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WELCOME.

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GOOD AFTERNOON, EVERYONE.

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THANK YOU FOR JOINING IN THIS

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SESSION OF THE WEDNESDAY

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AFTERNOON LECTURE SERIES.

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AND IT'S A REAL PLEASURE AND

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HONOR FOR ME, I'M IN THE

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INTRAMURAL DIVISION OF NICHD, TO

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INTRODUCE TODAY'S SPEAKER,

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HARMIT MALIK, WHO COMES TO US

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FROM THE FRED HUTCH CANCER

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RESEARCH CENTER IN SEATTLE,

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WHERE HE'S PROFESSOR AND

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COASSOCIATE PROFESSOR AND

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INVESTIGATOR OF THE HOWARD

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HUGHES MEDICAL INSTITUTE.

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HARMIT STUDIES THE CAUSE AND

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CONES QENSES OF GENETIC

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CONFLICTS THAT TAKE PLACE

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BETWEEN DIFFERENT GENOMES, AND

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HE'S INTERESTED IN UNDERSTANDING

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THESE WHAT HE CALLS MOLECULAR

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ARMS RACES AND HOW THEY DRIVE

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INNOVATION FROM THE PERSPECTIVE

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OF BOTH EVOLUTIONARY BIOLOGY AND

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HUMAN DISEASE.

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HARMIT AND HIS COLLEAGUES HAVE

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USED AN EVOLUTIONARY LENS TO

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DISSECT AND DISCOVER ADAPTATION

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STRATEGIES AND THIS WORK HAS

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HELPED FOUND THE FIELD.

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THE OTHER AREA OF RESEARCH IN

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HARMIT'S LAB IS THE STUDY OF

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RAPID EVOLUTION IN GENES

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INVOLVED IN ESSENTIAL CELLULAR

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PROCESSES SUCH AS CHROMOSOME

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SEGREGATION AND HIGH TOE CON ANL

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BIOLOGY.

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HE PROPOSED A MODEL -- THE

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UNEXPECTEDLY RAPID EVOLUTION OF

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16 DRCENTOMERIC PROTEINS.

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HE RECEIVED HIS

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UNDERGRADUATE DEGREE FROM THE

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IIT BOMBAY, AND IN HIS FINAL

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YEAR WAS INTERESTED IN A NEW

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COURSE TITLED AN INTRODUCTION TO

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MOLECULAR BIOLOGY.

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HIS CORE REQUIREMENTS PREVENTED

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HIM FROM ACTUALLY TAKING THAT

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COURSE FOR CREDIT BUT HIS

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TEACHER OFFERED TO TEACH HIM THE

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COURSE ONE ON ONE IN THE

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AFTERNOON PROVIDED HARMIT KEPTD

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KEPTUP WITH THE READINGS.

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HARMIT DID THAT AND OF COURSE

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MORE BECAUSE THAT TOGETHER WITH

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THE SIMULTANEOUS READING OF THE

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SELFISH GENE BY RICHARD DAWKINS

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SPARRED A DEEP INTEREST IN

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TRANSPOSABLE ELEMENTS THAT LED

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HIM TO A PH.D. AT THE UNIVERSITY

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OF ROCHESTER FOLLOWED BY A

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POSTDOC AT THE FRED HUTCH, WHERE

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HE STARTED HIS WORK ON EVOLUTION

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OF CENTROMERES.

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HE STARTED HIS LAB IN 2003 AT

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THE HUTCH AND HAS STAYED THERE

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EVER SINCE.

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HE HAS RECEIVED A WIDE NUMBER OF

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AWARDS, I'M ONLY GOING TO NAME A

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FEW.

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THE PTHE WAS RECIPIENT OF THEAWD

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COMPANY RESEARCH AWARD FROM THE

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AMERICAN SOCIETY OF

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MICROBIOLOGY.

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HE'S AN HHMI INVESTIGATOR AND I

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WANT TO SPECIFICALLY MENTION THE

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AWARD FOR EXCELLENCE IN LIFE

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SCIENCES NAMED AFTER THE

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FOUNDING FATHER OF MOLECULAR

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BIOLOGY RESEARCH IN INDIA.

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HE WAS INDUCTED INTO THE

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NATIONAL ACADEMY OF SCIENCES AND

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THE AMERICAN ACADEMY OF ARTS AND

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SCIENCES.

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HARMIT IS ALSO VERY KEEN TO

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PROMOTE INCLUSION IN SCIENCE AND

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IS ACTIVE ON SOCIAL MEDIA

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ENCOURAGING PEOPLE TO GET

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INVOLVED IN SCIENCE AND BREAKING

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DOWN THE BARRIERS OF ENTRY INTO

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SCIENCE.

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THEY BUILD ROLE MODELS AND BUILD

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COMMUNITY THAT IS PARTICULARLY

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INSPIRING FOR YOUNGER

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RESEARCHERS AND FOR THAT, WE

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HAVE TO BE COLLECTIVELY THANKFUL

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FOR FOLKS LIKE HARMIT.

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THANK YOU FOR COMING, LOOK

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FORWARD TO YOUR SEMINAR.

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[APPLAUSE]

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>> THANK YOU VERY MUCH.

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I FEEL A LITTLE BUI BIT CHEATED

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BECAUSE I WAS ASSURED THERE

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WOULD BE NO MORE THAN 20 PEOPLE

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IN THE AUDITORIUM AND I'M PRETTY

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SURE THAT ISN'T TRUE.

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I WAS TOLD THERE ARE GOING TO BE

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COFFEE AND COOKIES AFTER THE

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THING, SO YOU JUST HAVE TO WAIT

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FOR ABOUT AN HOUR.

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IT IS ALSO THE LONGEST DAY OF

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THE YEAR AND I HOPE TO NOT MAKE

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IT SEEM EVEN LONGER.

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[LAUGHTER]

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SO TODAY I'M ACTUALLY GOING TO

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TELL BUT SOME OF THE WORK THAT

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WE'RE DOING IN MY LAB ON HOST

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APT VIANTIVIRAL PROTEINS.

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I JUST WANT TO ADVERTISE IF YOU

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ARE KEEN TO GET MORE OF THIS,

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I'M ALSO GIVING A LECTURE IN THE

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NHGRI TOMORROW AND YOU ARE

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WELCOME TO ATTEND THAT AS WELL.

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SO BEFORE I GET INTO THE MEAT OF

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TODAY'S TALK, I JUST WANTED TO

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GIVE YOU AN INTRODUCTION INTO

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WHAT INSPIRES ALL OF THE WORK

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THAT GOES ON IN MY LAB.

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WHICH IS REALLY ABOUT GENETIC

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CONFLICTS.

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AND THE IDEA OF GENETIC

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CONFLICTS REALLY EMERGES FROM A

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VERY UNUSUAL SOURCE, SO I

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THOUGHT I'D SPEND A FEW MINUTES

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DISCUSSING THAT.

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WHICH IS THE FICTIONAL CHARACTER

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THE RED QUEEN IN THE BOOKS ABOUT

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ALICE'S ADVENTURES IN WONDERLAND

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WHERE AT ONE POINT IN RESPONSE

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TO ALICE'S COMPLAINT, THE RED

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QUEEN RETORTS THAT IT TAKES ALL

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THE RUNNING YOU CAN DO IN

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WONDERLAND TO KEEP IN THE SAME

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PLACE.

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THOSE OF YOU WHO RUN LABS CAN

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TOTALLY APPRECIATE THE RED QUEEN

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INTERACTION AS LIKE A REALLY

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IMPORTANT LESSON FOR LIFE.

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BUT UNSURPRISINGLY THIS ALSO WAS

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A VERY IMPORTANT LESSON FOR

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EVOLUTIONARY BIOLOGY AND LED TO

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THE FORMULATION OF THE RED QUEEN

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HYPOTHESIS, WHICH I LIKE TO

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THINK ABOUT AS THE SECOND SORT

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OF INCARNATION OF DAR VINNIAN

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THINKING IN EVOLUTIONARY -- IN

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THE ROLE OF NATURAL SELECTION

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AND HOW ORGANISMS ADAPT TO THEIR

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ENVIRONMENTS, THEY HAD

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PREDOMINANTLY FOCUSED ON THEIR

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ADAPTATION TO THEIR ABIOTIC

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ENVIRONMENT, AND IT WAS

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EXPLICITLY POINTED OUT THAT A

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LARGE PART OF THAT ENVIRONMENT

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IS ALSO MADE UP OF COMPETING

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SPECIES WHICH ARE OFTEN

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COMPETING FOR THE SAME FITNESS

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SPACE.

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SO IT WAS IMPOSSIBLE, FOR

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EXAMPLE, TO CONSIDER WHAT WAS

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GOING TO HAPPEN IN THE FITNESS

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OF THE SNOW LEOPARD POPULATION

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IF YOU FAIL TO CONSIDER WHAT WAS

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HAPPENING IN THE SNOW HARE

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POPULATION BECAUSE THE ADAPTIVE

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STRATEGIES DIRECTLY TIED IN WITH

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THE ADAPTIVE STRATEGIES OF THE

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OTHER.

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THE RED QUEEN HYPOTHESIS IS A

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VERY IMPORTANT -- EVERYTHING

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FROM ECOLOGY TO PUBLIC HEALTH

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AND WHAT LABS LIKE MINE ARE VERY

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INTERESTED IN IS ADOPTING THIS

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INTO MOLECULAR TERMS.

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SO I'M GOING TO MAKE A VERY

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SMALL LEAP BETWEEN ARMS RACES

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THAT OCCUR BETWEEN PREY AND

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PREDATORS VERSUS ARMS RACES THAT

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OCCUR BETWEEN ANTIVIRAL PROTEINS

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AND TODAY'S LECTURE IS GOING TO

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BE EXCLUSIVELY ON INNATE

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ANTIVIRAL PROTEINS, AND VIRAL

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PROTEINS.

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I'LL JUST POINT OUT THAT IN THIS

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HIGH RESOLUTION STRUCTURE OF AN

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ANTIVIRAL PROTEIN RECOGNIZING A

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VIRAL PROTEIN BY SOME SORT OF

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EPITOPE RECOGNITION, IT'S GOING

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TO ENCOUNTER THE VIRUSES AS SOON

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AS THEY ENTER THE CELL,

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EXTINGUISH THE VIRUS FROM THE

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CELL EVENTUALLY FROM THE

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ORGANISM, AND EVENTUALLY FROM

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THE SPECIES.

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THIS, OF COURSE, PUT A LOT OF

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DARWINIAN PRESSURE TO RAPIDLY

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EVOLVE TO A NEW STATE THAT IS NO

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LONGER CAPABLE OF BEING

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RECOGNIZED OR ANTAGONIZED, AND

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THIS CAN HAPPEN AT THE LEVEL OF

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A SINGLE AMINO ACID MUTATION,

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WHICH, GIVEN THE VERY RAPID

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MUTATION RATES AFFORDED TO

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VIRUSES, CAN HAPPEN VERY

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QUICKLY.

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OVER TIME THIS WILL ACTUALLY

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FORCE THE ANTIVIRAL PROTEIN TO

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RE-ESTABLISH ITS ANTAGONISM --

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MUTATION BUT THIS IS A MUCH

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SLOWER STEP BECAUSE WE NEED TO

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RELY ON GENERATIONAL MUTATION

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TIME WHICH IS, OF COURSE, MUCH

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SLOWER IN SPECIES SUCH AS OURS.

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SO A QUESTION THAT OFTEN ARISES

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IS HOW IS IT POSSIBLE TO THINK

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ABOUT THESE AS CONTEMPORANEOUS

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ARMS RACES WHERE ONE PARTY IS SO

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MUCH MORE ADAPTED EVOLUTION AND

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MUTATION THAN THE OTHER.

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AND THE RESPONSE IS THAT IF THIS

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IS A 1 TO 1 INTERACTION IT WOULD

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BE GAME OVER, JUST BECAUSE THE

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INHERENT ASYMMETRIC NATURE OF

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THESE ARMS RACES BUT LUCKILY FOR

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US, IT'S NOT A ONE TO ONE

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INTERACTION.

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IN FACT, WE HAVE NEARLY 200

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ANTIVIRAL PROTEINS ENCODED AND

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OFTEN TRIGGERED BY THE

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INTERFERON SYSTEM, THAT

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BASICALLY ARE DEDICATED TO THE

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JOB OF INTERROGATING INCOMING

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PATHOGENIC VIRUSES AND BACTERIA,

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AND BASICALLY EXPUNGING THEM.

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AND REALLY FOR THE HOST TO WIN,

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IT REALLY ONLY NEEDS TO WIN ONE

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OF THESE INTERACTIONS IN ORDER

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TO DO ITS JOB.

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WHEREAS FOR A VIRUS, EVEN THE

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VERY RAPIDLY INVOLVING RNA

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VIRUS, IT NEEDS TO RUN THE

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ENTIRE GAUNTLET OF ANTIVIRAL

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PROTEINS PROVIDED AND THAT'S

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WHERE THE MATH BEGINS TO ADD UP.

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ANTIVIRAL PROTEINS ALSO DON'T

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ENCOUNTER JUST ONE PATHOGENIC

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WILD VARIANT AS WE'VE ALREADY

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SEEN MULTIPLE PATHOGENIC

260
00:08:31,160 --> 00:08:33,200
VARIANTS OF THE SAME VIRUS

261
00:08:33,200 --> 00:08:34,600
MULTIPLE TIMES.

262
00:08:34,600 --> 00:08:36,600
AND IF YOU USE PUBLIC TRANSPORT,

263
00:08:36,600 --> 00:08:37,920
YOU PROBABLY ENCOUNTER THEM ON A

264
00:08:37,920 --> 00:08:39,200
WEEKLY BASIS OR IF YOU HAVE KIDS

265
00:08:39,200 --> 00:08:39,760
IN DAYCARE.

266
00:08:39,760 --> 00:08:41,280
THOSE ARE THE REAL FRONT LINES

267
00:08:41,280 --> 00:08:43,040
OF INFECTIOUS DISEASE IN OUR

268
00:08:43,040 --> 00:08:44,600
SPECIES.

269
00:08:44,600 --> 00:08:45,880
AND SO REALLY YOU BEGIN TO

270
00:08:45,880 --> 00:08:47,960
APPRECIATE THAT ANTIVIRAL

271
00:08:47,960 --> 00:08:49,160
PROTEINS AND VIRAL PROTEINS ARE

272
00:08:49,160 --> 00:08:51,240
LOCKED IN THIS MANY TO MANY

273
00:08:51,240 --> 00:08:52,120
INTERACTION BUT EVEN IF YOU WERE

274
00:08:52,120 --> 00:08:54,640
TO FOCUS ON THE FOCAL 1 TO

275
00:08:54,640 --> 00:08:55,320
1 INTERACTION YOU'LL APPRECIATE

276
00:08:55,320 --> 00:08:56,920
THAT THIS IS A RELENTLESS ENGINE

277
00:08:56,920 --> 00:08:58,280
FOR FORWARD EVOLUTION.

278
00:08:58,280 --> 00:08:59,600
AND WHAT DRIVES THIS ENGINE IS

279
00:08:59,600 --> 00:09:01,320
THE FACT THAT ONE PARTY IS

280
00:09:01,320 --> 00:09:02,960
ALWAYS ON THE LOSING SIDE OF

281
00:09:02,960 --> 00:09:05,240
THIS ARMS RACE, RESULTING IN

282
00:09:05,240 --> 00:09:06,920
GENETIC INNOVATION BEING

283
00:09:06,920 --> 00:09:08,760
CONSTANTLY SPURRED BY THE NATURE

284
00:09:08,760 --> 00:09:09,760
OF THIS INTERACTION.

285
00:09:09,760 --> 00:09:11,600
SO THERE'S ALWAYS GOING TO BE AN

286
00:09:11,600 --> 00:09:12,240
EVOLUTIONARY ADVANTAGE TO BE

287
00:09:12,240 --> 00:09:13,440
GAINED BY THIS INNOVATION, AND

288
00:09:13,440 --> 00:09:14,960
WHAT LABS LIKE MINE ARE TRYING

289
00:09:14,960 --> 00:09:16,960
TO DO IN A NUTSHELL IS LOOK

290
00:09:16,960 --> 00:09:18,600
BACKWARDS IN THE SEQUENCES OF

291
00:09:18,600 --> 00:09:20,640
VIRAL PROTEINS AND THE SEQUENCES

292
00:09:20,640 --> 00:09:22,440
OF ANTIVIRAL PROTEINS TO TRY TO

293
00:09:22,440 --> 00:09:23,880
RECONSTRUCT THE STEPS THAT TOOK

294
00:09:23,880 --> 00:09:24,840
PLACE IN THE COURSE OF THESE

295
00:09:24,840 --> 00:09:28,480
ARMS RACES AND UNDERSTAND THAT

296
00:09:28,480 --> 00:09:31,520
BIOCHEMICAL AND BIOLOGICAL

297
00:09:31,520 --> 00:09:31,760
OUTCOMES.

298
00:09:31,760 --> 00:09:32,920
ONE SPECIAL TYPE OF INNOVATION

299
00:09:32,920 --> 00:09:35,240
THAT IS QUITE EASY TO IMAGINE IS

300
00:09:35,240 --> 00:09:37,960
FOCUSING ON PROTEIN CODING IMEEN

301
00:09:37,960 --> 00:09:39,360
INNOVATION AND THIS IS JUST A

302
00:09:39,360 --> 00:09:40,800
BRIEF PRIMER FOR THOSE OF YOU

303
00:09:40,800 --> 00:09:43,920
WHO DON'T THINK ABOUT THIS ON AA

304
00:09:43,920 --> 00:09:45,080
DAILY BASIS WHERE IF YOU WERE TO

305
00:09:45,080 --> 00:09:49,360
CONSIDER A HYPOTHETICAL PIECE OF

306
00:09:49,360 --> 00:09:50,880
A PROTEIN CODING GENE, WE CAN

307
00:09:50,880 --> 00:09:52,320
CLASSIFY ALL OF THE NUCLEOTIDE

308
00:09:52,320 --> 00:09:53,960
SUBSTITUTIONS THAT OCCUR HERE

309
00:09:53,960 --> 00:09:55,160
OVER EVOLUTIONARY TIME INTO

310
00:09:55,160 --> 00:09:58,640
THOSE THAT WILL NOT ALTER THE

311
00:09:58,640 --> 00:10:00,960
AMINO ACID ENCODED, SILENT OR

312
00:10:00,960 --> 00:10:03,640
SYNONYMOUS CHANGES VERSUS THOSE

313
00:10:03,640 --> 00:10:05,120
THAT INSTANTLY ALTER THE GENE

314
00:10:05,120 --> 00:10:06,560
BECAUSE OF THE NATURE OF THE

315
00:10:06,560 --> 00:10:08,400
AMINO ACID SUBSTITUTION.

316
00:10:08,400 --> 00:10:10,280
WE CALL THESE NON-SYNONYMOUS OR

317
00:10:10,280 --> 00:10:10,800
REPLACEMENT CHANGES.

318
00:10:10,800 --> 00:10:13,000
NOW NORMALIZED AS DS AND DN, WE

319
00:10:13,000 --> 00:10:15,880
HAVE DIFFERENT WAYS OF VIEWING

320
00:10:15,880 --> 00:10:19,000
WHAT ARE THE EVOLUTIONARY EVOLUS

321
00:10:19,000 --> 00:10:20,600
THAT HAVE DRIVEN EACH OF THESE

322
00:10:20,600 --> 00:10:20,840
CHANGES.

323
00:10:20,840 --> 00:10:22,120
WE MAKE THE ASSUMPTION THAT

324
00:10:22,120 --> 00:10:23,520
SILENT OR SYNONYMOUS CHANGES ARE

325
00:10:23,520 --> 00:10:24,720
REALLY NOT VISIBLE TO NATURAL

326
00:10:24,720 --> 00:10:26,120
SELECTION.

327
00:10:26,120 --> 00:10:27,840
WE DO SO IN SPITE OF THE FACT WE

328
00:10:27,840 --> 00:10:29,440
KNOW THIS ASSUMPTION IS WRONG,

329
00:10:29,440 --> 00:10:31,360
THERE ARE MANY, MANY GOOD

330
00:10:31,360 --> 00:10:32,720
EXAMPLES WHERE SYNONYMOUS

331
00:10:32,720 --> 00:10:34,800
CHANGES WITH CAN AFFECT PROTEIN

332
00:10:34,800 --> 00:10:35,760
TRANSLATION RATES AND EVEN

333
00:10:35,760 --> 00:10:37,200
PROTEIN STABILITY BUT WE

334
00:10:37,200 --> 00:10:38,280
NONETHELESS MAKE THIS ASSUMPTION

335
00:10:38,280 --> 00:10:41,240
BECAUSE AS A FIRST ORDER OF

336
00:10:41,240 --> 00:10:45,400
APPROXIMATION, AN AVERAGE SILENT

337
00:10:45,400 --> 00:10:48,920
CHANGE IS MUCH MORE BENIGN THAN

338
00:10:48,920 --> 00:10:50,440
A REPLACEMENT CHANGE.

339
00:10:50,440 --> 00:10:52,400
AS A PROXY OF ALMOST LIKE A

340
00:10:52,400 --> 00:10:53,720
CLOCK-LIKE FASHION, THE LONGER

341
00:10:53,720 --> 00:10:56,040
TIME OF DIVERGENCE, THE MORE

342
00:10:56,040 --> 00:10:57,880
YOUR DS IS GOING TO DIVERGE.

343
00:10:57,880 --> 00:10:59,800
YET AS NATURAL SELECTION WILL

344
00:10:59,800 --> 00:11:00,840
DICTATE WHAT WILL HAPPEN WITH

345
00:11:00,840 --> 00:11:02,680
THE DN TERM, IF YOU DO NOT

346
00:11:02,680 --> 00:11:03,800
TOLERATE AMINO ACID CHANGES

347
00:11:03,800 --> 00:11:05,720
YOU'LL BASICALLY HAVE A DN WHICH

348
00:11:05,720 --> 00:11:07,920
IS MUCH LESS THAN YOU'D EXPECT

349
00:11:07,920 --> 00:11:09,920
AR AS IF YOU FAVOR REPLACEMENT

350
00:11:09,920 --> 00:11:11,560
CHANGES YOU'D HAVE A DN THAT'S

351
00:11:11,560 --> 00:11:12,400
MUCH HIGHER THAN WHAT YOU

352
00:11:12,400 --> 00:11:12,720
EXPECT.

353
00:11:12,720 --> 00:11:14,400
THOSE OF YOU USED TO LOOKING AT

354
00:11:14,400 --> 00:11:15,600
PROTEIN ALIGNMENTS INHERENTLY

355
00:11:15,600 --> 00:11:17,000
USE THIS TOOL, EVEN THOUGH YOU

356
00:11:17,000 --> 00:11:18,960
MIGHT NOT BE THINKING OF THIS AS

357
00:11:18,960 --> 00:11:20,840
THE DN/DS TOOL, BECAUSE WHEN

358
00:11:20,840 --> 00:11:21,960
YOUR EYE IS DRAWN TO THOSE

359
00:11:21,960 --> 00:11:23,480
POSITIONS THAT ARE COMPLETELY

360
00:11:23,480 --> 00:11:25,000
FROZEN IN EVOLUTION, DESPITE

361
00:11:25,000 --> 00:11:26,800
MILLIONS OF YEARS OF DIVERGENCE,

362
00:11:26,800 --> 00:11:28,840
LET'S SAY CATALYTIC RESIDUES OF

363
00:11:28,840 --> 00:11:30,280
AN ENZYME, WHAT YOU'RE DOING IS

364
00:11:30,280 --> 00:11:31,480
MAKING A MATHEMATICAL

365
00:11:31,480 --> 00:11:32,440
CALCULATION OF THE NUMBER OF

366
00:11:32,440 --> 00:11:33,240
MUTATIONS THAT MUST HAVE

367
00:11:33,240 --> 00:11:35,880
OCCURRED THAT ALTERED THE AMINO

368
00:11:35,880 --> 00:11:37,080
ACID, AT THOSE CRITICAL

369
00:11:37,080 --> 00:11:38,480
POSITIONS, BUT ALL OF THOSE WERE

370
00:11:38,480 --> 00:11:39,800
PURGED BECAUSE THEY WERE

371
00:11:39,800 --> 00:11:40,320
DELETERIOUS FOR FUNCTION.

372
00:11:40,320 --> 00:11:42,640
IN OTHER WORDS, WE USE THIS

373
00:11:42,640 --> 00:11:44,560
PROXY OF HOW SELECTION HAS ACTED

374
00:11:44,560 --> 00:11:47,320
TO PURIFY THE POPULATION OF

375
00:11:47,320 --> 00:11:49,120
PRESUMED DELETERIOUS AMINO ACID

376
00:11:49,120 --> 00:11:51,160
CHANGES OR A PROXY OF HIGH

377
00:11:51,160 --> 00:11:52,040
EVOLUTIONARY CONSERVATION FOR

378
00:11:52,040 --> 00:11:52,480
FUNCTION.

379
00:11:52,480 --> 00:11:54,880
SO IF IT'S HIGHLY CONSERVED IN

380
00:11:54,880 --> 00:11:55,600
EVOLUTION, DESPITE MILLIONS OF

381
00:11:55,600 --> 00:11:57,200
YEARS OF DIVERGENCE, IT MUST BE

382
00:11:57,200 --> 00:11:58,600
IMPORTANT TO HAVE ESSENTIALLY

383
00:11:58,600 --> 00:12:00,240
SURVIVED MUTATION.

384
00:12:00,240 --> 00:12:02,440
BUT WE SOMETIMES MAKE THE

385
00:12:02,440 --> 00:12:03,520
MISTAKEN ASSUMPTION THAT THINGS

386
00:12:03,520 --> 00:12:05,520
THAT ARE NOT CONSERVATIVE

387
00:12:05,520 --> 00:12:06,840
EVOLUTION MUST, THEREFORE, NOT

388
00:12:06,840 --> 00:12:07,400
BE IMPORTANT.

