BMS 500 MOLECULAR AND CELL BIOLOGY FALL 2013

Meets 9:00-10:50 AM Monday and Thursday Room 1041, David Axelrod Institute Course Description This course will examine essential cellular processes at the molecular level by providing historical perspective and using examples from the current literature. Emphasis is on processes involving DNA and RNA, with topics including DNA structure and function, replication, transposition, RNA interference, and transcriptional regulation; in addition, post-transcriptional regulation, translation, and intracellular trafficking will also be touched on. An outline is presented below. Objectives Students will expand their familiarity with basic concepts and gain new knowledge of more advanced material relevant to the topics to be covered (see Course Description). At the conclusion of the course, students will be able to understand and critique scientific literature and seminars in the relevant areas, and will have increased knowledge that they may apply to their specific areas of research. Students will be graded using exams that test their ability to synthesize the concepts and approaches they have learned, and to apply them to real or simulated experimental data, and on writing assignments that will test students’ ability to apply the concepts they have learned to the scientific literature. Course Web Site Lecture and reading material will be made available on the course web site, which is on SUNY Albany’s electronic reserves http://eres.ulib.albany.edu. Access requires a current UAlbany netID. The course is listed as BMS500. Office hours M-F, 9-5; meetings should be arranged with individual instructors, who may be contacted by email or phone, as this is a team-taught course. Grading scheme A-E; three non-cumulative exams of equal weight plus 3-4 written assignments that will each count the equivalent of 15-30% of an exam. Course requirements Readings from the scientific literature will be assigned by individual instructors. Exams will be given on October 3rd, November 7th, and December 12th. Exams are open book, but materials must be taken out of your bag or backpack before the beginning of the exam. Exam questions will primarily be short answers and short essays and will require problem solving. Course grades are determined based on exam performance and on written assignments, with class participation also considered.

Detailed syllabus: DNA structure: The content and complexity of the human genome will be examined. Genome size, unique and repetitive sequence content, and gene number and function will be discussed. Other topics include the increased genetic complexity provided by features of the proteome and the transciptome and human genetic variation and disease risk. Consequences of DNA mutation in human disease will be examined in discussion of transmission genetics and Mendelian inheritance and the analysis of human pedigrees. Nonmendelian and epigenetic inheritance will also be discussed. The structure and topology of DNA and the importance of chromatin structure is covered.

DNA replication. These lectures will cover the molecular mechanisms of DNA replication. Mechanisms of replication in bacteria and eukaryotes including detailed consideration of initiation and termination are covered. The replication of chromatin and the retention of epigenetic "marks" and developmental memory and telomere structure and replication are also discussed.

Transposition. In this unit, students will explore the impact that transposons have on eukaryotic genome evolution, organization and stability and the role that transposons play in human disease. We will examine the selfish DNA hypothesis and the mutualistic relationship that exists between transposons and their hosts. Cell Cycle: Topics covered will include: classical analysis of yeast cell cycle mutants, oocyte maturation, MPF, CSF, cyclins, and the convergence of these fields. The components of mammalian cell cycle machinery, common themes in cell cycle dysregulation in cancer, role of tumor suppressors in cell cycle regulation and checkpoints are also discussed.

Transcriptional regulation: Both prokaryotic and eukaryotic transcription will be discussed, with emphasis on basic principles and new technologies and advances in understanding. Material on prokaryotic transcription will include discussion of genetic and biochemical approaches to studying transcriptional regulation, and mechanisms of transcriptional initiation, elongation and termination. Discussion of eukaryotic transcription will include the role of transcriptional activators, co-activators, and the basic transcription machinery, and how they function in transcriptional regulation. Genome-wide approaches will be an important topic. In addition, the role of chromatin in transcriptional regulation will be covered in some depth.

Gene silencing: Topics covered will include: forms of gene silencing, the discovery of RNAi, RNAi mutants in C. elegans, RNAi biochemistry and the importance of microRNAs in development. RNA processing and RNA function: The difference between a primary transcript produced by RNA polymerase and a mature transcript poised for translation is significant. Furthermore, our understanding of functional roles for RNA and its production beyond mRNA production has expanded vastly in recently years. In this short unit, students will choose among topics including RNA splicing, long non-coding RNA transcripts, RNA stability, self splicing RNAs, RNA modification of mRNA and tRNA, and RNA editing to focus on one aspect of RNA processing/function in a group project or paper.

Protein translation: The structure and function of the basic components that participate in protein synthesis will be introduced, including tRNA and ribosomes. The problems of tRNA identity and decoding the genetic code will be discussed. Impact of advancements in the structural studies of ribosome in understanding mRNA decoding on the small ribosomal subunit will be discussed. The four main steps in protein synthesis will be discussed. Molecular mimicry between tRNA and various protein factors will be outlined and discussed. The mechanism of action of several antibiotics in inhibiting the steps of translation will be discussed.

Intracellular trafficking: A brief overview of cell structures with emphasis on the spatial and topological organization of the various membrane-bound intracellular compartments and the problems this creates for the movement of proteins between these compartments. Mechanisms

for translocating proteins across intracellular membranes in trafficking proteins between intracellular compartments will also be discussed.

BMS 500 MOLECULAR AND CELL BIOLOGY FALL 2013

9:00-10:50 AM

Room 1041, David Axelrod Institute

Day Date Lecture Topic Instructor Monday 26-Aug 1 Human genome sequence Glaser Thursday 29-Aug 2 Human genome variation Glaser Monday 2-Sep No Class Thursday 5-Sep No Class (Rosh Hashanah) Monday 9-Sep 3 DNA and chromatin structure Glaser

Thursday 12-Sep 4 DNA replication Wolfgang

Monday 16-Sep 5 DNA replication Wolfgang

Thursday 19-Sep 6 Cell cycle Conklin

Monday 23-Sep 7 Cell cycle Conklin

Thursday 26-Sep 8 Transposition Curcio Monday 30-Sep 9 Transposition/Review (1 hr

each) Curcio/Glaser, Wolfgang, Conklin

Thursday 3-Oct Exam 1

Monday 7-Oct 10 Transcriptional regulation (Prokaryotic)

Wade

Thursday 10-Oct 11 Transcriptional regulation (Prokaryotic)

Wade

Monday 14-Oct No Class (Columbus Day)

Thursday 17-Oct 12 Transcriptional regulation (Prokaryotic)

Wade

Monday 21-Oct 13 Transcriptional regulation (Prokaryotic/Eukaryotic)

Morse

Thursday 24-Oct 14 Transcriptional regulation (Eukaryotic)

Morse

Monday 28-Oct 15 Transcriptional regulation (Eukaryotic)

Morse

Thursday 31-Oct 16 Gene silencing Conklin Monday 4-Nov Review Thursday 7-Nov Exam 2 Monday 11-Nov 17 RNA processing TBD

Thursday 14-Nov 18 RNA processing TBD Monday 18-Nov 19 Protein translation Agrawal

Thursday 21-Nov 20 Protein translation Agrawal

Monday 25-Nov 21 Intracellular trafficking Mazurkiewicz Thursday 28-Nov No Class Monday 2-Dec 22 Intracellular trafficking Mazurkiewicz Thursday 5-Dec 23 Intracellular trafficking Mazurkiewicz Monday 9-Dec Review Thursday 12-Dec Exam 3

Instructors: Doug Conklin CRC dconklin@albany.edu 591-7154 Bill Wolfgang DAI wwolfgan@wadsworth.org 486-1156 Bob Glaser Griffin glaser@wadsworth.org 485-6483 Joan Curcio CMS curcio@wadsworth.org 473-4213 Joe Wade CMS jwade@wadsworth.org 474-5727 Randy Morse CMS morse@wadsworth.org 486-3116 Raj Agrawal ESP agrawal@wadsworth.org 486-5797 Joe Mazurkiewicz AMC MazurkJ@mail.amc.edu 262-5381

BIOLOGICAL BASIS OF PUBLIC HEALTH BMS505, Fall 2012

Syllabus

Location and meeting times Mo/We 10:30am – 11:50am, George Auditorium

Course Director:

Martin Tenniswood, PhD Department of Biomedical Sciences School of Public Health University at Albany, SUNY Tel: (518)591-7200 mtenniswood@albany.edu

Course Description: This course is designed to introduce students with no or minimal formal training in biological sciences an overview of the field with an emphasis on its application to significant public health problems. The primary emphasis of this course is to provide the necessary information to individuals with diverse backgrounds so that they have a good working knowledge of biomedical sciences and how it influences our lives and shapes public health. This course will provide an introduction to the field of biomedical sciences through discussion of disorders of public health relevance, including infectious and transmissible vectors, genetic disease and chronic disorders such as type II diabetes and obesity . Prerequisite: One semester of college science, e.g., biology, chemistry, physics or a comparable course. Learning objectives for BMS505:

You will be able to describe the role of biomedical sciences in the ecological model of public health. You will learn to understand and communicate basic biological and genetic terminologies. You will learn about emerging biological technologies and how they can be applied to diagnosis and

prevention of human disease. You will learn to identify the political, legal, social, ethical and economic issues associated with

integrating basic biology into public health. You will learn where to locate and how to acquire accurate and practical biological information that

impacts public health issues. You will be able to describe the role of the New York State Department of Health and the Wadsworth

Laboratories in the control of infectious and genetic diseases in New York State. You will be able to explain the use of laboratory procedures for understanding and diagnosing selected

infectious diseases and genetic conditions. You will be able to describe existing and proposed programs in newborn, carrier, and cancer screening,

and discuss pros and cons of each program, including medical, economic, ethical, legal, social and political factors.

