exam 3

In vivo

(of a process) performed or taking place in a living organism

In vitro

(of a process) performed or taking place in a test tube, culture dish, or elsewhere outside a living organism

Article: New 'prime' genome editor could surpass CRISPR -Science (10/21/2019)

-"Prime-editing" is a newer version of CRISPR that could make it possible to insert or delete specific sequences at genome targets with less collateral damage, more targeting flexibility and greater editing precision -Liu and his post-doc tested 175 different edits in human and mouse cells, and were able to correct mutations that cause sickle-cell anemia and Tay-Sachs disease, and other DNA mutations that other genome-editing systems could not fix or fix efficiently -Has the potential to correct 89% of known disease-causing genetic variations in DNA -Better than base editing which could only make certain base changes, prime editing can change any of the bases into any other base -Prime editors can make repairs in non-dividing cells, can remove a precise number of nucleotides, insert missing nucleotides or replace a string of disease-causing nucleotides with nucleotides supplied by CRISPR -Prime editing has three parts-the pegRNA-prime editing guide RNA, which targets specific location and contains nucleotides that will substitute for the disease-causing ones, a hobbled Cas9 enzyme, that cuts one but not both strands, and the enzyme reverse transcriptase fused to Cas9, which transfers the RNA nucleotides carried by the pegRNAand transforms them into DNA nucleotides, which replace those at the target site -Net result is a permanent edit that has been copied from the information encoded in the pegRNA -Delivering the large construct of RNA and enzymes into living cells will be difficult, and no one has yet shown it to work in an animal model

Article: Study sheds more light on genes 'on/off' switches -Science Daily (02/26/2019)

-2% of the genome is protein coding, a large portion of the remaining DNA controls the expression of genes, switching them on and off -Every cell has the same DNA, and what makes a muscle cell different from a brain cell is which genes are turned on or off -Using a sophisticated computational method to investigate genetic variation in noncoding DNA and how this change's a person's susceptibility to disease -Compare five types of regulatory regions and examine how they behave in different cell types -Epigenomics looks at how other factors than DNA regulate gene expression -Enhancers and promoters are gene regulatory elements that boost/initiate the rate of transcription -Findings suggest that enhancers and promoters that are cell-specific could make it easier for transcription to occur under certain environmental conditions by making the cell's chromatin relax making transcription more accessible

Article: Scientists Call for Global Moratorium on Creating Gene-Edited Babies -NPR (03/13/2019)

-A group of 18 prominent scientists and bioethicists are calling for a global moratorium on any attempts to bring gene-edited babies into the world -Including all clinical uses of human germline editing -Prompted by announcement of scientist in China, He Jiankui, that used CRISPR to create the world's first gene-edited babies, edited to protect them from the AIDS virus -Announcement widely condemned as unethical and irresponsible, talks about how could have been prevented, and what should be done to try to prevent more researchers from going rogue -Propose of five-year moratorium for every country, allow for creation of an "international framework" for how to proceed responsibly -Basic research using CRISPR would continue to determine safety and effectiveness of editing DNA in human embryos -US federal law prohibits the creation of gene-edited babies, 30 other countries have similar prohibitions, many others do not -Other scientists are concerned that moratorium might be too strong of a word, and complicates future discussions

Article: European Commission proposes relaxing GMO regs for COVID-19 vaccines -Regulatory Focus (06/18/2020)

-A proposal to adjust EU regulation of GMOs would relax requirements for vaccines under development for SARS-CoV-2, allowing GMO-containing candidate vaccines and coronavirus therapeutics to proceed with clinical trials -The objective of this policy change is to ensure that clinical trials with medicinal products for human use containing GMOs and intended for treatment or prevention of COVID-19 can start quickly, to protect human health -Some vaccines in development contain attenuated viruses, or live vectors, which fall under the EU GMO regulations -Plan to include an environmental risk assessment as part of the marketing authorization procedure for products that fall under the relaxed GMO regulations -Heterogeneous approaches to regulating GMOs should not hinder clinical trials having the most promise to speed development of a vaccine -The European Medicines Agency (EMA) will continue to assess environmental impacts in parallel with its quality, safety, and efficacy assessments, and written authorization is required for each member state, along with good clinical practice, ethical trial conduct, and good manufacturing is still mandatory -The proposed derogation would also allow distribution of medicinal products containing GMOs under a compassionate use of Regulation -The proposed derogation is only for the duration of the pandemic and applies only to medicinal products intended to prevent or treat COVID-19

Article: GMO Pros and Cons: Backed by Evidence -Healthline (07/02/2020)