389
00:12:07,400 --> 00:12:09,320
IN FACT, MY ENTIRE LAB STUDY

390
00:12:09,320 --> 00:12:11,080
CASES WHERE THE RATE OF AMINO

391
00:12:11,080 --> 00:12:12,160
ACID CHANGE MUCH EXCEEDS WHAT

392
00:12:12,160 --> 00:12:14,040
YOU WOULD EXPECT BY CHANCE

393
00:12:14,040 --> 00:12:15,480
ALONE, AND THAT'S ACTING NOT

394
00:12:15,480 --> 00:12:18,880
BECAUSE YOU SUDDENLY BECOME MUCH

395
00:12:18,880 --> 00:12:20,920
MORE SENSITIVE TO DS-TYPE

396
00:12:20,920 --> 00:12:21,960
CHANGES, BUT THAT'S OCCURRING

397
00:12:21,960 --> 00:12:24,160
BECAUSE SELECTION IS NOW ACTING

398
00:12:24,160 --> 00:12:25,720
POSITIVELY TO ACCELERATE THE

399
00:12:25,720 --> 00:12:27,840
RATE OF FIXATION OF AMINO ACID

400
00:12:27,840 --> 00:12:28,920
ALTERING MUTATIONS BECAUSE THEY

401
00:12:28,920 --> 00:12:31,800
WERE BENEFICIAL IN THE CONTEXT

402
00:12:31,800 --> 00:12:32,680
THAT THEY OCCURRED.

403
00:12:32,680 --> 00:12:33,800
WE WOULD MAKE THE CASE TODAY

404
00:12:33,800 --> 00:12:35,840
THAT JUST LIKE HIGH EVOLUTIONARY

405
00:12:35,840 --> 00:12:36,920
CONSERVATION IS A PROXY FOR

406
00:12:36,920 --> 00:12:38,680
FUNCTIONAL IMPORTANCE, THIS

407
00:12:38,680 --> 00:12:40,520
CONSTANT RELENTLESS SIGNATURE OF

408
00:12:40,520 --> 00:12:41,880
INNOVATION AT THE AMINO ACID

409
00:12:41,880 --> 00:12:43,480
LEVEL IS ALSO A PROXY FOR

410
00:12:43,480 --> 00:12:44,480
FUNCTIONAL IMPORTANCE, BUT THIS

411
00:12:44,480 --> 00:12:48,000
ONE IS A I LO  LOT MORE SPECIFIT

412
00:12:48,000 --> 00:12:52,440
YES NE TGENETIC CONFLICTS.

413
00:12:52,440 --> 00:12:54,120
WE CAN USE THIS TO APPLY TO ALL

414
00:12:54,120 --> 00:12:55,320
PROTEIN CODING GENES IN THE

415
00:12:55,320 --> 00:12:57,520
GENOME, WE CAN DO THIS IN OUR

416
00:12:57,520 --> 00:13:02,080
SPECIES, WE CAN DO THIS IN

417
00:13:02,080 --> 00:13:03,320
DROSOPHILA OR WHATEVER YOUR

418
00:13:03,320 --> 00:13:04,280
FAVORITE SPECIES IS.

419
00:13:04,280 --> 00:13:05,600
WE SEE THE OVERWHELMING

420
00:13:05,600 --> 00:13:06,920
SIGNATURE IS THAT OF PURIFYING

421
00:13:06,920 --> 00:13:07,600
SELECTION.

422
00:13:07,600 --> 00:13:10,200
ONCE AGAIN, IF THE ONLY EFFECT

423
00:13:10,200 --> 00:13:11,560
WAS ABOUT MUTATION, THEN ALL OF

424
00:13:11,560 --> 00:13:13,040
THE GENES WOULD BE PILED UP

425
00:13:13,040 --> 00:13:17,480
AROUND THIS DOTTED LINE OF DN/DS

426
00:13:17,480 --> 00:13:18,760
EQUALS 1, BUT BECAUSE MOST

427
00:13:18,760 --> 00:13:19,840
PROTEIN CODING GENES ARE

428
00:13:19,840 --> 00:13:21,360
BASICALLY IN THIS LEFTWARD

429
00:13:21,360 --> 00:13:22,800
HISTOGRAM, THIS GAP BETWEEN THE

430
00:13:22,800 --> 00:13:24,240
BOTTOM LINE ON THE HISTOGRAM

431
00:13:24,240 --> 00:13:25,640
REALLY INDICATES HOW NATURAL

432
00:13:25,640 --> 00:13:28,720
SELECTION I HAS ACTUALLY PURGED

433
00:13:28,720 --> 00:13:32,160
ALL OF THE AMINO ACIDS THAT HAVE

434
00:13:32,160 --> 00:13:33,760
PROBABLY TAKEN -- AMINO ACID

435
00:13:33,760 --> 00:13:37,920
MUTATIONS TAKING PLACE PRESUMED

436
00:13:37,920 --> 00:13:39,000
DELETERIOUS AND PURGED OUT WHICH

437
00:13:39,000 --> 00:13:40,320
IS WHY WE DON'T SEE THEM

438
00:13:40,320 --> 00:13:40,800
ANYMORE.

439
00:13:40,800 --> 00:13:42,760
BUT EVEN IN THIS WHOLE SORT OF

440
00:13:42,760 --> 00:13:44,920
CRUDE DN/DS AVERAGE, YOU CAN SEE

441
00:13:44,920 --> 00:13:46,760
THERE'S A BLIP OF GENES WHICH IS

442
00:13:46,760 --> 00:13:49,880
VERY MUCH IN THE -- BREAKING THE

443
00:13:49,880 --> 00:13:51,080
SPEED LIMIT, IF YOU WILL, THAT

444
00:13:51,080 --> 00:13:54,200
IS IMPOSED BY MUTATION.

445
00:13:54,200 --> 00:13:55,880
UNSURPRISINGLY IMMUNITY GENES

446
00:13:55,880 --> 00:13:57,840
ARE UNSURPRISINGLY REPRESENTED

447
00:13:57,840 --> 00:13:59,480
IN THIS CATEGORY.

448
00:13:59,480 --> 00:14:01,560
INNATE IMMUNE GENES THAT DEFEND

449
00:14:01,560 --> 00:14:04,400
AGAINST VIRUSES AND BACTERIA ARE

450
00:14:04,400 --> 00:14:05,160
HEAVILY OVERREPRESENTED HERE.

451
00:14:05,160 --> 00:14:06,600
THAT'S WHAT I'M GOING TO FOCUS

452
00:14:06,600 --> 00:14:09,000
ON FOR TODAY'S LECTURE.

453
00:14:09,000 --> 00:14:10,200
WEE ALSO INTERESTED IN CATEGORY

454
00:14:10,200 --> 00:14:12,400
OF GENES THAT DON'T MAKE ANY

455
00:14:12,400 --> 00:14:13,400
SENSE -- THAT'S ACTUALLY THE

456
00:14:13,400 --> 00:14:14,800
TOPIC FOR TOMORROW'S LECTURE.

457
00:14:14,800 --> 00:14:17,240
RETURNING TO THIS SORT OF HOW TO

458
00:14:17,240 --> 00:14:18,520
THINK ABOUT PURIFYING SELECTION

459
00:14:18,520 --> 00:14:20,160
AND POSITIVE SELECTION ON A SORT

460
00:14:20,160 --> 00:14:21,880
OF BIOCHEMICAL BASIS, LET'S

461
00:14:21,880 --> 00:14:23,560
IMAGINE AN INTERACTION BETWEEN

462
00:14:23,560 --> 00:14:25,720
TWO HOST PROTEINS WHOSE

463
00:14:25,720 --> 00:14:26,840
INTERACTION IS REALLY IMPORTANT.

464
00:14:26,840 --> 00:14:28,680
LET'S SAY FOR A SIGNAL

465
00:14:28,680 --> 00:14:29,240
TRANSDUCTION PATHWAY.

466
00:14:29,240 --> 00:14:31,000
NOW WE CAN IMAGINE MUTATIONS

467
00:14:31,000 --> 00:14:32,080
WILL OCCUR EITHER IN ONE PROTEIN

468
00:14:32,080 --> 00:14:34,400
OR THE OTHER PROTEIN THAT MIGHT

469
00:14:34,400 --> 00:14:35,600
PERTURB THIS INTERACTION BUT

470
00:14:35,600 --> 00:14:38,160
THAT WOULD BE DL DELETERIOUS

471
00:14:38,160 --> 00:14:40,200
BECAUSE YOU'RE ESSENTIALLY

472
00:14:40,200 --> 00:14:42,600
BREAKING THE SIGNAL TRANSDUCTION

473
00:14:42,600 --> 00:14:44,360
PATHWAY AND GIVEN BOTH ARE RARE

474
00:14:44,360 --> 00:14:46,120
IN THE POPULATION, IS

475
00:14:46,120 --> 00:14:47,120
EXCEEDINGLY RARE, WHICH MEANS

476
00:14:47,120 --> 00:14:48,640
THAT YOU WILL COME BACK MILLIONS

477
00:14:48,640 --> 00:14:50,160
OF YEARS LATER AND FIND THAT

478
00:14:50,160 --> 00:14:51,600
PURIFYING SELECTION IS LARGELY

479
00:14:51,600 --> 00:14:53,040
MAINTAINED THE INTERACTION

480
00:14:53,040 --> 00:14:54,080
INTERFACE BECAUSE THAT IS SO

481
00:14:54,080 --> 00:14:55,440
IMPORTANT IN THE COURSE OF

482
00:14:55,440 --> 00:14:56,400
EVOLUTION.

483
00:14:56,400 --> 00:14:59,480
SO THIS PARTICULAR PROTEIN HAS

484
00:14:59,480 --> 00:15:01,440
BASICALLY BEEN LEFT UNCHANGED BY

485
00:15:01,440 --> 00:15:01,960
NATURAL SELECTION.

486
00:15:01,960 --> 00:15:03,280
IN CONTRAST, IF YOU IMAGINE WHAT

487
00:15:03,280 --> 00:15:05,480
HAPPENS IN A HOST-VIRUS ARMS

488
00:15:05,480 --> 00:15:07,800
RACE, HERE WE BASICALLY BOUNCE

489
00:15:07,800 --> 00:15:08,640
BETWEEN TWO STATES BETWEEN THE

490
00:15:08,640 --> 00:15:11,360
HOST RINNING VERSUS THE VIRUS

491
00:15:11,360 --> 00:15:12,560
WINNING, AND BECAUSE WHAT'S IN

492
00:15:12,560 --> 00:15:13,560
THE BENEFIT OF THE HOST IS

493
00:15:13,560 --> 00:15:15,160
ACTUALLY TO THE DETRIMENT OF THE

494
00:15:15,160 --> 00:15:17,120
VIRUS AND VICE VERSA, SO ONCE

495
00:15:17,120 --> 00:15:19,000
AGAIN WE'VE GOT A

496
00:15:19,000 --> 00:15:19,840
PROTEIN-PROTEIN INTERACTION

497
00:15:19,840 --> 00:15:22,240
INTERFACE, BUT THIS ONE CANNOT

498
00:15:22,240 --> 00:15:24,560
STAY STABLE AND IT'S CONSTANTLY

499
00:15:24,560 --> 00:15:26,440
CHISELED AWAY BY ADAPTIVE

500
00:15:26,440 --> 00:15:27,400
EVOLUTION, EITHER ON THE HOST

501
00:15:27,400 --> 00:15:29,040
SIDE OR THE VIRUS SIDE, AND

502
00:15:29,040 --> 00:15:30,240
MOREOVER, IF YOU'RE EVEN PAYING

503
00:15:30,240 --> 00:15:31,240
ATTENTION TO THIS CARTOON

504
00:15:31,240 --> 00:15:32,520
EXAMPLE, YOU CAN APPRECIATE THAT

505
00:15:32,520 --> 00:15:34,080
WE DON'T EXPECT RAPID EVOLUTION

506
00:15:34,080 --> 00:15:36,280
TO BE RANDOMLY DISTRIBUTED OVER

507
00:15:36,280 --> 00:15:39,960
THESE PROTEINS, BUT I IN FACT,

508
00:15:39,960 --> 00:15:41,880
CONCENTRATED ALL THOSE RESIDUES

509
00:15:41,880 --> 00:15:43,800
OR DOMAINS -- THE BINDING

510
00:15:43,800 --> 00:15:45,360
AFFINITY BETWEEN THE HOST AND

511
00:15:45,360 --> 00:15:45,880
PROTEIN INTERACTIONS.

512
00:15:45,880 --> 00:15:47,400
SO MANY YEARS AGO, ARMED WITH

513
00:15:47,400 --> 00:15:50,480
NOTHING MORE THAN THIS, WE

514
00:15:50,480 --> 00:15:51,880
WONDERED IF WE COULD ACTUALLY

515
00:15:51,880 --> 00:15:53,200
SIMPLY ASK WHERE POSITIVE

516
00:15:53,200 --> 00:15:54,600
SELECTION OCCURS ON THE SURFACE

517
00:15:54,600 --> 00:15:57,240
OF THE PROTEINS AS A FIRST ORDER

518
00:15:57,240 --> 00:15:58,880
PREDICTOR OF WHAT THE

519
00:15:58,880 --> 00:16:00,000
INTERACTION SURFACE IS BETWEEN

520
00:16:00,000 --> 00:16:01,280
HOST AND VIRAL PROTEINS MIGHT BE

521
00:16:01,280 --> 00:16:01,680
LIKE.

522
00:16:01,680 --> 00:16:03,160
SO IN OTHER WORDS, RATHER THAN

523
00:16:03,160 --> 00:16:05,760
FOCUSING ON THE MOST -- PARTS OF

524
00:16:05,760 --> 00:16:07,440
PROTEINS LIKE MOST MOLECULAR

525
00:16:07,440 --> 00:16:08,840
BIOLOGISTS, HERE WE'RE ACTUALLY

526
00:16:08,840 --> 00:16:12,240
FOCUSED ON THE LEAST -- PARTS OF

527
00:16:12,240 --> 00:16:13,320
THE PROTEIN IN ORDER TO

528
00:16:13,320 --> 00:16:15,080
DETERMINE WHAT THE SPECIFICITY

529
00:16:15,080 --> 00:16:16,400
DOMAINS MIGHT BE.

530
00:16:16,400 --> 00:16:17,960
ALONG THE WAY WE REALIZED WE

531
00:16:17,960 --> 00:16:19,280
LEARNED A LOT ABOUT

532
00:16:19,280 --> 00:16:19,960
SUSCEPTIBILITY DETERMINANTS WHEN

533
00:16:19,960 --> 00:16:20,560
WE DO THIS.

534
00:16:20,560 --> 00:16:22,640
SO THERE ARE MANY INSTANCES

535
00:16:22,640 --> 00:16:23,720
WHERE ONE PARTICULAR VIRUS IS

536
00:16:23,720 --> 00:16:25,720
HIGHLY PATHOGENIC TO ONE SPECIES

537
00:16:25,720 --> 00:16:28,120
BUT VERY CLOSELY RELATED SPECIES

538
00:16:28,120 --> 00:16:30,520
IS ALMOST COMPLETELY IMMUNE.

539
00:16:30,520 --> 00:16:32,840
AND WE REALLY SORT OF

540
00:16:32,840 --> 00:16:33,720
HYPOTHESIZED IN THE EARLY DAYS

541
00:16:33,720 --> 00:16:35,880
OF GENOMICS, THIS MUST BE

542
00:16:35,880 --> 00:16:37,320
BECAUSE OUR GENE REPERTOIRES ARE

543
00:16:37,320 --> 00:16:37,960
ACTUALLY DIFFERENT.

544
00:16:37,960 --> 00:16:39,680
IT TURNS OUT THEY'RE NOT TOTALLY

545
00:16:39,680 --> 00:16:40,360
DIFFERENT, THEY'RE BASICALLY

546
00:16:40,360 --> 00:16:45,200
ALMOST THE SAME, BUT THE --

547
00:16:45,200 --> 00:16:46,600
WE'VE EACH ENCOUNTERED A

548
00:16:46,600 --> 00:16:48,040
DIFFERENT PRIVATE HISTORY OF

549
00:16:48,040 --> 00:16:48,920
PATHOGENIC VIRUSES.

550
00:16:48,920 --> 00:16:50,440
AND WHAT'S REALLY SPECTACULAR

551
00:16:50,440 --> 00:16:54,680
IS, WE CAN COMPLETELY GRAFT THIS

552
00:16:54,680 --> 00:16:56,360
TUNING FROM ONE SHE SHE'S INTO

553
00:16:56,360 --> 00:16:58,640
THE OTHER JUST BY MAKING SIGNAL

554
00:16:58,640 --> 00:16:59,760
AMINO ACID CHANGES AT THE

555
00:16:59,760 --> 00:17:00,600
CRITICAL INTERFACES AND THAT'S

556
00:17:00,600 --> 00:17:01,640
WHAT I'M GOING TO SHOW YOU

557
00:17:01,640 --> 00:17:02,160
TODAY.

558
00:17:02,160 --> 00:17:03,880
WE'VE DONE THIS FOR NEARLY A

559
00:17:03,880 --> 00:17:05,200
DOZEN ANTIVIRAL PROTEINS.

560
00:17:05,200 --> 00:17:06,520
THEY ALL HAVE COMPLETELY

561
00:17:06,520 --> 00:17:07,400
DIFFERENT MECHANISMS.

562
00:17:07,400 --> 00:17:09,280
SOME OF THEM ARE UBIQUITIN

563
00:17:09,280 --> 00:17:11,480
LIGASES, SOME OF THEM ARE DEAM

564
00:17:11,480 --> 00:17:12,880
NAISES, SOME OF THES ARE PROTEIN

565
00:17:12,880 --> 00:17:13,280
KINASE.

566
00:17:13,280 --> 00:17:14,920
THEY ALL WORK AGAINST COMPLETELY

567
00:17:14,920 --> 00:17:17,120
DIFFERENT CLASSES OF VIRUSES

568
00:17:17,120 --> 00:17:17,680
ENTIRELY.

569
00:17:17,680 --> 00:17:19,640
AND YET IN EACH CASE, WE CAN USE

570
00:17:19,640 --> 00:17:22,360
THIS POSITIVE SELECTION DRIVEN

571
00:17:22,360 --> 00:17:24,120
APPROACH TO CORRECTLY PREDICT

572
00:17:24,120 --> 00:17:25,680
THE INTERACTION SURFACE AND

573
00:17:25,680 --> 00:17:27,640
GRAFT CHANGES THAT WILL MAKE THE

574
00:17:27,640 --> 00:17:28,920
HOSE MORE FROM A LOSING SIDE TO

575
00:17:28,920 --> 00:17:30,800
A WINNING SIDE, WHICH MEANS THAT

576
00:17:30,800 --> 00:17:32,560
REALLY THE RATE LIMITING STEP TO

577
00:17:32,560 --> 00:17:34,000
DICTATE THE COURSE OF THE VIRUS

578
00:17:34,000 --> 00:17:35,640
INFECTION IN ALL OF THESE CASES

579
00:17:35,640 --> 00:17:37,960
IS WHAT IS THE BINDING AFFINITY

580
00:17:37,960 --> 00:17:39,040
OF THE INITIAL INTERACTIONS

581
00:17:39,040 --> 00:17:40,240
BETWEEN THE VIRAL AND THE

582
00:17:40,240 --> 00:17:41,960
IMMUNITY PROTEINS, WHICH IS WHY

583
00:17:41,960 --> 00:17:45,360
THIS APPROACH IS ACTUALLY SO

584
00:17:45,360 --> 00:17:46,680
CONSEQUENTIAL.

585
00:17:46,680 --> 00:17:47,920
IF YOU'D LIKE TO READ A LITTLE

586
00:17:47,920 --> 00:17:49,640
BIT MORE ABOUT THIS, HERE'S A

587
00:17:49,640 --> 00:17:51,080
SLIGHTLY OUT OF DATE REVIEW

588
00:17:51,080 --> 00:17:54,440
WRITTEN BY A FORMER POSTDOC,

589
00:17:54,440 --> 00:17:58,960
MATADOR TEE, IMATT DOHERTY, IN .

590
00:17:58,960 --> 00:18:02,000
TODAY I'M GOING TO PRESENT TWO

591
00:18:02,000 --> 00:18:05,280
VIGNETTES.

592
00:18:05,280 --> 00:18:06,600
THE FIRST PROTEIN I'VE CHOSEN TO

593
00:18:06,600 --> 00:18:09,680
TALK TO YOU ABOUT IS A PROTEIN

594
00:18:09,680 --> 00:18:10,440
CALLED TRIM5ALPHA, BECAUSE THIS

595
00:18:10,440 --> 00:18:12,200
IS ACTUALLY WHAT I USE TO GET

596
00:18:12,200 --> 00:18:13,240
INTO THE BUSINESS MYSELF WHEN I

597
00:18:13,240 --> 00:18:16,080
WAS STARTING MY LAB MORE THAN

598
00:18:16,080 --> 00:18:19,880
TWO DECADES AGO NOW ALMOST.

599
00:18:19,880 --> 00:18:21,800
SO TRIM5 WAS ACTUALLY DISCOVERED

600
00:18:21,800 --> 00:18:26,440
IN A BEAUTIFUL SCREEN DONE, ALL

601
00:18:26,440 --> 00:18:28,320
MONKEYS LIKE RHESUS MACAQUES

602
00:18:28,320 --> 00:18:29,840
CANNOT GET INFECTED WITH HIV-1

603
00:18:29,840 --> 00:18:31,600
AND THIS PROTECTION IS ACTUALLY

604
00:18:31,600 --> 00:18:32,560
AT THE CELLULAR LEVEL.

605
00:18:32,560 --> 00:18:36,000
IT TURNS OUT WHEN HIV-1 ENTERS

606
00:18:36,000 --> 00:18:38,400
THE SHELL AND SHEDS ITS ENVELOPE

607
00:18:38,400 --> 00:18:42,000
AT THE CELL SURFACE, IT ENTERS

608
00:18:42,000 --> 00:18:46,160
THIS PROTEINACEOUS -- TRIM 5 IS

609
00:18:46,160 --> 00:18:47,920
ACTUALLY A CYTOPLASMIC SENT NIL

610
00:18:47,920 --> 00:18:49,440
WHICH IS BASICALLY ALWAYS

611
00:18:49,440 --> 00:18:50,720
EXPRESSED, ALWAYS AROUND, AND IT

612
00:18:50,720 --> 00:18:54,040
INTERCEDES AND FORMS A

613
00:18:54,040 --> 00:18:54,680
LATTICE-LIKE STRUCTURE, LEADING

614
00:18:54,680 --> 00:18:57,880
TO THE RAPID DEGRADATION OF THIS

615
00:18:57,880 --> 00:18:59,120
RETROVIRAL CAPSID.

616
00:18:59,120 --> 00:19:02,040
PREVENTING THE VIRUS FROM

617
00:19:02,040 --> 00:19:04,200
UNDERGOING ITS OTHERWISE NORMAL

618
00:19:04,200 --> 00:19:05,000
CYCLE.

619
00:19:05,000 --> 00:19:08,720
THE ENTIRE SUCCESS OF TRIM 5 IS

620
00:19:08,720 --> 00:19:12,200
DICTATED BY THE KINETICS OF THE

621
00:19:12,200 --> 00:19:13,400
INTERACTION OF THE TRIM

622
00:19:13,400 --> 00:19:14,480
5 PROTEIN TO THE CAPSID CORE.

623
00:19:14,480 --> 00:19:18,000
SO THE REASON RHESUS IS SO

624
00:19:18,000 --> 00:19:20,840
SUCCESSFUL IS IT HAS EXTREMELY

625
00:19:20,840 --> 00:19:24,040
HIGH AIF I WANT FOR THE CAPSID.

626
00:19:24,040 --> 00:19:26,760
 -- WHICH IS PROTECTIVE AGAINST

627
00:19:26,760 --> 00:19:27,840
MANY RETROVIRUSES BUT OUR

628
00:19:27,840 --> 00:19:29,480
VERSION IS NOT EFFECTIVE AT

629
00:19:29,480 --> 00:19:30,800
CORRECTLY BINDING THE HIV-1

630
00:19:30,800 --> 00:19:32,320
CAPSID, WHICH IS WHY WE DO NOT

631
00:19:32,320 --> 00:19:33,880
HAVE BIOLOGICALLY MEANINGFUL

632
00:19:33,880 --> 00:19:35,720
PROTECTION AFFORDED BY THE HUMAN

633
00:19:35,720 --> 00:19:36,800
VERSION OF TRIM 5.

634
00:19:36,800 --> 00:19:39,760
SO MANY YEARS AGO, ARMED WITH

635
00:19:39,760 --> 00:19:41,200
THIS SORT OF PARADIGM OF OUR

636
00:19:41,200 --> 00:19:42,520
GENETIC CONFLICTS AND ARMS

637
00:19:42,520 --> 00:19:43,800
RACES, THIS TIME BETWEEN TRIM

638
00:19:43,800 --> 00:19:47,880
5 AND THE CAPSID GENE OF HIV-1,

639
00:19:47,880 --> 00:19:49,120
WE THOUGHT WE COULD ACTUALLY

640
00:19:49,120 --> 00:19:50,960
PREDICT WHAT THE INTERACTION

641
00:19:50,960 --> 00:19:52,160
INTERPHASE BETWEEN TRIM 5 AND

642
00:19:52,160 --> 00:19:54,000
CAPSID WOULD BE, AGAIN BY TAKING

643
00:19:54,000 --> 00:19:56,640
A LOOK AT WHERE THE RAPID

644
00:19:56,640 --> 00:19:57,920
EVOLUTION OF TRIM 5 MIGHT HAVE

645
00:19:57,920 --> 00:19:58,480
TAKEN PLACE.

646
00:19:58,480 --> 00:20:01,440
AND TO OUR SURPRISE, EVEN THOUGH

647
00:20:01,440 --> 00:20:04,320
TRIM 5 IS NEARLY 600 AMINO

648
00:20:04,320 --> 00:20:05,840
ACIDS, ALMOST ALL OF THE RAPID

649
00:20:05,840 --> 00:20:07,240
EVOLUTION IN TRIM 5 OCCURS IN

650
00:20:07,240 --> 00:20:09,760
THIS VERY TIGHT WIN DOLE, 11

651
00:20:09,760 --> 00:20:11,200
AMINO ACID STRETCH IN HUMANS,

652
00:20:11,200 --> 00:20:14,040
WHICH IS A 13 AMINO STRETCH IN

653
00:20:14,040 --> 00:20:14,800
RHESUS.