Public Health Biology Competencies for BMS505:

1. Specify the role of the immune system in population health. 2. Describe how behavior alters human biology. 3. Identify the ethical, social and legal issues implied by public health biology. 4. Explain the biological and molecular basis of public health. 5. Explain the role of biology in the ecological model of population-based health. 6. Explain how genetics and genomics affect disease processes and public health policy and practice. 7. Articulate how biological, chemical and physical agents affect human health.

8. Apply biological principles to development and implementation of disease prevention, control or

management programs. 9. Apply evidence-based biological and molecular concepts to inform public health laws, policies and

regulations. 10. Integrate general biological and molecular concepts into public health.

Public Health Biology Illustrative Competencies for BMS505: The ability to incorporate public health biology – the biological and molecular context of public health into public health practice. 1. Specify the role of the immune system in population health.

a) Explain what a vaccine is and why we have effective vaccines for some infectious disease but not all. b) Explain the function of the immune system. c) Identify immune responses to pathogens, manipulation of immune response for vaccines or

immunotherapy, and failure or aberrant immune responses. d) Explain the biological principles and vaccination strategies that allowed smallpox eradication. e) Describe the role, benefits, and limitations of vaccines in assuring the health of populations.

2. Describe how behavior alters human biology. a) Describe the influences of environment and human physiology on behavioral health, including:

genetics, substance use, family, culture, ethnicity, trauma, cognition, and developmental status. b) Relate biological and genetic changes resulting from smoking. c) Analyze the interaction of genetics, lifestyle, and the environment in the health of a population.

3. Identify the ethical, social and legal issues implied by public health biology. a) Assess the pros and cons of using individual information in the design, implementation, and evaluation

of public health activities and initiatives. b) Discuss the biological underpinnings and public health issues of drug interactions in diverse

populations. 4. Explain the biological and molecular basis of public health.

a) Explain the biological and molecular characteristics of cancer, heart disease, stroke, aging, and other chronic diseases.

b) Integrate general biological and molecular principles into public health problems such as infectious disease, disease susceptibility and drug resistance, and assisted reproduction.

c) Explain the relationships among nutrition, physical activity, and health. 5. Explain the role of biology in the ecological model of population-based health.

a) Discuss the biology of major determinants of national and global public health, e.g. smoking, obesity, malnutrition.

b) Relate the biological factors with other components of the ecological model for emerging infections in the global environment.

6. Explain how genetics and genomics affect disease processes and public health policy and practice. a) Define the basic terms, vocabulary, and underlying principles associated with genetics and genomics. b) Integrate traditional approaches in genetics with genomic and proteomic approaches. c) Determine the role of genetic factors in the susceptibility to and progression of disease. d) Discuss cancer as a genetic disease. e) Explain the genetic changes that are key in generating emerging infectious diseases such as avian flu.

7. Calculate how biological, chemical, and physical agents affect human health. a) Describe human, molecular, cellular, and physiological interactions with exogenous agents. b) Discuss environmental factors affecting expression of determinates of susceptibility to disease during

development. c) Describe the various ways by which chemicals can directly or indirectly affect human health. d) Discuss the effects of chemicals on the ecosystem, for example, global warming and the ozone layer.

8. Apply biological principles to development and implementation of disease prevention, control or management of programs. a) Assess biological principles of public health laboratory tests. b) Describe the ecological principles of disease and how these principles affect the likelihood of control. c) Assess factors that affect accessibility, adequacy, and safety of the food supply and the relationship to

the assessment and analysis of community food systems.

9. Apply evidence-based biological and molecular concepts to inform public health laws, policies, and

regulations. a) Determine appropriate use of data, statistical methods, and laboratory procedures for problem

identification and resolution, and program planning, implementation and evaluation. b) Discuss population dynamics in terms of reproduction, assisted reproduction, fecundity, selection, allele

frequencies, fitness and evolution. c) Discuss the principles of cell biology and development underlying the potential and controversy

surrounding stem cells. 10. Integrate general biological and molecular concepts into public health.

a) Discuss the evolution of concepts about health and the cause of disease. b) Discuss the multiple factors that influence infectious disease epidemics. c) Integrate biological approaches to air, food, and water safety.

Evaluation: Exams: (2) 50% (25% each) Exams will be take home open book, short essay questions. Exam questions will focus on the biological aspects of the course. Term Papers (2): (25% each) Two term papers (3-5 pages) on a choice of topics applying information from the course to important public Health issues will be required of each student. Grading Scale: A = 93-100 A- = 90-92 B+ = 87-89 B = 83-88 B- = 80-82 C+ = 77-79 C = 73-78 C- = 70-72 D+ = 67-69 D = 63-68 D- = 60-62 E = 0-59 Note 1: The “earned” grad of “E” is treated mathematically as a “30”. Note 2: Plagiarism without proper citation from any and all sources will result in a grade of “E” for the course. Consult the Graduate Student Bulletins or the course Instructors if you have any questions.

SCHEDULE Lecture 1 Monday August 26 Introduction

How do we measure health? “Top 10” Diseases by socioeconomic status Organization and Logistics

Lecture 2 Wednesday August 28 Obesity and Diet

BMI, Food/caloric Intake Glucose and Insulin

Monday September 2 LABOR DAY (No Class)

Lecture 3 Wednesday September 4 Physiology of Digestion

Metabolism of polysaccharides and fats Intervention Strategies

Lecture 4 Monday September 9 What’s in your diet?

High Fructose Corn Syrup Physiological and Psychological Effects

Lecture 5 Wednesday September 11 Type II Diabetes

Incidence, Treatment and Health Implications Public Health Implications

Lecture 6 Monday September 16 Health Implications of Our Diets

Hypertension and cardiovascular disease

Lecture 7 Wednesday September 18 Cells: The Basic Units of Life

Eukaryotic Cells Membrane Structure

Lecture 8 Monday September 23 Cells: The Basic Units of Life

Tissue Organization

Lecture 9 Wednesday September 25 Cells: The Basic Units of Life

Prokaryotes (aka Bacteria) Mycobacteria The Microbiome

Lecture 10 Monday September 30 Biomolecules

Nucleic Acids

Lecture 11 Wednesday October 2 Biomolecules

Proteins

Lecture 12 Monday October 7 The Central Dogma

Replication Transcription Translation

Lecture 13 Wednesday October 9 Life and Death of the Cell

Mitosis (Cell Division) Apoptosis (Cell Death)

Monday October 14 COLUMBUS DAY (No Class)

Lecture 14 Wednesday October 16 Meiosis and Fertilization

Spermatogenesis/Oogenesis Fertilization

Lecture 15 Monday October 21 Genetic Diseases

PKU, Sickle Cell Anemia Newborn Screening Pre-natal Diagnosis

Lecture 16 Wednesday October 23 Cancer

DNA Damage/DNA Repair Adduct formation (smoking)

Lecture 17 Monday October 28 Cancer

Chemoprevention

Lecture 18 Wednesday October 30 Viruses and Viral Diseases

Virus Structure

Lecture 19 Monday November 4 Viral Diseases

Influenza

Lecture 20 Wednesday November 6 Viral Diseases

HIV/AIDS

Lecture 21 Monday November 11 Immunology

Innate Immunity

Lecture 22 Wednesday November 13 Immunology

Acquired Immunity Immunoglobulin Synthesis

Lecture 23 Monday November 18 Vaccination

Passive Immunity Active Immunity

Lecture 24 Wednesday November 20

Vaccination and Autism

Lecture 25 Monday November 25 Endemic Diseases

Malaria Tuberculosis

Wednesday November 27 THANKSGIVING (No Class)

Lecture 26 Monday December 2 Endemic Diseases

Malaria Tuberculosis

Lecture 27 Wednesday December 4 Endemic Diseases

Schistosomiasis Trypanosomiasis

BMS505–BiologicalBasisofPublicHealth

ContactInformation:

Instructor: HeidiAtkinson,Ph.D.

CourseNumber: BMS505–BiologicalBasisofPublicHealth

Semester: Fall2013

MailingAddress:UniversityatAlbany,SchoolofPublicHealth1UniversityPlace,GECEastRensselaerNY12144

PrivateCommunications:

Forprivatecommunicationwithme,pleaseuseemail.Anythingotherthanaprivatecommunicationsshouldbepostedinthe'Askaquestion'discussionortheappropriatecourseareas.

Phone: 518‐788‐8036

LogonSchedule:Iwillbeloggingonandrespondingtoemailorpostedquestionsatleastonceadayeverydayoftheweek.

Overview:

Thiscourseisdesignedtoprovideanoverviewofthefieldofbiologywithanemphasisonsignificantpublichealthproblems.Thiscoursefocusesonprovidingthedetailsandbackgroundnecessaryforabasicunderstandingofbiologicalknowledgeandthetechnologythatsurroundsit.Theprimaryemphasisofthiscourseistoprovidethenecessaryinformationtoindividualswithdiversebackgroundssothattheyhaveagoodworkingknowledgeofbiomedicalsciencesandhowitinfluencesourlivesandshapespublichealth.Thiscoursewillprovideanintroductiontothefieldofbiomedicalsciencesbyprovidinginformationaboutdisordersofpublichealthrelevance,includinginfectiousandtransmissiblevectors,geneticdisease,andchronicdisorders.

CourseObjectives:

Bytheendofthesemesteryouwillbeableto:

1.Specifytheroleoftheimmunesysteminpopulationhealth.

a)Explainwhatavaccineisandwhywehaveeffectivevaccinesforsomeinfectiousdiseasebutnotall.

b)Explainthefunctionoftheimmunesystem.

c)Identifyimmuneresponsestopathogens,manipulationofimmuneresponseforvaccinesorimmunotherapy,andfailureoraberrantimmuneresponses.

d)Explainthebiologicalprinciplesandvaccinationstrategiesthatallowedsmallpoxeradication.

e)Describetherole,benefits,andlimitationsofvaccinesinassuringthehealthofpopulations.

