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Intro Bio Week 9

by: thersh

Intro Bio Week 9 BIOL 1010


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Notes from week 9 of class
Introduction to Biology
Stephanie Hutchins
Class Notes
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This 53 page Class Notes was uploaded by thersh on Monday April 4, 2016. The Class Notes belongs to BIOL 1010 at Rensselaer Polytechnic Institute taught by Stephanie Hutchins in Fall 2016. Since its upload, it has received 16 views. For similar materials see Introduction to Biology in Biology at Rensselaer Polytechnic Institute.


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Date Created: 04/04/16
Emerging Infectious Diseases (EID). Where do they originate? What do we do? Why do we care? Global richness map of the geographic origins of EID events from 1940 – 2004. The Realities in Global Trends •EIDs are a significant burden on global economies & public health. •EID emergence thought to be driven by socio-economic environmental & ecological factors. Definition of a Pandemic: Tracking pandemic – occurring over wide geographical area and affecting an exceptionally high proportion of the population. zoonotic diseases or zoonosis: infectious diseases that can be transmitted from other vertebrate animals to humans. May be direct or via a vector. Zoonotic Diseases: Five Stages through which pathogens of animals evolve to cause disease in humans. Critical transitions: •Stage 1 to Stage 2: from animal to human •Stages 3 & 4: pathogen’s ability to sustain cycles of human to human transmissions Ex. modern Ebola outbreaks are stage 3. 2007 Nature 447, 279-283. Global Trends Results •EIDs events have risen significantly over time. •Peak 1980s attributed to HIV. •EIDs dominated by zoonoses (60.3%). •71.8% of zoonoses originate in wildlife (SARs, Ebola) and this trend is increasing. •54.3% caused by bacteria or rickettsia. •25.4% by viruses or prions. •Drug-resistant microbes are Increasing. •Data reveal substantial risk of zoonotic & vector-borne EIDs at lower altitudes (below equator) where reporting effort low. 2008 Nature 451, 990-994 List of NIAID Emerging and Re-emerging Diseases Group I—Pathogens Newly Recognized in the Past Two Decades Acanthamebiasis Australian bat lyssavirus Babesia, atypical Group II—Re-emerging Bartonella henselae Ehrlichiosis Pathogens Encephalitozoon cuniculi Enterovirus 71 Clostridium difficile Encephalitozoon hellem Mumps virus Enterocytozoon bieneusi Helicobacter pylori Streptococcus, Group A Hendra or equine morbilli virus Staphylococcus aureus Hepatitis C Hepatitis E Human herpesvirus 8 Human herpesvirus 6 Lyme borreliosis Parvovirus B19 Why are many EIDs linked to Viruses? Viruses have •High rate of mutation, contact between species, spread from isolated populations. •RNA viruses – unusually high rates of mutation lack the proofreading mechanisms seen in DNA replication •Examples of RNA virus EIDs: common cold, measles, mumps, polio HIV or AIDs Ebola – hemorrhagic fever West Nile & other emerging viruses causing encephalitis SARS – severe acute respiratory syndrome (2002-2003) •Examples of DNA virus EIDs: hepatitis, chicken pox, herpes infections Ebola virus Infectious Disease Cycle & Persistence Resistance Spread Dependent on duration of Outbreak infectivity in host. •Rate of infection of new hosts. •Rate of development of host protective immunity •Population density, size, and structure: may eradicate locally but persists regionally. How does an Influenza Pandemic Occur? Video Experts predict next epidemic will start in animals. USA Today. October 22, 2008. First known case Swine Flu (H1N1): March 28, 2009. First known case US: April 17, 2009 th April 26 : New Zealand, France, Israel, Brazil, Spain report cases. 