654
00:20:14,800 --> 00:20:16,400
SO IT'S ALMOST AS IF YOU

655
00:20:16,400 --> 00:20:17,640
BASICALLY FOCUSED ALL OF THE

656
00:20:17,640 --> 00:20:20,040
ENERGY OR ALL OF THE SUBSEQUENT

657
00:20:20,040 --> 00:20:21,760
INTERACTIONS DOWN TO JUST ONE

658
00:20:21,760 --> 00:20:23,320
DOMAIN OF THE V1 LOOP.

659
00:20:23,320 --> 00:20:27,160
AS I POINTED OUT EARLIER, HUMAN

660
00:20:27,160 --> 00:20:28,800
TRIM 5 -- ONLY TWOFOLD

661
00:20:28,800 --> 00:20:30,280
PROTECTION AGAINST HIV-1 IN

662
00:20:30,280 --> 00:20:32,680
SIMILAR ASSAYS, WHEREAS RHESUS

663
00:20:32,680 --> 00:20:35,280
TRIM 5 ENCODES NEARLY 100 FOLD

664
00:20:35,280 --> 00:20:37,920
PROTECTION, WHICH OBVIOUS IS

665
00:20:37,920 --> 00:20:38,880
BIOLOGICALLY PROTECTIVE.

666
00:20:38,880 --> 00:20:39,960
INTERESTINGLY, HOWEVER, JUST

667
00:20:39,960 --> 00:20:41,360
TAKING THE V1 LOOP, WHICH

668
00:20:41,360 --> 00:20:43,560
REMEMBER IS THE MOST RAPIDLY

669
00:20:43,560 --> 00:20:45,760
EVOLVING PART OF TRIM 5 AND

670
00:20:45,760 --> 00:20:48,600
SWAPPING IT FROM RHESUS INTO

671
00:20:48,600 --> 00:20:50,400
HUMAN IS ABLE TO CONFER NEARLY

672
00:20:50,400 --> 00:20:51,680
COMPLETE PROTECTION IN THE

673
00:20:51,680 --> 00:20:53,560
OTHERWISE INEFFECTIVE HUMAN TRIM

674
00:20:53,560 --> 00:20:54,040
5 BACKBONE.

675
00:20:54,040 --> 00:20:56,640
THIS IS ONE OF THOSE EXAMPLES WE

676
00:20:56,640 --> 00:20:58,080
YOU CAN SEE HOW RAPID EVOLUTION

677
00:20:58,080 --> 00:20:59,640
CAN GUIDE US TO THE INTERFACES

678
00:20:59,640 --> 00:21:01,200
WHERE WE CAN ACTUALLY GRAFT

679
00:21:01,200 --> 00:21:02,680
SPECIFICITY FROM ONE BACKBONE

680
00:21:02,680 --> 00:21:03,520
INTO THE OTHER.

681
00:21:03,520 --> 00:21:05,880
EVEN MORE SPECTACULARLY, JUST

682
00:21:05,880 --> 00:21:07,680
ONE AMINO ACID CHANGE AT ONE OF

683
00:21:07,680 --> 00:21:10,600
THESE CRITICAL POSITIONS, THIS

684
00:21:10,600 --> 00:21:12,560
PROLINE AND SORT OF AN ARGININE

685
00:21:12,560 --> 00:21:15,720
IS ABLE TO CONFER WHAT WOULD BE

686
00:21:15,720 --> 00:21:16,400
BIOLOGICALLY MEANINGFUL

687
00:21:16,400 --> 00:21:17,880
PROTECTION IN THE HUMAN TRIM

688
00:21:17,880 --> 00:21:18,680
5 BACKBONE.

689
00:21:18,680 --> 00:21:19,640
YES?

690
00:21:19,640 --> 00:21:20,360
>> [INAUDIBLE]

691
00:21:20,360 --> 00:21:23,040
>> THIS IS THE QUALIFIED
UNIT OF

692
00:21:23,040 --> 00:21:23,480
PROTECTION.

693
00:21:23,480 --> 00:21:24,600
I'LL TALK MORE ABOUT THE ASSAY

694
00:21:24,600 --> 00:21:25,440
IN A FEW MINUTES.

695
00:21:25,440 --> 00:21:28,480
BUT THIS IS JUST A FULL

696
00:21:28,480 --> 00:21:29,480
PROTECTION RELATIVE TO AN EMPTY

697
00:21:29,480 --> 00:21:33,560
VECTOR CONTROL.

698
00:21:33,560 --> 00:21:35,080
SO THIS JUST BASICALLY PROVIDES

699
00:21:35,080 --> 00:21:36,720
THE EXAMPLE THAT YOU CAN HAVE

700
00:21:36,720 --> 00:21:37,960
SINGLE AMINO ACID CHANGES THAT

701
00:21:37,960 --> 00:21:40,120
COULD ACTUALLY BE MEANINGFULLY

702
00:21:40,120 --> 00:21:40,760
PROTECTIVE.

703
00:21:40,760 --> 00:21:42,120
I'LL JUST PREEMPT THE QUESTIONS

704
00:21:42,120 --> 00:21:44,640
HERE THAT UNFORTUNATELY, WE DO

705
00:21:44,640 --> 00:21:46,040
NOT HAVE ANY STANDING RADIATION

706
00:21:46,040 --> 00:21:48,320
IN THE V1 LOOP THAT WOULD BE

707
00:21:48,320 --> 00:21:50,200
PROTECTIVE AGAINST HIV-1 DUE TO

708
00:21:50,200 --> 00:21:52,400
AN ADAPTIVE SWEEP THAT WENT

709
00:21:52,400 --> 00:21:53,400
THROUGH TRIM 5 RIGHT OF THE OUT

710
00:21:53,400 --> 00:21:55,480
OF AFRICA SORT OF MIGRATION OF

711
00:21:55,480 --> 00:21:59,080
HUMANS, WE WIPED OUT ALL

712
00:21:59,080 --> 00:22:00,480
POLYMORPHISMS AND WE'VE NOT

713
00:22:00,480 --> 00:22:02,040
RECOVERED ENOUGH TO BE

714
00:22:02,040 --> 00:22:03,240
PROTECTIVE LANDSCAPE HERE.

715
00:22:03,240 --> 00:22:05,960
HOWEVER, TRIM 5 IS VERY

716
00:22:05,960 --> 00:22:09,880
POLYMORPHIC IN ORWELL MONKEYS.

717
00:22:09,880 --> 00:22:11,760
THIS PROJECT STARTED OFF WITH

718
00:22:11,760 --> 00:22:14,600
THIS VERY OLD STUDY WHERE WE

719
00:22:14,600 --> 00:22:16,240
SHOWED -- CAN BE RAPIDLY EVOLVE

720
00:22:16,240 --> 00:22:19,000
AND CONFER PROTECTION, BUT A NEW

721
00:22:19,000 --> 00:22:20,840
POSTDOC JOINED THE LAB AND SHE

722
00:22:20,840 --> 00:22:22,960
WAS REREADING ALL THE OLD LAB

723
00:22:22,960 --> 00:22:24,480
PAPERS AND SHE BASICALLY

724
00:22:24,480 --> 00:22:26,000
REALIZED YOU CALL THIS RAPID

725
00:22:26,000 --> 00:22:27,400
EVOLUTION BUT THERE'S NOT THAT

726
00:22:27,400 --> 00:22:29,520
MANY CHANGES IF YOU THINK ABOUT

727
00:22:29,520 --> 00:22:31,000
THEM, IT'S ALSO AS IF EVOLUTION

728
00:22:31,000 --> 00:22:32,400
IS MOVING WITHIN A BOX WHERE

729
00:22:32,400 --> 00:22:36,640
ONLY A FEW AMINO ACID -- IS THAT

730
00:22:36,640 --> 00:22:39,040
CONSTRAINED OR AN INSTANCE WHERE

731
00:22:39,040 --> 00:22:41,520
HELPFUL MUTATIONS ARE REALLY

732
00:22:41,520 --> 00:22:43,320
RARE, OR THESE ARE THE MUTATIONS

733
00:22:43,320 --> 00:22:44,720
THAT HAPPENED TO GET FIXED AND

734
00:22:44,720 --> 00:22:46,600
MAYBE THERE'S A WIDE SPECTRUM OF

735
00:22:46,600 --> 00:22:47,880
MUTATIONS TO CHOOSE FROM.

736
00:22:47,880 --> 00:22:48,680
IRONICALLY, WE DON'T HAVE THE

737
00:22:48,680 --> 00:22:50,200
MEANS TO DISTINGUISH BETWEEN

738
00:22:50,200 --> 00:22:51,320
THOSE POSSIBILITIES BECAUSE WE

739
00:22:51,320 --> 00:22:53,360
ARE LOOKING AT ALL OF THE

740
00:22:53,360 --> 00:22:54,120
SUCCESSFUL TRIM 5 VARIANTS,

741
00:22:54,120 --> 00:22:54,480
RIGHT?

742
00:22:54,480 --> 00:22:56,000
THESE ARE ALL VARIANTS THAT

743
00:22:56,000 --> 00:22:57,240
FOUGHT OFF SOMETHING AND HAVE

744
00:22:57,240 --> 00:22:57,560
SURVIVED.

745
00:22:57,560 --> 00:23:00,520
SO WE CAN SEPARATE MUTATION FROM

746
00:23:00,520 --> 00:23:00,960
SELECTION.

747
00:23:00,960 --> 00:23:02,400
SO SHE DECIDED THAT THAT'S THE

748
00:23:02,400 --> 00:23:04,240
PROJECT SHE WANTED TO DO, MOSTLY

749
00:23:04,240 --> 00:23:05,440
TO PROVE MY EARLIER DISCUSSION

750
00:23:05,440 --> 00:23:06,640
TO BE WRONG.

751
00:23:06,640 --> 00:23:09,640
SO THIS IS THE WORK I'M GOING TO

752
00:23:09,640 --> 00:23:10,040
DESCRIBE TODAY.

753
00:23:10,040 --> 00:23:11,440
SO SHE REALLY WANTED TO ASK THAT

754
00:23:11,440 --> 00:23:13,440
IF I WERE TO LIKEN THE

755
00:23:13,440 --> 00:23:17,920
EVOLUTIONARY LANDSCAPE OF TRIM S

756
00:23:17,920 --> 00:23:21,640
THE SEQUENCE ACCESS OF TRIM

757
00:23:21,640 --> 00:23:22,480
5 MUTATION, WHERE THE HEIGHT OF

758
00:23:22,480 --> 00:23:24,720
THE PEAK DETERMINES HOW MUCH THE

759
00:23:24,720 --> 00:23:25,800
HIV-1 RESTRICTION IS OCCURRING,

760
00:23:25,800 --> 00:23:27,120
YOU CAN SEE THAT RHESUS HAPPENS

761
00:23:27,120 --> 00:23:29,400
TO BE ON ONE OF THE PEAKS, AND

762
00:23:29,400 --> 00:23:30,440
HUMAN TRIM 5 HAPPENS TO BE IN

763
00:23:30,440 --> 00:23:31,520
ONE OF THE VALLEYS.

764
00:23:31,520 --> 00:23:35,360
SO SHE WANTED TO ASK ARE --

765
00:23:35,360 --> 00:23:37,480
SOLUTION JUST VERY RARE, AND IF

766
00:23:37,480 --> 00:23:39,280
YOU OWE KUR ON A WINNING

767
00:23:39,280 --> 00:23:41,600
SOLUTION, IS THAT VERY THA

768
00:23:41,600 --> 00:23:43,560
MUTATIONALLY FRAGILE OR

769
00:23:43,560 --> 00:23:44,080
RESILIENT?

770
00:23:44,080 --> 00:23:45,440
SO TO DO THIS, SHE NEEDED TO

771
00:23:45,440 --> 00:23:46,240
ACTUALLY DO AN EXPERIMENT WHERE

772
00:23:46,240 --> 00:23:47,640
SHE WOULD INTRODUCE ALL POSSIBLE

773
00:23:47,640 --> 00:23:49,040
MUTATIONS AND THEN SUBJECT THEM

774
00:23:49,040 --> 00:23:51,760
TO SELECTION, AND WE CAN DO THAT

775
00:23:51,760 --> 00:23:53,640
THANKS TO NICE ADVANCES IN DEEP

776
00:23:53,640 --> 00:23:55,920
MUTATIONAL SCANNING METHODS

777
00:23:55,920 --> 00:23:57,480
PIONEERED BY STAN FIELDS AND

778
00:23:57,480 --> 00:23:57,920
OTHERS.

779
00:23:57,920 --> 00:24:00,120
SO IN THIS CASE, WE DID NOT

780
00:24:00,120 --> 00:24:02,080
ACTUALLY DO A SCAN OF THE ENTIRE

781
00:24:02,080 --> 00:24:03,280
TRIM 5 BECAUSE WE WERE ONLY

782
00:24:03,280 --> 00:24:05,560
INTERESTED IN THE V1 LOOP SO WE

783
00:24:05,560 --> 00:24:07,320
INTRODUCED ALL POSSIBLE SINGLE

784
00:24:07,320 --> 00:24:10,400
AMINO ACID CHANGES IN THE 

785
00:24:10,400 --> 00:24:12,440
V1 LOOP OF HUMAN TRIM 5 AND WE

786
00:24:12,440 --> 00:24:14,880
INTRODUCED ALL OF THESE VARIANTS

787
00:24:14,880 --> 00:24:16,200
INTO CAT CELLS.

788
00:24:16,200 --> 00:24:18,160
THE CHOICE OF CAT CELLS IS

789
00:24:18,160 --> 00:24:19,360
PARTLY HISTORICAL.

790
00:24:19,360 --> 00:24:22,160
THAT'S THE CELL LINE -- USED TO

791
00:24:22,160 --> 00:24:23,720
DO HIS INITIAL TRIM

792
00:24:23,720 --> 00:24:25,360
5 EXPERIMENTS BUT THAT TURNS OUT

793
00:24:25,360 --> 00:24:27,240
TO BE VERY FORTUITOUS THAT HE

794
00:24:27,240 --> 00:24:28,680
DID THAT BECAUSE CATS AND DOGS

795
00:24:28,680 --> 00:24:29,960
HAVE INDEPENDENTLY LOST THEIR

796
00:24:29,960 --> 00:24:31,520
TRIM 5 FOR REASONS WE CANNOT

797
00:24:31,520 --> 00:24:32,920
ACTUALLY DISCUSS IN THE Q &
A

798
00:24:32,920 --> 00:24:34,360
SECTION, WHICH MEANS THAT ALL OF

799
00:24:34,360 --> 00:24:37,200
THESE CAT CELLS EACH HAS NOW AN

800
00:24:37,200 --> 00:24:40,040
INDIVIDUAL HUMAN TRIM 5 VARIANT,

801
00:24:40,040 --> 00:24:41,920
EACH SLIGHTLY DIFFERENT AT THE

802
00:24:41,920 --> 00:24:43,800
V1 LOOP, AND THAT'S ALL THE TRIM

803
00:24:43,800 --> 00:24:45,000
5 THAT THEY'RE CAPABLE OF

804
00:24:45,000 --> 00:24:45,400
ENCODING.

805
00:24:45,400 --> 00:24:47,400
SO WE SUBJECTED THIS POPULATION

806
00:24:47,400 --> 00:24:49,880
OF CAT CELLS EACH ENCODING A

807
00:24:49,880 --> 00:24:52,000
DIFFERENT HUMAN TRIM 5 TO

808
00:24:52,000 --> 00:24:54,240
INFECTION WITH HIV-1, BUT THIS

809
00:24:54,240 --> 00:24:56,120
HIV-1 HAS BEEN ENGINEERED TO

810
00:24:56,120 --> 00:24:58,000
ONLY ENCODE GSP UPON

811
00:24:58,000 --> 00:24:59,520
INTEGRATION, SO IT DOESN'T HAVE

812
00:24:59,520 --> 00:25:01,600
THE HIV-1 GENOME, IT JUST HAS

813
00:25:01,600 --> 00:25:03,760
THE ABILITY TO INTRODUCE GSP

814
00:25:03,760 --> 00:25:04,320
UPON INTEGRATION.

815
00:25:04,320 --> 00:25:06,440
FOR THE AFICIONADOS I SHOULD

816
00:25:06,440 --> 00:25:08,520
POINT OUT THAT WE DO THIS AS A

817
00:25:08,520 --> 00:25:09,720
HIGH MULTIPLICITY OF INFECTION

818
00:25:09,720 --> 00:25:11,240
BECAUSE WE WANT TO MAXIMIZE

819
00:25:11,240 --> 00:25:13,360
INFECTION RATES IN THIS ASSAY.

820
00:25:13,360 --> 00:25:15,280
SO THIS ASSAY IS GOING TO RESULT

821
00:25:15,280 --> 00:25:18,120
IN TWO CONSEQUENCES.

822
00:25:18,120 --> 00:25:19,320
CONSEQUENCE NUMBER ONE IS YOU'RE

823
00:25:19,320 --> 00:25:20,520
GOING TO TURN CELLS GREEN.

824
00:25:20,520 --> 00:25:22,960
THIS MEANS YOU ARE NOT ABLE TO

825
00:25:22,960 --> 00:25:25,440
PREVENT HIV-1 FROM INTEGRATING

826
00:25:25,440 --> 00:25:27,320
THIS GENOME INTO THE CELL, THAT

827
00:25:27,320 --> 00:25:30,280
MEANS YOU DO NOT HAVE A --

828
00:25:30,280 --> 00:25:30,520
VARIANT.

829
00:25:30,520 --> 00:25:31,840
WE'RE INTERESTED IN THE

830
00:25:31,840 --> 00:25:33,120
NON-GREEN CELLS BECAUSE FOR SOME

831
00:25:33,120 --> 00:25:35,360
REASON, THEY WERE PROTECTED

832
00:25:35,360 --> 00:25:37,640
AGAINST HIV-1, WHICH IS WHY HIV

833
00:25:37,640 --> 00:25:38,840
WAS NOT ABLE TO INTEGRATE INTO

834
00:25:38,840 --> 00:25:39,320
THE GENOME.

835
00:25:39,320 --> 00:25:41,480
SO THIS WOULD BE ENCODING

836
00:25:41,480 --> 00:25:42,360
RESTRICTOR VARIANTS OF TRIM 5,

837
00:25:42,360 --> 00:25:43,680
IT'S JUST WHAT WE ARE INTERESTED

838
00:25:43,680 --> 00:25:46,160
IN, BUT WE ARE ALSO CONVINCED

839
00:25:46,160 --> 00:25:47,960
THAT THERE ARE PROBABLY

840
00:25:47,960 --> 00:25:49,680
UNINFECTED CELLS WHICH, DESPITE

841
00:25:49,680 --> 00:25:52,120
OUR BEST EFFORTS, DID NOT GET

842
00:25:52,120 --> 00:25:54,400
INFECTED WITH HIV WHEN THOSE

843
00:25:54,400 --> 00:25:55,480
WOULD BE A SOURCE OF NOISE AND

844
00:25:55,480 --> 00:25:58,120
WE WANT TO ELIMINATE THEM.

845
00:25:58,120 --> 00:26:02,840
SO SHE SORTED ALL OF THE PF --

846
00:26:02,840 --> 00:26:04,000
NEGATIVE CELLS, SUBJECTED THEM

847
00:26:04,000 --> 00:26:04,480
TO INFECTION.

848
00:26:04,480 --> 00:26:06,560
NOW IT'S VERY UNLIKELY THAT A

849
00:26:06,560 --> 00:26:09,400
CELERY MAINS UNINFECTED IN BOTH

850
00:26:09,400 --> 00:26:10,400
ROUNDS.

851
00:26:10,400 --> 00:26:11,720
SIMPLY BY SEQUENCING THE

852
00:26:11,720 --> 00:26:13,240
STARTING POOL AND ENDING TOOL,

853
00:26:13,240 --> 00:26:15,120
SHE GETS ENRICHMENT SCORES FOR

854
00:26:15,120 --> 00:26:18,360
HOW LIKELY IS IT THAT YOU HAVE A

855
00:26:18,360 --> 00:26:20,680
PROTECTIVE TRIM 5 ALLELE

856
00:26:20,680 --> 00:26:23,440
VARIANT, WE HAVE TESTED ALL

857
00:26:23,440 --> 00:26:24,400
POSSIBLE -- AND I A SED THEM IN

858
00:26:24,400 --> 00:26:27,800
TERMS OF THEIR ENRICHMENT

859
00:26:27,800 --> 00:26:28,600
RELATIVE TO THE BACKGROUND.

860
00:26:28,600 --> 00:26:32,640
THIS IS SORT OF JUST A SANITY

861
00:26:32,640 --> 00:26:34,600
CHECK HERE, WE'VE DONE TWO

862
00:26:34,600 --> 00:26:35,520
BIOLOGICAL REPLICATES OF THIS.

863
00:26:35,520 --> 00:26:36,920
THE SCORES ARE BEAUTIFULLY

864
00:26:36,920 --> 00:26:37,480
CORRELATED.

865
00:26:37,480 --> 00:26:39,560
SO THAT'S OF COURSE VERY

866
00:26:39,560 --> 00:26:40,320
REASSURING.

867
00:26:40,320 --> 00:26:41,680
A SECOND SANITY CHECK CAME WHEN

868
00:26:41,680 --> 00:26:43,200
WE BASICALLY LOOKED AT THE

869
00:26:43,200 --> 00:26:44,600
ENRICHMENT SCORES ON THIS WATER

870
00:26:44,600 --> 00:26:48,520
FOLLOW PLOT, WHERE THE LEFT --

871
00:26:48,520 --> 00:26:49,560
THE MORE RESTRICTIVE YOU ARE.

872
00:26:49,560 --> 00:26:51,600
YOU'LL NOTICE THAT THE WILD TYPE

873
00:26:51,600 --> 00:26:53,360
HUMAN TRIM 5 IS HERE IN THE

874
00:26:53,360 --> 00:26:53,680
CLUSTER.

875
00:26:53,680 --> 00:26:56,400
THERE'S ACTUALLY MORE THAN ONE

876
00:26:56,400 --> 00:26:57,760
TRIM 5 VARIANT THAT ARE

877
00:26:57,760 --> 00:26:58,480
DIFFERENT AT SYNONYMOUS

878
00:26:58,480 --> 00:26:59,040
POSITIONS.

879
00:26:59,040 --> 00:27:00,160
THEY'RE BASICALLY IDENTICAL

880
00:27:00,160 --> 00:27:01,800
BECAUSE THEY ENCODE THE SAME

881
00:27:01,800 --> 00:27:05,840
PROTEIN, EVEN THOUGH I TOLD YOU

882
00:27:05,840 --> 00:27:07,600
THAT HUMAN TRIM 5 IS VERY POOR

883
00:27:07,600 --> 00:27:09,480
AGAINST HIV-1 YOU'LL NOTICE IT

884
00:27:09,480 --> 00:27:12,400
IS STILL STATISTICALLY BETTER

885
00:27:12,400 --> 00:27:15,480
THAN TRIM 5 VARIANTS THAT STOCK

886
00:27:15,480 --> 00:27:16,880
CODONS -- THIS IS A VERY

887
00:27:16,880 --> 00:27:17,960
REASSURING KIND OF STEP THAT WE

888
00:27:17,960 --> 00:27:20,480
ARE MAKING A BIOLOGICALLY

889
00:27:20,480 --> 00:27:21,360
MEANINGFUL PREDICTION ABOUT

890
00:27:21,360 --> 00:27:21,720
RESTRICTION.

891
00:27:21,720 --> 00:27:23,360
WHAT ABOUT TESTING INDIVIDUAL

892
00:27:23,360 --> 00:27:24,000
VARIANTS?

893
00:27:24,000 --> 00:27:25,000
THIS IS ACTUALLY IN RESPONSE TO

894
00:27:25,000 --> 00:27:26,040
THE QUESTION ABOUT THE NATURE OF

895
00:27:26,040 --> 00:27:26,520
THE ASSAY.

896
00:27:26,520 --> 00:27:29,280
SO THE NATURE OF THE ASSAY IS WE

897
00:27:29,280 --> 00:27:30,800
BASICALLY INFECT CELLS WITH

898
00:27:30,800 --> 00:27:37,680
INCREASING VIRAL DOSES BECAUSE

899
00:27:37,680 --> 00:27:40,560
ESSENTIALLY WE'RE ABLE TO

900
00:27:40,560 --> 00:27:41,560
OVERCOME -- IN THE ABSENCE OF

901
00:27:41,560 --> 00:27:42,960
ANY TRIM 5, IT TAKES ABOUT THIS

902
00:27:42,960 --> 00:27:44,840
MUCH VIRUS TO INFECT 10% OF THE

903
00:27:44,840 --> 00:27:45,680
CELLS.

904
00:27:45,680 --> 00:27:47,760
IN THE PRESENCE OF HUMAN TRIM 5,

905
00:27:47,760 --> 00:27:49,320
THIS SHIFT RIGHT WARD, BECAUSE

906
00:27:49,320 --> 00:27:51,080
YOU NEED A LITTLE BIT MORE VIRUS

907
00:27:51,080 --> 00:27:52,920
TO INFECT 10% OF THE CELLS.

908
00:27:52,920 --> 00:27:54,320
WITH RHESUS, IT WOULD SHIFT EVEN

909
00:27:54,320 --> 00:27:54,960
MORE RIGHT WARD.

910
00:27:54,960 --> 00:27:56,560
SO THESE ARE UNITS OF SELECTION

911
00:27:56,560 --> 00:27:58,840
FOR HOW MUCH RESTRICTIVE

912
00:27:58,840 --> 00:28:00,400
POTENTIAL IS PROVIDED BY

913
00:28:00,400 --> 00:28:02,560
INDIVIDUAL VARIANTS IN THE

914
00:28:02,560 --> 00:28:08,000
COURSE OF THEIR HIV-1

915
00:28:08,000 --> 00:28:08,600
PROTECTION.