-According to the USDA, GMO seeds are used to plant over 90% of maize, cotton and soy in the US, meaning many of us likely eat foods containing GMOs -GMO crops use recombinant DNA technology to add genes for various reasons, such as improving their growth, nutritional content, sustainability, pest resistance, and ease of farming -The FDA, EPA and USDA maintain that GMOs are safe for human and animal consumption ---Advantages of GMO foods: -Made to express genes that protects them against pests and insects, such as the Bt gene, which comes from the naturally occurring bacteria known as Bacillus thuringiensis (Bt), this gene produces a protein that is toxic to several pests and insects, giving the GMO plant resistance, reducing the need for pesticides as often, studies from 2014 show GMO technology reduced chemical pesticide use by 37%, increased crop yield 22% -GMO crops have been modified with genes that help survive stressful conditions (ex-droughts), and resist diseases (ex-blights), resulting in higher yields, lowering costs for farmers and consumers -Genetic modification can increase nutritional value (ex-Golden Rice with increased Vitamin A), or enhance flavor and appearance (ex-non-browning apples) ---Safety and Concerns: -Some concern GMO foods may trigger allergies, due to foreign genes, no reported allergic reactions to GMO foods currently on the market -Concerns GMO foods may aid in progression of cancer, because cancer is caused by mutations people fear foods with added genes may affect your DNA, no current research ties GMO intake to cancer, but no long-term human studies -Environmental concerns include plants becoming resistance to herbicides over time creating superweeds, and more herbicides being used to kill resistant weeds -Roundup and its active ingredient, glyphosate have been linked to various diseases in animal and test-tube studies ---How to Identify GMO foods -In the US currently no regulations mandate labeling of GMO foods, but as of January 2022 the USDA will require food manufacturers to label all foods containing GMO ingredients, using the label "bioengineered food" instead of "GMO" -Any food labeled "100% Organic" does not contain any GMO ingredients, but if labeled "Organic" it may contain GMOs, in the EU foods with more than 0.9% GMO ingredients must list "genetically modified" on them

Article: Binge Drinking in Adolescence may Increase Risk for Anxiety Later in Life -Science Daily (03/11/2019)

-Alcohol exposure early in life has lasting effects on the brain and increases the risk of psychological problems in adulthood, due to abnormal epigenetic programming -Changes connectivity in the brain, in the amygdala, which is involved in emotional regulation and anxiety, in ways we don't yet understand -Epigenetic alterations are required for normal development of the brain, but can be modified in response to environmental, and social factors, including alcohol and stress -Adolescent rats were exposed to ethanol for two days on and two days off, or saline in controls, for two weeks, then assessed for anxiety, the rats exposed to alcohol exhibited anxious behavior later in life, even if binge drinking stopped in late adolescence -Had lower levels of Arc protein in the amygdala, which is important for normal development of synaptic connections in the brain, 40% fewer neuronal connections in these rats, caused by epigenetic changes

Article: CRISPR: Gene editing and beyond -Nature (10/31/2017)

-CRISPR has revolutionized gene editing -Powerful tool for genetic research -Two components: DNA cutting protein:Cas9 & RNA molecule: Guide RNA-together cut specific sections of DNA -First identify PAM, unwind double helix, guide RNA matches specific sequence, Cas9 makes knicks and double-strand breaks, DNA repair -Great tool for knocking out specific genes -Other things: transport enzymes to specific sequences, base editing, introduce stop codons, promote gene transcription, gene silencing, attach fluorescent proteins to find particular DNA sequences, visual 3-D architecture, paint chromosomes to follow position, and many more

Article: A Look into the Epigenetics of the Coronavirus Infection -What is Epigenetics? (03/10/2020)

-Emerging viral infections are a major threat to global public health, with the last two decades dealing with fatal outbreaks of Swine Flu, Ebola, Zika virus and now COVID-19 -Viruses are constantly changing, difficult to treat, and require the host's immune system to clear the infection and while vaccines and anti-viral drugs help lower the mortality rate but are not always available and/or have harmful side effects -Scientists are studying epigenetics to better understand the mechanism of these viruses, and develop treatments -COVID-19 is an RNA type virus, which show strong associations with RNA modifications, including adenosine methylation (m6A, m6Am, 2'-O-me) playing an important role in the viral life cycle -Viruses in this family of coronaviruses and influenza are not able to change the genetic sequence, but can alter the epigenome, allowing the virus to defeat a host's immune response and successfully spread infection -Coronaviruses are common in humans and animals, usually cause mild to moderate upper-respiratory infections, but have been linked to severe illnesses -The CDC says it is rare for animal coronaviruses to infect people and then spread from person to person, but this has now happened with SARS-CoV, MERS-CoVand COVID-19, as well as the Avian Flu (H5N1) and Swine flu (H1N1) -1n 2018 study in PNAS, found an epigenetic mechanism responsible for "switching off" virus fighting systems in the host in both MERS-CoVand H5N1, specifically DNA methylation suppressing antigen presenting molecules -Another study found SARS-CoVand MERS-CoVcan delay or offset pathogen recognition, and interferon-stimulated gene (ISG) expression levels by making unique proteins that prevent immune signaling in the host

Article: When genetic engineering came of age: World's first GMO-GE insulin approved 35 years ago -Genetic Literacy Project (10/30/2017)

-FDA approved human insulin synthesized in genetically engineered bacteria 35 years ago-the world's first recombinant DNA drug product -Starting in 1922, insulin in crude form was obtained from pig and cow pancreases, which differ slightly in composition from human insulin, but lifted the death sentence previously imposed on diabetics -In 1970's supply of animal pancreases declined, as insulin-requiring diabetes grew, fear of shortages -At same time the new, powerful tool of recombinant DNA technology, or "genetic engineering" became available, offered promise of unlimited amounts of insulin, identical to humans -Eli Lilly and Company starting using recombinant DNA technology to produce extremely pure synthetic human insulin, and clinical trials started in 1980, the product performed superbly -Market approved in 1982, in only five months vs normal 30.5 months, and it was brand new technology, major step forward in the "scientific and commercial viability" of recombinant DNA technology

