtexture}} of the plastic affects how cells grow.
Published	12/01/2023	Cap goes {{c1::face down}} on sterile surfaces to prevent attachment of free floating microbes.
Published	12/01/2023	{{c1::Confluency}} is the percentage of cells covering the bottom of the cell culture disk
Published	12/01/2023	The incubator is kept at {{c1::5% CO2}} to {{c1::maintain the pH of the cell media}}
Published	12/01/2023	Trypsin is used to {{c1::detach the cells from the plate}}
Published	12/01/2023	{{c2::Higher}} confluence means {{c1::faster growing cells}} because of cell signaling
Published	12/01/2023	Solid waste that touches our CHO K1 cells goes {{c1::in the orange biohazard bags}}
Published	12/01/2023	Solid waste that does not touchh cells {{c1::can go in the regular trash}}
Published	12/01/2023	We used {{c1::an inverted microscope}} to visualize CHO K1 cells.
Published	12/01/2023	{{c1::Genomic}} medicine is {{c2::using someones genome for their clinical care.}}
Published	12/01/2023	Sickle cell disease: Caused by a {{c1::missense}} mutationConverts {{c2::glutamic acid}} to {{c2::valine}}The hemoglobin molecule&…
Published	12/01/2023	Beta-Thalassemia:Caused by a {{c1::nucleotide substitution}} or {{c1::deletion}} mutationResults in the absence/reduction of {{c2::beta-glob…
Published	12/01/2023	{{c1::Autologous}}: obtained from the same individual
Published	12/01/2023	{{c1::Myeloablative conditioning}}: {{c2::Destruction of hematopoietic cells (in bone marrow)}}
Published	12/01/2023	{{c2::Vase/Veno-occulusive event}}: Microciruclation {{c1::obstructed/blocked by sickle cell RBCs}}
Published	12/01/2023	CTX001 is an {{c1::autologous drug}}. It is edited with {{c2::CRISPR Cas9 ribonucleoprotein}} which silences {{c1::BCL11A}} in Beta Thalasse…
Published	12/01/2023	{{c1::Morbidity}} is how many people suffer from the disease while {{c1::mortality}} is how many deaths
Published	12/01/2023	Morbidity vs fetal hemoglobin in Beta Thalassemia: Studies found that {{c1::lower}} fetal hemoglobin lead to {{c2::higher}} morbidityTherefore, {…
Published	12/01/2023	By using CTX001: Acheive high levels of {{c1::allelic editing and durable engraftment}}High levels of {{c1::fetal hemoglobin}}Elimination of {{c2…
Published	12/01/2023	Tips for data presentation: {{c1::Power poses}}{{c1::Practice}}{{c2::Don't read off your slides}}{{c2::No cue cards}}{{c3::Project your voice}}{{…
Published	12/01/2023	Denser gels with higher % agarose are better for {{c1::smaller/shorter}} samples
Published	12/01/2023	What brain region do opioids stimulate to release dopamine? {{c1::Ventral Tegmental Area/ Reward area}}
Published	12/01/2023	The function of the ANKK1 gene is {{c1::to synthesize dopamine}}
Published	12/01/2023	{{c1::Monoclonal antibodies}} are FDA-approved drugs produced through {{c2::cell culture}}
Published	12/01/2023	FBS has necessary {{c1::survival factors for cell culture}} but we dont know exactly which factors
Published	12/01/2023	Dopamine release in the {{c1::Nucleus Accumbens}} and {{c2::Prefrontal Cortex}} causes euphoria
Published	12/01/2023	Drug users have fewer {{c1::dopamine}} receptors
Published	12/01/2023	Not everyone responds to opioids in the same way. Some people are {{c1::more at risk}} for {{c1::developing a substance use disorder}} from opioid use…
Published	12/01/2023	A {{c1::high}} ORT score reflects a higher risk of developing a Substance Use Disorder. We may not recommend opioids for individuals with really high …
Published	12/01/2023	The restriction enzyme used to cleave the PCR product in the opioid lab was called {{c1::TaqI}}. This enzyme cuts a PCR product with the {{c2::C}…
Published	12/01/2023	Expected PCR product sizes: {{c1::PCR Product}}: {{c3::532}} base pairsAfter Restriction Enzyme digest: {{c1::TT}} genotype: {{c3::532}} bas…
Published	12/01/2023	Opioid study participants included {{c1::heroin-dependent}} patients from three drug treatment centers. The {{c1::control group}} contained healt…
Published	12/01/2023	THe Orange G dye used in gel electrophoresis functions to {{c1:: visually track the progression of the same down the gel}}
Published	12/01/2023	Components of gel electrophoresis: {{c1::Colored Dye}}{{c1::Thickening agent}}{{c1::EDTA}}
Published	12/01/2023	The purpose of {{c1::EDTA}} in gel electrophoresis is to {{c1::bind any cations like Mg2+}} and stop all subsequent enzyme reactions ({{c2::nucleases}…
Published	12/01/2023	{{c1::Ethidium Bromide}} {{c2::binds to DNA}} and a UV light illuminates the dye, used to visualize the results of gel electrophoresis.
Published	12/01/2023	Genetics can affect how we: {{c1::Respond}} to drugs{{c1::Absorb}} drugs{{c2::Metabolize}} drugs{{c2::Excrete}} drugs
Published	12/01/2023	{{c1::Immortalized}} cell lines are cells that have been manipulated to {{c2::proliferate indefinitely}} and can thus be cultured for long period…
Published	12/01/2023	The doubling time for CHO K1 cells is pretty fast, approximately {{c1::14-17 hours}}
Published	12/01/2023	How confluence affects growth and behavior in cell culture with immortalized cells: Immortalized cells often do not exhibit {{c1::contact inhibit…
Published	12/01/2023	What is in cell media?{{c1::pH}} buffersProteins ({{c2::to inhibit proteases}}, {{c2::stabilize}} media, or bind {{c2::toxins}}){{c1::Carbohydrates}}{…
Published	12/01/2023	Biosafety cabinet rules: {{c1::Alarms and Blowers}} always onGlass never {{c2::open above level that causes alarm}}Clean cabinent before and…
Published	12/01/2023	Beta Thalassemia is a spectrum of mutations that result in {{c1::reduced}} or {{c1::absent }} adult hemoglobin
Published	12/01/2023	Turning off {{c2::BCL11a}} expression in Beta Thalassemia and Sickle Cell disease results in the restoration of {{c1::gamma globin expression}}
Published	12/01/2023	Enhancer regions can be {{c1::anywhere}} in the genome
Published	12/01/2023	{{c2::CRISPR Cas9}} causes formation of site-specific {{c1::double stranded break}} in the DNA
Published	12/01/2023	{{c1::Non-homologous end joining}} repairs DNA cut by CRISP Cas9
Published	12/01/2023	Pain is measured using {{c1::a scale from 1-10}} in conjunction with {{c1::facial expressions}}.
Published	12/01/2023	{{c2::Non-steroidal anti-inflammatory}} drugs are {{c1::analgesics}}, however, there is a {{c1::ceiling/limit}} to how much pain they can treat
Published	12/01/2023	{{c2::Receptor downregulation}}: {{c1::reduction of dopamine receptors}} in the brain to {{c1::adjust to the increased dopamine in the system}} from {…
Published	12/01/2023	The ANKK1 gene may affect the expression of dopamine receptors because this gene {{c1::is next to the receptor that codes for the receptor}}
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