2.Describehowbehavioraltershumanbiology.

a)Relatebasicprinciplesofcellbiology,biochemistry,andgeneticstoproblemsinmentalhealth.

b)Describetheinfluencesofenvironmentandhumanphysiologyonbehavioralhealth,including:genetics,substanceuse,family,culture,ethnicity,trauma,cognition,anddevelopmentalstatus.

c)Relatebiologicalandgeneticchangesresultingfromsmoking.

d)Analyzetheinteractionofgenetics,lifestyle,andtheenvironmentinthehealthofapopulation.

3.Identifytheethical,socialandlegalissuesimpliedbypublichealthbiology.

a)Assesstheprosandconsofusingindividualinformationinthedesign,implementation,andevaluationofpublichealthactivitiesandinitiatives.

b)Discussthebiologicalunderpinningsandpublichealthissuesofdruginteractionsindiversepopulations.

4.Explainthebiologicalandmolecularbasisofpublichealth.

a)Explainthebiologicalandmolecularcharacteristicsofcancer,heartdisease,stroke,aging,andotherchronicdiseases.

b)Integrategeneralbiologicalandmolecularprinciplesintopublichealthproblemssuchasinfectiousdisease,diseasesusceptibility,drugresistance,andassistedreproduction.

c)Explaintherelationshipsamongnutrition,physicalactivity,andhealth.

5.Explaintheroleofbiologyintheecologicalmodelofpopulation‐basedhealth.

a)Discussthebiologyofmajordeterminantsofnationalandglobalpublichealth,e.g.smoking,obesity,malnutrition.

b)Relatethebiologicalfactorswithothercomponentsoftheecologicalmodelforemerginginfectionsintheglobalenvironment.

6.Explainhowgeneticsandgenomicsaffectdiseaseprocessesandpublichealthpolicyandpractice.

a)Definethebasicterms,vocabulary,andunderlyingprinciplesassociatedwithgeneticsandgenomics.

b)Integratetraditionalapproachesingeneticswithgenomicandproteomicapproaches.

c)Determinetheroleofgeneticfactorsinthesusceptibilitytoandprogressionofdisease.

d)Discusscancerasageneticdisease.

e)Explainthegeneticchangesthatarekeyingeneratingemerginginfectiousdiseasessuchasavianflu.

7.Articulatehowbiological,chemical,andphysicalagentsaffecthumanhealth.

a)Describehumanmolecular,cellular,andphysiologicalinteractionswithexogenousagents.

b)Discussenvironmentalfactorsaffectingexpressionofdeterminatesofsusceptibilitytodiseaseduringdevelopment.

c)Describethevariouswaysbywhichchemicalscandirectlyorindirectlyaffecthumanhealth.

d)Discusstheeffectsofchemicalsontheecosystem,forexampleglobalwarmingandtheozonelayer.

8.Applybiologicalprinciplestodevelopmentandimplementationofdiseaseprevention,control,ormanagementofprograms.

a)Assessbiologicalprinciplesofpublichealthlaboratorytests.

b)Describetheecologicalprinciplesofdiseaseandhowtheseprinciplesaffectthelikelihoodofcontrol.

c)Assessfactorsthataffectaccessibility,adequacy,andsafetyofthefoodsupplyandtherelationshiptotheassessmentandanalysisofcommunityfoodsystems.

9.Applyevidence‐basedbiologicalandmolecularconceptstoinformpublichealthlaws,policies,andregulations.

a)Determineappropriateuseofdata,statisticalmethods,andlaboratoryproceduresforproblemidentificationandresolution,andprogramplanning,implementationandevaluation.

b)Discusspopulationdynamicsintermsofreproduction,assistedreproduction,fecundity,selection,allelefrequencies,fitnessandevolution.

c)Discusstheprinciplesofcellbiologyanddevelopmentunderlyingthepotentialandcontroversysurroundingstemcells.

10.Integrategeneralbiologicalandmolecularconceptsintopublichealth.

a)Discusstheevolutionofconceptsabouthealthandthecauseofdisease.

b)Discussthemultiplefactorsthatinfluenceinfectiousdiseaseepidemics.

c)Integratebiologicalapproachestoair,food,andwatersafety.

Readings:

Thereisnorequiredtextbookforthiscourse.AllreadingswillbepostedonBlackboardorlinkstoaccessthereadingsontheWebwillbeprovided.

TheclassnotesandothermaterialsarebasedontheFall2012coursedevelopedbyDaynaManiccia,DrPH,MS,AssistantProfessor,ProgramDirector,HealthServicesAdministration,CoordinatorUndergraduatePublicHealth,TheSageCollegesandMartinTenniswood,Ph.D.,EmpireInnovationsProfessor,DepartmentofBiomedicalSciences,Gen*NY*SisCenterofExcellenceinCancerGenomics,SchoolofPublicHealth,UniversityatAlbany.Drs.TenniswoodandManicciagraciouslyprovidedthematerialsforuseinthiscourse.

Courselearningactivitiesandhowyouwillbeevaluated

Severalactivitieswillbeincorporatedintoyoufinalgrade.Duringthecourseofthesemesteryouwilltake2exams,writeseveralbriefpapers,participateinonlinediscussions/reflectionsandcompleteseveralbriefassignments.

Coursegradeswillbedeterminedasfollows:

Briefpapers(3total)30% Reflections/discussions(minimumof5)30% Exams(2total)30% Assignments10%

Briefdescriptionofcourselearningactivities(amoredetaileddescriptionwillbeprovidedwhentheactivityisassigned).

Briefpapers‐Thesepaperswillbe2‐3pagesinlengthandwillrequireyoutoapplyinformationfromthecoursetoimportantpublichealthissues.

Reflections/discussions‐Fortheseassignmentsyouwillbegivenaquestionandaskedtopostyourresponsetothediscussionboard.Youwillalsopostresponsesonotherstudent’sdiscussionthreadinamannerthatbroadensthediscussionandbuildstheknowledgebasefortopicathand.

Exams‐Examswillbeacombinationofshortanswer,multiplechoice,andmatchingquestionsandwilltestyourknowledgeofthematerialcoveredduringthesemester.

Assignments‐Thesewillbebriefactivitiesthataregenerallydueduringtheperiodthatthemoduleisactive..

No‐faultopportunities:

Sincetheremaybetimesinyourlifewhenmissinganassignmentisunavoidableoryouarenotabletoperformyourbest,youhavethefollowing“no‐faults”touse.

1‐Theduedateofeachassignmentwillbeclearlynoted.Todoyourbestinthisclassyoushouldsubmitallassignmentsontime.However,lateassignmentswillbeaccepted.Ifyouchoosetosubmitanassignmentsaftertheduedate5%willbedeductedfromyourfinalscoreformissingtheduedateandanadditional5%willbedeductedforevery24hourstheassignmentislate.Nomake‐upopportunitiesexist.AllassignmentsmustbesubmittedviaBlackboard.

2‐Ifyoubecomeseriouslyillduringthesemesterorhaveunforeseeablelifeproblemsthatrequireyoutomisssomanyassignmentsthatitwillruinyourgrade,youandIwillscheduleaspecialmeetinginordertomakearrangementsforyoutodropthecourse.Donotwaittocontactme.

CourseExpectations:

Whatyoucanexpectofme

YoucanexpectthatIwill....

Holdyoutoahighstandard. Challengeyouintellectually. Provideconstructivefeedbackonassignments. Logontothecoursedailyandrespondtoquestions. Beresponsivetorequestsforhelp.Pleaseallowmeatleast24hourstorespondtoemails‐

ifyoudonotgetaresponsetoanemailwithin24hours,feelfreetoemailmeagain. Referyoutoothersourceswhenadditionalhelpisneeded.

WhatIexpectofyou

Iexpectthatyouwill.... Completeallmodulesontime. Dotherequiredreadingsandassignmentsontime. Submitassignmentsthatrepresentyourbestwork,completedonyourown. Providethoughtfuldiscussionpointsthatarerelevantandsupportedbyfactual

information. Writewell(usepropergrammar,professionalwritingstyle,andcorrectspelling) Contactmeifyouneedhelp,whilegivingmesufficienttimetohelpyou. Sharewithmeanyspecialneedsthatyouhavethatcouldaffectyourperformanceinthe

course.

ClassPolicies

Assignments:Allassignmentsareduebytheassigneddate.Youmayturnassignmentsinlatebut,ifyouchoosetodoso,5%willbedeductedfromyourfinalscoreformissingtheduedateandanadditional5%willbedeductedforevery24hourstheassignmentislate.DonotwaituntilthelastminutetocompleteorsubmitassignmentssincetheHelpDeskisnotopenonweekendandImay

notbecheckingemail.Atechnicalproblemisnotavalidexcuseforsubmittingassignmentslate‐youwilllosepointsifyourassignmentislatebecauseyouwerehavingtechnicaldifficulties.Noexceptionsandnomake‐upopportunitiesexist.

Academicintegrity:Studentsareexpectedtobeethicalandhonestincarryingoutallassignmentsandcourserequirements.AsperUniversitypolicyplagiarism,cheatingonexams,multiplesubmissionofthesamework,forgery,sabotage,unauthorizedcollaborationwithotherstudents,falsificationofwork,briberyoruseofpurchasedresearchservicereportswithoutappropriatenotation,andtheft,damage,ormisuseoflibraryorcomputerresourcesareconsideredformsofacademicdishonesty.Attemptstocommitsuchactsshallalsoconstituteacademicdishonesty.Academicdishonestywill,atminimum,resultinafailinggradeontheassignment/examandmayresultinafailinggradeinthecourse.Academicdishonestywillbereportedtothestudent’sdepartmentChairperson,andtheAssociateDeanforAcademicAffairs.PleasebeadvisedthatprofessorsarerequiredtoreportinstancesofacademicdishonestytotheDeanofGraduateStudies.