Article: Licking Rat Babes -Fact of the Day (09/22/2017)

-Mother rat's who lick their young more result in those offspring being more nurturing -High-licking mothers offspring tend to me more calm, less aggressive and less strange sexual behaviors, while low-licking mothers are more aggressive and exhibit strange sexual behaviors -Switched babies from high-licking to low-licking and found those offspring licked their offspring less, so not passed in genes, passed epigenetically; while low-licking babies switched to high-licking mother and they had offspring that were more nurturing -More licking, more love, more proteins in brain, less stressed animals -Link between maternal behavior and stress

Article: Scientists Can Design 'Better' Babies. Should They? -New York Times (06/10/2018)

-News about genetically edited embryos ignites alarm, worried about designer babies -Similar fears were ignited when the first IVF (test tube babies) was performed, a slippery slope -Researchers had to be careful, but first IVF baby came to term and was healthy -Then was considered a miracle baby, and a revolution in science, a Nobel Prize winning event, now millions of couples around the world have used IVF to have babies -Pre-implantation genetic diagnosis can now be done prior to IVF -PGD can be used to select the sex, which is illegal in many countries, and cost more than $10,000, also using to choose babies with blue eyes, up to 30 shades of blue eyes -What is the social impact of these technologies? -Embryo editing, medical breakthrough or a dangerous road? -Using CRISPR also ignited concerns, MWD, US Congress banned edited embryos -Traits that people want to change are not well enough understood....YET -Would change not only their traits but all of their descendants -Must be sure we have breaks, and stopping points, can't have the Wild West, but also not paralyzed by fear

Article: CRISPR Treatment inserted Directly into the Body for the First Time -Nature (03/05/2020)

-Person with genetic condition that causes blindness was the first to receive a CRISPR-Cas9 gene therapy administered directly into their body -Used to remove the mutations that cause the rare genetic condition Leber Congenital Amaurosis 10 (LCA10) -There is currently no treatment, and it is the leading cause of blindness in children -The components of CRISPR-Cas9 were encoded into the genome of a virus and injected directly into the eye, near photoreceptor cells -Previous CRISPR-Cas9 has been done in humans but the cells were removed from the body, corrected and then infused back into the body -The name of the clinical trial is called BRILLIANCE -Gene editing is used to delete a mutation in the gene CEP290 that is responsible for LCA10 -Have touse gene editing because the gene is too large to fit into a virus for gene therapy applications -Mutations in CEP290 disable light-sensing cells called photoreceptors in the retina, but the cells are still present and alive in people with LCA10, so it is hopeful that this will reactivate those cells

Article: Paternal Exercise Epigenetically Enhances Expression and Inheritance of a Key Gene Involved in Learning and Memory -What is Epigenetics? (02/19/2019)

-Physical exercise can reprogram the epigenome, by regulating gene expression in the hippocampus, important for learning and memory -Exercising before exposure to a sub-threshold learning event can transform that event into a long-term memory by altering expression of bdnf(brain-derived neurotrophic factor), by two mechanisms-DNA methylation and histone acetylation -Exercise increases histone acetylation and bdnf expression and primes brain for learning and memory -Toxins, psychological stress and high-fat diets are environmental insults that perturb the epigenetic landscape can lead to inheritance of disease in subsequent generations-up to the 4th generation -Maternal and paternal exercise training can restore aberrant inheritance of disease linked to diet-induced obesity in subsequent generation -8-week pre-mating diet and exercise intervention restored healthy phenotypes of offspring

Article: Can a roommate's genes influence your health? -Live Science (01/25/2017)

-Quantified social genetic effects (SGE) in laboratory mice -Over 40 traits in the mice were believed to be influenced by their neighbors including rate of growth, lung function, blood biochemistry -Genetic variation in cage mates can explain up to 29% of variation in anxiety, wound healing, immune function and body weight -SGE are important components of health and disease, and we need to stop looking at individual's in isolation, and look at social partners when looking at health issues -An example in humans, morning person living with a night owl, morning person might get sick more because lack of sleep from staying up late with roommate

Article: RNA-Seq shows thrombotic complications in Covid-19 patients linked to platelet hyper-reactivity -clinical omics (07/01/2020)

-SARS-CoV-2 infection induces functional changes in platelets that make them more likely to aggregate and cause blood clots according to a recent study at U of Utah, some of these changes could explain some of disease's most dangerous complications, heart attacks/strokes -Findings suggest inflammatory proteins produced during COVID-19 infection make platelets hyperreactive and more likely to form blood clots -Researchers studied 41 COVID-19 patients hospitalized, 17 in ICU, including 9 on ventilators, and compared to blood samples from age and sex matched healthy individuals -Using differential gene expression analysis, they found altered platelet gene expression and functional responses in patients infected with SARS-CoV-2 -RNA sequencing demonstrated distinctive changes in gene expression profiles of circulating platelets of COVID-19 patients -Pathway analysis showed differential gene expression changes in pathways involved in protein ubiquitination, antigen presentation and mitochondrial dysfunction -Platelets of patients with COVID-19 also aggregated more readily, altering how they interact with the immune system, likely contributing to inflammation -The SARS-CoV-2 binding receptor, ACE2, was not detected in platelets of infected patients, suggesting platelets may take up the virus independently of ACE2 -The study's lead author says that inflammation due to the infection could be genetically altering megakaryocytes, the cells that produce platelets, making them hyperactive

