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Home , Michael Rosbash, Tasuku Honjo

Zebrafish heart WELCOME

BISC 336-

Left: Franklind, R. X-diffraction, Right: Crick, F. Watson, J. Original DNA model Genetic engineering is being used…. Genetic engineering is being used…. A. To design babies

B. To cure disease

C. Make food

D. Get rid of Mosquitos

E. On my roommate Genetic engineering should be used…. A. To fix cosmetic traits

B. Only on somatic cells

C. On Food

D. On Mosquitos

E. On my roommate I’m excited about having my genome sequenced because…

A. To see if I possess the smart gene

B. So I can get a cool looking poster

C. See where my ancestors come from

D. See what diseases I might get

E. See what medicine I should take for my back • Introductions • What is genetics • Mendel’s Postulates and the Mono-hybrid cross • Course logistics • Meiosis Learning outcomes: – Appreciate the integral nature of genetics in underpinning daily biological and medical practice – Describe how chromosomes segregate during Meiosis, Explain why this is important to genetics? – Explain genetics as an independent field of study and methodology – Explain what Mendel’s postulates reveal about the nature of inheritance and gene – Explain what Mendel did differently Why is genetics important? What is the genetic basis of disease? Why is genetics important?

What is the value of genetic testing? Why is genetics important?

What can genetic counselors predict? Why is genetics important? What can genetic counselors predict? Why is genetics important? How can DNA bring justice? Why is genetics important?

Can genetic testing resolve other types of disputes? Why is genetics important?

What am I eating? Why is genetics important? Are mutations good or evil? Who am I?

Name: Joshua Bloomekatz, Ph.D.

Assistant Professor and Geneticist here at the University of Mississippi in the Biology department - How does the heart form? - What is the basis for congenital and adult heart disease? - How does the heart form? - What is the basis for congenital and adult heart disease?

Zebrafish embryo

Human heart - How does the heart form? - What is the basis for congenital and adult heart disease?

Advantages of the zebrafish embryo: • Controlled crosses • Large number of embryos from a single cross • Cheap • Ability to make specific mutations • External fertilization and growth • Translucent: good for visualizing processes in real-time, live

Zebrafish embryo - How does the heart form? - What is the basis for congenital and adult heart disease?

Zebrafish embryo Auman et al. 2007 Who are you? • Introduce yourself to your neighbor (and possible study partner)

• Tell your neighbor -

• What about genetics is important for you

• What previous experience have you had with genetics?

• What is a gene? (not jeans)

• I did well in a previous class, because I did ______.

Who are you?

Survey- • If you haven’t had a chance to answer this, please do so, it will help me tailor the class to your needs. • Introductions • What is genetics • Mendel’s Postulates and the Mono-hybrid cross • Course logistics • Meiosis What is genetics:

Technical Definition: Study of inheritance • How are traits inherited? • Why do we look like our parents?

• Study of genes and their functions • Why do certain mutations cause certain diseases? • How does mutation underlie evolution? • How do genes function together to perform molecular, cellular, tissue and organismal functions?

Methodology: A way of thinking and investigating • The use of genetics (mutations) to study biological processes. What is genetics: Study of inheritance and methodology

What are the kind of questions do Geneticist ask?

• How are traits inherited? • Why do you look like your parents? • Family health is a large determinate of individual health • Why is it you’re more likely to have heart disease or cancer if your mother or father has it?

• Methodology? • Example: Breakthrough prizes • Example: anti-cholesterol drugs-PCSK9 • Zebrafish heart development • Frank Bennett and Adrian Krainer - • Using antisense oligonucleotide therapy to treat children with SMA (Spinal Muscular Atrophy)

• Angelika Amon- • What is the consequence of aneuploidy in Cancer

• Xiawei Zhaung - Superresolution microscopy • BISC 579 - Illuminating the invisible

• James Chen - Biochemist, how is exogenous DNA sensed and destroyed by the immune system