StudentsshouldbecomefamiliarwiththeUniversity’sdefinitionsandpoliciesasdetailedintheGraduateBulletinandintheUniversity’sCommunityRightsandResponsibilities.TheUniversity’sCommunityRightsandResponsibilitiesisavailableatthefollowingwebaddresshttp://www.albany.edu/judicial_affairs/standardsofconduct.html.

PleasealsoreadtheGraduateBulletin,andgoon‐linetotheAlbanyLibraryWebsitehttp://library.albany.edu/usered/ncplaga/index.html,wherethereismoreinformationonwhatconstitutesplagiarismandhowtoavoidit.Foranyassignment,feelfreetoconsultwiththemetogetclarificationaboutpotentialplagiarismissues,PRIORtohandinginyourassignment.

AsanassignmentyouarerequiredtocompletetheAlbanyLibrary’sPlagiarismTutorial,“Plagiarism101”.YouMUSTcompletethetutorialforthisclassevenifyouhavecompleteditforanotherclassthis,orinaprior,semester.Thisassignmentisnotgradedbutisworth5%ofyourfinalgradeandisduebytheendofthefirstModule.

Studentsshouldsubmitworkthatrepresentsthebestoftheirabilitiesandthathasbeencompletedwithoutcollaborationwithotherstudents.Unauthorizedcollaborationisconsideredacademicdishonestyandcanresultinafailinggradeforthecourse.AsperUniversitypolicy,theburdenonavoidingplagiarismfallssolelyonthestudent.

Respectforothers:Iexpecteveryonetoberespectfulofoneanother.Therefore,Iaskyoupleasebecourteoustoyourfellowstudents.Pleaserefrainfromprofanity,inappropriatelanguage,slander,anddiscrimination.Idonotexpectstudentstoagree‐infact,Iencourageexpressionofdifferingviewpoints‐thisenhanceslearningandincreasesdiscussion.However,Iexpectthatyouwillalwaysberespectfulofthediverseopinionsandviewsofyourclassmates,evenifyoudisagreewiththem.NOTE:Iwillremoveanypoststhatareoffensiveorinappropriateandwillcontactthestudentwho'spostwasremoved.

Pleaseobserveproper"netiquette"‐‐courteousandappropriateformsofcommunicationandinteractionovertheInternet(withinyouronlinecourse).Thismeansnopersonalattacks,obscenelanguage,orintolerantexpression.Allviewpointsshouldberespected.FormoreinformationaboutNetiquettefeelfreetovisitthefollowingsite:http://www.albion.com/netiquette/corerules.html

NOTE:Ireservetherighttoremoveanyquestionableoroffensivematerialfrompublicareasofthiscourse.

Disability:Anystudentinthiscoursewhohasadisabilitythatmaypreventhim/herfromfullydemonstratinghis/herabilitiesshouldcontacttheinstructorbythesecondweekofclasstodiscussaccommodationsnecessarytoensurefullparticipationandfacilitateyoureducationalexperience.

Syllabus:Tentativemoduledatesandassignmentduedatesareprovidedinthissyllabus.Ifneeded,theduedatesmaybealteredtobetterallowustoachievethecoursegoals.Additionalassignmentsmaybeaddedduringthesemester.Therefore,thissyllabusshouldbeconsideredaguideandmaybemodified.Ifthesyllabusismodified,studentswillbegivennoticeinatimelyfashion.Studentsareresponsibletoapprisethemselvesofchangestothesyllabus.

BMS 506: Introduction to Immunology (3 credits)

Syllabus

Course Director: Bill Lee; leew@wadsworth.org; 473-3543.

Meeting time and location: Tuesday 3:30-5:30; DAI teaching laboratory

Participating Faculty:

Wadsworth Center: Bill Lee

Albany College of Pharmacy: Eric Yager

Albany Medical Center: Kathleen Busman-Sahay and Jeff Kennedy

Course Description: This is an introductory immunology course designed for non-

majors, or individuals beginning their study in the field. Lectures on fundamental

immunological processes will be presented and these will be followed by discussion of

historical and current literature. The goal of the formal lectures will be to provide

students with the fundamental knowledge of the immune system. Quizzes on the formal

lecture material and the required reading will be used to evaluate the students’ learning,

and will be given the week following each lecture. Students may also be asked to

submit essays the literature discussion sessions toward the latter part of the course.

Learning objectives:

• Develop a basic understanding of fundamental immunological processes.

• Identify the major cellular and tissue components which comprise the innate and

adaptive immune system

• Demonstrate an understanding of how white blood cells, including lymphocytes,

develop from undifferentiated precursors

• Learn how highly variable lymphocyte receptors are generated from a limited amount

of genetic information.

• Acquire a basic understanding of the fundamental of the Major Histocompatibility

Complex

• Understand how immune responses by CD4 and CD8 T cells, and B cells, are initiated

and regulated

• Be able to discuss how the immune system distinguishes self from non-self

• Gain experience at reading and evaluating the scientific literature in immunology

Prerequisite: Introduction to Cell and Molecular Biology or permission from the

instructor. Students should be familiar with basic principles of biomedical sciences.

Textbook: Immunology, by Kuby et al. 6th edition.

Grading: Weekly quizzes on lecture material (40%), participation/essay questions

(20%), final exam (40%).

Tuesdays 3:30-5:30

date Lecture # TOPIC LECTURER chapter

1/29/2013 1o/ce s a d

organs/hematopoiesis Bill Lee 1,2

2/5/2013 2 Innate immunity Eric Yager 3, 7

2/12/2013 3 Antigens and antibodies Bill Lee 4

2/19/2013 4 Ig genes/diversity Bill Lee 5

2/26/2013 5 Immunological techniques Bill Lee 6

3/5/2013 6 MHC and Ag processing Kathleen Busman-Sahay 83/12/2013 7 T cells Eric Yager 9, 10

3/19/2013

3/26/2013 8 B cells/leukocytes Bill Lee 11

4/2/2013 9 Immune cell functions Eric Yager 12, 14

4/9/2013 10 papers/discussion Eric Yager

4/16/2013 11 papers/discussion Eric Yager/Kathleen Busman-Sahay

4/23/2013 12 papers/discussion Bill Lee

4/30/2013 13 Immunological diseases Jeff Kennedy

5/7/2013 14 papers/discussion Jeff Kennedy

5/14/2013 15

Grading

Quizzes 40

Participation/Discussion questions 20

Final 40

Course organization Spring 2013

Winter Break

Final exam

Spring 2013 BMS 556

Biodefense Laboratory Sciences

9:00 -12:00 Wednesdays (1 Credit)

Dr. Christina Egan (BMS) Course Director

Course Policies

Justification: The School of Public Health at the State University of New York (SUNY) at Albany is proposing the introduction of a Certificate in Biodefense. The proposed Certificate has been designed to attract graduate students already enrolled in the Biomedical Sciences program through the SUNY at Albany as well as prospective students and post-doctoral fellows applying for the Biodefense Training grant program. In addition, the biodefense certification program will be offered to current Wadsworth Center employees in order to meet continuing education needs. Purpose/Learning Objectives: Students should gain an understanding and appreciation for issues impacting Biodefense Laboratory processing and regulation. Inclusive in this will be; understanding of Biosafety Levels (BSL), appropriate personal protective equipment for defined BSL, working in biosafety cabinets, decontamination methods, amplification and detection methods, and general biosecurity practices. The students in this course will gain an understanding of the role of the laboratory in a bioterrorism event. Course Description: This course will provide an introduction to the procedures and methods to safely and securely work with these agents in the laboratory. Overviews and use of diagnostic methods will be presented including culture, immunoassay and nucleic acid amplification. The laboratories are designed to give students an understanding of the testing flow used for biothreat analysis and emerging infectious disease as well as some of the specialized techniques and technology that the Wadsworth Center has used in real-world testing of these types of samples. The students will take analysis from the beginning stages of specimen/sample arrival through rapid and confirmatory testing that will be taught throughout the laboratories. Faculty: Course Director- Dr. Christina Egan eganc@wadsworth.org Additional Instructors- Mr. Alan Antenucci aantenuc@wadsworth.org

Mr. David Hill djh08@health.state.ny.us Mr. Michael Perry mperry@wadsworth.org

Dr. Nick Mantis nmantis@wadsworth.org Dr. Lisa Mingle lam27@health.state.ny.us

Mr. Alan Dupois apd05@health.state.ny.us

Ms. Danielle Wrobleski dxw12@health.state.ny.us

Suggested Texts No text book is available for the breadth of topics in this course. Reading and study material will be compiled from open literature sources and distributed to students at beginning of each section. Selected sections from the following texts and resources will be utilized: Biosafety in Microbiological and Biomedical Laboratories, 5th Edition. 2003. Jonathan Richmond and Robert McKinney, Eds. US Government Printing Office, Washington, DC. Bioterrorism: Guidelines for Medical and Public Health Management. 2002. Donald Henderson, Thomas Inglesby, Tara O’Toole, Eds. AMA Press, Chicago, IL. Manual of Clinical Microbiology, 8th Edition. 2002. Murray, baron, Jorgensen, Pfaller, Yolken Eds. ASM Press, Washington, DC. Websites: http://www.bt.cdc.gov/ This is an excellent resource for information on bioterrorism select agents and public health emergency preparedness and response. http://www.hopkins-biodefense.org/. This is the website for the Center for Civilian Biodefense Strategies Homework and Help: All course instructors will have at least 2 hours per week available for students with questions or requesting addition tutoring. Homework will be primarily reading assigned materials. Meets: Wednesdays for 3 hours Grading: A-C, E Student Evaluation: Students will be evaluated using a comprehensive final written exam (40%), and a hands-on lab practical exam (30%), class participation (20%), and laboratory notebook and laboratory assignments (10%).