86 deaths in Mexico attributed to swine flu. June 11 : Pandemic declared by WHO. The first influenza pandemic in the last 40 years. th July 14 : WHO authorizes pharmacy companies to manufacture vaccines. August 27 : US colleges see spike in number of cases. September 4 : WHO announced 625 deaths in the last week. th October 5 : vaccine ready. October 24: President declares a national emergency . Attendance exercise: Why did the President declare a national emergency concerning swine flu? What is the greatest fear of scientists and policy makers? Swine Flu or H1N1 is an influenza A virus containing 11 viral genes. Genome consists of 8 segments of single stranded RNA. Genes encoded include: polymerase PB2 polymerase PB1& PB1-F2 polymerase PA hemagglutinin HA nuclear protein NP neuraminidase NA matrix proteins M1 & M2 Neumann et al. 2009. Nature 459, 931-939. nonstructural proteins NS1 & 2 Schematic diagram of the influenza viral life cycle. Animation: Influenza Virus Replication Figure 2: G Neumann et al. Nature 459, 931-939 (2009) Where did most recent H1N1 come from? Original reservoir was birds 1918: human influenza A (H1N1) pandemic – transfer from chickens 1918: Cedar Rapids Swine Show influenza A transmitted to pigs from humans. 1931: documented infectious transmission 1933: used ferret model to document transmissibility for human & swine viruses. 1918-present: evolution of virus in humans. 1957: H1N1 abruptly disappeared from humans. Morens et al. 2009. NEJM 361. 225-229. Genesis of 2009 Swine-origin H1N1 Influenza Viruses. Neumann et al. 2009. Nature 459, 931-939. Monitoring for Influenza viruses MSNBC Video: H1N1 Virus We can watch virus evolution. This requires large-scale sequencing of viruses isolated from patients. After this, bioinformatic analysis shows which ones are evolving most rapidly. These are, on evolutionary principles, the most likely to be problematic in the future. video backup link US Vaccine Evaluation Centers Prevention and Control Possibility #1 Prevention and Control Possibility #2 A Antiviral drugs interfere with viral specific proteins: adamantanes: block ion channel formed by M proteins (M proteins used for escape from endosome). adamantanes bound B Oseltamivir (Tamiflu) and aznamivir: neuraminidase inhibitors block release of new virus particles. Attendance exercise: Why did the President declare a national emergency concerning swine flu? What is the greatest fear of scientists and policy makers? Dengue Fever on the watch list. Why? Video from ABC News (copy of the Video link) •Caused by one of 4 different, but related viruses. •Carried by mosquito, Aedes aegypti •4-6 days for symptoms to appear. • Often referred to as break-back fever + Why? Local copy of the video Antibiotic resistance: MRSA Infections •Methicillin-resistant Staphylococcus aureus. •Resistant to broad range of antibiotics. •Harmless unless enters body through cut or wound. •Deadly to those with weakened immune systems. •Hospitals, assisted living facilities. •Teams, locker rooms. •2M people/year infected in hospitals. ~100,000 deaths. Kellen Winslow, Oct 21, 2008 MRSA Infections – RPI News: August 16, 2010 •Develop antimicrobial coatings for hospital surfaces •Carbon nanotube-enzyme conjugates made with Lysostaphin, a cell wall degrading enzyme •Lysostaphin from non-pathogenic strains of Staph bacteria had >99% MRSA killed within 2 hours. R Pangule et al. JS Dordick 2010 ACS Nano 4, 3993-4000. Antibiotics: An Uphill Battle www.CEN-ONLINE.orgApril 14, 2008 •Short period of effectiveness. •Emerging drug-resistant pathogens. •Cost of R&D without promise of profit margin. •Mother nature more clever than humans! •Focus on natural products- novel compounds The Need for New Ideas Focus on Under Developed Nations •Focus on Tuberculosis- second most lethal infectious disease •Bill and Melinda Gates Foundation – October 21, 2008 •X PRIZE to fight tuberculosis worldwide-effective diagnosis Control of Gene Expression Eukaryotic cell Animation: Chime YouTube Version Windows media (get plugin) Gene Expression: The process by which information flows from DNA to RNA to protein or genotype to phenotype. E. coli as model organism to understand prokaryotic gene expression. Features of prokaryotic transcriptional regulation •Ability to change metabolic activities in response to the environment. •Capability to induce/repress entire enzyme pathways- genome organization. •Examples of regulated gene networks: lac operon, trp operon Lac operon: Proteins interacting with DNA turn prokaryotic genes on & off. First regulation discovered by François Jacob and Jacques Monod in 1961 • Lactose is a disaccharide that can be broken down into two monosaccharides used in glycolytic pathway •Lactose is not always present in the diet. •If present, three enzymes are needed to convert it to a useful metabolite •The genes for the enzymes are physically linked on the genome •Regulate transcription based upon presence or absence of lactose. •Microbes are efficient!! Lactose operon is not transcribed in the absence of lactose. 