Article: COVID-19: Could gut bacteria be involved? -Medical News Today (06/26/2020)

-Scientists have implicated gut bacteria in a number of conditions from Type 2 diabetes to depression, and a recent paper outlined previous research that demonstrates a link between lung health and gut bacteria -Some pieces of evidence that support a link between the gut and COVID-19 have been provided -GI symptoms are a common feature of COVID-19, with one study showing more than half of patients having digestive symptoms -Another link involves ACE-2 receptors, which are SARS-CoV-2's entry point into the cells, which are expressed only in a few anatomical locations including the lungs and GI tract, as well as detecting SARS-CoV-2 in the stool of people with COVID-19 -New paper in Virus Research outlines how microbiome might influence the risk of developing or severity of COVID-19 including: the gut-lung axis, which is cross-talk that occurs between gut microbiota and the lungs; gut bacteria and the immune system, with the composition of balanced gut microbiota being known to have a major influence on the effectiveness of lung immunity; the role of nutrition, with diet playing a major role in shaping composition of GI bacteria -A recent study analyzed stool samples from 15 individuals with COVID-19 2 to 3 times/week and compared to healthy individuals, and 6 people with pneumonia and no COVID-19, and found at all time points patients with COVID-19 had significant alterations in fecal microbiomes compared with controls -Currently, no firm evidence to suggest that SARS-CoV-2 interacts with gut bacteria in a meaningful way, or that the microbiome influences the severity of COVID-19, but based on evidence so far seems a credible theory that requires further research

Article: Your Questions about Italy's GMO Mosquito Experiment Answered -NPR (03/01/2019)

-Scientists released genetically engineered mosquitoes in a high-security lab in Italy, designed to spread a genetic mutation, using CRISPR -Engineered mosquitoes carry a genetic mutation that is lethal to its species, and could be a potent weapon in the war against malaria, but still concerns of unintended consequences -Transforms the mosquitoes (1/2 male and ½ female) mouth is male so they can not bite, and reproductive organs are mutated and can not produce eggs -Would release in Africa to breed with the wild-type mosquitoes to wipe them out, to hopefully eradicate the disease -Funded by Bill and Melinda Gates Foundation, want to use to wipe out other diseases, but others fear that they could wreak havoc if released into the wild -Food chain worries-100's of mosquito species so only getting rid of one should be fine -If altered to not lay eggs, how will the mutation spread?-only become infertile when they inherit two copies of the mutation, they will mate with wild-type mosquitoes, eventually crashing the population-within 7-11 generations -Vaccine more money worthy?-have been trying without success-malaria still kills 429,000 people yearly -Many arguments against?-ecosystems are too complex to predict what might happen in the wild, safer options -How are we informing?-Target Malaria outreach program to educate native Africans -Pass the gene drive to other species?-no gene flow between non-malaria mosquitoes so not likely

Article: Serotonin can regulate gene expression inside neurons -Science Daily (03/13/2019)

-Serontonin, a neurotransmitter known for passing signals between neurons in the brain, can also regulate gene expression in an unexpected way -Thought that neurotransmitters act solely through the activation of membrane receptors in the brain the regulate brain cell activity -DNA is wrapped around histone proteins, when wound tight no transcription, when the gene is not wound as tightly the gene is more likely to be expressed -Found that a protein called tissue transglutaminase 2 can directly attach serotonin molecules to histone proteins, which loosens the spool to allow robust gene expression -Does this dual role of serotonin play a role in the regulation of mood? -Could this knowledge be used to develop better medications for depression and other mood disorders? -Does dopamine also have a similar dual role in the brain? -Exciting new area of research on gene regulation and the complexity of it

Article: What is Genetically Modified Food? -Scientific American (08/07/2013)

-Strange genetically modified organisms like glow-in-the-dark pigs, featherless chickens, goats that produce spider silk -Genetically modified foods are scary to people -Started 10,000 years ago with domestication of animals, and artificial selection of traits in plants and animals -Modern genetic modification makes cisgenic, or transgenic organisms, by transferring DNA -Modern examples include corn that makes insect toxins, tomatoes with antifreeze proteins from fish, cows that make human milk -Current GMO foods have been tested and deemed safe, but newer GMO's not tested

Article: Civil War Battlefield Natural Therapies Found to be Effective against Modern-Day Multidrug-Resistant Bacteria -Genetic Engineering & Biotechnology News (05/22/2019)