916
00:28:08,600 --> 00:28:09,800
WHAT'S REALLY NICE IS EVEN

917
00:28:09,800 --> 00:28:11,080
THOUGH SHE TESTED ONLY A HANDFUL

918
00:28:11,080 --> 00:28:15,440
OF THESE VARIANTS, SHE FOUND THE

919
00:28:15,440 --> 00:28:16,680
RESTRICTION BEAUTIFULLY

920
00:28:16,680 --> 00:28:18,520
CORRELATED WITH THE POOR

921
00:28:18,520 --> 00:28:20,480
ENRICHMENT SCORE THEY FOUND IN

922
00:28:20,480 --> 00:28:21,480
HER ONE PART EXPERIMENT WHICH

923
00:28:21,480 --> 00:28:22,600
MEANT THAT THE ASSAY EVEN THOUGH

924
00:28:22,600 --> 00:28:23,800
IT WAS DONE ALL TOGETHER WAS A

925
00:28:23,800 --> 00:28:25,000
BEAUTIFUL KIND OF REFLECTION OF

926
00:28:25,000 --> 00:28:26,200
WHAT THE ACTUAL CONSTRAINTS

927
00:28:26,200 --> 00:28:31,640
MIGHT BE.

928
00:28:31,640 --> 00:28:34,520
SO I WANT TO RETURN TO THIS

929
00:28:34,520 --> 00:28:35,800
WATERFALL PLOT BECAUSE ONE OF

930
00:28:35,800 --> 00:28:36,960
THE SURPRISING THINGS TO US WAS

931
00:28:36,960 --> 00:28:39,240
WE MADE RANDOM MUTATIONS IN THE

932
00:28:39,240 --> 00:28:41,880
V1 LOOP HOPING SOME OF THEM

933
00:28:41,880 --> 00:28:43,440
WOULD BE BETTER, SOME WORSE.

934
00:28:43,440 --> 00:28:44,960
WE FOUND THAT NEARLY 60% OF

935
00:28:44,960 --> 00:28:46,600
THESE RANDOM VARIANTS WERE

936
00:28:46,600 --> 00:28:49,040
ACTUALLY BETTER THAN WILD TYPE

937
00:28:49,040 --> 00:28:50,440
HUMAN TRIM 5 WHICH MEANT THAT

938
00:28:50,440 --> 00:28:52,720
FOR SOME SORT OF UNFORTUNATE

939
00:28:52,720 --> 00:28:54,040
CIRCUMSTANCES WE WERE SITTING IN

940
00:28:54,040 --> 00:28:55,800
THIS VALLEY BUT WE COULD EASILY

941
00:28:55,800 --> 00:28:57,760
BE GO UP A PEAK WHERE WE WOULD

942
00:28:57,760 --> 00:28:59,240
BE PROTECTED WITH JUST A SINGLE

943
00:28:59,240 --> 00:29:00,760
AMINO ACID CHANGE.

944
00:29:00,760 --> 00:29:05,280
SEVTHAT WOULD BE BIOLOGICALLY

945
00:29:05,280 --> 00:29:06,160
MEANINGFUL PROTECTION SO IT WAS

946
00:29:06,160 --> 00:29:07,560
NOT THE CASE THAT HELPFUL

947
00:29:07,560 --> 00:29:09,560
MUTATIONS WERE RARE HERE.

948
00:29:09,560 --> 00:29:11,080
SO WE BECAME VERY INTERESTED IN

949
00:29:11,080 --> 00:29:13,040
UNDERSTANDING WH WHAT'S THE

950
00:29:13,040 --> 00:29:14,040
BIOCHEMICAL BASIS FOR THIS?

951
00:29:14,040 --> 00:29:15,800
BECAUSE THIS SEEMS LIKE, YOU

952
00:29:15,800 --> 00:29:16,800
KNOW, HUMAN TRIM 5 SHOULD BE

953
00:29:16,800 --> 00:29:18,760
DOING A LOT BETTER, AND SO TO DO

954
00:29:18,760 --> 00:29:22,840
THAT, WE BASICALLY MODELED OUR

955
00:29:22,840 --> 00:29:25,200
RESTRICTERS ON THIS KIND OF 2 BY

956
00:29:25,200 --> 00:29:27,400
2 PLOT HERE WHERE THE ROWS

957
00:29:27,400 --> 00:29:30,120
INDICATE EACH POSITION IN THE V.

958
00:29:30,120 --> 00:29:31,400
THE ARROW HEADS JUST INDICATE

959
00:29:31,400 --> 00:29:32,480
THOSE RAPIDLY EVOLVING POSITIONS

960
00:29:32,480 --> 00:29:34,160
THAT I TOLD YOU ABOUT, AND EACH

961
00:29:34,160 --> 00:29:37,280
COLUMN REFERS TO MUTATIONS TO A

962
00:29:37,280 --> 00:29:39,200
PARTICULAR AMINO ACID WITH EACH

963
00:29:39,200 --> 00:29:42,520
OF THE 20 AMINO ACIDS AND CODONS

964
00:29:42,520 --> 00:29:44,600
BECAUSE WE COULD NOT -- THAT IN

965
00:29:44,600 --> 00:29:45,800
OUR MUTATIONAL STRATEGY.

966
00:29:45,800 --> 00:29:47,840
SO WHAT WOULD YOU EXPECT HERE?

967
00:29:47,840 --> 00:29:51,160
THE BLUER YOU ARE, THE MORE

968
00:29:51,160 --> 00:29:54,640
RESTRICTIVE YOU ARE.

969
00:29:54,640 --> 00:29:58,480
OVER THE ENTIRE DIAGRAM IS

970
00:29:58,480 --> 00:29:59,120
DECIDEDLY -- CERTAINLY NOT THAT

971
00:29:59,120 --> 00:30:01,720
HE PROBABLY MADE ANY MONEY OFF.

972
00:30:01,720 --> 00:30:04,080
THAT'S BECAUSE WE HAD THESE VERY

973
00:30:04,080 --> 00:30:05,400
ROW-LIKE AND COLUMN-LIKE

974
00:30:05,400 --> 00:30:07,760
STRUCTURES IN OUR GRAFTING.

975
00:30:07,760 --> 00:30:09,440
SO THE TWO THAT ARE MOST OBVIOUS

976
00:30:09,440 --> 00:30:11,400
IS THAT HUMAN TRIM 5 HAS THESE

977
00:30:11,400 --> 00:30:15,000
DOUBLE ARGININES AT POSITION 33.

978
00:30:15,000 --> 00:30:17,360
IT TURNS OUT THAT ANY AMINO ACID

979
00:30:17,360 --> 00:30:18,760
OTHER THAN AN ARGININE OR A

980
00:30:18,760 --> 00:30:21,280
LYSINE WOULD BE PROTECTIVE.

981
00:30:21,280 --> 00:30:24,040
SO WE'RE SORT OF LIKE DOUBLY

982
00:30:24,040 --> 00:30:26,240
UNFORTUNATE FOR THESE TWO

983
00:30:26,240 --> 00:30:27,440
ARGININES AR WITH WE WOULD BE

984
00:30:27,440 --> 00:30:28,200
BETTER WITH ANYTHING ELSE AT

985
00:30:28,200 --> 00:30:29,520
THESE POSITIONS AND REALLY

986
00:30:29,520 --> 00:30:30,720
UNDERSCORING THAT, YOU CAN ALSO

987
00:30:30,720 --> 00:30:33,560
SEE THAT AT ANY POSITION,

988
00:30:33,560 --> 00:30:35,760
MUTATION TO ACIDIC RESIDUE, A D

989
00:30:35,760 --> 00:30:46,280
OR AN E, WOULD BE ACTUALLY

990
00:30:46,560 --> 00:30:46,920
PROTECTIVE.

991
00:30:46,920 --> 00:30:50,240
I DRAW YOUR ATTENTION TO THIS

992
00:30:50,240 --> 00:30:53,720
ABSOLUTELY CONSERVED GLYCINE

993
00:30:53,720 --> 00:30:55,800
RESIDUE ACROSS ALL MAMMALS AND

994
00:30:55,800 --> 00:30:58,880
YET GLYCINE IS ONE OF THE WORST

995
00:30:58,880 --> 00:31:01,520
RESIDUES TO HAVE AT THIS PO

996
00:31:01,520 --> 00:31:02,640
POSITION IN TERMS OF PROTECTION.

997
00:31:02,640 --> 00:31:03,720
THE REASON I'M NOT GOING TO

998
00:31:03,720 --> 00:31:05,360
FOCUS ON GLYCINE TODAY IS

999
00:31:05,360 --> 00:31:07,440
BECAUSE CHARGE CAN EXPLAIN 90%

1000
00:31:07,440 --> 00:31:09,320
OF WHAT WE SEE ON THIS PLOT.

1001
00:31:09,320 --> 00:31:12,040
SO TO HIGHLIGHT THAT IN

1002
00:31:12,040 --> 00:31:14,320
AGGREGATE TERMS, WILD TYPE

1003
00:31:14,320 --> 00:31:15,760
HAS -- OF PLUS TO.

1004
00:31:15,760 --> 00:31:18,520
IF YOU MAKE THE V1 LOOK MORE

1005
00:31:18,520 --> 00:31:19,560
POSITIVELY CHARGED YOU MAKE IT

1006
00:31:19,560 --> 00:31:21,440
WORSE, BUT AS YOU MAKE THE

1007
00:31:21,440 --> 00:31:22,880
V1 LOOP LESS AND LESS POSITIVELY

1008
00:31:22,880 --> 00:31:24,200
CHARGED, YOU GET MORE AND MORE

1009
00:31:24,200 --> 00:31:24,840
PROTECTIVE.

1010
00:31:24,840 --> 00:31:26,400
SO EVEN THOUGH WE'VE KNOWN ABOUT

1011
00:31:26,400 --> 00:31:28,680
TRIM 5 FOR NEARLY 20 YEARS NOW,

1012
00:31:28,680 --> 00:31:31,880
IT TURNS OUT THAT THE MUTATION

1013
00:31:31,880 --> 00:31:33,280
STRATEGY ALLOWED US TO ACTUALLY

1014
00:31:33,280 --> 00:31:35,040
PREDICT THAT IN FACT THE KEY

1015
00:31:35,040 --> 00:31:38,240
DETERMINANT ABOUT WHETHER TRIM R

1016
00:31:38,240 --> 00:31:43,080
NOT AGAINST HIV-1 IS THE

1017
00:31:43,080 --> 00:31:45,480
POSITIVE CHARGE -- AND A

1018
00:31:45,480 --> 00:31:47,960
PRESUMED POSITIVELY CHARGED --

1019
00:31:47,960 --> 00:31:49,080
CAPSID, AND JENNETTE IS NOW

1020
00:31:49,080 --> 00:31:50,520
DOING SIMILAR EXPERIMENTS ON THE

1021
00:31:50,520 --> 00:31:52,160
CAPSID SIDE IN HER OWN LAB TO

1022
00:31:52,160 --> 00:31:54,440
BASICALLY FULLY KIND OF

1023
00:31:54,440 --> 00:31:56,000
FORMULATE THIS OPINION.

1024
00:31:56,000 --> 00:31:58,200
SO AGAIN RETURNING TO THIS GLASS

1025
00:31:58,200 --> 00:32:01,680
HALF FULL, GLASS HALF EMPTY

1026
00:32:01,680 --> 00:32:02,920
HYPOTHESIS, 30% OF RANDOM

1027
00:32:02,920 --> 00:32:04,120
MUTATIONS CAN CONFER PROTECTION.

1028
00:32:04,120 --> 00:32:06,520
SO THIS IS AN INDICATION THAT

1029
00:32:06,520 --> 00:32:07,840
WINNING SOLUTIONS ARE NOT RARE.

1030
00:32:07,840 --> 00:32:12,120
SO WHAT WE SAW WHEN WE ASSESSED

1031
00:32:12,120 --> 00:32:15,200
PRIMATE TRIM 5s WAS A SMALL

1032
00:32:15,200 --> 00:32:17,840
TIP OF THE ICEBERG OF A GIANT

1033
00:32:17,840 --> 00:32:19,360
ICEBERG OF POSSIBLE RANDOM

1034
00:32:19,360 --> 00:32:20,040
MUTATIONS.

1035
00:32:20,040 --> 00:32:22,880
SO NEXT SHE TURNED HER ATTENTION

1036
00:32:22,880 --> 00:32:24,200
TO WHAT ABOUT TRIM 5 ALREADY IN

1037
00:32:24,200 --> 00:32:26,360
A WINNING POSITION, IS THAT A

1038
00:32:26,360 --> 00:32:28,440
MUTATIONALLY FRAGILE OR

1039
00:32:28,440 --> 00:32:28,880
RESILIENT SOLUTION?

1040
00:32:28,880 --> 00:32:30,640
IN OTHER WORDS, IF YOU GUYS ARE

1041
00:32:30,640 --> 00:32:32,880
SKIERS IN THE AUDIENCE, YOU ARE

1042
00:32:32,880 --> 00:32:36,680
ON A BLACK DIE MONDAY SKI SLOPE,

1043
00:32:36,680 --> 00:32:39,120
EVERY -- DOWN THE FITNESS LAND

1044
00:32:39,120 --> 00:32:39,760
LANDSCAPE.

1045
00:32:39,760 --> 00:32:41,400
OR ARE YOU ON ONE OF THOSE BUNNY

1046
00:32:41,400 --> 00:32:43,400
SLOPES WHERE YOU LEARN HOW TO

1047
00:32:43,400 --> 00:32:44,600
SKI, EVERYTHING IS QUITE GENERAL

1048
00:32:44,600 --> 00:32:45,840
10 AND UNLIKELY TO BREAK ANY

1049
00:32:45,840 --> 00:32:46,560
BONES HERE.

1050
00:32:46,560 --> 00:32:48,120
SO TO DO THIS, SHE DID A

1051
00:32:48,120 --> 00:32:48,680
RECIPROCAL VERSION OF THE

1052
00:32:48,680 --> 00:32:48,960
EXPERIMENT.

1053
00:32:48,960 --> 00:32:55,640
THIS TIME FOCUSING ON RHESUS --

1054
00:32:55,640 --> 00:32:58,480
AND NOW MUTATING EACH OF THE

1055
00:32:58,480 --> 00:33:00,040
V1 RESIDUES AND DOING THE SAME

1056
00:33:00,040 --> 00:33:02,640
INFECTION WITH HIV-1 GFP BUT

1057
00:33:02,640 --> 00:33:03,480
THIS TIME REMEMBER WE STARTED

1058
00:33:03,480 --> 00:33:05,080
OFF WITH SOMETHING THAT WAS

1059
00:33:05,080 --> 00:33:06,320
ALREADY PROTECTIVE AGAINST

1060
00:33:06,320 --> 00:33:07,800
HIV-1, SO NOW WE ARE INTERESTED

1061
00:33:07,800 --> 00:33:09,240
IN THE GREEN CELLS, BECAUSE

1062
00:33:09,240 --> 00:33:10,920
THESE ARE VARIANTS THAT HAVE

1063
00:33:10,920 --> 00:33:12,440
LOST THEIR PROTECTION, SO IT'S

1064
00:33:12,440 --> 00:33:13,760
THE OPPOSITE OF THE ASSAY THAT

1065
00:33:13,760 --> 00:33:15,840
WE DID EARLIER, WHERE WE DNT

1066
00:33:15,840 --> 00:33:17,040
WANT THE GREEN CELLS, NOW WE

1067
00:33:17,040 --> 00:33:17,920
WANT THE GREEN CELLS BECAUSE

1068
00:33:17,920 --> 00:33:20,880
THESE ARE THE LOSS OF FUNCTION

1069
00:33:20,880 --> 00:33:22,960
MUTATIONS THAT ARE INTRODUCED

1070
00:33:22,960 --> 00:33:23,400
INTO RHESUS.

1071
00:33:23,400 --> 00:33:26,440
SO AGAIN IN RHESUS IS

1072
00:33:26,440 --> 00:33:27,920
MUTATIONALLY FRAGILE WE WOULD

1073
00:33:27,920 --> 00:33:29,120
PREDICT MOST WE MADE IN THE

1074
00:33:29,120 --> 00:33:30,080
V1 LOOP WOULD BE LOSS OF

1075
00:33:30,080 --> 00:33:30,640
FUNCTION.

1076
00:33:30,640 --> 00:33:34,560
TO OUR SURPRISE, TH THERE WERE Y

1077
00:33:34,560 --> 00:33:35,880
FEW LOSS OF FUNCTION MUTATIONS.

1078
00:33:35,880 --> 00:33:37,640
IN FACT, THE ONLY MUTATIONS WE

1079
00:33:37,640 --> 00:33:40,960
FOUND THAT WERE IN THE LEFT-HAND

1080
00:33:40,960 --> 00:33:42,640
SIDE ENRICHED FOR THE

1081
00:33:42,640 --> 00:33:45,240
NON-RESTRICTORS, WERE THE TRIM

1082
00:33:45,240 --> 00:33:47,320
5 -- WE HAD MADE TRUNCATION

1083
00:33:47,320 --> 00:33:48,280
MUTATIONS IN THE TRIM 5.

1084
00:33:48,280 --> 00:33:50,040
MOST OF THE RHESUS TRIM

1085
00:33:50,040 --> 00:33:51,360
5 VARIANTS WERE JUST AS GOOD AS

1086
00:33:51,360 --> 00:33:52,600
THE WILD TYPE RHESUS.

1087
00:33:52,600 --> 00:33:59,160
IN FACT, 51% ARE NOT

1088
00:33:59,160 --> 00:34:00,600
DISTINGUISHLIABLE FROM WILD TYPE

1089
00:34:00,600 --> 00:34:01,040
RHESUS.

1090
00:34:01,040 --> 00:34:02,480
WHICH MEANS AMAZINGLY EVEN

1091
00:34:02,480 --> 00:34:06,520
THOUGH THIS IS A PRIMARY LIGAND

1092
00:34:06,520 --> 00:34:08,480
INTERACTION -- IT'S MUTATIONALLY

1093
00:34:08,480 --> 00:34:09,920
RESILIENT ENOUGH THAT IT CAN

1094
00:34:09,920 --> 00:34:11,360
TOLERATE MUTATIONS WITHOUT

1095
00:34:11,360 --> 00:34:13,200
LOSINGITY BASE INTERACTION WITH

1096
00:34:13,200 --> 00:34:14,400
THE HIV-1 CAPSID.

1097
00:34:14,400 --> 00:34:17,280
IS THIS A GENERALLY MUTATIONALLY

1098
00:34:17,280 --> 00:34:18,280
RESILIENT PHENOMENON OR IS THIS

1099
00:34:18,280 --> 00:34:20,680
SOMETHING THAT HAS AN

1100
00:34:20,680 --> 00:34:23,120
EVOLUTIONARY SELECTIVE PROPERTY

1101
00:34:23,120 --> 00:34:24,680
LIKE RHESUS ON TRIM 5?

1102
00:34:24,680 --> 00:34:26,840
WE THOUGHT WE COULD ASK THAT

1103
00:34:26,840 --> 00:34:28,280
QUESTION BY ASKING WHAT IF WE

1104
00:34:28,280 --> 00:34:30,680
WERE TO ENGINEER NEW RESTRICTION

1105
00:34:30,680 --> 00:34:32,760
AND REQUESTS WHETHER THAT IS

1106
00:34:32,760 --> 00:34:33,320
MUTATIONALLY RESILIENT.

1107
00:34:33,320 --> 00:34:34,480
WE CAN DO THAT BECAUSE REMEMBER

1108
00:34:34,480 --> 00:34:36,520
I SHOWED YOU A SINGLE AMINO ACID

1109
00:34:36,520 --> 00:34:38,360
CHANGED FROM RHESUS INTO HUMAN

1110
00:34:38,360 --> 00:34:39,760
TRIM 5 CAN PROVIDE YOU

1111
00:34:39,760 --> 00:34:41,560
SUBSTANTIAL RESTRICTION.

1112
00:34:41,560 --> 00:34:44,840
SO JENNETTE DID YET ANOTHER SCAN

1113
00:34:44,840 --> 00:34:47,160
OF THIS VERY HUMAN TRIM 5 WHERE

1114
00:34:47,160 --> 00:34:48,040
THIS PARTICULAR POSITION HAS

1115
00:34:48,040 --> 00:34:50,000
BEEN CHANGED FROM AN ARGININE TO

1116
00:34:50,000 --> 00:34:51,240
A PROLINE, REMOVING ONE OF THOSE

1117
00:34:51,240 --> 00:34:52,640
ARGININES THAT I TOLD YOU ARE SO

1118
00:34:52,640 --> 00:34:53,960
BAD FOR RESTRICTION.

1119
00:34:53,960 --> 00:34:56,160
AND WHEN SHE DID THAT, SHE

1120
00:34:56,160 --> 00:34:57,840
FOUND, ONCE AGAIN, THAT THIS

1121
00:34:57,840 --> 00:35:00,680
NEWLY ENGINEERED TRIM 5 IS JUST

1122
00:35:00,680 --> 00:35:01,320
AS RESILIENT.

1123
00:35:01,320 --> 00:35:03,280
SO ONCE YOU GO UP THE FITNESS

1124
00:35:03,280 --> 00:35:05,720
LANDSCAPE, IT'S NOT INEVITABLE

1125
00:35:05,720 --> 00:35:07,480
THAT THE NEXT IS GOING TO DRIVE

1126
00:35:07,480 --> 00:35:09,440
YOU -- THIS IS A PRETTY

1127
00:35:09,440 --> 00:35:10,200
INTERESTING PROPERTY THAT HAS

1128
00:35:10,200 --> 00:35:13,520
BEEN GRAFTED WE THINK BECAUSE OF

1129
00:35:13,520 --> 00:35:16,240
ITS INTERACTIONS WITH RAPIDLY

1130
00:35:16,240 --> 00:35:18,280
CHANGING VIRAL PATHOGENS SO THE

1131
00:35:18,280 --> 00:35:19,000
TWO SORT OF QUESTIONS THAT SHE

1132
00:35:19,000 --> 00:35:20,560
WANTED TO ASK, HOW RARE ARE

1133
00:35:20,560 --> 00:35:21,280
WINNING SOLUTIONS.

1134
00:35:21,280 --> 00:35:23,280
THAT WAS A SU SURPRISE BEING

1135
00:35:23,280 --> 00:35:24,640
THEY'RE NOT RARE AT ALL.

1136
00:35:24,640 --> 00:35:27,040
IN FACT EVOLUTION TURNED OUT TO

1137
00:35:27,040 --> 00:35:29,640
BE MISLEADING, AND MANY

1138
00:35:29,640 --> 00:35:31,880
SOLUTIONS TURN OUT TO BE QUITE

1139
00:35:31,880 --> 00:35:34,120
STABLE AND NOT AT ALL

1140
00:35:34,120 --> 00:35:34,680
MUTATIONALLY FRAGILE.

1141
00:35:34,680 --> 00:35:36,320
I JUST WANT TO CONTRAST WHAT SHE

1142
00:35:36,320 --> 00:35:38,200
HAS FOUND HERE WITH WHAT OTHERS

1143
00:35:38,200 --> 00:35:40,400
HAVE FOUND WHEN THEY DO SCANNING

1144
00:35:40,400 --> 00:35:42,120
WITH PROTEIN-PROTEIN INTERACTION

1145
00:35:42,120 --> 00:35:42,600
INTERFACES.

1146
00:35:42,600 --> 00:35:43,960
IN PARTICULAR WHEN YOU COME TO

1147
00:35:43,960 --> 00:35:47,680
LILIGAND BINDING INTERACTIONS,

1148
00:35:47,680 --> 00:35:49,120
WHAT PEOPLE HAVE FOUND IS AS YOU

1149
00:35:49,120 --> 00:35:51,080
GET CLOSER AND CLOSER TO THE

1150
00:35:51,080 --> 00:35:52,440
LIGAND BINDING DOMAIN, YOU GET

1151
00:35:52,440 --> 00:35:55,000
MORE AND MORE DEVASTATING

1152
00:35:55,000 --> 00:35:58,640
EFFECTS OF -- YOU HAVE ALMOST A

1153
00:35:58,640 --> 00:36:01,840
LOCK AND KEY-TYPE MECHANISM

1154
00:36:01,840 --> 00:36:04,040
WHERE ANY NEED THE LOCK YOU NEED

1155
00:36:04,040 --> 00:36:05,320
FOR THE LIGAND INTERACTION.

1156
00:36:05,320 --> 00:36:07,320
IN CONTRAST TO THIS, WE HAVE

1157
00:36:07,320 --> 00:36:11,360
THESE ROLLING HEADLINE -- WHICH

1158
00:36:11,360 --> 00:36:13,920
YOU CAN SEE WOULD BE VERY HUGELY

1159
00:36:13,920 --> 00:36:14,960
BENEFICIAL FOR ANTIVIRAL

1160
00:36:14,960 --> 00:36:16,520
PROTEINS TO ACTUALLY HAVE,

1161
00:36:16,520 --> 00:36:18,160
BECAUSE YOU'RE BASICALLY PLAYING

1162
00:36:18,160 --> 00:36:20,360
THESE AFFINITY-BASED ARMS RACES

1163
00:36:20,360 --> 00:36:22,360
WITH CHANGING VIRAL PATHOGENS.

1164
00:36:22,360 --> 00:36:25,200
SO THIS IS ONE OF THOSE REGIMES

1165
00:36:25,200 --> 00:36:26,640
WHERE IT EASY TO MAKE A

1166
00:36:26,640 --> 00:36:27,600
RESTRICTION HAPPEN BUT HOW TO

1167
00:36:27,600 --> 00:36:30,720
BREAK THE RESTRICTIONS ONCE YOU

1168
00:36:30,720 --> 00:36:32,600
GET MEANS YOU CAN GENERATE

1169
00:36:32,600 --> 00:36:33,160
STANDING VARIATION WITHOUT A

1170
00:36:33,160 --> 00:36:34,760
HUGE COST TO YOUR STANDING SORT

1171
00:36:34,760 --> 00:36:38,200
OF RESTRICTION PR PROFILE AND TE

1172
00:36:38,200 --> 00:36:39,560
STANDING VARIANTS ARE LIKELY TO

1173
00:36:39,560 --> 00:36:42,600
BE BENEFICIAL, WHEN YOU

1174
00:36:42,600 --> 00:36:44,120
ENCOUNTER A NOW VARIANT OR

1175
00:36:44,120 --> 00:36:44,720
PATHOGEN ENTIRELY.