$3 million dollars each The : 2018

•: and / Forward genetic techniques/“speed up evolution” to optimize enzymes

•Nobel Prize in Medicine: James Allison and : Treat Cancer by inhibiting CTLA-4 an Only 1 million dollars integral part of the immune system. (James Allison used mutations to see the function of CTLA-4) Nobel Prize in medicine Won by geneticists throughout time 1933: 1935: 1946: Hermann Muller 1958: George Beadler, , 1959: , 1962: , , Frederick Wilkins 1965: Francois Jacob, Andre Lwoff, 1966: Cancer - treatments 1968: Robert Holley, Har Khorana, Marshal Nirenberg 1969: Max Delbruck, , 1975: , , Howard Temin 1978: , Daniel Natans, Hamilton Smith 1980: , George Snell 1983: Barbara McClintock 1986: Stanley Cohen, Rita Levi-Montalcini 1987: 1989: Michael Bishop, Harold Varmus Nobel Prize in medicine Won by geneticists throughout time (contd) 1993: Richard Roberts, Phillip Sharp 1995: Christiane Nusslein-Volhard, Eric Wischaus 1996: Stanley Prusiner 2001: , 2002: , Robert Horvitz, 2006: , 2007: , , 2009: , Carol Greider, Jack Szostak 2012: , 2013: , , Thomas Sudhof 2016: Yoshinoriz Ohsumi 2017: Jeffry Hall, , Michael Young 2018: James Allison, Tasuku Honjo

30/108 - 28% • Methodology-Example-PCSK9 • Why does atherosclerosis occur? Why do some people have higher risk of atherosclerosis than others?

NHLBI Individuals with PCSK9 mutations have very high LDL levels

Abifadel et al. 2003 Involved Jackson, MS Heart Study Individuals with PCSK9 mutations have very low LDL levels and low incidence Of coronary heart disease

The new england journal of medicine

original article

Sequence Variations in PCSK9, Low LDL, and Protection against Coronary Heart Disease

Jonathan C. Cohen, Ph.D., Eric Boerwinkle, Ph.D., Thomas H. Mosley, Jr., Ph.D., and Helen H. Hobbs, M.D.

ABSTRACT

Background From the Donald W. Reynolds Cardio- A low plasma level of low-density lipoprotein (LDL) cholesterol is associated with vascular Clinical Research Center (J.C.C., reduced risk of coronary heart disease (CHD), but the effect of lifelong reductions H.H.H.), the Center for Human Nutrition (J.C.C.), the Departments of Internal in plasma LDL cholesterol is not known. We examined the effect of DNA-sequence Medicine (J.C.C., H.H.H.) and Molecular variations that reduce plasma levels of LDL cholesterol on the incidence of coronary Genetics (H.H.H.), and the Howard events in a large population. Hughes Medical Institute (H.H.H.), Uni- versity of Texas Southwestern Medical Center, Dallas; the Human Genetics Cen- Methods ter and Institute of Molecular Medicine, We compared the incidence of CHD (myocardial infarction, fatal CHD, or coronary University of Texas Health Science Center, Houston (E.B.); and the Department of revascularization) over a 15-year interval in the Atherosclerosis Risk in Communi- Medicine, University of Mississippi Med- ties study according to the presence or absence of sequence variants in the propro- ical Center, Jackson (T.H.M.). Address tein convertase subtilisin/kexin type 9 serine protease gene (PCSK9) that are associ- reprint requests to Dr. Hobbs at the N Engl J Med 2006;354:1264-72 Howard Hughes Medical Institute, Uni- ated with reduced plasma levels of LDL cholesterol. versity of Texas Southwestern Medical LDL levels Center, 5323 Harry Hines Blvd., Dallas Results TX 75390-9046, or at helen.hobbs@ utsouthwestern.edu. Of the 3363 black subjects examined, 2.6 percent had nonsense mutations in PCSK9; these mutations were associated with a 28 percent reduction in mean LDL choles- N Engl J Med 2006;354:1264-72. terol and an 88 percent reduction in the risk of CHD (P = 0.008 for the reduction; Copyright © 2006 Massachusetts Medical Society. hazard ratio, 0.11; 95 percent confidence interval, 0.02 to 0.81; P = 0.03). Of the 9524 white subjects examined, 3.2 percent had a sequence variation in PCSK9 that was associated with a 15 percent reduction in LDL cholesterol and a 47 percent reduc- tion in the risk of CHD (hazard ratio, 0.50; 95 percent confidence interval, 0.32 to 0.79; P = 0.003).

Conclusions These data indicate that moderate lifelong reduction in the plasma level of LDL cholesterol is associated with a substantial reduction in the incidence of coronary events, even in populations with a high prevalence of non–lipid-related cardiovas- cular risk factors.