Course Evaluations: Following completion of course, students will be asked to evaluate course for content, presentations, materials, lecturers, and overall utility.

BMS 556 Biodefense/Emerging Infectious Diseases Laboratory Sciences Course Syllabus Laboratory 1- Mr. David Hill/Dr. Christina Egan (Wadsworth) Course overview/ BSL Levels/Biosafety Practices Biosafety review, Working in a BSL3 laboratory, Entry/Exit procedures for BSL3 laboratory, Safety in a BSL3 laboratory, Biosecurity, Select agent regulations. Class participants will review these principles, tour the BSL3 laboratory, and then enter, dress, and practice the use of proper microbiological practices in the mock BSL3 laboratory. Laboratory 2-Dr. Christina Egan (Wadsworth) Biosafety Cabinet Techniques Sterile aseptic technique, proper biosafety and use of the biosafety cabinet. Students will grow bacterial strains and learn to quantitate organisms. Students will also learn how environmental biothreat samples are processed in a BSL3 laboratory. Laboratory 3- Mr. Alan Dupuis (Wadsworth) Viral Culture Methods I Viral culture techniques will be taught in this lab. Students will learn how to perform plaque assays to determine cytopathic effect and proper aseptic cell culture technique. Laboratory 4- Mr. Alan Dupuis (Wadsworth) Viral Culture Methods II Using the techniques of Viral Culture Methods I, advanced virology methods will be covered in this lab. Students will learn how to perform Tissue Culture Infecting Dose (TCID50) and virus neutralization assays. Laboratory 5- Mr. Michael Perry (Wadsworth) BSL3 Training/Bacterial Culture Students will experience working within a BSL3 environment. They will gain experience and knowledge in the PPE and practices that are necessary for working within a high containment laboratory. They will process environmental samples for the detection of bacterial pathogens within the BSL3 laboratory. Students will learn how to perform and interpret routine bacteriological staining techniques such as Gram and Wayson staining. Students will also visualize bacterial cells using direct fluorescent antibody staining to identify biothreat organisms such as Bacillus anthracis that were isolated from Laboratory #2. Laboratory 6- Mr. Alan Antenucci (Wadsworth) BSL3-Glovebox Training Students will become familiarized with working in a BSL3 Glovebox. Laboratory 7- Mr. Alan Antenucci (Wadsworth) BSL3-Advanced High Containment Training Students will become familiarized with working in a mobile BSL3 laboratory using a BSL3 glovebox. They will obtain additional high containment training. Laboratory 8- Lab Practicum

Laboratory 9-Dr. Nick Mantis (Wadsworth) Antibody Based methods Antibody-based assays will be reviewed such as ELISAs, Western blots, immunofluorescence, and microsphere immunoassays. Students will learn how to measure antibodies in serum and mucosal secretions from mice that react with ricin and staphylococcal enterotoxin B as well as how to perform cytotoxicity assays and ELISAs for toxin identification. Laboratory 10- Mr. Michael Perry (Wadsworth) Spectroscopy Methods/Emerging Technologies Microscopy and spectroscopy methods such as Fourier-Transform Infrared (FTIR) and mass spectroscopy will be reviewed in this laboratory. Students will also learn how to use the Illuminator system to rule-out and identify various environmental powders using the environmental samples that were processed in laboratory #2. Laboratory 11-Ms. Danielle Wroblewski (Wadsworth) DNA isolation techniques in BSL3 laboratory Discuss DNA and RNA techniques, chemistry of extractions, commercially available kits, robotic instrumentation, Samples types (clinical, food, water, and powders), and PCR inhibition. Students will extract bacterial DNA in the BSL3 laboratory. DNA will also be quantitated. Students will also learn how DNA extractions on performed on various environmental sample and will perform DNA extraction on samples processed in laboratory #2. Observe robotic extraction utilized for Biodefense Protocols. Laboratory 12-Dr. Lisa Mingle(Wadsworth) Nucleic Acid Based Methods I Basic PCR concepts, RT-PCR applications, example of multiplex PCR will be covered in this laboratory. Students in this laboratory will learn how to perform a conventional and real-time PCR assays for B. anthracis using the samples that they processed and extracted in laboratory #10. Laboratory 13-Ms. Danielle Wroblewski (Wadsworth) Nucleic Acid Based Methods II Advanced molecular PCR based technologies will be covered in this class including sequencing and pyrosequencing as well as other technologies used for strain typing. Students in this laboratory will learn how to perform these types of assays utilizing DNA samples that were extracted in laboratory #10. Laboratory 14-All- Comprehensive Exam/Lab Practical

Laboratory Topic Instructor Date

1 Course overview/ BSL Levels/Biosafety Practices Hill/Egan Jan 30

2 Biosafety cabinet training/BSL 3 Practices Egan Feb. 6

3 Virology Culture Methods I Dupuis Feb. 13

4 Virology Culture Methods II Dupuis Feb 20

5 BSL3 training/Bacterial Culture Perry Feb 27

6 BSL3 Glovebox training Antenucci March 6

7 BSL3 Glovebox/AHRF Training Antenucci March 13

8 Practicum All March 27

9 Antibody Based methods Mantis April 3

10 Spectroscopic Methods/Emerging technologies Perry April 10

11 DNA isolation techniques in BSL3 laboratory Wroblewski April 17

12 Nucleic acid Based Methods I Mingle April 24

13 Nucleic acid Based Methods II Wroblewski May 1

14 FINAL Comprehensive Exam All May 8

BMS 557 ‐ Emerging Infectious Diseases Spring 2013 

 Time: 12:30‐1:30 PM, Wednesdays Location: DAI Classroom (Rm 1041) ‐ David Axelrod Institute, 120 New Scotland Ave  Course coordinators:  Linda Styer, Ph.D. (Office: DAI 5001, Work Phone: 474‐2163, e‐mail: lms24@health.state.ny.us)  Course Goals: At the end of the course, students will be able to: 

1) Define ‘emerging infectious disease’ and describe factors that have allowed disease emergence 2) Be familiar with basic principles of infectious disease epidemiology, including the importance of ongoing 

surveillance and outbreak investigation 3) Understand the basic biology, epidemiology, diagnostics, treatment/control for specific emerging 

infectious diseases, including, if applicable, recent outbreaks within New York State. 4) Appreciate the important role of public health practitioners in monitoring, diagnosing and controlling 

emerging infectious diseases   

Course Schedule:  

Date  Lecture   Topic  Instructor  Email 

Jan 23  1  Introduction to EIDs  Styer  lms24@health.state.ny.us 

Topic 1: Emergence of pandemic zoonoses from host switching 

Jan 30  2  SARS   Masters  masters@wadsworth.org 

Feb 6  3  Influenza: a continually emerging pathogen  St. George  kxs16@health.state.ny.us 

Feb 13  4  HIV   Styer  lms24@health.state.ny.us 

Feb 20  5  Student presentations  Students   

EXAM 1 (lectures 1‐4) will be sent to you on Wed, Feb 20; it is due by 12:30pm on Wed, Feb 27.   

Topic 2: Emergence due to changes in medicine or industry 

Feb 27  6  Emergence of antimicrobial resistance  Escuyer  vee01@health.state.ny.us 

Mar 6   7  Food‐borne pathogens  Musser  kam22@health.state.ny.us 

Mar 13  8  Hepatitis C virus   Parker  mmp09@health.state.ny.us 

Mar 20  Break – No Classes 

Mar 27  9  Emerging fungal infections   Ramani  rxr15@health.state.ny.us 

Apr 3  10  Student presentations  Students   

EXAM 2 (lectures 6‐9) will be sent to you on Wed, Apr 3; it is due by 12:30pm on Wed, Apr 10.   

Topic 3: Emergence due to changing environments and travel  

Apr 10  11  Zoonoses associated with rodents  Eidson  mxe04@health.state.ny.us 

Apr 17  12  Emerging parasitic diseases  Madison‐Antenucci  susanma@wadsworth.org 

Apr 24  13  Emerging mosquito‐borne viruses  Ciota  atc04@health.state.ny.us 

May 1  14  White‐nose syndrome in bats   Rudd  rjr06@health.state.ny.us 

May 8  15  Emerging tick‐borne infections   Backenson  bpb01@health.state.ny.us 

EXAM 3 (lectures 11‐15) will be sent to you on Thurs, May 9; it is due by 12:30pm on Thurs, May 16.   

 Reading Materials: Since there is no text book for the course, articles, handouts and lecture contents will be the required reading materials.  These materials will be emailed to you and/or available on Blackboard.   