1176
00:36:44,720 --> 00:36:46,120
SO WHAT I HAVEN'T TELL YOU SO

1177
00:36:46,120 --> 00:36:47,120
FAR BUT I WILL RIGHT NOW IS THAT

1178
00:36:47,120 --> 00:36:48,520
THERE'S A REASON WHY WE THINK

1179
00:36:48,520 --> 00:36:49,880
THAT ANTIVIRAL PROTEINS LIKE

1180
00:36:49,880 --> 00:36:52,280
TRIM 5 HAVE THIS VERY UNUSUAL

1181
00:36:52,280 --> 00:36:53,600
ROLLING HILL-LIKE LANDSCAPE,

1182
00:36:53,600 --> 00:36:56,000
WHICH IS THAT THE V1 LOOP EVEN

1183
00:36:56,000 --> 00:36:58,000
IN STRUCTURAL ANALYSIS IS

1184
00:36:58,000 --> 00:36:59,480
BASICALLY UNSTRUSTRUCTURED.

1185
00:36:59,480 --> 00:37:01,280
WHAT THAT MEANS IS THAT IT'S

1186
00:37:01,280 --> 00:37:03,840
REALLY AN ENSEMBLE OF MANY

1187
00:37:03,840 --> 00:37:04,440
DIFFERENT STRUCTURAL STATES

1188
00:37:04,440 --> 00:37:06,560
WHICH WE CANNOT REALLY CAPTURE

1189
00:37:06,560 --> 00:37:08,240
IN ONE PARTICULAR STRUCTURE.

1190
00:37:08,240 --> 00:37:09,880
UNLIKE THE REST OF TRIM 5 WHICH

1191
00:37:09,880 --> 00:37:11,080
IS QUITE NICELY STRUCTURED.

1192
00:37:11,080 --> 00:37:14,680
YOU CAN MABLG IN THIS SITUATIONS

1193
00:37:14,680 --> 00:37:16,040
SITUATION, IT'S ACTUALLY ONE OF

1194
00:37:16,040 --> 00:37:19,080
THE SUBSETS IS ACTUALLY CAPABLE

1195
00:37:19,080 --> 00:37:20,400
OF INTERACTING WITH THE HIV-1

1196
00:37:20,400 --> 00:37:21,720
CAPSID AND THAT'S WHERE WE GET

1197
00:37:21,720 --> 00:37:23,080
THE SPECIFICITY FROM.

1198
00:37:23,080 --> 00:37:23,960
HOWEVER, NO SINGLE MUTATION IS

1199
00:37:23,960 --> 00:37:25,480
GOING TO COMPLETELY BREAK THIS

1200
00:37:25,480 --> 00:37:27,560
ENSEMBLE OF STATES.

1201
00:37:27,560 --> 00:37:29,120
IN FACT, THE VERY FEW MUTATIONS

1202
00:37:29,120 --> 00:37:30,520
THAT DID BREAK THIS ENSEMBLE OF

1203
00:37:30,520 --> 00:37:32,560
STATES IN RHESUS TRIM 5 HAPPEN

1204
00:37:32,560 --> 00:37:33,680
TO BE THINGS WHERE WE HAD

1205
00:37:33,680 --> 00:37:34,680
INTRODUCED PROLINES, WHICH THOSE

1206
00:37:34,680 --> 00:37:36,120
OF YOU WHO ARE SORT OF

1207
00:37:36,120 --> 00:37:37,240
BIOCHEMICALLY INCLINED CAN

1208
00:37:37,240 --> 00:37:38,360
APPRECIATE WOULD BE A BAD THING

1209
00:37:38,360 --> 00:37:41,080
TO INTRODUCE INTO AN

1210
00:37:41,080 --> 00:37:41,920
UNSTRUCTURED LOOP IN ORDER TO

1211
00:37:41,920 --> 00:37:44,080
SORT OF IMPOSE STRUCTURE INTO

1212
00:37:44,080 --> 00:37:44,600
THAT.

1213
00:37:44,600 --> 00:37:45,960
THIS SHOULD BE VERY FAMILIAR TO

1214
00:37:45,960 --> 00:37:48,800
THOSE OF YOU WHO REMEMBER YOUR

1215
00:37:48,800 --> 00:37:49,760
IMEU KNOLL COURSES BECAUSE THIS

1216
00:37:49,760 --> 00:37:52,080
IS EXACTLY WHAT HAPPENS IN THE

1217
00:37:52,080 --> 00:37:54,640
COURSE OF SORT OF AFFINITY

1218
00:37:54,640 --> 00:37:56,680
MATURATION FOR ANTIBODIES, WHERE

1219
00:37:56,680 --> 00:37:58,200
ANTIGEN RECOGNITION SITES START

1220
00:37:58,200 --> 00:38:00,120
OFF IN THIS ENSEMBLE OF

1221
00:38:00,120 --> 00:38:01,320
UNSTRUCTURED STATES, AND AS YOU

1222
00:38:01,320 --> 00:38:02,800
GET MORE AND MORE MATURE AND YOU

1223
00:38:02,800 --> 00:38:04,320
SORT OF GET LESS AND LESS

1224
00:38:04,320 --> 00:38:07,680
DIVERSE IN YOUR EPITOPE

1225
00:38:07,680 --> 00:38:08,680
RECOGNITION, YOU GET MORE AND

1226
00:38:08,680 --> 00:38:12,440
MORE STRUCTURED AND DEFINED, BUT

1227
00:38:12,440 --> 00:38:14,040
REALLY YOU START OFF IN THESE

1228
00:38:14,040 --> 00:38:15,440
ENSEMBLE STATES WHICH GIVES YOU

1229
00:38:15,440 --> 00:38:17,240
THE MAXIMUM ABILITY TO SORT OF

1230
00:38:17,240 --> 00:38:18,360
DIVERGE INTO THESE MULTIPLE KIND

1231
00:38:18,360 --> 00:38:19,800
OF VALLEYS OF AFFINITY

1232
00:38:19,800 --> 00:38:20,440
MATURATION.

1233
00:38:20,440 --> 00:38:22,960
IN FACT, TRIM 5 IS NOT THE ONLY

1234
00:38:22,960 --> 00:38:24,520
PROTEIN THAT WE SEE THIS IN.

1235
00:38:24,520 --> 00:38:26,320
I'M GOING TO SORT OF SWITCH TO

1236
00:38:26,320 --> 00:38:28,040
OUR SECOND VIGNETTE NOW AND

1237
00:38:28,040 --> 00:38:30,720
FOCUS ON ANOTHER ANTIVIRAL GENE

1238
00:38:30,720 --> 00:38:32,360
CALLED MXA JUST TO MAKE A

1239
00:38:32,360 --> 00:38:33,120
DIFFERENT POINT, WHERE ONCE

1240
00:38:33,120 --> 00:38:34,560
AGAIN THE HERO OF THE STORY, IF

1241
00:38:34,560 --> 00:38:36,160
YOU WILL, HAPPENS TO BE THIS

1242
00:38:36,160 --> 00:38:37,720
UNSTRUCTURED LOOP CALLED LOOP

1243
00:38:37,720 --> 00:38:39,600
L4, WHICH IS THE PRIMARY

1244
00:38:39,600 --> 00:38:41,800
DETERMINANT FOR AFFINITY FOR A

1245
00:38:41,800 --> 00:38:42,800
COMPLETELY DIFFERENT CLASS OF

1246
00:38:42,800 --> 00:38:43,760
VIRUS AS WELL.

1247
00:38:43,760 --> 00:38:44,880
SO THE DISORDERED LOOPS REALLY

1248
00:38:44,880 --> 00:38:46,440
PROVIDE THE EVOLUTIONARY

1249
00:38:46,440 --> 00:38:47,960
FLEXIBILITY THAT ALLOWS THESE

1250
00:38:47,960 --> 00:38:49,240
ANTIVIRAL PROTEINS TO KEEP PACE

1251
00:38:49,240 --> 00:38:53,760
WITH CHANGING VIRAL PATHOGENS.

1252
00:38:53,760 --> 00:38:55,080
SO WHAT IS MXA?

1253
00:38:55,080 --> 00:38:56,640
IT'S AN INTERFERON TRIGGER GENE

1254
00:38:56,640 --> 00:38:58,400
WHICH IS ONE OF THOSE MANY ALARM

1255
00:38:58,400 --> 00:39:00,120
GENES THAT YOU TURN ON WHEN YOU

1256
00:39:00,120 --> 00:39:04,200
SENSE THAT SOME VIRAL PATHOGEN

1257
00:39:04,200 --> 00:39:06,560
IS TAKING OVER YOUR BODY.

1258
00:39:06,560 --> 00:39:08,080
MXA HAPPENS TO AB VERY CLOSE

1259
00:39:08,080 --> 00:39:09,800
RELATIVE IN EVOLUTIONARY TERMS

1260
00:39:09,800 --> 00:39:13,920
OF A PROTEIN CALLED DYNAMIN,

1261
00:39:13,920 --> 00:39:18,640
IMPORTANT FOR MEDIATING ENDO

1262
00:39:18,640 --> 00:39:20,280
CYTOSIS AS THEY RE-ENTER THE

1263
00:39:20,280 --> 00:39:22,600
CYTOPLASM.

1264
00:39:22,600 --> 00:39:24,480
MXA IS NOT ESSENTIAL AND IS

1265
00:39:24,480 --> 00:39:26,240
ACTUALLY DEDICATED TO A ROLE IN

1266
00:39:26,240 --> 00:39:28,200
ANTIVIRAL IMMUNITY.

1267
00:39:28,200 --> 00:39:30,520
PEOPLE IN THE IMMUNOLOGY WORLD

1268
00:39:30,520 --> 00:39:32,480
REALLY REVERE MXA BECAUSE IT'S

1269
00:39:32,480 --> 00:39:34,400
THE VERY FIRST INNATE ANTIVIRAL

1270
00:39:34,400 --> 00:39:35,680
PROTEIN TO BE DISCOVERED IN

1271
00:39:35,680 --> 00:39:36,120
MAMMALS.

1272
00:39:36,120 --> 00:39:37,960
IT WAS DISCOVERED BECAUSE OF A

1273
00:39:37,960 --> 00:39:39,240
HAPPY ACCIDENT, LET'S CALL IT

1274
00:39:39,240 --> 00:39:41,320
THAT, OF MOUSE BREEDING WHERE

1275
00:39:41,320 --> 00:39:42,600
MOST LABORATORY STRAINS OF MICE

1276
00:39:42,600 --> 00:39:46,560
HAPPEN TO BE DELETED FOR THE MX

1277
00:39:46,560 --> 00:39:47,000
LOCUS.

1278
00:39:47,000 --> 00:39:48,800
THIS WAS DISCOVERED MANY YEARS

1279
00:39:48,800 --> 00:39:52,400
LATER, WHICH MAKES THESE STRAINS

1280
00:39:52,400 --> 00:39:54,840
EXQUISITELY SUSCEPTIBLE TO BOTH

1281
00:39:54,840 --> 00:39:56,800
HUMAN AND BIRD INFLUENZA.

1282
00:39:56,800 --> 00:39:57,880
MOST STRAINS ARE DEAD WITHIN

1283
00:39:57,880 --> 00:39:58,760
FOUR DAYS OF INFECTION.

1284
00:39:58,760 --> 00:39:59,880
THIS IS A PRETTY SIGNIFICANT

1285
00:39:59,880 --> 00:40:00,440
INFECTION.

1286
00:40:00,440 --> 00:40:01,560
WHEREAS IF YOU WERE TO RESTORE

1287
00:40:01,560 --> 00:40:04,880
THE MOUSE MX1 GENE OR EVEN BRING

1288
00:40:04,880 --> 00:40:08,520
IN THE HUMAN MXA GENE, YOU CAN

1289
00:40:08,520 --> 00:40:09,120
COMPLETELY PROTECT THESE MICE

1290
00:40:09,120 --> 00:40:11,560
AND YOU CAN DO SO EVEN IN MICE

1291
00:40:11,560 --> 00:40:13,320
THAT ARE MUTATED FOR THE

1292
00:40:13,320 --> 00:40:15,160
INTERFERON RECEPTOR, WHICH MEANS

1293
00:40:15,160 --> 00:40:16,320
THAT NOW YOU DON'T HAVE ACCESS

1294
00:40:16,320 --> 00:40:18,800
TO THOSE 200 GENES THAT PROTECT

1295
00:40:18,800 --> 00:40:19,760
AGAINST VIRUSES.

1296
00:40:19,760 --> 00:40:21,200
YOU ONLY HAVE ACCESS TO ONE

1297
00:40:21,200 --> 00:40:23,200
GENE, MXA, AND THAT IS

1298
00:40:23,200 --> 00:40:24,680
SUFFICIENT TO PROTECT YOU LONG

1299
00:40:24,680 --> 00:40:27,440
ENOUGH FOR THE ADAPTIVE IMMUNE

1300
00:40:27,440 --> 00:40:29,040
SYSTEM TO KICK IN AND PROTECT

1301
00:40:29,040 --> 00:40:29,440
YOU.

1302
00:40:29,440 --> 00:40:32,480
SO REMEMBER LIKE THE JOB FOR

1303
00:40:32,480 --> 00:40:34,120
TRIM 5 AND MXA IS NOT TO CLEANSE

1304
00:40:34,120 --> 00:40:36,040
THE BODY OF THE PARTICULAR VIRAL

1305
00:40:36,040 --> 00:40:36,600
INFECTION.

1306
00:40:36,600 --> 00:40:38,200
IT'S JUST TO DELAY THE VIRAL

1307
00:40:38,200 --> 00:40:40,160
INFECTION LONG ENOUGH FOR THE

1308
00:40:40,160 --> 00:40:41,400
ADAPTIVE IMMUNE SYSTEM TO KICK

1309
00:40:41,400 --> 00:40:42,520
IN, EDUCATE ITSELF AND THEN

1310
00:40:42,520 --> 00:40:43,600
CLEANSE THE BODY OF THE

1311
00:40:43,600 --> 00:40:44,040
INFECTION.

1312
00:40:44,040 --> 00:40:46,360
THAT'S REALLY THE PRIMARY JOB OF

1313
00:40:46,360 --> 00:40:50,640
INNATE IMMUNITY IN VERTEBRATES.

1314
00:40:50,640 --> 00:40:52,600
SO WHAT IS MXA ACTING AGAINST?

1315
00:40:52,600 --> 00:40:54,600
I TOLD YOU IT ALREADY WORKS

1316
00:40:54,600 --> 00:40:56,040
AGAINST INFLUENZA AND SUBSEQUENT

1317
00:40:56,040 --> 00:40:57,360
STUDIES SHOW IT ACTUALLY WORKS

1318
00:40:57,360 --> 00:40:58,560
BY RECOGNIZING THE NUCLEAR

1319
00:40:58,560 --> 00:40:59,880
PROTEIN OF INFLUENZA, WHICH IS

1320
00:40:59,880 --> 00:41:01,000
THE PROTEIN THAT ACTS ALMOST

1321
00:41:01,000 --> 00:41:03,840
LIKE A HISTONE TO WRAP AROUND

1322
00:41:03,840 --> 00:41:05,480
THE RNA AND MEDIATE BOTH

1323
00:41:05,480 --> 00:41:06,400
TRANSCRIPTION AND REPLICATION OF

1324
00:41:06,400 --> 00:41:08,560
THIS RNA VIRUS.

1325
00:41:08,560 --> 00:41:11,000
SO I'M GOING TO SORT OF -- IT

1326
00:41:11,000 --> 00:41:12,640
WORKS A LOT LIKE TRIM 5 SO I'M

1327
00:41:12,640 --> 00:41:13,640
ACTUALLY GOING TO JUST GO

1328
00:41:13,640 --> 00:41:16,720
THROUGH THIS SORT OF SENSE OF

1329
00:41:16,720 --> 00:41:17,920
DEJA VU.

1330
00:41:17,920 --> 00:41:19,560
PATRICK MITCHELL, FORMER

1331
00:41:19,560 --> 00:41:21,840
GRADUATE STUDENT IN THE LAB

1332
00:41:21,840 --> 00:41:24,600
REALLY FOCUSED ON MXA BECAUSE

1333
00:41:24,600 --> 00:41:25,920
DESPITE DISCOVERY NEARLY FOUR

1334
00:41:25,920 --> 00:41:27,360
DECADES AGO, WE HAD NO IDEA WHAT

1335
00:41:27,360 --> 00:41:29,000
IT'S USING TO INTERACT WITH THE

1336
00:41:29,000 --> 00:41:31,440
MP PROTEIN.

1337
00:41:31,440 --> 00:41:32,560
 THE

1338
00:41:32,560 --> 00:41:33,640
NP PROTEIN.

1339
00:41:33,640 --> 00:41:36,480
SO ONCE AGAIN, WE USED THIS

1340
00:41:36,480 --> 00:41:37,800
EVOLUTION-GUIDED APPROACH WHERE

1341
00:41:37,800 --> 00:41:39,560
WE REALIZE THAT THERE WERE

1342
00:41:39,560 --> 00:41:40,560
REALLY TWO HOT SPOTS FOR

1343
00:41:40,560 --> 00:41:41,920
POSITIVE SELECTION, AND ONE OF

1344
00:41:41,920 --> 00:41:43,680
THEM HAPPENED TO BE THIS

1345
00:41:43,680 --> 00:41:45,440
UNSTRUCTURED LOOP CALLED LOOP

1346
00:41:45,440 --> 00:41:46,880
L4, WHICH I'VE DRAWN IN HERE

1347
00:41:46,880 --> 00:41:48,160
WITH MY ARTIST'S RENDITION,

1348
00:41:48,160 --> 00:41:49,280
WHICH HAD THE MAJORITY OF

1349
00:41:49,280 --> 00:41:51,160
POSITIVELY SELECTED SITES IN

1350
00:41:51,160 --> 00:41:52,920
THIS, AND WE WONDERED WHETHER

1351
00:41:52,920 --> 00:41:54,760
THIS WAS, IN FACT, THE MISSING

1352
00:41:54,760 --> 00:41:56,920
SPECIFICITY DOMAIN THAT ALLOWED

1353
00:41:56,920 --> 00:41:59,440
MXA TO BIND THE NUCLEAR PROTEINS

1354
00:41:59,440 --> 00:42:00,000
OF INFLUENZA.

1355
00:42:00,000 --> 00:42:01,360
AND INDEED, PATRICK SHOWED THAT

1356
00:42:01,360 --> 00:42:05,320
WITH AN INFLUENCE -- WHERE IN

1357
00:42:05,320 --> 00:42:08,640
THE ABSENCE OF MXA YOU HAVE 100%

1358
00:42:08,640 --> 00:42:10,680
INFECTION, HUMAN MXA IS VERY,

1359
00:42:10,680 --> 00:42:10,960
VERY GOOD.

1360
00:42:10,960 --> 00:42:12,520
IN FACT, IT'S STILL THE VERY

1361
00:42:12,520 --> 00:42:15,280
BEST MXA VARIANT WE'VE FOUND

1362
00:42:15,280 --> 00:42:15,880
AGAINST -- VIRUS.

1363
00:42:15,880 --> 00:42:17,320
WE HAVE NO IDEA WHY BECAUSE THIS

1364
00:42:17,320 --> 00:42:20,120
IS A VIRUS THAT INFECTS MICE BUT

1365
00:42:20,120 --> 00:42:21,720
DOES NOT INFECT HUMANS.

1366
00:42:21,720 --> 00:42:24,160
HUMAN MXA, STRONG PROTECTION SO

1367
00:42:24,160 --> 00:42:26,680
IT'S THE OPPOSITE OF TRIM 5.

1368
00:42:26,680 --> 00:42:28,000
AFRICAN GREEN MONKEY IS NOT

1369
00:42:28,000 --> 00:42:28,600
PROTECTED.

1370
00:42:28,600 --> 00:42:31,160
THESE ARE 90% IDENTICAL AT THE

1371
00:42:31,160 --> 00:42:32,760
AMINO ACID LEVEL AND YET ONE IS

1372
00:42:32,760 --> 00:42:33,840
COMPLETELY PROTECTIVE, THE OTHER

1373
00:42:33,840 --> 00:42:35,040
IS COMPLETELY NOT PROTECTIVE.

1374
00:42:35,040 --> 00:42:36,400
JUST LIKE WHAT YOU CAN SEE FROM

1375
00:42:36,400 --> 00:42:38,440
THE TRIM 5 STORY, SWAPPING IN

1376
00:42:38,440 --> 00:42:40,320
THE MOST RAPIDLY EVOLVING PARTS

1377
00:42:40,320 --> 00:42:43,720
OF THE LOOP L4 REGION BETWEEN

1378
00:42:43,720 --> 00:42:44,960
THESE TWO BACKBONES IS ABLE TO

1379
00:42:44,960 --> 00:42:49,680
CONFER PROTECTION -- YET AGAIN A

1380
00:42:49,680 --> 00:42:53,520
SINGLE AMINO ACID RESIDUE OUT OF

1381
00:42:53,520 --> 00:42:54,720
THE -- IS ABLE TO CONVERT WHAT

1382
00:42:54,720 --> 00:42:56,480
WAS A LOSING SITUATION WITH

1383
00:42:56,480 --> 00:42:59,120
AFRICAN GREEN MONKEY MXA INTO

1384
00:42:59,120 --> 00:43:00,760
ESSENTIALLY A COMPLETELY

1385
00:43:00,760 --> 00:43:02,160
PROTECTIVE SITUATION, HUMAN

1386
00:43:02,160 --> 00:43:02,400
LIFE.

1387
00:43:02,400 --> 00:43:03,960
SO JUST TO REITERATE THAT WE ARE

1388
00:43:03,960 --> 00:43:05,520
ABLE TO USE EVOLUTION-GUIDED

1389
00:43:05,520 --> 00:43:08,240
APPROACH TO IDENTIFIED LOOP L4.

1390
00:43:08,240 --> 00:43:09,800
IT DOES MEDIATE THE TARGET

1391
00:43:09,800 --> 00:43:11,560
RECOGNITION AND SINGLE RESIDUE

1392
00:43:11,560 --> 00:43:13,440
CHANGES CAN DRASTICALLY ALTER

1393
00:43:13,440 --> 00:43:15,480
THE ANTIVIRAL ACTIVITY HERE.

1394
00:43:15,480 --> 00:43:17,400
SO UP TO THIS POINT, EVERYTHING

1395
00:43:17,400 --> 00:43:19,040
I'VE TOLD YOU HAS BEEN A

1396
00:43:19,040 --> 00:43:20,040
RETROSPECTIVE VIEW, WHICH IS

1397
00:43:20,040 --> 00:43:21,120
BASICALLY I'M LOOKING BACKWARDS

1398
00:43:21,120 --> 00:43:23,800
IN EVOLUTION, I'M TRYING TO

1399
00:43:23,800 --> 00:43:25,480
DECIPHER READING THE TEA LEAVES

1400
00:43:25,480 --> 00:43:26,920
OF WHETHER CHANGES HAVE OCCURRED

1401
00:43:26,920 --> 00:43:28,120
AND DESAI FER WHAT THE

1402
00:43:28,120 --> 00:43:28,960
INTERACTION INTERFACES MIGHT BE.

1403
00:43:28,960 --> 00:43:30,520
AND YOU KNOW, I WAS PERFECTLY

1404
00:43:30,520 --> 00:43:31,400
HAPPY TO DO THIS FOR THE

1405
00:43:31,400 --> 00:43:35,040
REMAINDER OF MY CAREER, BUT YOU

1406
00:43:35,040 --> 00:43:36,240
KNOW, GRADUATE STUDENTS COME IN

1407
00:43:36,240 --> 00:43:37,680
AND LIKE YEAH THAT'S BEEN DONE

1408
00:43:37,680 --> 00:43:38,600
BEFORE, I WANT TO DO SOMETHING

1409
00:43:38,600 --> 00:43:39,520
ELSE, WHICH IS WHAT ARE YOU

1410
00:43:39,520 --> 00:43:40,440
GOING TO USE THIS FOR?

1411
00:43:40,440 --> 00:43:42,000
I WAS LIKE WELL I'M GOING TO USE

1412
00:43:42,000 --> 00:43:43,160
THIS TO KEEP MY JOB.

1413
00:43:43,160 --> 00:43:44,640
THAT'S LIKE AN IMPORTANT, LIKE,

1414
00:43:44,640 --> 00:43:45,600
IMPORTANT TASK TO BEGIN.

1415
00:43:45,600 --> 00:43:47,240
SHE SAID NO, NO, BECAUSE YOU

1416
00:43:47,240 --> 00:43:49,000
LEARNED ALL OF THIS STUFF FROM

1417
00:43:49,000 --> 00:43:50,520
EVOLUTION, CAN YOU USE THIS TO

1418
00:43:50,520 --> 00:43:53,200
MAKE SORT OF A MORE SORT OF

1419
00:43:53,200 --> 00:43:55,680
DESIGNER SPECIFICITY INTO A

1420
00:43:55,680 --> 00:43:56,480
ANTIVIRAL PROTEIN THAT DOESN'T

1421
00:43:56,480 --> 00:43:56,800
HAVE IT.

1422
00:43:56,800 --> 00:43:58,800
THIS IS PRE-COVID SO WE WEREN'T

1423
00:43:58,800 --> 00:44:01,080
EVEN THINKING ABOUT SARS COV BUT

1424
00:44:01,080 --> 00:44:02,720
THAT WOULD BE, OF COURSE, VERY

1425
00:44:02,720 --> 00:44:03,960
USEFUL SO WE WONDERED CAN WE USE

1426
00:44:03,960 --> 00:44:05,560
THE SAME PLAY BOOK OF POSITIVE

1427
00:44:05,560 --> 00:44:06,840
SELECTION IDENTIFIED THROUGH

1428
00:44:06,840 --> 00:44:08,920
THIS RETROSPECTIVE ANALYSIS TO

1429
00:44:08,920 --> 00:44:10,600
NOW GO AFTER NEW SPECIFICITIES

1430
00:44:10,600 --> 00:44:14,720
IN THE LABORATORY TO ACTUALLY

1431
00:44:14,720 --> 00:44:15,680
ELICIT THAT AND WHAT IS THE

1432
00:44:15,680 --> 00:44:17,640
LANDSCAPE OF THAT NEW ADAPTIVE

1433
00:44:17,640 --> 00:44:18,400
LANDSCAPE WHICH MIGHT BE

1434
00:44:18,400 --> 00:44:21,440
REVEALED FROM THESE EXPERIMENTS.

1435
00:44:21,440 --> 00:44:23,640
SO THIS IS WHAT SHE DECIDED TO

1436
00:44:23,640 --> 00:44:24,240
DO.