-Studies by scientists at Emory University suggest that traditional plant-based remedies used during the Civil War to treat soldiers' wounds could represent a source of modern-day antibiotics for some of the most dangerous multidrug-resistant bacteria -Conventional medicine was scarce during the 1861-1865 war, and the Confederate Surgeon General commissioned a guide on medicinal plants that were native to the southern US, which were used by Native Americans -Tested extracts from three of the plants in the guide and confirmed their antiseptic properties and showed they prevent growth of one or more multi-drug resistant bacteria -Antiseptic was defined as a tonic useful in preventing external or internal modification, onions were used to treat powder burns, now scientists know that onions and garlic contain antimicrobial agents that impact two features of bacterial pathogenicity, quorum sensing and biofilm formation -Biofilms comprise communities of bacteria and polysacchariesthat physically protect microorganisms from antibiotics, quorum sensing is a form of bacterial cell-cell communication through which organisms can secrete chemical signals and toxins, or become pathogenic, which is triggered in response to population density, both of which have therapeutic value in the absence of new antibiotics -More Civil War soldiers died from disease than in battle, and amputation was common to treat infected wounds

Article: First Successful Gene Drive in Mammals -The Scientist (01/23/2019)

-Study published in Nature used CRISPR-Cas9 to alter the female mouse germline and drive the expression of white fur and a red fluorescent protein -Normal mouse breeding takes a long time, so wanted to use CRISPR to make desired modifications -Targeted the tyrosinasegene, which affects coat color, and added the RFP protein, and introduced the transgene into the population that would activate cas9 at different times and in different places during sperm, egg and embryo development -Breeding animals that produced white animals that glowed red indicated they had cut Tyrosinaseand repaired it with the copy of their engineered gene -Best result, which was 72% was when Cas9 was activated during egg development, while activation during early embryogenesis or sperm development led to insertions and deletions at Cas9 target sites -Want to use this for pest control, and use less animals to make transgenic animals, but won't work if can't make it work in males

Article: After a century, insulin is still expensive-could DIYers change that? -The Conversation (09/13/2018)

-The patent for insulin cost $1 in 1921, and now people pay $400/month for insulin, driving some uninsured patients to desperate and dangerous measures -DIYer's are working to solve the insulin affordability problem, by figuring out how to do it patent-free -It's not patents, its regulations making it expensive -Discovering and developing drugs is expensive, patents help companies recoup the cost for a limited time, once the patent expires off-brand versions and competition can drive costs down -Today, insulin is made from genetic engineering, also made to be faster acting, or longer lasting, new pumps, pens, and devices each with their own patent -Insulin is a biologic drug, produced by living organisms, by biomanufacturing, which is more inconsistent than chemical synthesis -If a new company wants to make insulin they have to they have to do expensive clinical trials with it, which can cost up to $250 million -One company making a "generic" insulin and for 15% cheaper, compared to normal 80% cheaper for generic -Patients try to ration or use crowd-funding, and now DIYersmight make their own insulation which would not have to be patented

Article: Antibiotic resistance: the hidden threat lurking behind Covid-19 -STAT (03/23/2020)

-There is a larger threat lurking behind the current coronavirus outbreak, antibiotic resistance (AR), which currently kills hundreds of thousands of people each year and will further complicate care for patients with COVID-19 -The pipeline of drugs to fight antibiotic resistance is nearly dry -2.8 million deaths each year, and 35,000 deaths/year caused by AR, and these bacteria live in hospitals and medical facilities, putting all patients at risk -Patients at greatest risk for AR infection are those already vulnerable to illness from viral lung infections like influenza,SARS and Covid-19 -In 2009 H1N1 influenza pandemic between 29-55% of deaths were due to secondary bacterial infections, virus weakens then hard-to-treat bacteria take hold -New coronavirus data shows 1 in 7 patients hospitalized with Covid-19 has acquired a dangerous secondary bacterial infection, 50% of patients who have died had these secondary infections -AR could become an enormous force of additional sickness and death across the healthcare system -17 years ago the arsenal of antibiotics to treat AR-infections was not sufficient to manage a large outbreak of drug-resistant bacteria, since then AR bacteria have become more widespread, more deadly, far more difficult to treat, and antibiotics to manage them have barely increased -Why don't we have more antibiotics? Developing new antibiotics can cost more than $1 billion, and cost can't be recovered by widespread use or they will lose their effectiveness -Hospital reimbursement systems generally discourage use of new antibiotics, even when patients need them, because they are too expensive -Developing an Innovative Strategy for Antimicrobial Resistant Microorganisms (DISARM) Act is a bipartisan bill that would reform Medicare reimbursement to make it easier for hospitals to use the appropriate antibiotic for the patient, despite cost

Article: Can a 'Poop Transplant' Change Your Weight? -Live Science (05/2017)

-Transplanting the feces of one mouse to another mouse changed the recipient mouse so they either gained or lost weight -Could Fecal microbiotiatransplantations (FMTs) or transpoosions have the same affect on humans? -Two studies performed to look at this possibility both used patients who had been infected with Clostridium difficile (C. diff) and received fecal transplants from healthy donors to prevent severe diarrhea -One study on humans showed the fecal transplants from healthy BMI donors could lead to weight loss that was maintained a year after the procedure -Another study with 70 patients who received FMT's to treat C diff found no effect from various BMI donors did not show statistically significant changes in patients' BMIs -It is still unclear what the results of having a fecal transplant from an obese donor vs a healthy weight donor has on the gut microbiome

Article: Immigrating to the U.S.? Get ready for a New Gut Microbiome (and maybe more pounds) -NPR (11/01/2018)