Grading Policies Exams (130 points) There will be 3 take home exams.  Each lecture will contribute one 10 point essay question to the exams.  Exam 1 (lectures 1‐4) will be e‐mailed to students on Feb 20 and will be due by 12:30 pm on Feb 27.  Exam 2 (lectures 6‐9) will be e‐mailed to students on Apr 3 and will be due by 12:30pm on Apr 10.  Exam 3 (lectures 11‐15) will be e‐mailed to students on May 9 and will be due by 12:30pm on May 16. Five points will be deducted for each day that an exam is late.    Attendance and Participation (20 points) Students earn 1 point for attending each lecture (15 points total).  You can earn up to an additional 5 points for class participation.  Participation points will be assigned at the end of the semester at the discretion of the course director.      Student Presentation (50 points) 

1) Pick a published paper that either (1) discusses a recent (within the last 20 years) infectious disease outbreak, preferably one that will not be covered in class or (2) discusses another aspect of emerging infectious diseases and is referenced in the Lancet Series on zoonoses (Lancet 2012 380:1936‐1965).   

2) Sign up for a presentation date on Blackboard (maximum of 3 student presentations/date) and enter your paper information.     

3) Send your paper to the other students in the class.  Lead a 15‐20 min discussion of your paper in class.             Points Take‐home exams (10 pts/lecture)            130 pts (65%)   Attendance (1 pt/class) and participation (5 pts)         20 pts (10%)   Presentation                  50 pts (25%)                      200 pts  Grading Scale for Course: Note: Grades will be posted on Blackboard  

Grade  A  A‐  B+ B B‐ C+ C C‐  D 

Hi %  100%  92.4%  89.4% 87.4% 82.4% 79.4% 77.4% 72.4%  69.4%

Hi Pts  200  184.9  178.9 174.9 164.9 158.9 154.9 144.9  138.9

Lo %  92.5%  89.5%  87.5% 82.5% 79.5% 77.5% 72.5% 69.5%  59.5%

Lo Pts  185.0  179.0  175.0 165.0 159.0 155.0 145.0 139.0  119.0

BMS 590: Lab Rotation

Fall 2013

Information Booklet

Contents: Expectations, Syllabus, and Evaluation Forms

Valerie Bolivar, PhD, Course Director

3 credits

Expectations: A. Course Description

The aims of the laboratory rotation course are: (1) To allow the student to interact with scientists working on a variety of research problems. (2) To introduce the student to laboratory techniques and principles. (3) To give students and laboratory staff a chance to interact intellectually and socially. (4) To aid the student in selecting a mentor for graduate research.

Each rotation will consist of a small research project developed in consultation with the mentor. It is expected that the student will spend a minimum of 10 hours per week in the rotation. Some mentors may expect more than this, and the student and mentor should discuss expectations prior to agreeing on the rotation, bearing in mind other student obligations such as coursework and service work that is required for the SUNY assistantships that are the source of support for most students during the first year. At the end of the rotation a written report is submitted and evaluated.

REPEAT ROTATIONS IN THE SAME LABORATORY ARE NOT PERMITTED.

Please keep in mind that: • Rotations should be in laboratories that are funded to accept students or have a

reasonable likelihood of obtaining such funding in the near future. • Students should consider the fit of the laboratory. • Students should consider the fit of the project.

B. Student Obligations

A student may choose to work in the laboratory of any faculty member within the Department of Biomedical Sciences. Special permission may be given to a student who wishes to do a rotation with a faculty member in one of the school's other departments. Students should make their choice based on the written descriptions of faculty research. Students should also view the BMS web site: http://www.albany.edu/sph/bms.php for faculty research interests. Students are strongly encouraged to meet with some of the faculty on an individual basis to help them decide on rotation mentors. For the first rotation, students should fill out the STUDENT FACULTY AGREEMENT form, give it to the rotation mentor to complete, and then give to Dr. Bolivar. Students must decide on their first rotation mentor by Tuesday Sept 3rd, but are encouraged to decide as early as possible. Please indicate your choice for the second rotation by completing the rotation agreement form by Friday, October 18th. This will help avoid conflicts, such as two students desiring to do a second rotation with a faculty member who only has space for one.

Students are required to write a brief report (2-3 pages) describing their research project for only one of the two rotations. Generally this will include an Introduction describing the research and its purpose, a Methods section, a section including Results and Discussion (alternatively, these two sections may be separate), and a short reference list. Properly formatted Figures and Tables should be included as appropriate. This report should be given to the research mentor near the end of the rotation for editing. THE FINAL EDITED VERSION OF THE REPORT

MUST BE SUBMITTED TO DR. BOLIVAR BY EMAIL BY DEC 16TH

IN ORDER TO ALLOW REVIEW TIME PRIOR TO GRADES BEING POSTED. The rotation reports are considered in the student's grade for the rotation. The student is responsible for submitting this report and failure to do so will result in an incomplete (and eventually unsatisfactory) grade. Students will also have their notebooks evaluated by their rotation mentors as part of their rotation requirement, and will discuss their performance with the mentor at the end of the rotation. At the end of the rotation, the student fills out a STUDENT EVALUATION OF MENTOR form to provide constructive feedback, whether positive or negative, about the laboratory experience. C. Research Mentor Obligations The research mentor is responsible for assigning a small project, which the student should be able to make tangible progress on in the limited time frame of a rotation (a minimum of 10 hrs per week). The mentor should take the time to ensure that the student understands how the project fits into the larger scheme of the laboratory's overall goals. The mentor should meet on a regular basis (at least weekly) with the student to monitor progress during the rotation.

It is very important for the mentor to recognize that some of the new students may have limited laboratory experience, and to take responsibility for making sure the student is aware of proper procedures for laboratory safety (use of protective clothing/safety glasses, handling toxic compounds and suspected carcinogens).

At the end of the rotation, the mentor fills out a MENTOR EVALUATION OF STUDENT form, taking into account the student's time in the laboratory, laboratory notebook and final report. The students will be given copies of this form in class and additional copies can be obtained from the departmental web site. The rotation mentor must also meet with the student to discuss the evaluation that is given, point by point. In order to meet SUNY grading deadlines, this evaluation must be submitted on the final day of class.

Any questions on rotation procedures should be directed to the BMS office (Tony Torres, axt12@wadsworth.org, Room 5200, CMS) or the course director (Valerie Bolivar, bolivar@wadsworth.org, Room 5243, CMS).

D. Fall 2013 Lab Rotation Schedule Students are required to rotate in two laboratories. Rotation times are outlined below. The grading is S (Satisfactory)/U (Unsatisfactory). Grades for rotations will be based on the written and oral reports, in addition to mentor evaluations. The grading policy for this course requires attendance at all scheduled meetings and completion of presentations and written reports at required deadlines. The rotation schedule is designed to allow the maximum lab experience within the framework of courses and additional graduate responsibilities. The program can be adjusted for exceptional circumstances. PLEASE NOTE THAT A SATISFACTORY GRADE IN BOTH ROTATIONS MUST BE ATTAINED TO FULFILL THE ROTATION REQUIREMENT.

E. Detailed Class Schedule (ATTENDANCE IS MANDATORY)

Date Purpose Time Room Aug 27 Overview of Rotations and Class 9:30-10:30 DAI Classroom 1041 Sept 10 Describe Rotation #1 9:30-10:30 DAI Classroom 1041 Sept 24 Invited Faculty Talks (Rotation 2 Mentors) 9:30-10:30 DAI Classroom 1041 Oct 1 Discussion of Progress 9:30-10:30 DAI Classroom 1041 Oct 8 Invited Faculty Talks (Rotation 2 Mentors) 9:30-10:30 DAI Classroom 1041 Oct 22 Rotation 1 Oral Final Summary (EVAL) 9:30-10:30 DAI Classroom 1041 Oct 29 Describe Rotation #2 9:30-10:30 DAI Classroom 1041 Nov 19 Discussion of Progress 9:30-10:30 DAI Classroom 1041 Dec 3 Rotation Report Info Session 9:30-10:30 DAI Classroom 1041 Dec 10 Rotation 2 Oral Final Summary (EVAL) 9:30-10:30 DAI Classroom 1041

DATES ROTATION LENGTH

STUDENT/MENTOR EVALUATION FORMS DUE

FINAL / EDITED ROTATION REPORT

DUE Rotation 1 Aug 30- Oct 18 7 weeks Oct 22 (in class) Rotation 2 Oct 21 - Dec 6 7 weeks Dec 10 (in class) Dec 16 (email)

NEUROANATOMY AND NERVOUS SYSTEM DISORDERS BMS 612 (call #3391); NEU 605

Abigail Snyder-Keller, course director; DAI 2031, 402-2623; snykell@wadsworth.org (FALL 2013: Tu, Th 11:00 - 12:30; MS134A @AMC)

SYLLABUS AUG 27 Overview of the nervous system: Basic features of the CNS and PNS (Dr. Abigail Snyder-Keller) 29 Ventricular system; blood supply; meninges (Dr. Snyder-Keller) SEPT 3 Spinal cord; brainstem; cranial nerves (Dr. Snyder-Keller) 6 NO CLASS 10 Hypothalamus; autonomic nervous system (Dr. Lauren Jacobson)

12 Cortex; thalamus (Dr. Russ Ferland) 17 Visual system (Dr. Russ Ferland) 19 Somatosensory system (Dr. Phillip Albrecht)

24 Brain imaging (Dr. Snyder-Keller) 26 EXAM 1 (until 1:00) ***in MS 518***

OCT 1 Overview of motor systems: Pyramidal tract (Dr. Snyder-Keller) 3 Motor systems: Spinal reflexes and spinal cord injury (Dr. Jon Wolpaw) 8 Cerebellum and vestibular system (Dr. Wilson Crone)

10 Motor systems: basal ganglia (Dr. Snyder-Keller)

15 Limbic system (Dr. Lauren Jacobson) 17 Huntington's disease (Dr. Don Higgins) ***in MS 518*** 22 Parkinson's disease (Dr. Rick Keller) 24 Epilepsy (Dr. Yunfei Huang)

29 EXAM 2 (until 1:00)

31 Stroke; Ischemia (Dr. Paul Feustel)

NOV 5 Depression; Manic-depressive illness (Dr. Jeff Carlson) 7 Schizophrenia (Dr. Jeff Carlson) 12 NO CLASS – NEUROSCIENCE MTNG

14 NS plasticity: Experimental lesions; regeneration; sprouting (Dr. Jonathan Carp) 19 Alzheimer's disease (Dr. David Carpenter)

21 Genetics of Neurological diseases (Dr. Anne Messer)

26 Developmental Disorders (Dr. Valerie Bolivar) 28 NO CLASS – THANKSGIVING DEC 3 Drug Addiction (Dr. Stanley Glick) 5 OPEN - REVIEW?