3 enzymes located together on the chromosome and regulated as single unit. β-galatosidase-lacZ galactose permease-lacY thiogalatoside transacetylase-LacA Regulatory regions precede the genes encoding the enzymes Lac operon: alternative states depending upon presence or absence of lactose. Model of induction. •Lactose present– operon is active and available for transcription because lactose binds to the repressor protein inducing a conformational change •Repressor•Lactose complex cannot bind to operator and RNA polymerase binds & initiates transcription. Attendance Exercise There is a mutation such that the nucleotide sequence of the operator is changed. The lac repressor protein will not bind. a. Explain what happens to transcription of the lac operon when lactose is present? b. Explain what happens to transcription of the lac operon when lactose is absent? Unifying theme: Transcription of many prokaryotic genes is up regulated as a group or turned off as a group. However, there are alternatives to the lac example of induction. •trp operon repressor requires binding of tryptophan to the repressor protein for repression of transcription. •There are also operons controlled by activators which assist RNA polymerase binding. Eukaryotic mechanisms of gene regulation 1.All cells contain the same genotype. Differential gene expression leads to different cell types. 2.Multiple mechanisms to regulate gene expression. •DNA packing. Prevents access of the DNA for transcription. •Eukaryotic transcription has multiple enhancers, silencers, and variety of proteins that are assembled into a complex. •Alternative RNA splicing leads to multiple mRNAs for translation. •microRNAs and RNA interference. •Translation and later events also regulated. Differentiation in cell types in multicellular organisms is due to differential gene expression DNA packing prevents access of the DNA for transcription. X-chromosome inactivation: In female mammals, one X chromosome is inactivated in all cells except gametes. •Occurs early in embryonic development. •Random which X is inactivated. •Inactive X referred to as Barr body. Gene expression during embryogenesis Video: NOVA Life’s Greatest Miracle chapter 3 (on the bottom part of the video pop- up, mouse over the slider and select episode 3) “The embryo Takes Shape” Eukaryotic transcription complexes have multiple proteins and regulatory factors . • Regulation of gene expression for development. •Important first studies from Drosophila melanogaster. •Identify mutants that developed abnormally. •Normal head with eyes and antenna shown on the left. •Abnormal development on the right with legs in place of antenna Early development of head-tail polarity. protein gradients Post transcriptional regulation: Alternative RNA splicing results in multiple transcripts from the same gene. Standard splicing to remove introns Example of alternative splicing Role of microRNAs (miRNA) in gene expression. •Discovered 1993 •Small single-stranded RNA (20-26 nucleotides long) •Associate with protein complex and complementary mRNA sequence •Imperfect base pairing is allowed •Estimated that expression of 1/3 of human genes are regulated by ~1000 miRNAs Gene expression regulated at later stages. •mRNA degradation: t 1/2of transcripts variable. prokaryotic: very short, minutes, because mRNA lasting for too long could have negative impact on environmental change. eukaryotic: variable, hours to months and can be regulated particularly by hormones •translation highly regulated inhibitory protein blocks transcription of hemoglobin mRNA if heme supply is low (iron containing compund that binds oxygen) Post-translational Regulation Protein Activation example Insulin activation •Insulin synthesized in pancreas. •Proinsulin is inactive. Multiple levels of regulation in Eukaryotic cells •In the nucleus & in cytoplasm. •Before & after translation. •Novel regulatory mechanisms are still being discovered. DNA Microarrays picomoles DNA


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