1437
00:44:24,240 --> 00:44:25,320
SHE AGAIN CAME TO MY LAB

1438
00:44:25,320 --> 00:44:26,760
FOLLOWING UP ON PATRICK'S WORK

1439
00:44:26,760 --> 00:44:27,680
AND SHE SAID I'M REALLY

1440
00:44:27,680 --> 00:44:29,240
INTERESTED IN LOOP L4, BUT I'M

1441
00:44:29,240 --> 00:44:31,880
NOT INTERESTED IN THE 20 ODD

1442
00:44:31,880 --> 00:44:33,320
PRIMATE SEQUENCES THAT YOU'VE

1443
00:44:33,320 --> 00:44:34,520
SEQUENCED BECAUSE THAT'S A VERY

1444
00:44:34,520 --> 00:44:41,800
SMALL SUBSET OF THE POSSIBLE

1445
00:44:41,800 --> 00:44:42,240
COMBINATORIAL SPACE.

1446
00:44:42,240 --> 00:44:47,800
I WANT TO EXPLORE WHAT ARE THE

1447
00:44:47,800 --> 00:44:50,560
POSSIBLE STATES THAT MIGHT BE

1448
00:44:50,560 --> 00:44:53,040
REVEALED BY THIS APPROACH.

1449
00:44:53,040 --> 00:44:54,360
SO I SAID THIS SOUNDS LIKE A

1450
00:44:54,360 --> 00:44:56,440
GOOD IDEA, WE SHOULD DO THIS.

1451
00:44:56,440 --> 00:44:57,920
THIS WAS MANY YEARS AGO.

1452
00:44:57,920 --> 00:45:00,480
THIS WOULD NOW BE LIKE A PHONE

1453
00:45:00,480 --> 00:45:02,680
CALL TO TWIST BIOSCIENCES AWAY

1454
00:45:02,680 --> 00:45:06,240
BUT UNFORTUNATELY THAT WAS NOT

1455
00:45:06,240 --> 00:45:07,960
ROSSAN A'S GOOD LUCK, SO SHE

1456
00:45:07,960 --> 00:45:09,840
ASSESSED THEM INDIVIDUALLY IN

1457
00:45:09,840 --> 00:45:12,200
TRIPLICATE FOR FUNCTIONALITY AND

1458
00:45:12,200 --> 00:45:13,160
SHE DID ABOUT A THOUSAND

1459
00:45:13,160 --> 00:45:13,440
VARIANTS.

1460
00:45:13,440 --> 00:45:14,360
THIS WAS A LOT OF WORK.

1461
00:45:14,360 --> 00:45:15,640
I'M NOT GOING TO SORT OF DENY

1462
00:45:15,640 --> 00:45:16,840
THAT THIS WAS A LOT OF EFFORT

1463
00:45:16,840 --> 00:45:20,320
THAT SHE DID IN THIS PART.

1464
00:45:20,320 --> 00:45:21,680
AND IT WAS VERY DISAPPOINTING.

1465
00:45:21,680 --> 00:45:23,200
SO WHAT SHE FOUND WAS THAT 95%

1466
00:45:23,200 --> 00:45:26,280
OF THE VARIANTS WERE ACTUALLY

1467
00:45:26,280 --> 00:45:27,640
WORSE THAN WILD TYPE MXA.

1468
00:45:27,640 --> 00:45:29,200
SO EVEN THOUGH WE HAD STARTED

1469
00:45:29,200 --> 00:45:31,160
WITH HUMAN MXA, WHICH IS VERY

1470
00:45:31,160 --> 00:45:32,720
GOOD, AND WE HAD ONLY MESSED

1471
00:45:32,720 --> 00:45:34,120
WITH THE RAPIDLY EVOLVING

1472
00:45:34,120 --> 00:45:35,680
POSITIONS, IT TURNS OUT YOU CAN

1473
00:45:35,680 --> 00:45:40,440
STILL BREAK MXA QUITE EASILY.

1474
00:45:40,440 --> 00:45:42,320
AND ABOUT 5% WERE ABOUT AS GOOD

1475
00:45:42,320 --> 00:45:44,720
AS WILD TYPE MXA AND THEN WE HAD

1476
00:45:44,720 --> 00:45:46,080
A FEW VARIANTS THAT WERE

1477
00:45:46,080 --> 00:45:47,800
SLIGHTLY BETTER EVEN THAN WILD

1478
00:45:47,800 --> 00:45:48,800
TYPE MXA.

1479
00:45:48,800 --> 00:45:50,440
SO THIS WAS LIKE ONE OF THOSE

1480
00:45:50,440 --> 00:45:52,240
DEEPLY DEPRESSING SERIES OF LAB

1481
00:45:52,240 --> 00:45:54,360
MEETINGS WHERE YOU SORT OF GET

1482
00:45:54,360 --> 00:45:55,600
THESE ACCUSATORY LOOKS ABOUT

1483
00:45:55,600 --> 00:45:56,640
GRADUATE STUDENTS ABOUT HOW YOU

1484
00:45:56,640 --> 00:45:57,840
SHOULD HAVE REALLY TOLD ME

1485
00:45:57,840 --> 00:45:59,120
BETTER THINGS TO DO, AND THEN WE

1486
00:45:59,120 --> 00:46:00,920
SORT OF REALIZED AFTER THAT HAD

1487
00:46:00,920 --> 00:46:02,200
ENDED THAT WE SHOULD LOOK AT THE

1488
00:46:02,200 --> 00:46:04,040
VARIANTS THAT DID HAVE SOME

1489
00:46:04,040 --> 00:46:05,360
ACTIVITY, AND IT TURNS OUT THAT

1490
00:46:05,360 --> 00:46:08,000
ALL OF THOSE VARIANTS ACTUALLY

1491
00:46:08,000 --> 00:46:10,000
HAVE THIS RESIDUE RESTRICTION,

1492
00:46:10,000 --> 00:46:12,640
WHICH IS THAT THEY NEED TO HAVE

1493
00:46:12,640 --> 00:46:16,760
A PHENYL ALANINE, TYROSINE OR

1494
00:46:16,760 --> 00:46:18,720
TRYPTOPHAN -- THOSE OF YOU THAT

1495
00:46:18,720 --> 00:46:20,040
REMEMBER IT WAS EXACTLY THE SAME

1496
00:46:20,040 --> 00:46:21,120
RESIDUE THAT PATRICK HAD

1497
00:46:21,120 --> 00:46:24,680
ACTUALLY MUTATED FROM HUMAN INTO

1498
00:46:24,680 --> 00:46:26,080
AFER GANGRENE MONKEY TO CONFER

1499
00:46:26,080 --> 00:46:26,520
PROTECTION.

1500
00:46:26,520 --> 00:46:29,200
SO THE MORAL OF THE STORY IS WE

1501
00:46:29,200 --> 00:46:31,040
SHOULD DEFINITELY REREAD OUR OWN

1502
00:46:31,040 --> 00:46:31,760
PAPERS BEFORE EMBARKING ON THE

1503
00:46:31,760 --> 00:46:32,440
NEXT STUDY.

1504
00:46:32,440 --> 00:46:34,480
SO MY SUCCESSFUL CONTRIBUTION TO

1505
00:46:34,480 --> 00:46:36,880
THIS PROJECT WAS TO CONVINCE

1506
00:46:36,880 --> 00:46:38,680
ROSSANA TO NOT QUIT GRAD SCHOOL

1507
00:46:38,680 --> 00:46:40,720
AND REDO THE SCREEN AGAIN BUT

1508
00:46:40,720 --> 00:46:43,760
GUIDED BY THIS APPROACH WHERE

1509
00:46:43,760 --> 00:46:45,320
SHE ALREADY FOUND PHENYL ALANINE

1510
00:46:45,320 --> 00:46:46,840
IS PRETTY GOOD, TYROSINE IS EVEN

1511
00:46:46,840 --> 00:46:48,320
BETTER AND TRYPTOPHAN CAN WORK

1512
00:46:48,320 --> 00:46:49,840
BUT IT'S ACTUALLY NOT AS GOOD

1513
00:46:49,840 --> 00:46:51,520
COMPARED TO THE OTHER

1514
00:46:51,520 --> 00:46:54,320
HYDROPHOBIC RES KNEWS SO WE

1515
00:46:54,320 --> 00:46:57,600
DECIDED -- PHENYL ALANINE AND TO

1516
00:46:57,600 --> 00:46:58,560
SWEETEN THE POT A LITTLE BIT I

1517
00:46:58,560 --> 00:47:01,120
HAD A ROTATION STUDENT JOIN

1518
00:47:01,120 --> 00:47:02,640
ROSSANA AND THEY SAID WE'RE ONLY

1519
00:47:02,640 --> 00:47:04,240
GOING DO ABOUT 250 VARIANTS

1520
00:47:04,240 --> 00:47:05,560
BECAUSE WE'RE GOING TO TEST THEM

1521
00:47:05,560 --> 00:47:06,320
INDIVIDUALLY, AND THIS COULD

1522
00:47:06,320 --> 00:47:07,640
HAVE GONE REALLY BADLY BUT

1523
00:47:07,640 --> 00:47:09,720
LUCKILY FOR ME, IT DID NOT.

1524
00:47:09,720 --> 00:47:12,160
SO NOW 70% OF THE VARIANTS WERE

1525
00:47:12,160 --> 00:47:15,360
AS GOOD OR BETTER THAN HUMAN MXA

1526
00:47:15,360 --> 00:47:16,880
BECAUSE WE HAD NOW HONORED THE

1527
00:47:16,880 --> 00:47:19,120
REQUIREMENT OF A HYDROPHOBIC

1528
00:47:19,120 --> 00:47:20,360
AROMATIC RESIDUE AT THE CRITICAL

1529
00:47:20,360 --> 00:47:20,840
POSITION.

1530
00:47:20,840 --> 00:47:23,320
AND WE STILL HAVE ABOUT 30% OF

1531
00:47:23,320 --> 00:47:24,760
VARIANTS THAT ARE WORSE THAN

1532
00:47:24,760 --> 00:47:25,760
WHAT YOU'D EXPECT.

1533
00:47:25,760 --> 00:47:27,360
AND I WOULD BE REALLY INTERESTED

1534
00:47:27,360 --> 00:47:29,280
IN ANSWERING WHY THAT IS.

1535
00:47:29,280 --> 00:47:30,360
BUT OF COURSE WE NEVER DID THAT

1536
00:47:30,360 --> 00:47:32,000
BECAUSE WE REALIZED THAT WE HAD

1537
00:47:32,000 --> 00:47:34,200
NOW NEARLY TWO DOZEN VARIANTS

1538
00:47:34,200 --> 00:47:35,600
THAT WERE SIGNIFICANTLY BETTER

1539
00:47:35,600 --> 00:47:37,880
THAN WILD TYPE HUMAN MXA, WHICH

1540
00:47:37,880 --> 00:47:40,640
IS THE VERY BEST NATURAL

1541
00:47:40,640 --> 00:47:44,280
RESTRICTOR OF THE VIRUS WE HAVE

1542
00:47:44,280 --> 00:47:45,280
IN OUR ARSENAL.

1543
00:47:45,280 --> 00:47:48,480
THIS IS SHOWN IN TRIPLICATE

1544
00:47:48,480 --> 00:47:48,800
AGAIN.

1545
00:47:48,800 --> 00:47:50,800
WE USE THIS AS A CONTROL

1546
00:47:50,800 --> 00:47:51,800
NORMALIZED TO ONE.

1547
00:47:51,800 --> 00:47:54,120
WILD TYPE HUMAN MXA AT THIS

1548
00:47:54,120 --> 00:47:56,360
LEVEL OF PROTECTION IS TENFOLD

1549
00:47:56,360 --> 00:47:58,080
PROTECTION, REALLY, REALLY GOOD

1550
00:47:58,080 --> 00:47:58,840
PROTECTION.

1551
00:47:58,840 --> 00:48:01,160
HERE'S OUR INITIAL FIVE SITE

1552
00:48:01,160 --> 00:48:03,480
SCREEN AND HERE IS NOW OUR FOUR

1553
00:48:03,480 --> 00:48:04,560
SITE SCREEN WHERE YOU FIX THE

1554
00:48:04,560 --> 00:48:05,120
PHENYL ALANINE.

1555
00:48:05,120 --> 00:48:06,400
SO I JUST WANT TO YOU APPRECIATE

1556
00:48:06,400 --> 00:48:08,280
WHAT WE'VE DONE HERE.

1557
00:48:08,280 --> 00:48:11,760
WE ARRIVED AT LOOP L4 BY A

1558
00:48:11,760 --> 00:48:12,400
RETROSPECTIVE ANALYSIS THAT

1559
00:48:12,400 --> 00:48:13,040
IDENTIFIED THESE POSITIONS.

1560
00:48:13,040 --> 00:48:14,840
WE HAVE NOW JUST ALLOWED THOSE

1561
00:48:14,840 --> 00:48:15,480
POSITIONS, FOUR OF THOSE

1562
00:48:15,480 --> 00:48:17,160
POSITIONS TO MUTATE, AND WE NOW

1563
00:48:17,160 --> 00:48:20,400
HAVE 10 TO 20 FOLD BETTER

1564
00:48:20,400 --> 00:48:21,920
PROTECTIVE VERSIONS OF MXA JUST

1565
00:48:21,920 --> 00:48:23,520
BY TAKING THIS EVOLUTIONARY SORT

1566
00:48:23,520 --> 00:48:25,560
OF HANDBOOK AND JUST ALLOWING

1567
00:48:25,560 --> 00:48:27,000
MOLECULAR BIOLOGY IN THE LAB TO

1568
00:48:27,000 --> 00:48:29,160
TELL US ABOUT ALLOWING US TO

1569
00:48:29,160 --> 00:48:30,960
SCREEN MORE VARIANTS OF THAT

1570
00:48:30,960 --> 00:48:31,400
TIME.

1571
00:48:31,400 --> 00:48:32,640
I JUST WANT TO POINT OUT

1572
00:48:32,640 --> 00:48:34,480
FOCUSING ON THE THREE VERY BEST

1573
00:48:34,480 --> 00:48:35,800
SUPER RESTRICTORS WE HAVE ON THE

1574
00:48:35,800 --> 00:48:38,480
RIGHT HERE THAT THESE SUPER

1575
00:48:38,480 --> 00:48:39,360
RESTRICTIVE VARIANTS ARE BETTER

1576
00:48:39,360 --> 00:48:42,280
AT ALL LEVELS OF ECK PRETION TO

1577
00:48:42,280 --> 00:48:44,560
SHE OUTPERFORM WILD TYPE MXA

1578
00:48:44,560 --> 00:48:46,080
WHERE I'M GOING TO FOUND LIKE

1579
00:48:46,080 --> 00:48:47,520
VERY BEST NATURAL RESTRICTOR AND

1580
00:48:47,520 --> 00:48:48,560
THESE VARIANTS WE HAVE IN THE

1581
00:48:48,560 --> 00:48:50,520
LAB CAN OUTPERFORM THEM

1582
00:48:50,520 --> 00:48:53,160
SIGNIFICANTLY AT ALL LEVELS OF

1583
00:48:53,160 --> 00:48:55,880
EXPRESSION, AND UNSURPRISINGLY

1584
00:48:55,880 --> 00:48:57,280
BUT STILL REASSURINGLY, THE

1585
00:48:57,280 --> 00:49:00,160
REASON THEY OUTPERFORM THIS IS

1586
00:49:00,160 --> 00:49:03,120
BECAUSE OF HIGHER AVIDITY WITH

1587
00:49:03,120 --> 00:49:05,000
THE PROTEIN OF THE VIRUS.

1588
00:49:05,000 --> 00:49:06,520
SO HERE YOU CAN SEE THAT WILD

1589
00:49:06,520 --> 00:49:08,680
TYPE MXA HAS THE REALLY NICE

1590
00:49:08,680 --> 00:49:12,480
ABILITY TO -- DURING VIRALLY

1591
00:49:12,480 --> 00:49:14,280
INFECTED CELLS BUT EACH OF THE

1592
00:49:14,280 --> 00:49:15,720
SUPER RESTRICTORS IS MUCH MORE

1593
00:49:15,720 --> 00:49:18,680
AVID BINDER OF THE NP PROTEIN

1594
00:49:18,680 --> 00:49:20,800
AND THAT MAKES IT A MUCH MORE

1595
00:49:20,800 --> 00:49:21,920
AVID RESTRICTOR OF THE VIRUS

1596
00:49:21,920 --> 00:49:24,240
ITSELF.

1597
00:49:24,240 --> 00:49:26,360
SO LET'S RETURN BACK TO THIS

1598
00:49:26,360 --> 00:49:28,480
SORT OF DIAGRAM WHERE WE HAVE

1599
00:49:28,480 --> 00:49:30,080
NOW THE FIVE SITE AND FOUR SITE

1600
00:49:30,080 --> 00:49:31,160
MUTATIONS THAT ARE BENEFICIAL.

1601
00:49:31,160 --> 00:49:32,600
THIS IS THE POINT IN THE TALK

1602
00:49:32,600 --> 00:49:34,640
WHERE I OFTEN GET ASKED, NOW YOU

1603
00:49:34,640 --> 00:49:38,560
COULD USE DEEP LEARNING TO

1604
00:49:38,560 --> 00:49:39,680
ACTUALLY LIKE FIGURE OUT WHAT IS

1605
00:49:39,680 --> 00:49:40,680
THE SECRET HERE?

1606
00:49:40,680 --> 00:49:42,360
WHAT COULD YOU DO?

1607
00:49:42,360 --> 00:49:43,680
THAT'S THE POINT OF THE TALK

1608
00:49:43,680 --> 00:49:45,320
WHERE I TELL YOU THIS IS NOT A

1609
00:49:45,320 --> 00:49:45,760
REPRESENTATIVE SET.

1610
00:49:45,760 --> 00:49:48,120
THIS IS LITERALLY ALL THE

1611
00:49:48,120 --> 00:49:51,280
VARIANTS WE FOUND AT THE END WE

1612
00:49:51,280 --> 00:49:52,760
COULD CERTAINLY FIND MORE BUT

1613
00:49:52,760 --> 00:49:53,800
THAT WOULD REQUIRE HER TO DOM

1614
00:49:53,800 --> 00:49:55,640
BACK TO GRAD SCHOOL, WHICH IS

1615
00:49:55,640 --> 00:49:56,520
NOT HAPPENING.

1616
00:49:56,520 --> 00:50:00,880
SO WE USED MY VERSION OF SHALLOW

1617
00:50:00,880 --> 00:50:02,920
LEARNING, WHICH IS THE P.I.

1618
00:50:02,920 --> 00:50:04,120
STARES AT THESE VARIANTS FOR A

1619
00:50:04,120 --> 00:50:05,680
LONG TIME AND ALLOWS PATTERNS TO

1620
00:50:05,680 --> 00:50:06,240
EMERGE.

1621
00:50:06,240 --> 00:50:07,080
ACTUALLY THIS DID WORK IN THIS

1622
00:50:07,080 --> 00:50:09,320
CASE BECAUSE WE REALIZED THAT

1623
00:50:09,320 --> 00:50:11,960
THE Q RESIDUE THAT GLUTAMATED AT

1624
00:50:11,960 --> 00:50:12,680
THE FIRST POSITION WAS ACTUALLY

1625
00:50:12,680 --> 00:50:14,920
KIND OF OVERREPRESENT THE HERE,

1626
00:50:14,920 --> 00:50:16,200
IN SPITE OF THE FACT THAT

1627
00:50:16,200 --> 00:50:18,280
GLUTAMATE ITSELF IS NOT THAT

1628
00:50:18,280 --> 00:50:19,560
WELL REPRESENTED IN THE GENETIC

1629
00:50:19,560 --> 00:50:22,480
CODE, SO WE SAID THE GLUTAMATE

1630
00:50:22,480 --> 00:50:24,440
AT THIS POSITION 540 MUST BE

1631
00:50:24,440 --> 00:50:24,880
CRITICAL.

1632
00:50:24,880 --> 00:50:28,000
SO JUST TO REMIND YOU AGAIN,

1633
00:50:28,000 --> 00:50:31,040
WILD TYPE MXA WITH THE FIVE

1634
00:50:31,040 --> 00:50:32,600
RESIDUES, RAPIDLY EVOLVING

1635
00:50:32,600 --> 00:50:32,880
POSITIONS.

1636
00:50:32,880 --> 00:50:34,760
A G TO Q MUTATION IS A SMALL

1637
00:50:34,760 --> 00:50:36,080
BUMP IN RESTRICTION BUT ACTUALLY

1638
00:50:36,080 --> 00:50:37,960
IF YOU TAKE EACH OF THE SUPER

1639
00:50:37,960 --> 00:50:39,320
RESTRICTORS THAT ALREADY HAVE A

1640
00:50:39,320 --> 00:50:41,120
QUEUE, REVERTING TO A WILD TYPE

1641
00:50:41,120 --> 00:50:43,400
VERSION, YOU LOSE THE SUPER

1642
00:50:43,400 --> 00:50:43,720
RESTRICTION.

1643
00:50:43,720 --> 00:50:44,440
SO THIS IS OUR FIRST EVIDENCE

1644
00:50:44,440 --> 00:50:48,160
THAT RESIDUE 540, IN ADDITION TO

1645
00:50:48,160 --> 00:50:50,520
RESIDUE 561, IS PLAYING A VERY

1646
00:50:50,520 --> 00:50:50,840
CRITICAL ROLE.

1647
00:50:50,840 --> 00:50:54,520
THAT PROMPTED US TO ASK OKAY

1648
00:50:54,520 --> 00:50:56,600
WHAT ABOUT OTHER AMINO ACIDS AT

1649
00:50:56,600 --> 00:50:57,360
THIS POSITION?

1650
00:50:57,360 --> 00:50:59,520
MAYBE WE SHOULD MUTATE THEM TO

1651
00:50:59,520 --> 00:51:00,440
ALL THAT ARE PRESENT.

1652
00:51:00,440 --> 00:51:01,760
SO WE DID THAT AND IT ACTUALLY

1653
00:51:01,760 --> 00:51:05,600
TURNS OUT THAT PROLINE IS

1654
00:51:05,600 --> 00:51:06,240
TERRIBLE, WE'RE NOT GOING TO

1655
00:51:06,240 --> 00:51:07,320
KIND OF DWELL ON THAT, THAT

1656
00:51:07,320 --> 00:51:09,320
TURNS OUT TO BE A UNIVERSALLY

1657
00:51:09,320 --> 00:51:09,640
TRUE THING.

1658
00:51:09,640 --> 00:51:11,920
BUT YOU CAN SEE THAT YOU CAN GO

1659
00:51:11,920 --> 00:51:13,200
FROM TRYPTOPHAN ON THIS END TO

1660
00:51:13,200 --> 00:51:15,520
ALANINE ON THIS END AND THAT'S A

1661
00:51:15,520 --> 00:51:16,880
TENFOLD DIFFERENCE IN

1662
00:51:16,880 --> 00:51:17,160
RESTRICTION.

1663
00:51:17,160 --> 00:51:19,080
THAT'S THE DIFFERENCE BETWEEN

1664
00:51:19,080 --> 00:51:20,160
PROTECTION AND NO PROTECTION, IF

1665
00:51:20,160 --> 00:51:22,160
YOU WILL, AND THAT'S JUST

1666
00:51:22,160 --> 00:51:23,600
HAPPENING WITH A SINGLE AMINO

1667
00:51:23,600 --> 00:51:25,720
ACID RESIDUE.

1668
00:51:25,720 --> 00:51:30,280
AND WE STARR STARED AT THIS VERD

1669
00:51:30,280 --> 00:51:31,920
TO DETERMINE ARE THERE ANY

1670
00:51:31,920 --> 00:51:33,520
BIOLOGICAL PATTERNS, ET CETERA,

1671
00:51:33,520 --> 00:51:35,200
AND NOTHING BECAME OBVIOUS UNTIL

1672
00:51:35,200 --> 00:51:36,480
AGAIN SHALLOW LEARNING CAME TO

1673
00:51:36,480 --> 00:51:38,560
THE RESCUE BECAUSE IT TURNS OUT

1674
00:51:38,560 --> 00:51:39,720
THAT -- ARE REALLY BAD IN THE

1675
00:51:39,720 --> 00:51:41,040
WILD TYPE CONTEXT BUT I

1676
00:51:41,040 --> 00:51:42,880
REMEMBERED THAT VAI LEAN AND

1677
00:51:42,880 --> 00:51:44,440
THREONINE WERE ACTUALLY PRESENT

1678
00:51:44,440 --> 00:51:46,800
IN TWO OF OUR BEST SUPER

1679
00:51:46,800 --> 00:51:48,640
RESTRICTORS SO SUDDENLY VISIONS

1680
00:51:48,640 --> 00:51:49,520
OF CONVERTING THOSE TO ALANINE

1681
00:51:49,520 --> 00:51:52,680
AND GETTING A SUPERDOOPER

1682
00:51:52,680 --> 00:51:53,720
RESTRICTOR LIKE WOW, THAT WOULD

1683
00:51:53,720 --> 00:51:55,160
MAKE A REALLY GREAT FINAL FIGURE

1684
00:51:55,160 --> 00:51:57,680
FOR A PAPER, SO THAT'S WHAT I

1685
00:51:57,680 --> 00:52:00,600
ENCOURAGED ROSSANA TO DO, LET'S

1686
00:52:00,600 --> 00:52:04,440
TAKE THE WILD TYPE RESIDUE IN

1687
00:52:04,440 --> 00:52:06,120
WHICH THERE'S THIS DRAMATIC

1688
00:52:06,120 --> 00:52:07,160
DIFFERENCE IN RESTRICTION, LET'S

1689
00:52:07,160 --> 00:52:09,360
DO THE SAME FOR THE SUPER

1690
00:52:09,360 --> 00:52:10,640
RESTRICTOR THAT ALREADY HAD A

1691
00:52:10,640 --> 00:52:12,520
VAI LEAN AN MAYBE WE CAN BUMP UP

1692
00:52:12,520 --> 00:52:13,600
THE RESTRICTION EVEN MORE.

1693
00:52:13,600 --> 00:52:15,560
OF COURSE THE OPPOSITE HAPPENED.