FINAL EXAM suggested date – Thursday 12/12 11:00-3:00

BMS 612 / NEU 605: NEUROANATOMY AND NERVOUS SYSTEM DISORDERS FALL 2013 — Abigail Snyder-Keller, course director Prerequisites: No specific course prerequisites, although some exposure to Neuroscience at either the undergraduate or graduate level is recommended. Course objectives and description:

The purpose of this course is twofold. First, to provide a comprehensive overview of the anatomy of the brain from a systems perspective. Second, to provide an introduction to the major neurological and psychiatric disorders with known brain pathology. Upon completion of the course, students will be expected to be able to: 1) Describe interactions between brain regions involved in specific sensory and motor systems, as well as in systems involved in more complex behaviors. 2) Identify pathophysiological processes that underlie the most common nervous system disorders.

The first half of the course covers basic neuroanatomy: the location and organization of individual structures is discussed as we work up the neuraxis, and then structures are combined into sensory, motor, and integrative systems for which function is also discussed. In the second half, individual disorders of the nervous system are presented, with an emphasis on known pathological bases, and also covering symptomatology and treatment strategies.

This course draws upon the expertise of numerous neuroscientists in the area. Most classes are in lecture format, with discussion as deemed appropriate by the instructor. An outline of the material covered will be provided as a handout for each class. The suggested text for the course, The Human Brain: An Introduction to Functional Anatomy, by John Nolte (6th ed., Mosby Inc., 2008) provides the best summary of the material presented in the first half of the course (basic neuroanatomy), although other books on the reading list provide a comparable overview, or can be used as supplements. Some instructors, particularly those teaching in the disorders part of the course, may provide a list of articles that will be appropriate reading material.

As part of their grade (see below and next page), students are asked to review a recent paper in class that relates to the particular brain region or disorder that is being covered that day. The paper should be chosen with the faculty member teaching that lecture, and that person will be responsible for assigning a grade, which will reflect the student’s performance in class, as well as a short report on the paper. The student will be given 15-20 min at the end of that class period, in which to present the paper. GRADING: Letter grade determined by total points obtained from the following:

Exam 1 (25%): fill-in, MC, T/F, matching, short answer, long answer

Exam 2 (25%): fill-in, MC, T/F, matching, short answer, long answer

Paper presentation and report (10%) - see attached explanation

EXAM 3 FINAL (40%): similar to Exams 1 and 2, with more short and long answer questions (i.e. requires more writing) and some review of earlier material.

BMS 612 / NEU 605 PAPER REPORT AND PRESENTATION 1. Select the topic (lecture) of greatest interest to you. NOTE: Only one presentation per class period, so selecting yours early will guarantee that you spend your time on something of interest! BUT... you cannot pick a topic that is what your research is on. Verify with Dr. Snyder-Keller that that class/topic is available - selections must be made through her. 2. Select a recent paper (last 1-2 years) in consultation with the instructor for that class period. 3. Present paper in last 15 minutes of that class. Distribute copies of the first page (containing the abstract) of the article to class members before you start. (NOTE: it’s a good idea to submit an outline of your presentation to the class instructor one week prior to your class presentation (or less if instructor agrees). This gives the instructor an opportunity to evaluate your understanding of the paper beforehand, and better guide you in your presentation. 4. Prepare a 2-3 page written report of the paper:

- summarize approach and results - discuss findings in terms of how they relate to our knowledge of that disorder and/or brain region - this is the most important part - revise your report after your class presentation; submit final paper to the class instructor AND the course director (Dr. Snyder-Keller) - due by the last day of classes (Dec. 5)

Grade will be determined by class presentation plus report. The final exam will include one 1-pt. T/F question (main point) about each paper. NOTE: As is the case with all of the writing you do, your write-up of the paper must be in your own words. Paraphrasing what is in the published paper – taking sentences and modifying them slightly so that it appears not to be plagiarized – will not earn you any points. If you must use a phrase from the paper verbatim – other than common-use phrasing - then it should be in quotes. What we are looking for is your own evaluation of the paper’s contribution to our knowledge of that topic, not just a restatement of the findings and the authors’ conclusions. Other sources can be used in your discussion, just be sure to reference them appropriately. _______________________________________________________________________

SUGGESTED TEXTS: (select one) RECOMMENDED: Nolte, John, The Human Brain: An Introduction to its Functional Anatomy, (6th ed., Mosby, Inc.) 2008. - available at Mary Jane Books, 215 Western Ave. ALTERNATIVES: Kiernan, John A., Barr’s Human Nervous System: An Anatomical Viewpoint (J.B. Lippincott Co.). Blumenfeld, Hal, Neuroanatomy through Clinical Cases (Sinauer Associates). Haines, D.E., Fundamental Neuroscience (Churchill Livingstone) Fitzgerald, M.T., Neuroanatomy: Basic and Clinical (Balliere Tindall) Martin, J.H., Neuroanatomy: Text and Atlas (Appleton & Lange)

FACULTY CONTACTS - NEUROANATOMY AND NERVOUS SYSTEM DISORDERS

NAME E-MAIL PHONE & LOCATION

Dr. Abigail Snyder-Keller snykell@wadsworth.org 402-2623 (WC-DAI)

Dr. Lauren Jacobson jacobsl@mail.amc.edu 262-4993 (AMC)\

Dr. Russell Ferland ferlanr@mail.amc.edu 262-0172 (AMC)

Dr. Phillip Albrecht albrecp@mail.amc.edu 262-5821 (AMC)

Dr. Jon Wolpaw wolpaw@wadsworth.org 473-3631 (WC-ESP)

Dr. Wilson Crone cronew@mail.amc.edu 262-5251 (AMC)

Dr. Rick Keller kellerr@mail.amc.edu 262-5253 (AMC)

Dr. Don Higgins donald.higgins@va.gov 626-6391 (VA)

Dr. Yunfei Huang huangy@mail.amc.edu 262-5873 (AMC)

Dr. Paul Feustel feustep@mail.amc.edu 262-5339 (AMC)

Dr. Jeff Carlson carlsoj@mail.amc.edu 262-5802 (AMC)

Dr. David Carpenter dcarpenter@albany.edu 525-2660 (SUNY SPH)

Dr. Anne Messer messer@wadsworth.org 473-7560 (WC-DAI)

Dr. Valerie Bolivar Bolivar@wadsworth.org 473-2207 (WC-CMS)

Dr. Jonathan Carp carpj@wadsworth.org 486-4911 (WC-ESP)

Dr. Stanley Glick glicks@mail.amc.edu 262-5303 (AMC)

***ELECTRONIC RESERVES: Slides and/or handouts can be found here (as pdfs), for viewing in greater detail.

For U Albany students:

http://www.albany.edu/MyUAlbany Electronic reserves now under Blackboard Logon using UAlbany NetID and password BMS 612 should come up under MyCourses on right Click on course, will see list of class #s, click to view pdf

For AMC students: the same lecture pdfs can be found on Sakai.

Click on NEU 605 13-14 Fal

BMS 502: Macromolecular Structure & Function (4 credits) Fall 2012

9 am – 10:50 am, David Axelrod Institute, Room 1041 Day Date Session Topic Professor Wed 28 Aug 1 Introduction and Molecular Graphics Pata Module 1: Fundamentals Fri 30 Aug 2 Structure I: Proteins Pata Wed 4 Sept 3 (RAT #1) Structure II: Other Macromolecules Pata Fri 6 Sept No Class - Rosh Hashana Break Wed 11 Sept 4 Function I: Binding Pata Fri 13 Sept 5 Function II: Kinetics Pata Wed 18 Sept 6 Function III: Enzyme Mechanism Pata Fri 20 Sept 7 Function IV: Mutations & Evolution Pata Wed 25 Sept 8 Exam Pata Module 2: Proteins & Protein Assemblies Fri 27 Sept 9 Protein Structure, Folding, and Engineering Banavali Wed 2 Oct 10 (RAT #2) Protein-protein Interactions & Inhibitor design Banavali Fri 4 Oct 11 Protein structure & function relationships - I Banavali Wed 9 Oct 12 Protein structure & function relationships - II Banavali Fri 11 Oct 13 Exam, presentation or project Banavali Module 3: The Cytoskeleton Wed 16 Oct 14 Cytoskeleton I Sui Fri 18 Oct 15 (RAT #3) Cytoskeleton II Sui Wed 23 Oct 16 Cytoskeleton III Sui Fri 25 Oct 17 Cytoskeleton IV Sui Wed 30 Oct 18 Exam, presentation or project Sui Module 4: Proteins & Membranes Fri 1 Nov 19 Membrane Proteins I Wagenknecht Wed 6 Nov 20 (RAT #4) Membrane Proteins II Wagenknecht Fri 8 Nov 21 Membrane Proteins III Wagenknecht Wed 13 Nov 22 Membrane Proteins IV Wagenknecht Fri 15 Nov 23 Exam, presentation or project Wagenknecht Wed 20 Nov – No Class - Thanksgiving Break Fri 22 Nov – No Class - Thanksgiving Break Module 5: Proteins & Nucleic Acids Wed 27 Nov 24 Proteins & Nucleic Acids I Pata Fri 29 Nov 25 (RAT #5) Proteins & Nucleic Acids II Pata Wed 4 Dec 26 Proteins & Nucleic Acids III Pata Fri 6 Dec 27 Proteins & Nucleic Acids IV Pata Wed 18 Dec 28 Exam Pata