1264 n engl j med 354;12 www.nejm.org march 23, 2006

The New England Journal of Medicine Downloaded from nejm.org on January 6, 2018. For personal use only. No other uses without permission. Copyright © 2006 Massachusetts Medical Society. All rights reserved. The new england journal of medicine

original article

Effect of a to PCSK9 on LDL Cholesterol

Evan A. Stein, M.D., Ph.D., Scott Mellis, M.D., Ph.D., George D. Yancopoulos, M.D., Ph.D., Neil Stahl, Ph.D., Douglas Logan, M.D., William B. Smith, M.D., Eleanor Lisbon, M.D., M.P.H., Maria Gutierrez, M.D., Cheryle Webb, M.D., Richard Wu, Ph.D., Yunling Du, Ph.D., Therese Kranz, R.N., M.B.A., Evelyn Gasparino, B.S., and Gary D. Swergold, M.D., Ph.D.

Abstract

Background From the Metabolic and Atherosclerosis Proprotein convertase subtilisin/kexin 9 (PCSK9), one of the serine proteases, binds to Research Center (E.A.S., C.W., T.K.) and low-density lipoprotein (LDL) receptors, leading to their accelerated degradation and the Medpace Clinical Pharmacology Unit (D.L.) — both in Cincinnati; Regeneron to increased LDL cholesterol levels. We report three phase 1 studies of a monoclonal Pharmaceuticals, Tarrytown, NY (S.M., antibody to PCSK9 designated as REGN727/SAR236553 (REGN727). G.D.Y., N.S., R.W., Y.D., E.G., G.D.S.); New Orleans Center for Clinical Research, Methods University of Tennessee Medical Center, In healthy volunteers, we performed two randomized, single ascending-dose studies Knoxville (W.B.S.); Quintiles, Overland Park, KS (E.L.); and Comprehensive Phase of REGN727 administered either intravenously (40 subjects) or subcutaneously One, Miramar, FL (M.G.). Address reprint (32 subjects), as compared with placebo. These studies were followed by a random- requests to Dr. Stein at the Metabolic ized, placebo-controlled, multiple-dose trial in adults with heterozygous familial and Atherosclerosis Research Center, 4685 Forest Ave., Cincinnati, OH 45212, hypercholesterolemia who were receiving atorvastatin (21 subjects) and those with or at [email protected]. nonfamilial hypercholesterolemia who were receiving treatment with atorvastatin (30 subjects) (baseline LDL cholesterol, >100 mg per deciliter [2.6 mmol per liter]) N Engl J Med 2012;366:1108-18. Copyright © 2012 Massachusetts Medical Society. or a modified diet alone (10 subjects) (baseline LDL cholesterol, >130 mg per deciliter [3.4 mmol per liter]). REGN727 doses of 50, 100, or 150 mg were administered subcutaneously on days 1, 29, and 43. The primary outcome for all studies was the occurrence of adverse events. The principal secondary outcome was the effect of REGN727 on the lipid profile. Results Among subjects receiving REGN727, there were no discontinuations because of ad- verse events. REGN727 significantly lowered LDL cholesterol levels in all the studies. In the multiple-dose study, REGN727 doses of 50, 100, and 150 mg reduced mea- sured LDL cholesterol levels in the combined atorvastatin-treated populations to 77.5 mg per deciliter (2.00 mmol per liter), 61.3 mg per deciliter (1.59 mmol per liter), and 53.8 mg per deciliter (1.39 mmol per liter), for a difference in the change from baseline of −39.2, −53.7, and −61.0 percentage points, respectively, as compared with placebo (P<0.001 for all comparisons). Conclusions In three phase 1 trials, a monoclonal antibody to PCSK9 significantly reduced LDL cholesterol levels in healthy volunteers and in subjects with familial or nonfamilial hy- percholesterolemia. (Funded by Regeneron Pharmaceuticals and Sanofi; ClinicalTrials .gov numbers, NCT01026597, NCT01074372, and NCT01161082.) N Engl J Med 2012;366:1108-18

1108 n engl j med 366;12 nejm.org march 22, 2012 The New England Journal of Medicine Downloaded from nejm.org on January 6, 2018. For personal use only. No other uses without permission. Copyright © 2012 Massachusetts Medical Society. All rights reserved. • Methodology- • What is important for the individual chambers to contract?