-When people immigrate to the US they begin to loose their native microbiome according to study that tracked digestive health of refugees coming to Minnesota from Southeast Asia -Some of the strains they lose are ones that help break down and get nutrients from fibers found in Southeast Asian staples -This loss of microbiome diversity is associated with more obesity (though it has not yet been shown to be the cause) -In a group of 19 refugees from Thailand a Western bacterial strain Bacteroides began to displace non-Western strain Prevotellawithin 6-9 months in the US -Tracking food logs researchers found an Americanized diet plays a role in disrupting immigrants' microbiomes, but don't explain most of the changes, possible other factors such as exposure to antibiotics, or changes to quality of drinking water, also affecting microbiome -Many immigrants worried about increased obesity despite little change to their diet -More research is needed to determine how moving from developing countries to westernized countries affects the microbiome and what the consequences are for health both in the short and long term

Protospacer adjacent motif (PAM)

2-6 base pair DNA sequence immediately following the DNA sequence targeted by the Cas9 nuclease in the CRISPR bacterial adaptive immune system. Cas9 will not successfully bind to or cleave the target DNA sequence if it is not followed by the PAM sequence

Genetically modified organism (GMO)

A popular term for a transgenic organism, usually referring to an agricultural plant or animal, in which genetic material is transferred from one organism to another

NAS

National Academy of Sciences

DNA cloning

The production of exact copies (clones) of a particular gene of DNA sequence using genetic engineering techniques. The DNA containing the target gene(s) is split into fragments using restriction enzymes

TALENs

Transcription Activator-Like Effector Nucleases are a class of engineered nuclease that can be used for gene editing

Conjugation

Type of horizontal gene transfer where bacteria connect to one another by a pilus and exchange genetic material, also known as "bacteria sex"

prime editing

a 'search-and-replace' genome editing technology that directly writes the genetic information into a targeted DNA site. It uses a fusion protein that contains a catalytically impaired Cas9 endonuclease fused to an engineered reverse transcriptase enzyme, and a prime editing guide RNA (pegRNA), capable of identifying the target site and providing the new genetic information to replace the target DNA nucleotides

Zinc-finger nucleases (ZFNs)

a class of engineered DNA-binding proteins that facilitate targeted editing of the genome by creating double-strand breaks in DNA at user-specified locations

antibiotic

a compound (natural or synthetic) that either kills bacteria or inhibits their growth

CRISPR (clustered regularly interspaced short palindromic repeats)

a family of DNA sequences in bacteria that contains snippets of DNA from viruses that have attacked the bacterium. These snippets are used by the bacterium to detect and destroy DNA from further attacks by similar viruses. These sequences play a key role in a bacterial defense system, and form the basis of a genome editing technology known as CRISPR/Cas9 that allows permanent modification of genes within organisms

Clinical medicine

a field on medicine that deals primarily with the practice and study of medicine based on the direct examination of the patient

Designer babies

a human embryo that has been genetically modified, usually following guidelines set by the parent or scientist, to produce desirable traits

Polylinker (multiple cloning site)

a multiple cloning site (MCS), also called a polylinker, is a short segment of DNA which contains many (up to ~20) restriction sites - a standard feature of engineered plasmids. Restriction sites within an MCS are typically unique, occurring only once within a given plasmid

Non-homologous end joining

a pathway that repairs double-strand breaks in DNA. NHEJ is referred to as "non-homologous" bc the break ends are directly ligated without the need for a homologous template, in contrast to homology directed repair, which requires a homologous sequence to guide repair

X chromosome inactivation

a process by which one of the copies of the X chromosome present in female mammals is inactivated. The inactive structure called heterochromatin

Transcription factors

a protein that controls the rate of transcription of genetic information from DNA to messenger RNA, by binding to a specific DNA sequence. The function of TFs is to regulate- turn on and off- genes in order to make sure that they are expressed in the right cell at the right time and in the right amount throughout the life of the cell and the organism

cloning vector (plasmid)

a small piece of DNA, taken from a virus, a plasmid, or the cell of higher organism, that can be stably maintained in an organism, and into which a foreign DNA fragment can be inserted for cloning purposes

Gene editing/Genome engineering

a type of genetic engineering in which DNA is inserted, deleted or replaced in the genome of a living organism using engineered nucleases, or "molecular scissors"

Homologous recombination

a type of genetic recombination in which nucleotide sequences are exchanged between two similar or identical molecules of DNA. It is most widely used by cells to accurately repair harmful breaks that occur on both strands of DNA, known as double-strand breaks

binary fission

a type of vertical gene transfer where a bacteria replicates its DNA and then divides into two cells each with its own copy of the original DNA

antibiotic resistance

ability to survive and reproduce in the presence of an antibiotic

alternative splicing

alternative splicing, or differential splicing, is a regulated process during gene expression that results in a single gene coding for multiple proteins. In this process, particular exons of a gene may be included within or excluded from the final, processed mRNA produced from that gene

Xist (X-inactive specific transcript)

an RNA gene on the X chromosome of the placental mammals that acts as a major effector of the X inactivation process

Cas9

an RNA-guided DNA endonuclease enzyme associated with the CRISPR adaptive immunity system to memorize and later interrogate and cleave foreign DNA, such as invading bacteriophage DNA or plasmid DNA

sticky ends

an end of a DNA double helix at which a few unpaired nucleotides of one strand extend beyond the other, created by using restriction enzymes during gene cloning

blunt ends

an end of a DNA helix at which nucleotides do not extend beyond the other, created by using restriction enzymes during gene cloning

restriction enzymes (endonucleases)

an enzyme produced chiefly by certain bacteria, having the property of cleaving DNA molecules at or near a specific sequence of bases