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SYLLABUS SYNOPSIS This course presents an integrated approach to investigating the structure and function of biological macromolecules. The course is primarily intended for students who are undertaking graduate-level research in the biomedical sciences, and is designed to bridge the gap that frequently exists between undergraduate biochemistry lectures and graduate level thesis and dissertation research. COURSE DESCRIPTION The first module of the course covers the fundamental aspects of macromolecular structure and function. The next three modules focus on three major types of macromolecular interactions (protein-protein, protein-nucleic acid, and protein-membrane) and the distinctive aspects of each type of interaction. The final module focusses on the structure and function of the cytoskeleton, linking the study of individual molecules to cellular architecture. Topics for in-depth study in each module will be determined by the instructor, and may change from year to year, but will be drawn from the wide variety of disciplines encompassed by research in the Department of Biomedical Sciences, including infectious disease and immunology, cancer, neurobiology, molecular genetics, cell biology, biochemistry and structural biology. A significant fraction of in-class time will be devoted to individual and group exercises that will provide students with opportunities to demonstrate their knowledge of macromolecular structure and function by analyzing experimental methods and results from the primary research literature, evaluating alternative approaches, and designing further experiments. Unless otherwise noted, all sessions will be held from 9:00 AM to 10:50 AM in Room 1041 of the David Axelrod Institute at 120 New Scotland Avenue, Albany, NY. LEARNING OBJECTIVES An overarching objective is that students will become motivated self-learners with the resources to delve more deeply into the study of macromolecular structure and function as it relates to their own research. After taking this course, students will: - know the fundamental principles of macromolecular structure and function. - understand these fundamentals and how they can be used to study a wide range of biological questions. - be able apply this knowledge and understanding to investigate how changes in structure (e.g. mutations and modifications) produce changes in function. - be able to analyze data and interpret results of experiments relating to macromolecular structure and function. - be able to evaluate the advantages and limitations of different experimental approaches. - be able to integrate the knowledge and skills acquired to design new experimental approaches to study biological problems of interest and relevance to their own research.

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INSTRUCTORS (office hours by arrangement) Course Director: Dr. Janice Pata jpata@wadsworth.org 518-402-2595 CMS 2007 Additional Faculty: Dr. Nilesh Banavali banavali@wadsworth.org 518-474-0569 CMS 2008 Dr. Haixin Sui hsui@wadsworth.org 518-474-4235 ESP C265 Dr. Terry Wagenknecht terry@wadsworth.org 518-474-2450 ESP C300 COURSE REQUIREMENTS Prerequisites: Undergraduate-level courses in biochemistry and molecular biology are recommended. Students who are not enrolled in a graduate program with the Department of Biomedical Sciences should contact the course director prior to registering for this course. Reading material: The course will make extensive use of reviews and primary research articles from the scientific literature and will be provided to the students during the course. Course materials will be posted on UAlbany’s Blackboard system (version 9.1), which can be accessed at http://blackboard.albany.edu using your university username and password. Textbooks: Students should have access to comprehensive textbooks on biochemistry and molecular cell biology. Since the textbooks will primarily be used for background reading to supplement the other material, students should consult with the course director prior to investing in the purchase of textbooks. The following books will be available in the classroom:

Voet & Voet (2004) Biochemistry, 3rd Edition. [Wiley] Alberts et al. (2002) Molecular Biology of the Cell, 4th Edition. [Garland Science]

Note: There is a more recent addition of each of these books, so if you decide to purchase copies, be sure to get the 4th edition of Voet & Voet (2010) and the 5th edition of Alberts (2007). Computers & Internet Access: Students will need access to personal computers (Macintosh or Windows operating systems) with software for internet browsing (Firefox is the easiest to set up for network access from the classroom) as well as basic word processing and spreadsheet applications (e.g. Open Office, Microsoft Office, or iWork). The open-source programs JMol and PyMol will be used for visualizing and analyzing molecular structures. Other programs will be accessed through web-based interfaces. Internet access will be available in DAI 1041 during class and for work outside of class time. Each student should bring his/her own laptop computer to each session to use for in-class exercises. Students who do not have a laptop computer should notify the course director prior to the first class so that alternate arrangements can be made. REASONABLE ACCOMODATIONS Reasonable accommodations will be provided for students with documented physical, sensory, systemic, cognitive, learning and psychiatric disabilities. If you believe you have a disability requiring accommodation in this class, please notify the Director of the Disability Resource Center (Campus Center 137, 442-5490). That office will provide the course instructor with verification of your disability, and will recommend appropriate accommodations. See http://www.albany.edu/disability/ for more information.

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GRADING The course uses the A-E grading scheme. Grades will be determined based on the following Exams and Individual Assignments 40% Readiness Assessments Tests 30% Group Work 10% Peer Evaluation 10% Class Participation 10% Readiness Assessment Tests: At the beginning of each module, students will take a multiple-choice “Readiness Assessment Test” (RAT) that will cover the background material assigned in advance for that module. These tests are designed to help students to review material from their undergraduate courses and any background reading provided by the instructor that will serve as the foundation for the module, and to allow faculty to spend more class time on new concepts rather than going over material that is already familiar to the students. Students will have the opportunity to ask questions about the background reading prior to taking the RAT. Students will first take the RAT individually, then immediately re-take the same RAT as a group. Both the individual and group RATs will be graded. Group work and peer evaluation: During the first class session, students will be divided into groups of 5-7 students that will work together throughout the semester. Groups will be formed to distribute expertise as equitably as possible between the groups. To ensure that everyone has an incentive to contribute to the group work, each student will assess the contributions made by the other members of his/her group. Assesments will be done at the end of the first module and at the end of the semester. Only the final assessment will count towards the grade; the first assessment is to provide feedback so that students have a chance to improve group performance over the course of the semester. The assessment will take into consideration the following criteria about group members: Preparation: were they prepared when they came to class? Contribution: did they contribute productively to group discussions & work? Respect for others’ ideas: did they encourage others to contribute their ideas? Flexibility: were they flexible when disagreements occurred? ATTENDANCE Attendance at all class sessions is expected. Students should notify the other members of their group and the instructor if they know they will not be able to attend a session. Because of the group work that is to be done in class, attendance will be taken into account during the peer evaluation as it effects preparation for and contribution to group work. ACADEMIC INTEGRITY All students are expected to abide by the UAlbany policies on academic integrity, which can be found at http://www.albany.edu/graduatebulletin/admission_graduate_requirements.htm .

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DESCRIPTION OF MODULES Module 1: Fundamentals of Macromolecular Structure & Function This module will cover the building blocks and structures of the major constituents of cells: protein, nucleic acids, membranes, and polysaccharides; the biophysical properties of molecules that govern their behavior; how solution conditions (e.g. pH, ionic strength, temperature, hydrophobicity) affect molecular structure and function; the forces governing non-covalent interactions between molecules; energetics (free energy, enthalpy, entropy); the role of concenration on molecular interactions (law of mass action); how enzymes catalyze biochemical reactions; enzyme kinetics; mutations and evolution of proteins. There will be an emphasis on using molecular graphics programs to visuallize and analyze the three-dimensional structures of macromolecules. Module 2: Proteins and Protein Assemblies The principles of how proteins fold or assemble into functional structures and perform various biological roles, how they can be engineered and manipulated, and how small molecules can be designed to alter protein function by using protein structures will be explored. Different methods in protein structure prediction, quantifying protein-protein interactions, protein engineering and design, and inhibitor design will be presented. Case studies on structural and mutational analysis of proteins and protein-protein interactions, hormone function, antibody function, protein catalysts, proteins as cellular building material, proteins as molecular motors, and protein inhibitor design will be discussed. Individual and group projects will focus on structural analysis and prediction of protein-protein interfaces and/or novel inhibitor design by using known protein structures. Module 3: Cytoskeletal Structure & Function The critical functions and dynamic behaviors make the cytoskeleton research a frontier in cell biology. Different from general protein complexes that contain a defined and relatively small number of molecules, cytoskeleton filaments are long protein architecture assembled with thousands copies of the component protein(s). This module will review major research advances on the structure-function of cytoskeleton filaments, and explain how the knowledge was achieved by structural imaging methods, mainly electron microscopy. Besides advanced knowledge on cytoskeleton filaments, the application and basic principles of the involved structural imaging methods will also be discussed. Module 4: Membranes and Membrane Proteins The Proteins and Membranes Module introduces the basic kinetic and thermodynamic concepts regarding transport of metabolites across biological membranes. Specific examples of transporter proteins that carry out facilitated transport (e.g., ion channels) and active transport (e.g., ATP-powered pumps, electron transport chain), with emphasis on structural principles and molecular mechanisms of transport, will be discussed. Module 5: Nucleic Acids and Protein-Nucleic Acid Interactions This module is concerned with the principles of protein/DNA and protein/RNA interactions important mostly for the recognition of specific nucleic acid sequences but also relevant for the recognition of common nucleic acid geometries and structural motifs. The sequence and structure specific interactions via DNA and RNA binding motifs will be discussed in the context of transcriptional activators and repressors, DNA replication and repair proteins as well as commonly found RNA binding proteins. The implications of such recognition events for human disease and public health will also be discussed for most of the examples mentioned above.