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Auman et al. 2007 Genetics is a methodology: a way of knowing

• Genetics is its own discipline with its own terminology separate from other strands of biology

• Builds on its own knowledge: From patterns of inheritance genetics identifies principles of biological concepts

• Logical approach to elucidating principles of biology Clickr: Logic problem - What pattern belongs in the box?

?

http://www.indiabix.com/non-verbal-reasoning/pattern- completion/ Clickr: Logic problem - What pattern belongs in the box?

a.

b.

c. ?

d.

Why? What is the rule that the led you to the answer What are your assumptions? http://www.indiabix.com/non-verbal-reasoning/pattern- completion/ Clickr: Logic problems-

What direction is the bus traveling?

A) Left B) Right Clickr: Logic problems-

What direction is the bus traveling?

A) Left B) Right

What information are you missing? Where is that information? What rules are guiding these patterns?

x means to combine •Red x Red = Red •Blue x Blue = Blue •Yellow x Yellow = Yellow •Red x Blue = Red •Blue x Yellow = Blue •Red x Yellow = Red Clickr: Logic problems-

What rules are guiding these patterns?

•Red x Red = Red •Blue x Blue = Blue •Yellow x Yellow = Yellow •Red x Blue = Red •Blue x Yellow = Blue •Red x Yellow = Red

A. Red dominant to Yellow and Blue B. Blue dominant to Yellow C. Only one colored allowed D. Position dominants E. All of the above • Introductions • What is genetics • Mendel’s Postulates and the Mono-hybrid cross • Course logistics • Meiosis Mendel’s Postulates and the Mono-hybrid cross

The Question:

What are the principles/rules of inheritance?

Why do children look like their parents?

The mystery of the hybrid?

1822-1884 Lots of theories: Why do children look like their parents?

-Preformation: the homunculus

-The “blood” theory (Aristotle)

-The “jigsaw” theory

-The “blending” theory Lots of theories: Why do children look like their parents?

Leeuwenhoek’s drawing of sperm:

Victor Hartmann -- the drawing that inspired Mussorgsky to write the “Ballet of the Unhatched Chicks” from Pictures at an Exhibition

Observing but not experimenting Lots of theories: Why do children look like their parents?

Leeuwenhoek’s drawing of sperm:

What’s wrong with the logic? Lots of theories: Why do children look like their parents?

Leeuwenhoek’s drawing of sperm:

Leeuwenkoek hasn’t properly isolated his variables. He is conflating two variables? What are the two variables he is conflating? Lots of theories: Why do children look like their parents?

What are the two variables he is conflating?

A)Grey and White fur B)Fur color and Gender C)Genotype and Phenotype D)Genes and Gender E)Sperm and Dominant genes

Leeuwenkoek hasn’t properly isolated his variables. He is conflating two variables? The mystery of the hybrid?

“When Kolreuter compared them, he found a striking contrast. F1 hybrids for any given cross were alike, and in most of their characters were intermediate between the two parental species. F2 and back-crossed hybrids were all different, and they tended to be less like their parental hybrids and more like one or other of the originating species.”

Hybrids: • two types of characters: • intermediate and similar to a parent; • All hybrids alike • F2 not so

Joseph Kölreuter (1761)

R. Olby Origins of Mendelism Mendel in his own words: Hybrids are important

“Those who survey the work done “It requires indeed some courage in this department will arrive at to undertake a labor of such far– the conviction that among all the reaching extent; this appears, numerous experiments made, not however, to be the only right way one has been carried out to such by which we can finally reach the an extent and in such a way as to solution of a question the make it possible to determine the importance of which cannot be number of different forms under overestimated in connection which the offspring of the hybrids with the narrative of how living appear, or to arrange these forms beings develop.” with certainty according to their separate generations, or definitely to ascertain their numerical relations to each other.”

http://www.mendelweb.org/CollText/homepage.html What did Mendel do differently? • Performed controlled, reciprocal crosses

• Analyzed characters showing only two different forms (e.g. seed shape round or wrinkled, seed color yellow or green) -

• Reductionist - only looked at a single trait or two traits, isolate the variables • Worked with true-breeding lines