Nucleases

an enzyme that cleaves the chains of nucleotides in nucleic acids into smaller units

genomic imprinting

an epigenetic phenomenon that causes genes to be expressed in a parent-of-origin-specific manner. Forms of genomic imprinting have been demonstrated in fungi, plants and animals. As of 2014, there are about 150 imprinted genes known in the mouse and about half that in humans

Epiallele

any of a group of otherwise identical genes that differ in the extent of methylation, or a specific DNA methylation pattern of a genetic locus

promoter-proximal elements

any regulatory sequence in eukaryotic DNA that is located close to (within 200 base pairs) a promoter and binds a specific protein thereby modulating transcription of the associated protein coding gene

Translation research

applies findings from basic science to enhance human health and well-being

base editing

base editing is a new genome editing approach that uses the components from CRISPR systems with other enzymes to directly install point mutations into cellular DNA or RNA without making double-stranded DNA breaks (DSBs)

nucleosome

basic unit of DNA packaging in eukaryotes, consisting of a segment of DNA would in sequence around eight histone protein cores

epigenome

chemical modifications at the level of the genome

microbiome

collection of bacteria and fungi that live on and in another organism

DNA repair

collection of processes by which a cell identifies and corrects damage to the DNA molecules that encode its genome

chromatin

complex of nucleic acids (DNA or RNA) and proteins, which condenses to form a chromosome during cell division

chromatin (epigenetics)

complex of nucleic acids and proteins, which condenses to form a chromosome during cell division

epimutations

defined as abnormal transcriptional repression of active genes and/or abnormal activation of usually repressed genes caused by errors in epigenetic gene repression

dNTPs

deoxynucleotide triphosphates (adenine, guanine, cytosine, and thymine) bases that are added to gene cloning reactions

chromatin remodeling

dynamic modification of chromatin architecture to allow access of condensed genomic DNA to the regulatory machinery proteins, and thereby control gene expression

operon

functioning unit of DNA containing a cluster of genes under the control of a single promoter. The genes are transcribed together into an mRNA strand and either translated together in the cytoplasm, or undergo splicing to create monocistronic mRNAs that are translated separately, ie several strands of mRNA that each encode a single gene product. The result of this is that the genes contained in the operon are either expressed together or not at all

selectable marker

gene introduced into a cell, especially a bacterium or to cells in culture, that confers a trait suitable for artificial selection. They are a type of reporter gene used in laboratory microbiology, molecular biology, and genetic engineering to indicate the success of a transfection or other procedure meant to introduce foreign DNA into a cell. Selectable markers are often antibiotic resistance genes (an antibiotic resistance marker is a gene that produces a protein that provides cells expressing this protein with resistance to an antibiotic) Bacteria that have been subjected to a procedure to introduce foreign DNA are grown on a medium containing an antibiotic, and those bacterial colonies that can grow have successfully taken up and expressed the introduced genetic material

reporter gene

gene that researchers attach to a regulatory sequence of another gene of interest in bacteria, cell culture, animals or plants. Certain genes are chosen as reporters bc the characteristics they confer on organisms expressing them are easily identified and measured, or bc they are selectable markers. Reporter genes are often used as an indication of whether a certain gene has been taken up by or expressed in the cell or organism population

histone proteins

highly alkaline proteins found in eukaryotic cell nuclei that package and order the DNA into structural units called nucleosomes. They are the chief protein components of chromatin, acting as spools around which DNA winds, and playing a role in gene regulation. Without histones, the unwound DNA in chromosomes would be very long (a length to width ratio of more than 10 million to 1 in human DNA). For example, each human diploid cell (containing 23 pairs of chromosomes) has about 1.8 meters of DNA; wound on the histones, the diploid cell has about 90 micrometers of chromatin. When the diploid cells are duplicated and condensed during mitosis, the result is about 120 micrometers of chromosomes

Histone code

hypothesis that the transcription of genetic information encoded in DNA is in part regulated by chemical modifications to histone proteins, primarily on their unstructured ends. Together with similar modifications such as DNA methylation it is part of the epigenetic code

trans-acting DNA sequences

in the context of transcription regulation, a trans-acting element is usually a DNA sequence that contains a gene. This gene codes for a protein (or microRNA or other diffusible molecule) that will be used in the regulation of another target gene. The trans-acting gene may be on a different chromosome as the target gene, but the activity is via the intermediary protein or RNA that it encodes

DNA-binding domain

independently folded protein domain that contains at least one structural motif that recognizes double- or single-stranded DNA. A DBD can recognize a specific DNA sequence (a recognition sequence) or have a general affinity to DNA

euchromatin

lightly packed form of chromatin (DNA, RNA, and protein) that is enriched in genes, and is often (but not always) under active transcription. Euchromatin comprises the most active portion of the genome within the cell nucleus. 92% of the human genome is euchromatin

multigenic RNA

more than one gene encoded on a single RNA molecule

regulatory elements

nucleotide sequences of a gene that are involved in regulation of genetic transcription