1694
00:52:15,560 --> 00:52:18,600
SO THE SAME MUTATION IN A

1695
00:52:18,600 --> 00:52:19,920
DIFFERENT CONTEXT REMEMBER THESE

1696
00:52:19,920 --> 00:52:24,600
ARE OWL DIFFE ONLY DIFFERENT IN-

1697
00:52:24,600 --> 00:52:26,960
COMPARED TO THE 600 AMINO ACID

1698
00:52:26,960 --> 00:52:28,640
ASSAY PROTEIN HAVE COMPLETELY

1699
00:52:28,640 --> 00:52:29,680
OPPOSITE EFFECTS ON RESTRICTION

1700
00:52:29,680 --> 00:52:32,000
PRPROFILE, JUST AGAIN REFLECTING

1701
00:52:32,000 --> 00:52:34,280
THE UNPREDICTABLE NATURE OF THE

1702
00:52:34,280 --> 00:52:35,240
ENSEMBLE, ALSO REALLY

1703
00:52:35,240 --> 00:52:37,360
HIGHLIGHTING THAT THIS KIND OF

1704
00:52:37,360 --> 00:52:38,560
EPISTASIS MEANS WE WERE REALLY

1705
00:52:38,560 --> 00:52:42,360
LUCKY THAT WE DID IMI NIGH TORE

1706
00:52:42,360 --> 00:52:45,080
YAL -- RATHER THAN SINGLE

1707
00:52:45,080 --> 00:52:46,160
RESIDUE SCANNING.

1708
00:52:46,160 --> 00:52:47,040
BUT THAT LOSS OF FUNCTION

1709
00:52:47,040 --> 00:52:48,480
MUTATION ACTUALLY PERMITTED THE

1710
00:52:48,480 --> 00:52:49,960
GAIN OF FUNCTION SUBSEQUENT

1711
00:52:49,960 --> 00:52:51,160
MUTATIONS TO ACTUALLY OCCUR.

1712
00:52:51,160 --> 00:52:52,280
SO YOU HAD TO GO THROUGH THE

1713
00:52:52,280 --> 00:52:53,560
VALLEY TO GET TO THE PEAK THAT

1714
00:52:53,560 --> 00:52:59,360
WAS ACTUALLY AFFORDED.

1715
00:52:59,360 --> 00:53:00,760
JUST TO SUMMARIZE WHAT I TOLD

1716
00:53:00,760 --> 00:53:02,360
YOU SO FAR, WE STARTED WITH THIS

1717
00:53:02,360 --> 00:53:03,920
APPROACH WHERE WE LOOKED AT

1718
00:53:03,920 --> 00:53:06,960
EVOLUTION AND LOOKED AT LOOP

1719
00:53:06,960 --> 00:53:09,160
L4 -- TURNS OUT NOT JUST FOR TA

1720
00:53:09,160 --> 00:53:11,200
GOA DA VIRUS BUT INFLUENZA.

1721
00:53:11,200 --> 00:53:13,400
NOW ROSSANA HAS TAKEN THIS

1722
00:53:13,400 --> 00:53:14,760
APPROACH WHERE SHE'S MUTATED ALL

1723
00:53:14,760 --> 00:53:17,080
OF THE RESIDUES EXCEPT ONE AND

1724
00:53:17,080 --> 00:53:19,520
SHE'S NOW FOUND SUPER

1725
00:53:19,520 --> 00:53:20,080
RESTRICTORS.

1726
00:53:20,080 --> 00:53:22,320
I CAN GUARANTEE MOST OF YOU HAVE

1727
00:53:22,320 --> 00:53:25,720
NEVER HEARD OF THOGOTO VIRUS OR

1728
00:53:25,720 --> 00:53:27,440
WISH YOU WOULDN'T HAVE BUT YOU

1729
00:53:27,440 --> 00:53:29,080
ALL CARE ABOUT INFLUENZA VIRUS.

1730
00:53:29,080 --> 00:53:30,960
SO SUDDENLY VISIONS OF GRAND

1731
00:53:30,960 --> 00:53:32,320
FUNDING BEGAN DANCING IN MY HEAD

1732
00:53:32,320 --> 00:53:34,800
I SAID OH MY GOD, WHAT IF YOU'VE

1733
00:53:34,800 --> 00:53:36,960
DISCOVERED SUPER RESTRICTORS OF

1734
00:53:36,960 --> 00:53:37,520
INFLUENZA, WOULDN'T THAT BE

1735
00:53:37,520 --> 00:53:38,480
AMAZING.

1736
00:53:38,480 --> 00:53:39,600
AND MAYBE THAT'S WHAT THE WHOLE

1737
00:53:39,600 --> 00:53:41,880
STORY IS GOING TO BE ABOUT.

1738
00:53:41,880 --> 00:53:44,440
THAT'S WHEN ROSSANA TESTED MANY

1739
00:53:44,440 --> 00:53:47,200
OF HER SUPER RESTRICTORS AGAINST

1740
00:53:47,200 --> 00:53:49,800
THOGOTO VIRUS ON THE X AXIS

1741
00:53:49,800 --> 00:53:52,760
AGAINST THE -- HERE'S THE WILD

1742
00:53:52,760 --> 00:53:56,440
TYPE MMXA, AND YOU REALIZE WHAT

1743
00:53:56,440 --> 00:53:57,720
BECAME APPARENT TO US OVER LIKE

1744
00:53:57,720 --> 00:54:00,200
WEEKS OF DOING THIS THAT YOU

1745
00:54:00,200 --> 00:54:06,000
COULD GET REALLY GOOD AT THOGOTA

1746
00:54:06,000 --> 00:54:07,120
VIRUS BUT YOU'D GET WORSE AND

1747
00:54:07,120 --> 00:54:08,560
WORSE WITH INFLUENZA VIRUS.

1748
00:54:08,560 --> 00:54:09,720
SO EVEN THOUGH WE'RE MESSING

1749
00:54:09,720 --> 00:54:12,040
WITH THIS VERY SMALL LANDSCAPE

1750
00:54:12,040 --> 00:54:15,040
OF THE V1 LOOP, THERE IS THIS

1751
00:54:15,040 --> 00:54:16,480
SPECIFICITY TRADEOFF WHERE THE

1752
00:54:16,480 --> 00:54:18,200
WILD TYPE VERSION WE HAVE IN OUR

1753
00:54:18,200 --> 00:54:20,640
GENOME IS REALLY THE JACK OF ALL

1754
00:54:20,640 --> 00:54:22,360
TRADES VERSION AGAINST BOTH

1755
00:54:22,360 --> 00:54:22,840
VIRUSES.

1756
00:54:22,840 --> 00:54:24,400
YOU CAN GET BETTER BUT YOU OFTEN

1757
00:54:24,400 --> 00:54:26,040
DO SO AT THE EXPENSE OF THE

1758
00:54:26,040 --> 00:54:28,240
BREADTH OF RESTRICTION THAT MXA

1759
00:54:28,240 --> 00:54:29,000
CAN PROVIDE.

1760
00:54:29,000 --> 00:54:30,920
SO UNDAUNTED BY THIS, A NEW

1761
00:54:30,920 --> 00:54:33,000
GRADUATE STUDENT IN THE LAB, RI

1762
00:54:33,000 --> 00:54:37,600
CHRACHEL GEIGER, SAID I WANT TOO

1763
00:54:37,600 --> 00:54:39,480
THIS APPROACH BUT THIS TIME

1764
00:54:39,480 --> 00:54:41,120
AGAINST THE INFLUENZA VIRUSES

1765
00:54:41,120 --> 00:54:43,560
BECAUSE THAT'S THE ONES THAT I

1766
00:54:43,560 --> 00:54:45,200
CARE ABOUT.

1767
00:54:45,200 --> 00:54:47,200
LONG STORY SHORT, THIS WORKS

1768
00:54:47,200 --> 00:54:49,120
AGAINST INFLUENZA VIRUSES BUT WE

1769
00:54:49,120 --> 00:54:50,960
FIND COMPLETELY DIFFERENT

1770
00:54:50,960 --> 00:54:51,280
VARIANTS.

1771
00:54:51,280 --> 00:54:54,440
WE MADE THE JUDICIOUS CHOICE OF

1772
00:54:54,440 --> 00:54:56,400
ALLOWING ALL CRE HYDROPHOBIC

1773
00:54:56,400 --> 00:54:57,720
RESIDUES TO OCCUR IN THIS

1774
00:54:57,720 --> 00:54:59,280
LIBRARY AND THAT TURNED OUT TO

1775
00:54:59,280 --> 00:55:03,800
BE A VERY JUICE DI JUDICIOUS CHE

1776
00:55:03,800 --> 00:55:07,320
BECAUSE WHAT SHE DISCOVERED WAS

1777
00:55:07,320 --> 00:55:09,120
THE TRYPTOPHAN RESIDUE IS

1778
00:55:09,120 --> 00:55:10,560
OVERREPRESENTED AMONG THE

1779
00:55:10,560 --> 00:55:12,320
INFLUENZA SUPER RESTRICTORS, AND

1780
00:55:12,320 --> 00:55:14,760
THE TYROSINE RESIDUE IS

1781
00:55:14,760 --> 00:55:15,680
UNDERREPRESENTED AMONG THE

1782
00:55:15,680 --> 00:55:17,200
INFLUENCE IS A SUPER

1783
00:55:17,200 --> 00:55:17,520
RESTRICTORS.

1784
00:55:17,520 --> 00:55:20,040
IN FACT, THIS IS CLEARLY

1785
00:55:20,040 --> 00:55:22,360
APPARENT BY TAKING JUST ONE

1786
00:55:22,360 --> 00:55:23,520
VARIANT WHERE YOU'VE BASICALLY

1787
00:55:23,520 --> 00:55:25,480
MUTATED JUST THIS RESIDUE FROM A

1788
00:55:25,480 --> 00:55:28,640
TRYPTOPHAN, WHICH IS SUPER

1789
00:55:28,640 --> 00:55:29,480
RESTRICTIVE, AND A PHENYL AL

1790
00:55:29,480 --> 00:55:30,920
LEAN OR TYROSINE WHICH LOSES

1791
00:55:30,920 --> 00:55:32,200
THAT SUPER RESTRICTION, AND IF

1792
00:55:32,200 --> 00:55:34,840
YOU'LL RECALL, THIS IS EXACTLY

1793
00:55:34,840 --> 00:55:38,920
THE OPPOSITE OF WHAT SHE FOUND

1794
00:55:38,920 --> 00:55:43,920
WITH THE HYDROPHOBIC RESIDUE

1795
00:55:43,920 --> 00:55:44,200
PRESENCE.

1796
00:55:44,200 --> 00:55:46,080
SO IT TURNS OUT THIS TRADEOFF

1797
00:55:46,080 --> 00:55:47,720
OFTEN JUST COMES DOWN TO WHICH

1798
00:55:47,720 --> 00:55:49,560
HOE DREE PHOBIC RESIDUE DO YOU

1799
00:55:49,560 --> 00:55:52,800
HAVE FIXED OR NOT FIXED AT

1800
00:55:52,800 --> 00:55:53,200
RESIDUE 561?

1801
00:55:53,200 --> 00:55:55,800
IF IT'S A TRYPTOPHAN YOU'RE MUCH

1802
00:55:55,800 --> 00:55:58,040
MORE LIKELY TO BE AN INFLUENZA

1803
00:55:58,040 --> 00:56:01,000
VIRUS RESTRICT TORE, IF YOU'RE

1804
00:56:01,000 --> 00:56:02,200
PHENYL ALANINE, TURNS OUT YOU

1805
00:56:02,200 --> 00:56:04,040
STILL HAVE SOME PLAY, YOU CAN BE

1806
00:56:04,040 --> 00:56:05,320
BOTH, AND WE'RE HAPPY TO EXPLORE

1807
00:56:05,320 --> 00:56:06,000
THAT.

1808
00:56:06,000 --> 00:56:08,200
SO I JUST WANT TO TELL YOU THAT

1809
00:56:08,200 --> 00:56:09,600
THE JURY IS STILL OUT, WHETHER

1810
00:56:09,600 --> 00:56:11,120
WE CAN USE THIS APPROACH FOR

1811
00:56:11,120 --> 00:56:12,880
SUPER RESTRICTORS OF INFLEUN SHA

1812
00:56:12,880 --> 00:56:13,600
CYRUS.

1813
00:56:13,600 --> 00:56:14,920
WE'LL BE CONFIDENT WE'LL BE ABLE

1814
00:56:14,920 --> 00:56:16,360
TO DO THAT, AND THE NEXT STEP,

1815
00:56:16,360 --> 00:56:17,840
OF COURSE, IS TO GO AFTER

1816
00:56:17,840 --> 00:56:19,160
PANDEMIC STRAINS OF INFLUENZA

1817
00:56:19,160 --> 00:56:20,560
THAT BASICALLY HAVE ESCAPED

1818
00:56:20,560 --> 00:56:22,360
HUMAN MXA AND ASK, CAN WE USE

1819
00:56:22,360 --> 00:56:24,600
THE SAME APPROACH TO BRING THEM

1820
00:56:24,600 --> 00:56:27,600
BACK WITHIN THE REA STRICKTIVE

1821
00:56:27,600 --> 00:56:30,760
MANIFOLD OF MXA RESTRICTION?

1822
00:56:30,760 --> 00:56:32,040
SO HOPEFULLY I'VE CONVINCED YOU

1823
00:56:32,040 --> 00:56:35,320
TODAY THAT DISORDERED LOOPS EVEN

1824
00:56:35,320 --> 00:56:37,040
THOUGH THAT'S KIND OF MESSY FROM

1825
00:56:37,040 --> 00:56:37,800
A STRUCTURAL STANDPOINT ARE

1826
00:56:37,800 --> 00:56:39,440
REALLY AN IMPORTANT TOOL FOR

1827
00:56:39,440 --> 00:56:40,520
ANTIVIRAL PROTEINS THAT PROVIDE

1828
00:56:40,520 --> 00:56:41,960
BOTH THE EVOLUTIONARY

1829
00:56:41,960 --> 00:56:43,480
FLEXIBILITY AND THE ADAPTIVE

1830
00:56:43,480 --> 00:56:45,880
POTENTIAL THAT ALLOWS ANTIVIRAL

1831
00:56:45,880 --> 00:56:48,360
PROTEINS, EVEN SLOWLY EVOLVING,

1832
00:56:48,360 --> 00:56:50,320
MOST OF WHAT I TOLD YOU TODAY

1833
00:56:50,320 --> 00:56:54,160
ARE ONE ON ONE ARMS RACES, AND

1834
00:56:54,160 --> 00:56:56,000
THESE RED QUEEN CONFLICTS CAN

1835
00:56:56,000 --> 00:56:57,520
NEFORT THE LESS BE QUITE

1836
00:56:57,520 --> 00:56:57,960
SUCCESSFUL.

1837
00:56:57,960 --> 00:57:00,000
I JUST WANT TO CLOSE BY

1838
00:57:00,000 --> 00:57:01,000
ACKNOWLEDGING THE PEOPLE WHO DID

1839
00:57:01,000 --> 00:57:02,000
THE WORK.

1840
00:57:02,000 --> 00:57:03,920
ALL OF THIS WORK IS ACTUALLY THE

1841
00:57:03,920 --> 00:57:05,800
CONSEQUENCE OF A VERY INFLUENCE

1842
00:57:05,800 --> 00:57:07,320
SAL COFFEE THAT I HAD 20 YEARS

1843
00:57:07,320 --> 00:57:09,400
AGO WHEN I STARTED MY LAB WITH

1844
00:57:09,400 --> 00:57:11,680
MY SENIOR COULD LEAGUE, MICHAEL

1845
00:57:11,680 --> 00:57:12,440
EMERMAN.

1846
00:57:12,440 --> 00:57:15,040
I HOPE IT WAS NOT TOTALLY ON

1847
00:57:15,040 --> 00:57:17,040
VEES BUT I'M AN EVOLUTIONARY

1848
00:57:17,040 --> 00:57:18,440
BIOLOGIST BY TRAINING AND ALL OF

1849
00:57:18,440 --> 00:57:21,080
THIS IS A BEAUTIFUL SYMBIOSIS

1850
00:57:21,080 --> 00:57:25,880
BETWEEN A BIOLOGY DRIVEN LAB AND

1851
00:57:25,880 --> 00:57:27,400
EVOLUTION -- THERE ARE STUDENTS

1852
00:57:27,400 --> 00:57:29,040
IN MY LAB DOING EXPERIMENTS IN

1853
00:57:29,040 --> 00:57:30,440
WHICH I HAVE ABSOLUTELY NO

1854
00:57:30,440 --> 00:57:32,000
TRAINING IN DOING AND NO

1855
00:57:32,000 --> 00:57:32,800
BIOSAFETY ABILITY TO ACTUALLY

1856
00:57:32,800 --> 00:57:34,240
TRAIN THEM, BUT MICHAEL DOES,

1857
00:57:34,240 --> 00:57:35,240
AND THAT'S GOOD.

1858
00:57:35,240 --> 00:57:36,600
I ALSO WANT TO THANK JENNETTE

1859
00:57:36,600 --> 00:57:38,880
FOR LEADING ALL THE OF THE TRIM

1860
00:57:38,880 --> 00:57:40,200
5 WORK AND ACTUALLY RETRACING

1861
00:57:40,200 --> 00:57:41,560
OUR STEPS ON AN IMPORTANT STUDY

1862
00:57:41,560 --> 00:57:43,640
AND FINDING EVEN MORE INSIGHTS,

1863
00:57:43,640 --> 00:57:46,320
AND ROSANNA AND RACHEL FOR THE

1864
00:57:46,320 --> 00:57:46,880
SUPER RESTRICTOR.

1865
00:57:46,880 --> 00:57:47,320
THANK YOU VERY MUCH.

1866
00:57:47,320 --> 00:57:57,520
[APPLAUSE]

1867
00:57:58,200 --> 00:58:00,040
>> HELLO.

1868
00:58:00,040 --> 00:58:01,560
THANK YOU VERY MUCH FOR A VERY

1869
00:58:01,560 --> 00:58:01,960
BEAUTIFUL TALK.

1870
00:58:01,960 --> 00:58:03,400
I HAVE LIKE TWO QUICK QUESTIONS.

1871
00:58:03,400 --> 00:58:04,720
THE FIRST ONE ABOUT TRIM 5.

1872
00:58:04,720 --> 00:58:09,200
DO YOU THINK THE FACT THAT

1873
00:58:09,200 --> 00:58:11,280
HUMAN -- VERSION OF TRIM 5 IS

1874
00:58:11,280 --> 00:58:12,920
LIKELY A RESULT THAT IT'S BAD

1875
00:58:12,920 --> 00:58:15,720
FOR HIV BUT GOOD FOR OTHER RETRO

1876
00:58:15,720 --> 00:58:16,440
RETROVIRUSES?

1877
00:58:16,440 --> 00:58:17,640
>> EXCELLENT QUESTION.

1878
00:58:17,640 --> 00:58:18,680
I HAVE A WHOLE DIFFERENT PART OF

1879
00:58:18,680 --> 00:58:20,000
THE TALK WHERE IT TALKS ABOUT

1880
00:58:20,000 --> 00:58:22,640
WHY DID WE FIX THOSE DOUBLE

1881
00:58:22,640 --> 00:58:22,880
ARGININES.

1882
00:58:22,880 --> 00:58:25,160
THE SHORT ANSWER IS, DOUBLE

1883
00:58:25,160 --> 00:58:26,680
ARGININES SEEM TO BE BAD FOR HIV

1884
00:58:26,680 --> 00:58:29,080
AND FOR SIV, ALL THE SIVs

1885
00:58:29,080 --> 00:58:29,840
WE'VE TESTED.

1886
00:58:29,840 --> 00:58:31,560
SO WE ARE STILL ON THE HUNT

1887
00:58:31,560 --> 00:58:32,960
FOR -- THIS WAS CLEARLY DRIVEN

1888
00:58:32,960 --> 00:58:34,400
BY ADAPTIVE MUTATION, WHICH

1889
00:58:34,400 --> 00:58:35,760
MEANS THAT THIS WAS BENEFICIAL

1890
00:58:35,760 --> 00:58:38,360
WHEN IT OCCURRED THE DOUBLE

1891
00:58:38,360 --> 00:58:39,560
ARGININES, BUT WE STILL DON'T

1892
00:58:39,560 --> 00:58:41,080
HAVE WHAT WAS THE DRIVING FORCE

1893
00:58:41,080 --> 00:58:42,240
FOR THAT LEFT USING, WHETHER IT

1894
00:58:42,240 --> 00:58:44,440
WAS A VIRUS OR WHETHER IT WAS TO

1895
00:58:44,440 --> 00:58:45,880
DIMINISH SOME SORT OF AUTOIMMUNE

1896
00:58:45,880 --> 00:58:46,520
RESPONSE, WE DON'T KNOW.

1897
00:58:46,520 --> 00:58:47,040
>> THANK YOU.

1898
00:58:47,040 --> 00:58:49,240
AND THEN SECOND QUESTION RELATED

1899
00:58:49,240 --> 00:58:52,440
TO THAT, SO IF THERE SEEMS TO BE

1900
00:58:52,440 --> 00:58:54,120
SOME SORT OF LIKE HOW TO SAY

1901
00:58:54,120 --> 00:58:55,800
MUTUAL EXCLUSIVITY LIKE ONE IS

1902
00:58:55,800 --> 00:58:57,640
GOOD FOR ONE VIRUS, ANOTHER FOR

1903
00:58:57,640 --> 00:59:00,000
ANOTHER VIRUS, AS GENES LIKE

1904
00:59:00,000 --> 00:59:02,400
FREQUENTLY DUPLICATED IN THE

1905
00:59:02,400 --> 00:59:03,600
EVOLUTION BECAUSE THAT WOULD BE

1906
00:59:03,600 --> 00:59:05,520
VERY BENEFICIAL FOR THEM TO BE

1907
00:59:05,520 --> 00:59:06,160
EVOLVING SEPARATELY.

1908
00:59:06,160 --> 00:59:07,440
>> THIS IS AN EXCELLENT

1909
00:59:07,440 --> 00:59:07,720
QUESTION.

1910
00:59:07,720 --> 00:59:09,200
EVEN IF THERE WAS NO

1911
00:59:09,200 --> 00:59:11,280
SPECIFICITY, IT WOULD BE

1912
00:59:11,280 --> 00:59:13,880
MASSIVELY ADVANTAGEOUS TO HAVE

1913
00:59:13,880 --> 00:59:15,760
ALLELE IK -- AT EACH OF THESE.

1914
00:59:15,760 --> 00:59:17,400
THAT IS TRUE FOR TRIM 5, AND

1915
00:59:17,400 --> 00:59:20,320
IT'S ACTUALLY TRUE FOR MOST

1916
00:59:20,320 --> 00:59:20,960
SELF-RESPECTING ANTIVIRAL GENES

1917
00:59:20,960 --> 00:59:21,520
AMONG MAMMALS.

1918
00:59:21,520 --> 00:59:23,440
IT IS NOT TRUE FOR MXA, AND WE

1919
00:59:23,440 --> 00:59:24,440
DO NOT KNOW WHY.

1920
00:59:24,440 --> 00:59:27,160
I WOULD COMPLETELY AGREE WITH

1921
00:59:27,160 --> 00:59:29,120
YOUR PREDICTION THAT MXA SHOULD

1922
00:59:29,120 --> 00:59:30,760
DUPLICATE AND BASICALLY EACH

1923
00:59:30,760 --> 00:59:31,880
VERSION SHOULD SPECIALIZE FOR A

1924
00:59:31,880 --> 00:59:33,280
DIFFERENT VIRUS BECAUSE THEN IT

1925
00:59:33,280 --> 00:59:35,280
DOESN'T HAVE A TRADEOFF OR A

1926
00:59:35,280 --> 00:59:36,000
COMPROMISE.

1927
00:59:36,000 --> 00:59:36,960
WE DON'T UNDERSTAND THE NATURE

1928
00:59:36,960 --> 00:59:37,400
OF THE TRADEOFF.

1929
00:59:37,400 --> 00:59:38,480
THERE'S ANOTHER STUDENT IN THE

1930
00:59:38,480 --> 00:59:39,920
LAB WHO'S VERY INTERESTED IN WHY

1931
00:59:39,920 --> 00:59:41,200
THAT TRADEOFF IS OCCURRING.

1932
00:59:41,200 --> 00:59:42,840
EVERY MAMMAL, DESPITE MULTIPLE

1933
00:59:42,840 --> 00:59:44,960
ROUNDS OF DUPLICATION, HAS

1934
00:59:44,960 --> 00:59:47,200
2MXs, ONE THAT WORKS IN THE

1935
00:59:47,200 --> 00:59:48,240
CYTOPLASM AND ONE THAT WORKS IN

1936
00:59:48,240 --> 00:59:49,080
THE NUCLEUS.

1937
00:59:49,080 --> 00:59:50,000
THEY WORK ON COMPLETELY

1938
00:59:50,000 --> 00:59:51,360
DIFFERENT VIRUSES BUT THERE ARE

1939
00:59:51,360 --> 00:59:52,360
NOT CASE WHERE THERE ARE

1940
00:59:52,360 --> 00:59:54,120
MULTIPLE MX PARALOGS WITHIN THE

1941
00:59:54,120 --> 00:59:54,440
SAME.

1942
00:59:54,440 --> 00:59:56,040
SO WE ARE ACTIVELY CONSIDERING

1943
00:59:56,040 --> 00:59:58,360
THE PROSPECT THAT BECAUSE MX

1944
00:59:58,360 --> 01:00:00,360
ACTS AS AN OLIGOMER E HAVING --

1945
01:00:00,360 --> 01:00:02,800
IN THE SAME COMPARTMENT RUNS THE

1946
01:00:02,800 --> 01:00:05,360
RISK OF POISONING THE OL GER

1947
01:00:05,360 --> 01:00:06,520
MIEZATION BETWEEN THEM AND WE

1948
01:00:06,520 --> 01:00:07,640
MIGHT LOSE THE ACTIVITY AND

1949
01:00:07,640 --> 01:00:09,040
THAT'S SOMETHING WE'RE ACTIVELY

1950
01:00:09,040 --> 01:00:09,680
STUDYING RIGHT NOW.

1951
01:00:09,680 --> 01:00:10,720
>> THANK YOU.

1952
01:00:10,720 --> 01:00:12,240
>> THANK YOU SO MUCH.