• Analyzed large numbers of progeny in a rigorous, quantitative way

• Fortuitously, each difference analyzed was controlled by a single gene Chose good system Worked hard Was lucky! Monohybrid cross: round/wrinkled wrinkled X round P generation

round F1 generation

F2 generation 5474 1850 Monohybrid cross: round/wrinkled wrinkled X round P generation

round F1 generation

F2 generation 5474 1850

3 : 1 - Ratio Reciprocal monohybrid cross: round/wrinkled

round X wrinkled P generation

round F1 generation

F2 generation 3 : 1 Same results Stem height had 3:1 ratio

P X

tall dwarf

F1 X

tall

F2 3:1 tall:dwarf Observations from Mendel’s crosses:

P • Redundancy, not trait X specific tall dwarf • Traits are Binary (twos)

• F1s exhibit only one trait

F1 X • F2s can exhibit both traits

tall • F2s exhibit a 3:1 ratio

F2 3:1 tall:dwarf Mendel’s postulates

• Unit factors occur in pairs (DD) – Unit factors are Binary (twos) – Inherited characters are controlled by unit factors (genes) that exist in pairs in individual organisms • Dominance/Recessiveness (Dd) – F1s only exhibit only one trait – When two unlike alleles responsible for a single character are present in a single individual, one allele is dominant to the other, which is said to be recessive • Random segregation (D or d has equal chance) – F2s exhibit both traits, F2s exhibit a 3:1 ratio- – Put together these observations with Dominance/Recessiveness => During the formation of gametes (egg or pollen), the paired genes segregate randomly so that each gamete receives one or the other with equal likelihood • Introductions • What is genetics • Mendel’s Postulates and the Mono-hybrid cross • Course logistics • Meiosis Course logistics: Design of the course

• Pre-lecture reading • Lecture • Post-lecture questions

• Laboratory sections • Problem sets

• Blackboard Website for information: • Syllabus; grading, etc • Discussion board • Announcements • Problem sets - due end of class on Tuesday • Surveys

• Swipe for attendance first 2 weeks • Register your clicker for credit Supplemental Instruction (SI) sessions

•Lauren Bryd: •Wed 5:30-7:00 (Shoemaker 303), Sun 3:30-5:00 (Lamar 132)

•Rush Butler: •Tues - 5:30-7:00 (Bishop 107), Thurs 7:30-9:00 (Bishop107) How to do well:

• This course is difficult • Genetics is difficult: New way of thinking • Genetics is difficult: Information builds on itself Course logistics: How to do well • Genetics is difficult: New way of thinking • Genetics is hard

• Engage/work: Ask questions, be active, do problems • You will be asked to utilize your knowledge base: Not a memorization course • Use the concepts and Teach others • Ask yourself how would I explain this concept, how would I do this problem, how would I design this experiment • Different from “Do I understand…” • Think about how you learn and what you are learning- ”Meta-cognition” • Participate in the learning feedback circuit Course logistics: How to do well

• Think like a Geneticist • How would you design an experiment to figure this out • How do you know what you know? What experiments prove this, why? • What are the rules?

• Key in on the Lectures/Learning outcomes/ problem sets Course logistics: How to do well: what to study

Learning outcomes: – Appreciate the integral nature of genetics in underpinning daily biological and medical practice – Describe how chromosomes segregate during Meiosis, Explain why this is important to genetics? – Explain genetics as an independent field of study and methodology – Explain what Mendel’s postulates reveal about the nature of inheritance and gene – Explain what Mendel did differently Course logistics: My goals

• Present/teach the material in an engaging and interesting manner, revealing the relationship of the material to world around us

• Help students engage with the material by asking thought provoking questions and providing thought provoking assignments (Active-learning)

• Give lots of feedback (learning circuit)

• Empower students to learn Meiosis: at the heart of genetics

Chr. 1

What happens next? Meiosis: at the heart of genetics Meiosis: at the heart of genetics

What’s important? •Pairs of chromosomes (diploid, 2n) •Creation of tetrads and positioning during metaphase 1 •Different possible positioning of tetrad •How n changes 2n -> 4n -> 2n -> 1n •Crossing over, different ways Chiasmata can be resolved •Being able to follow the chromosomes Post-lecture questions

R r • Follow the texture locus with alleles R =round and r=wrinkled through meiosis and fertilization with another plant of the same genotype. What aspect of meiosis proves Mendel’s first 3 postulates

• Follow the texture locus with alleles R =round and R r T t r=wrinkled and the height locus with alleles T= tall and t=small on a separate chromosome through meiosis and fertilization. What aspect of meiosis proves Mendel’s fourth postulate of independent assortment?