Basic science research

often called fundamental or bench research - provides the foundation of knowledge for the applied science that follows

allosteric site

place on an enzyme where a molecule that is not a substrate may bind, thus changing the shape of the enzyme and influencing its ability to be active

cellular differentiation

process by which a cell becomes specialized in order to perform a specific function, as in the case of a liver cell, a blood cell, or a neuron. There are more than 250 general types of cells in the human body

Gene expression

process by which information from a gene is used in the synthesis of a functional gene product

methylation

process by which methyl groups are added to certain nucleotides in genomic DNA. This affects gene expression, as methylated DNA is not easily transcribed. The degree of methylation is passed on to daughter strands at mitosis by maintenance DNA methylases

acetylation

process where an acetyl functional group is transferred from one molecule to another. These reactions are typically catalysed by enzymes with "histone acetyltransfase" (HAT) or "histone deacetylase" (HDAC) activity

repressor

protein in which its binding to the operator inhibits the transcription of one or more genes

post-translational modifications

refers to the covalent and generally enzymatic modification of proteins following protein biosynthesis. Proteins are synthesized by ribosomes translating mRNA into polypeptide chains, which may undergo PTM to form the mature protein product

cis-acting DNA sequences

regions of non-coding DNA which regulate the transcription of neighboring genes. Cis-acting DNA sequences are found in the vicinity of the genes that they regulate, and typically regulate gene transcription by binding to transcription factors

Negative regulation

repressor protein binds to an operator to prevent a gene from being expressed. The absence of the repressor is required for transcription to occur

Operator

segment of DNA where the repressor binds to, thereby preventing the transcription of certain genes

Enhancers

short (50-1500bp) region of DNA that can be bound by proteins (activators) to increase the likelihood that transcription of a particular gene will occur. These proteins are usually referred to as transcription factors

primers

short, artificial DNA strands of about 18 to 25 nucleotides that match the beginning and end of the DNA fragment to be amplified. The primers anneal to the simple-stranded DNA template at these points. Once the primers bind, the DNA-Polymerase binds and begins the synthesis of the new DNA strand

plasmid

small circular piece of DNA

epigenetics

study of changes in organisms caused by modification of gene expression rather than alteration of the genetic code itself

PCR (polymerase chain reaction)

technique in molecular genetics that permits the analysis of any short sequence of DNA (or RNA) even in samples containing only minute quantities of DNA or RNA . PCR is used to reproduce (amplify) selected sections of DNA or RNA for analysis

transformation

the genetic alteration of a cell resulting from the direct uptake and incorporation of exogenous genetic material from its surroundings through the cell membrane(s)

recombinant DNA technology (biotechnology)

the joining together of DNA molecules from two different species to produce new genetic combinations that are of value to science, medicine, agriculture, and industry

Gene drives

the phenomenon in which the inheritance of a particular gene or set of genes is favorably biased. Gene drive can arise through a variety of mechanisms and results in its prevalence increasing in a population

transduction

the process by which foreign DNA is introduced into a cell by a virus or viral vector. An example is the viral transfer of DNA from one bacterium to another

transgenerational epigenetic inheritance

the transmission of informaiton from one generation of an organism to the next that affects the traits of offspring without alteration of the primary structure of DNA- in other words epigenetically

Taq polymerase

thermostable DNA polymerase named after the termophilic bacterium Thermus aquaticus from which it was originally isolated. It is frequently used in the polymerase chain reaction (PCR), a method for greatly amplifying the quantity of short segments of DNA

heterochromatin

tightly packed form of DNA or condensed DNA, which comes in multiple varieties. These varieties lie on a continuum between the two extremes of constitutive heterochromatin and facultative heterochromatin. Both play a role in the expression of genes. Because it is tightly packed, it was thought to be inaccessible to polymerases and therefore not transcribed

positive regualtion

transcription factor is required to bind at the promoter in order to enable RNA polymerase to initiate transcription

activator

transcriptional activator is a protein (transcription factor) that increases gene transcription of a gene or set of genes. Most activators are DNA-binding proteins that bind to enhancers or promoter-proximal elements

Horizontal Gene transfer

transmission of genetic material between unrelated bacteria

Vertical Gene Transfer

transmission of genetic material from parent bacteria to offspring bacteria

transduction (bacterial genetics-antibiotic resistance)

type of horizontal gene transfer that uses a virus to move the genetic material from one cell to another cell

transformation (bacterial genetics-antibiotic resistance)

type of horizontal gene transfer where a bacteria takes up DNA from its environment

In situ hybridization

type of hybridization that uses a labeled complementary DNA, RNA or modified nucleic acids strand to localize a specific DNA or RNA sequence in a portion or section of tissue, or, if the tissue is small enough, in the entire tissue, in cells, and in circulating tumor cells

adaptive immunity (acquired immunity)

uses specific antigens to strategically mount an immune response. Unlike the innate immune system, which attacks only based on the identification of general threats, the adaptive immunity is activated by exposure to pathogens, and uses an immunological memory to learn about the threat and enhance the immune response accordingly. The adaptive immune response is much slower to respond to threats and infections than the innate immune response, which is primed and ready to fight at all times

phenotypic variation

variability in phenotypes that exists in a population