1953
01:00:12,240 --> 01:00:13,320
VERY INTERESTING TALK.

1954
01:00:13,320 --> 01:00:16,240
MY QUESTION IS ABOUT THE KIND OF

1955
01:00:16,240 --> 01:00:17,240
SUPER RESTRICTORS AND THE

1956
01:00:17,240 --> 01:00:19,760
TRADEOFF YOU MENTIONED BETWEEN

1957
01:00:19,760 --> 01:00:22,440
THE THOGOTO VIRUS AND INFLUENZA.

1958
01:00:22,440 --> 01:00:26,120
WHEN YOU LOOK AT SPECIES -- HOST

1959
01:00:26,120 --> 01:00:27,400
SPECIES WHERE ONLY ONE OF THOSE

1960
01:00:27,400 --> 01:00:29,200
VIRUS FAMILIES HAVE CIRCULATED,

1961
01:00:29,200 --> 01:00:30,760
DO YOU SEE KIND OF A PREFERENCE

1962
01:00:30,760 --> 01:00:33,640
FOR ONE OR THE OTHER KIND OF

1963
01:00:33,640 --> 01:00:36,880
MUTATIONAL STATUS OF THE SUPER

1964
01:00:36,880 --> 01:00:37,320
RESTRICTORS?

1965
01:00:37,320 --> 01:00:38,000
>> THAT'S AN EXCELLENT
QUESTION.

1966
01:00:38,000 --> 01:00:39,200
SO WE DON'T HAVE THE ABILITY TO

1967
01:00:39,200 --> 01:00:40,640
MAKE THAT JUDGMENT QUITE SO

1968
01:00:40,640 --> 01:00:41,720
WELL.

1969
01:00:41,720 --> 01:00:45,880
BECAUSE AS I POINTED OUT, THE

1970
01:00:45,880 --> 01:00:46,640
THOGOTOVIRUS IS NOT SOMETHING

1971
01:00:46,640 --> 01:00:48,720
THAT IS PRESENT IN HUMAN

1972
01:00:48,720 --> 01:00:49,560
POPULATIONS, IT'S SOMETHING THAT

1973
01:00:49,560 --> 01:00:52,320
IS ENDEMIC IN EUROPEAN

1974
01:00:52,320 --> 01:00:53,200
POPULATIONS, BUT THAT DOESN'T

1975
01:00:53,200 --> 01:00:54,400
MEAN THAT IT WASN'T ABLE TO

1976
01:00:54,400 --> 01:00:55,240
ACTUALLY PROVIDE SOME

1977
01:00:55,240 --> 01:00:56,320
PROTECTION, SO IT'S REALLY LIKE

1978
01:00:56,320 --> 01:00:57,840
IF YOU WERE SUCCESSFUL, YOU

1979
01:00:57,840 --> 01:00:58,960
PROBABLY DON'T HAVE THE VIRUS

1980
01:00:58,960 --> 01:01:00,120
BECAUSE YOU'RE PROTECTED FROM

1981
01:01:00,120 --> 01:01:05,680
ZOO KNOW CYS --SO THAT'S HARD FO

1982
01:01:05,680 --> 01:01:05,960
RECONCILE.

1983
01:01:05,960 --> 01:01:07,360
I WILL ALSO POINT OUT THAT

1984
01:01:07,360 --> 01:01:08,760
INFLUENZA VIRUSES, AT LEAST IN

1985
01:01:08,760 --> 01:01:09,880
THEIR NORMAL COURSE OF

1986
01:01:09,880 --> 01:01:10,600
INFECTION, PROBABLY DIDN'T DRIVE

1987
01:01:10,600 --> 01:01:12,160
THE MAJORITY OF THE EVOLUTION

1988
01:01:12,160 --> 01:01:13,440
WE'VE SEEN BECAUSE AGAIN, THAT

1989
01:01:13,440 --> 01:01:15,320
WAS IN THE AFRICAN DIASPORA.

1990
01:01:15,320 --> 01:01:17,960
SO THERE ARE VIRUSES THAT HAVE

1991
01:01:17,960 --> 01:01:24,200
DRIVEN THIS BUT WE'RE USING

1992
01:01:24,200 --> 01:01:25,800
THOGOTO AND INFLUENZA VIRUSES

1993
01:01:25,800 --> 01:01:26,880
FOR WHAT THIS MIGHT HAVE BEEN.

1994
01:01:26,880 --> 01:01:27,280
>> THANK YOU.

1995
01:01:27,280 --> 01:01:29,200
>> IT SEEMED LIKE FOR TRIM
5,

1996
01:01:29,200 --> 01:01:30,800
THERE WAS NO EVOLUTIONARY

1997
01:01:30,800 --> 01:01:33,440
PRESSURE WITH REGARD TO HIV-1,

1998
01:01:33,440 --> 01:01:36,160
PROBABLY BECAUSE THE HISTORY WAS

1999
01:01:36,160 --> 01:01:37,000
TOO SHORT.

2000
01:01:37,000 --> 01:01:38,400
FOR MXA, OBVIOUSLY, THERE WAS A

2001
01:01:38,400 --> 01:01:40,400
LOT OF EVOLUTIONARY PRESSURE AND

2002
01:01:40,400 --> 01:01:42,120
YOU HINTED AT THE POSSIBILITY

2003
01:01:42,120 --> 01:01:44,120
THAT THERE COULD BE VERSIONS OF

2004
01:01:44,120 --> 01:01:48,400
MXA THAT WOULD TREAT INFLUENZA

2005
01:01:48,400 --> 01:01:49,800
AND THE OTHER VIRUSES PERHAPS

2006
01:01:49,800 --> 01:01:52,160
EQUALLY WELL AND BETTER THAN THE

2007
01:01:52,160 --> 01:01:52,960
WILD TYPE VERSION.

2008
01:01:52,960 --> 01:01:54,360
HAVE YOU LOOKED AT WHETHER

2009
01:01:54,360 --> 01:01:56,560
PERHAPS ANY OF THOSE MUTATIONS

2010
01:01:56,560 --> 01:02:01,000
THAT WOULD BE BETTER FROM AN

2011
01:02:01,000 --> 01:02:02,880
ANTIVIRAL PERSPECTIVE WOULD LEAD

2012
01:02:02,880 --> 01:02:05,240
TO RESPONSES IN THE ORGANISM

2013
01:02:05,240 --> 01:02:08,200
THAT WOULD BE DISADVANTAGE --

2014
01:02:08,200 --> 01:02:09,920
>> SORT OF TOXIC EFFECT --

2015
01:02:09,920 --> 01:02:12,640
>> YEAH, TOXIC EFFECTS OR

2016
01:02:12,640 --> 01:02:13,880
TRIGGER IMMUNE RESPONSES OR

2017
01:02:13,880 --> 01:02:14,560
WHATEVER, BECAUSE THAT SEEMS TO

2018
01:02:14,560 --> 01:02:16,480
BE ANOTHER POINT.

2019
01:02:16,480 --> 01:02:18,080
>> SO I WILL COMPLETELY
AGREE

2020
01:02:18,080 --> 01:02:18,520
WITH THAT.

2021
01:02:18,520 --> 01:02:19,800
THAT'S ACTUALLY, BY THE WAY,

2022
01:02:19,800 --> 01:02:22,320
TRUE OF TRIM 5 AS WELL, WHERE

2023
01:02:22,320 --> 01:02:24,520
TRIM 5 SAN E3 -- WITH A RAPIDLY

2024
01:02:24,520 --> 01:02:25,800
EVOLVING LIGAND SPECIFICITY

2025
01:02:25,800 --> 01:02:26,920
DOMAIN AND YOU CAN IMAGINE THAT

2026
01:02:26,920 --> 01:02:28,200
SOME OF THE ADAPTIVE LANDSCAPE

2027
01:02:28,200 --> 01:02:29,960
IS GOING TO BE RESTRICTIVE

2028
01:02:29,960 --> 01:02:31,600
BECAUSE OF THE CHANCES OF AN

2029
01:02:31,600 --> 01:02:33,680
INTERACTION WITH THE -- PROTEIN.

2030
01:02:33,680 --> 01:02:36,720
ALL OF OUR EXPERIMENTS ARE DONE

2031
01:02:36,720 --> 01:02:39,880
ON CELL LINES SO WE HAVE NOT

2032
01:02:39,880 --> 01:02:41,760
MANIPULATED -- EACH IS LIKE A

2033
01:02:41,760 --> 01:02:43,240
SIGNIFICANT INVESTMENT, AND

2034
01:02:43,240 --> 01:02:44,480
ASSESSING WHICH OF THE VARIANTS

2035
01:02:44,480 --> 01:02:46,520
THAT DIDN'T WORK, WE WANT TO

2036
01:02:46,520 --> 01:02:47,880
TEST, IS MORE PROBLEMATIC.

2037
01:02:47,880 --> 01:02:49,600
I WILL SAY, THOUGH, THAT

2038
01:02:49,600 --> 01:02:50,880
EVERYTHING IN OUR ASSAY, WE DID

2039
01:02:50,880 --> 01:02:52,680
NOT ACTUALLY SEE ANY

2040
01:02:52,680 --> 01:02:54,160
OVERTOXICITY WITH ANY OF THE

2041
01:02:54,160 --> 01:02:55,160
VARIANTS.

2042
01:02:55,160 --> 01:02:58,760
SO BOTH IN THE V1 LOOP OF TRIM E

2043
01:02:58,760 --> 01:03:00,720
ABLE TO ASSESS, BECAUSE WE

2044
01:03:00,720 --> 01:03:03,240
TESTED EACH OF THESE

2045
01:03:03,240 --> 01:03:04,800
INDIVIDUALLY, NEARLY 2,000

2046
01:03:04,800 --> 01:03:06,480
VARIANTS, IF THERE WAS A

2047
01:03:06,480 --> 01:03:08,240
TOXICITY VARIANT EFFECT, WE

2048
01:03:08,240 --> 01:03:09,360
WOULD HAVE NOTICED THAT.

2049
01:03:09,360 --> 01:03:11,440
THEY ALL APPEAR TO BE EXPRESSED

2050
01:03:11,440 --> 01:03:13,840
WELL AND ALL ARE CAPABLE OF

2051
01:03:13,840 --> 01:03:14,240
OLIGOMERIZATION.

2052
01:03:14,240 --> 01:03:16,760
THAT'S STILL ONLY ABOUT ONE MILL

2053
01:03:16,760 --> 01:03:20,160
YONTMILLIONTH.

2054
01:03:20,160 --> 01:03:22,440
I ALSO WANT TO MAKE A SMALL

2055
01:03:22,440 --> 01:03:24,280
CORRECTION ACTUALLY WITH MXA, WE

2056
01:03:24,280 --> 01:03:25,720
TONIGHT KNOW EXACTLY WHAT DROVE

2057
01:03:25,720 --> 01:03:27,120
IT BUT TRIM 5 WE HAVE A MUCH

2058
01:03:27,120 --> 01:03:28,760
BETTER SENSE OF WHAT DROVE IT

2059
01:03:28,760 --> 01:03:30,120
BECAUSE THE HUMAN TRIM 5 IS

2060
01:03:30,120 --> 01:03:32,760
VERY, VERY GOOD AT RESTRICTING

2061
01:03:32,760 --> 01:03:34,880
ANTEROPICK TROA PEEN -- LEUKEMIA

2062
01:03:34,880 --> 01:03:37,040
VIRUS, FOR MANY OF THE

2063
01:03:37,040 --> 01:03:38,160
ENDOGENOUS RETROVIRUSES WE HAVE

2064
01:03:38,160 --> 01:03:39,440
INTEGRATED INTO OUR GENOME.

2065
01:03:39,440 --> 01:03:40,680
ALMOST CERTAINLY, I DON'T THINK

2066
01:03:40,680 --> 01:03:44,920
THERE'S ANY AMBIGUITY, WERE

2067
01:03:44,920 --> 01:03:47,640
DRIVEN WITH THOSE ENDOGENOUS

2068
01:03:47,640 --> 01:03:48,000
RETROVIRUSES.

2069
01:03:48,000 --> 01:03:48,640
>> THANK YOU.

2070
01:03:48,640 --> 01:03:51,480
>> IT SEEMS TO ME THAT THE
BEST

2071
01:03:51,480 --> 01:03:53,760
STRATEGY FOR A VIRUS WOULD BE TO

2072
01:03:53,760 --> 01:03:57,680
NOT ONLY EVOLVE TO AVOID THE

2073
01:03:57,680 --> 01:03:59,000
RECOGNITION BY THE INNATE

2074
01:03:59,000 --> 01:04:01,720
IMMUNITY PROTEIN, BUT TO ALSO

2075
01:04:01,720 --> 01:04:03,160
EVOLVE SUCH THAT IT BECAME MORE

2076
01:04:03,160 --> 01:04:07,120
SIMILAR TO A HOST PROTEIN TO

2077
01:04:07,120 --> 01:04:08,200
ALMOST TAKE A HOST PROTEIN

2078
01:04:08,200 --> 01:04:10,160
HOSTAGE SO THAT IF THAT INNATE

2079
01:04:10,160 --> 01:04:12,720
IMMUNITY PROTEIN EVOLVES TO

2080
01:04:12,720 --> 01:04:14,440
CHASE IT AND HIT IT IN THE

2081
01:04:14,440 --> 01:04:15,880
FUTURE, IT'S GOING TO HAVE TO

2082
01:04:15,880 --> 01:04:18,280
SOMEHOW, LIKE, DO A SECOND STEP

2083
01:04:18,280 --> 01:04:19,880
TO AVOID HURTING ANOTHER HOST

2084
01:04:19,880 --> 01:04:20,280
PROTEIN.

2085
01:04:20,280 --> 01:04:21,760
SO IS THERE ANY EVIDENCE THAT

2086
01:04:21,760 --> 01:04:24,440
SOMETHING LIKE THAT EXISTS OR --

2087
01:04:24,440 --> 01:04:25,960
>> I'M SMILING BECAUSE TOM
IS IN

2088
01:04:25,960 --> 01:04:30,000
THE AUDIENCE AND HIS LAB HAS,

2089
01:04:30,000 --> 01:04:32,320
ALONG WITH MY LAB, STUDIED MANY

2090
01:04:32,320 --> 01:04:37,920
EXAMPLES OF VIRAL MIMIC RI,LY,

2091
01:04:37,920 --> 01:04:39,760
EXACTLY WHAT YOU'RE SAYING,

2092
01:04:39,760 --> 01:04:41,720
THEY'LL USE THEM AS DECOYS TO

2093
01:04:41,720 --> 01:04:43,160
ESSENTIALLY PREVENT ANTIVIRAL

2094
01:04:43,160 --> 01:04:44,920
PROTEINS, OFTEN THEY'LL STEAL

2095
01:04:44,920 --> 01:04:47,080
HOST GENES WITH JUST SUBSTRATES

2096
01:04:47,080 --> 01:04:49,400
OF ANTIVIRAL PROTEINS AND MAKE

2097
01:04:49,400 --> 01:04:51,000
VERSIONS THAT ARE CAPABLE OF

2098
01:04:51,000 --> 01:04:52,440
BEING BOUND BY THE ANTIVIRAL

2099
01:04:52,440 --> 01:04:53,840
PROTEINS BUT NOT CAPABLE OF

2100
01:04:53,840 --> 01:04:55,480
BEING CATALYZED, WHICH BASICALLY

2101
01:04:55,480 --> 01:04:57,240
TAKES THEM OUT OF THE PICTURE.

2102
01:04:57,240 --> 01:04:59,520
THIS HAS HAPPENED -- THIS IS A

2103
01:04:59,520 --> 01:05:01,080
VERY SEC SUS FELL STRATEGY THAT

2104
01:05:01,080 --> 01:05:02,280
MANY VIRUSES THAT HAVE THE

2105
01:05:02,280 --> 01:05:04,560
ABILITY TO HAVE LARGE GENOMES

2106
01:05:04,560 --> 01:05:06,200
LIKE DOUBLE SIDED DNA VIRUSES

2107
01:05:06,200 --> 01:05:07,840
HAVE EMPLOYED VERY, VERY

2108
01:05:07,840 --> 01:05:08,800
SUCCESSFULLY IN THE PAST.

2109
01:05:08,800 --> 01:05:10,880
THERE'S NO EVIDENCE FOR THAT FOR

2110
01:05:10,880 --> 01:05:13,960
MXA OR TRIM 5, BUT IN THEORY,

2111
01:05:13,960 --> 01:05:16,920
YOUR POINT IS WELL TAKEN THAT

2112
01:05:16,920 --> 01:05:18,600
MIMICRY IS A VERY, VERY GOOD

2113
01:05:18,600 --> 01:05:19,440
EVOLUTIONARY STRATEGY IN

2114
01:05:19,440 --> 01:05:22,120
GENERAL.

2115
01:05:22,120 --> 01:05:32,280
>> JUST SO INTERESTING
BECAUSE

2116
01:05:32,280 --> 01:05:33,880
YOU FOCUS ON THE FLEXIBLE LOOPS

2117
01:05:33,880 --> 01:05:34,680
BECAUSE THOSE ARE VERY

2118
01:05:34,680 --> 01:05:35,240
IMPORTANT.

2119
01:05:35,240 --> 01:05:38,920
IT WAS HERE IN MY LAB, WE

2120
01:05:38,920 --> 01:05:41,320
SHOWED -- FLEXIBLE LOOPS IN

2121
01:05:41,320 --> 01:05:42,960
PROTEIN STRUCTURES.

2122
01:05:42,960 --> 01:05:49,760
NOW WHAT I WANT TO ASK, YOU HAVE

2123
01:05:49,760 --> 01:05:53,760
A GLYCINE RESIDUE AND THE

2124
01:05:53,760 --> 01:05:57,520
GLYCINE CONFORMATION, YOU MUST

2125
01:05:57,520 --> 01:05:59,360
ANALYZE THE CONFIRMATION AT THAT

2126
01:05:59,360 --> 01:06:01,120
REGION AND THE DYNAMICS OF THE

2127
01:06:01,120 --> 01:06:01,560
CONFORMATION.

2128
01:06:01,560 --> 01:06:02,680
THAT'S VERY IMPORTANT.

2129
01:06:02,680 --> 01:06:03,560
GLYCINE CHAINS --

2130
01:06:03,560 --> 01:06:07,800
>> GLYCINE AND PROLINE ARE

2131
01:06:07,800 --> 01:06:09,520
INTERESTING AT BOTH ENDS OF THE

2132
01:06:09,520 --> 01:06:09,800
SPECTRUM.

2133
01:06:09,800 --> 01:06:10,920
>> THAT STUDY IS VERY
IMPORTANT.

2134
01:06:10,920 --> 01:06:12,880
>> I SHOULD POINT OUT THAT
WE

2135
01:06:12,880 --> 01:06:14,160
ACTUALLY NOT HAVE DONE MUCH IN

2136
01:06:14,160 --> 01:06:15,280
TERMS OF THE CONFORMATIONAL

2137
01:06:15,280 --> 01:06:16,960
STATE IN PART BECAUSE WE THINK

2138
01:06:16,960 --> 01:06:18,280
ABOUT -- WITH MXA WE'VE BEEN

2139
01:06:18,280 --> 01:06:19,920
THINKING MORE THAT IT'S ALMOST

2140
01:06:19,920 --> 01:06:22,880
LIKE AN UNSTRUCTURED LOOP THAT

2141
01:06:22,880 --> 01:06:23,840
BECOMES -- WHEN IT BOUND AND

2142
01:06:23,840 --> 01:06:25,760
THERE ARE NO CO-STRUCTURES OF

2143
01:06:25,760 --> 01:06:28,640
THE MXA WITH THE NP PROTEIN IN

2144
01:06:28,640 --> 01:06:29,640
PART BECAUSE IT WAS NOT STRONG

2145
01:06:29,640 --> 01:06:31,000
ENOUGH FOR A CRYSTAL STRUCTURE.

2146
01:06:31,000 --> 01:06:33,640
WE ARE HOPING THAT OUR -- WILL

2147
01:06:33,640 --> 01:06:35,120
HELP THAT BECAUSE WE HAVE 24

2148
01:06:35,120 --> 01:06:38,080
MORE AVID STRUCTURES AND WE ARE

2149
01:06:38,080 --> 01:06:38,960
ACTIVELY WORKING WITH

2150
01:06:38,960 --> 01:06:39,400
COLLEAGUES.

2151
01:06:39,400 --> 01:06:41,600
WE'VE BEEN TOLD THAT THE

2152
01:06:41,600 --> 01:06:42,760
CONFORMATIONAL STATUS IS

2153
01:06:42,760 --> 01:06:43,760
SOMETHING THAT IS REALLY THE

2154
01:06:43,760 --> 01:06:45,200
PURVIEW OF NMR.

2155
01:06:45,200 --> 01:06:46,680
THIS IS FAR TOO BIG FOR THAT.

2156
01:06:46,680 --> 01:06:48,320
BUT WE'RE HOPING THAT EVEN

2157
01:06:48,320 --> 01:06:49,760
CRYO-EM STUDIES MIGHT ACTUALLY

2158
01:06:49,760 --> 01:06:52,040
REVEAL A LITTLE BIT MORE ABOUT

2159
01:06:52,040 --> 01:06:53,040
THIS.

2160
01:06:53,040 --> 01:06:53,560
THANKS FOR THE QUESTION.

2161
01:06:53,560 --> 01:06:55,560
>> IT'S PART 2 OF THIS ONE

2162
01:06:55,560 --> 01:06:56,400
QUESTION FROM OUR COLLEAGUE IN

2163
01:06:56,400 --> 01:07:00,000
THE LIBRARY.

2164
01:07:00,000 --> 01:07:00,600
NATIONAL LIBRARY OF MEDICINE.

2165
01:07:00,600 --> 01:07:02,720
COULD THE STORY ABOUT THE TWO

2166
01:07:02,720 --> 01:07:04,840
ARGININES, RATHER THAN BEING AN

2167
01:07:04,840 --> 01:07:06,720
UNFORTUNATE COINCIDENCE, REFLECT

2168
01:07:06,720 --> 01:07:11,720
ADAPTATION TO HIV TO HUMANS?

2169
01:07:11,720 --> 01:07:14,880
>> IT'S NOT ABOUT
ADAPTATION TO

2170
01:07:14,880 --> 01:07:18,040
HIV OR REALLY TO ANY SIVs

2171
01:07:18,040 --> 01:07:18,920
WE'VE TESTED NEARLY A DOZEN

2172
01:07:18,920 --> 01:07:20,480
SIVs THAT COULD HAVE POSSIBLY

2173
01:07:20,480 --> 01:07:22,320
JUMPED INTO HUMANS BUT MAYBE

2174
01:07:22,320 --> 01:07:24,520
WERE PROTECTED BECAUSE WE HAD

2175
01:07:24,520 --> 01:07:26,600
THE DOUBLE ARGININES BUT IT WAS

2176
01:07:26,600 --> 01:07:27,240
CERTAINLY ADAPTIVE.

2177
01:07:27,240 --> 01:07:28,680
THIS IS AN UNFORTUNATE

2178
01:07:28,680 --> 01:07:30,960
COINCIDENCE ONLY WITH RESPECT TO

2179
01:07:30,960 --> 01:07:32,160
HIV SUSCEPTIBILITY BUT IT WAS

2180
01:07:32,160 --> 01:07:33,920
NOT AN UNFORTUNATE COINCIDENCE

2181
01:07:33,920 --> 01:07:35,440
BECAUSE BOTH OF THESE WERE

2182
01:07:35,440 --> 01:07:36,560
DELIBERATELY OCCURRED AND

2183
01:07:36,560 --> 01:07:37,760
DELIBERATELY SELECTED FOR IN THE

2184
01:07:37,760 --> 01:07:38,880
CONTEXT THAT THEY OCCURRED.

2185
01:07:38,880 --> 01:07:41,960
WE JUST DON'T KNOW SINCE THIS

2186
01:07:41,960 --> 01:07:45,120
HAPPENED IN THE COMMON ANCESTOR

2187
01:07:45,120 --> 01:07:47,880
OF CHIMPS, GUERILLAS AND HUMANS,

2188
01:07:47,880 --> 01:07:49,200
WE JUST DON'T KNOW WHAT THAT

2189
01:07:49,200 --> 01:07:51,080
AGENT WAS, WHETHER IT WAS A

2190
01:07:51,080 --> 01:07:53,240
VIRAL AGENT OR AUTOIMMUNE AGENT.

2191
01:07:53,240 --> 01:07:56,160
ONE OF THE PROBLEMS IS MAKING A

2192
01:07:56,160 --> 01:07:58,280
CONTEMPORANEOUS ARGUMENT FOR

2193
01:07:58,280 --> 01:07:59,160
WHAT DROVE THIS REQUIRES US TO

2194
01:07:59,160 --> 01:08:00,480
HAVE A PRETTY GOOD SINCE OF WHAT

2195
01:08:00,480 --> 01:08:02,440
THE VIRUSES WERE.

2196
01:08:02,440 --> 01:08:04,160
WITH RETROVIRUSES WE HAVE A

2197
01:08:04,160 --> 01:08:05,160
PRETTY GOOD SENSE OF THAT

2198
01:08:05,160 --> 01:08:07,000
BECAUSE MANY OF THEM INTEGRATED

2199
01:08:07,000 --> 01:08:09,320
INTO OUR GENOME BUT THINGS LIKE

2200
01:08:09,320 --> 01:08:10,760
HIV -- THEY'RE NOT GERMLINE

2201
01:08:10,760 --> 01:08:11,200
INTEGRATION EVENTS.

2202
01:08:11,200 --> 01:08:13,880
SO WE HAVE HALF THE MIRROR IMAGE

2203
01:08:13,880 --> 01:08:15,320
OF THE STORY.

2204
01:08:15,320 --> 01:08:17,280
WE KNOW ITS ADAPTATION BUT WE

2205
01:08:17,280 --> 01:08:18,240
DON'T KNOW WHAT CAUSED IT.

2206
01:08:18,240 --> 01:08:18,960
>> OKAY.

2207
01:08:18,960 --> 01:08:19,280
>> ALL RIGHT.

2208
01:08:19,280 --> 01:08:21,040
THANK YOU VERY MUCH FOR COMING.

2209
01:08:21,040 --> 01:08:27,880
[APPLAUSE]