microbial genetics & interactions 2011

MICROBIAL GENETICS & MICROBIAL INTERACTIONS

Last Lecture Sets for Examination 3

Thursday, September 15, 2011

LECTURE OUTLINE Microbial Genetics: OVERVIEW

Microbial Interactions

Principles of Disease and Epidemiology

Immunology and Its Applications

Environmental Microbiology

Applied and Industrial Microbiology

Reference: Tortora (10e) Chapters 8 and 9 for Microbial Genetics; Chapters 14-18/27-28 for Microbial Interactions)


MICROBIAL GENETICS


TERMS IN MICROBIAL GENETICS

Genome: All of the genetic material in a cell

Genomics: The molecular study of genomes

Genotype: The genes of an organism

Phenotype: Expression of the genes


OVERVIEW


IMPORTANT ENZYMES


REGULATION OF GENE EXPRESSION


MUTATIONS

A change in the genetic material

Mutations may be neutral, beneficial, or harmful

Mutagen: Agent that causes mutations

Spontaneous mutations: Occur in the absence of a mutagen


TYPES OF MUTATIONS: MISSENSE


TYPES OF MUTATIONS: NONSENSE


TYPES OF MUTATIONS: FRAMESHIFT


REPAIRING MUTATIONS

Ionizing radiation (X rays and gamma rays) causes the formation of ions that can react with nucleotides and the deoxyribose-phosphate backbone

Nucleotide excision repairs mutations.

UV radiation causes thymine dimers

Light-repair separates thymine dimers.


MUTATIONS IN THE LAB

FREQUENCY: Spontaneous mutation rate = 1 in 109 replicated base pairs or 1 in 106 replicated genes AND Mutagens increase to 10–5 or 10–3 per replicated gene

SELECTION:

Positive (direct) selection detects mutant cells because they grow or appear different

Negative (indirect) selection detects mutant cells because they do not grow.


CHARACTERIZING MUTATIONS


MUTAGENICITY TEST: AMES TEST


GENE TRANSFERS

ENDPOINT: RECOMBINATION

Vertical gene transfer: Occurs during reproduction between generations of cells

Horizontal gene transfer: The transfer of genes between cells of the same generation

CONJUGATION, TRANSFORMATION, TRANSDUCTION


CONJUGATION


TRANSFORMATION


TRANSDUCTION


EXTRACHROMOSOMAL INHERITANCE: PLASMIDS

Conjugative plasmid: Carries genes for sex pili and transfer of the plasmid

Dissimilation plasmids: Encode enzymes for catabolism of unusual compounds

R factors: Encode antibiotic resistance


EXTRACHROMOSOMAL INHERITANCE: TRANSPOSONS

Segments of DNA that can move from one region of DNA to another

Contain insertion sequences for cutting and resealing DNA (transposase)

Complex transposons carry other genes


BIOTECHNOLOGY: APPLICATIONS OF MICROBIAL GENETICS

Biotechnology: The use of microorganisms, cells, or cell components to make a product

Foods, antibiotics, vitamins, enzymes

Recombinant DNA technology: Insertion or modification of genes to produce desired proteins.


BIOTECHNOLOGY: APPLICATIONS OF MICROBIAL GENETICS


BENEFITS FROM BIOTECHNOLOGY


SAFETY ISSUES AND ETHICS

Avoid accidental release

Genetically modified crops must be safe for consumption and for the environment

Who will have access to an individual's genetic information?

ASSIGNMENT: GROUP WORK (of 4-5)

“Discuss one important safety and ethical issue associated with utilization of BIOTECHNOLOGY and come up with a position paper”


PRINCIPLES OF DISEASE AND EPIDEMIOLOGY

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MECHANISMS OF PATHOGENICITY


STAGES OF DISEASE


Reservoirs of infection: Humans, Animals and Non-living e.g. soil

Contact: Direct, Indirect, Droplets

TRANSMISSION & SOURCES OF INFECTION


Vehicles (inanimate)

Vectors (ticks, mosquitoes, fleas)

Mechanical (flies)



REPORTING DISEASES & SURVEILLANCE

MORBIDITY (The rate of incidence of a notifiable disease) = How many got sick?

MORTALITY (deaths from notifiable diseases) = How many died?



DALYs (disability-adjusted life year)

Estimate the number of years of life lost due to premature death and any years lost in disability

Used by policy makers to determine the level of funding for prevention programs, treatment efforts, and research



PREVALENCE (The total number of cases of a disease in a given population at a specific time)

INCIDENCE (number of new cases during some time period)


IMMUNOLOGY & ITS APPLICATIONS

Q: Why do you think your

lymph nodes swell when

there is infection?


MIAN FUNCTION OF IMMUNE SYSTEM = DISCRIMINATION


INFLAMMATION


THE COMPLEMENT SYSTEM


CLASSICAL, ALTERNATIVE AND LECTIN PATHWAYS


INTEGRATION

Although the innate mechanisms do not improve with repeated exposure to infection as do the acquired, they play a vital role since they are intimately linked to the acquired systems by two different pathways which all but encapsulate the whole of immunology. Antibody, complement and polymorphs give protection against most extracellular organisms, while T-cells, soluble cytokines, macrophages and NK cells deal with intracellular infections


VACCINES : GLOBAL CHALLENGES

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PASSIVE AND ACTIVE IMMUNIZATION


VACCINES AND IMMUNOLOGIC MEMORY


COMMON VACCINES (HUMANS)


VACCINES AND POLIO ERADICATION EFFORTS


VACCINES AND MEASLES


VACCINES : TOXOIDS


MONOCLONAL ANTIBODIES


ANTIGENIC PEPTIDES


RECOMBINANT VACCINES


VACCINES & HERD

IMMUNITY

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ECOLOGICAL RELATIONSHIPS AND MICROBES

ANTAGONISM


ECOLOGICAL RELATIONSHIPS AND MICROBES (Fungi and algae)


ECOLOGICAL RELATIONSHIPS AND MICROBES : bacteria & legumes


ECOLOGICAL RELATIONSHIPS AND MICROBES : ruminants and microbes


ECOLOGICAL RELATIONSHIPS AND MICROBES : fungi and plants


ENVIRONMENTAL MICROBIOLOGY: RESEARCH AREAS


MICROBES AND THE BIOGEOCHEMICAL CYCLES


N2Nitrogen - fixation Ammonia (NH3)

Nitrate ion (NO3-) Pseudmonas N2

Nitrite ion (NO2-) Nitrobacter Nitrate ion (NO3

- )

Ammonium ion (NH4+) Nitrosomonas Nitrite ion (NO2

- )

Amino acids (–NH2)Microbial ammonification Ammonia (NH3)

Proteins and waste products Microbial decomposition Amino acids


MICROBES AND THE BIOGEOCHEMICAL CYCLES


Proteins and waste products Amino acidsMicrobial decomposition

Amino acids (–SH) Microbial dissimilation H2S

H2SThiobacillus SO4

2– (for energy)

SO42– Microbial & plant assimilation Amino acids


APPLIED AND INDUSTRIAL MICROBIOLOGY

Bioremediation

Use of microbes to detoxify or degrade pollutants; enhanced by nitrogen and phosphorus fertilizer

Bioaugmentation

Addition of specific microbes to degrade of pollutant

Composting

Arranging organic waste to promote microbial degradation


APPLIED AND INDUSTRIAL MICROBIOLOGY: BIOFILMS


APPLIED AND INDUSTRIAL MICROBIOLOGY: BIOLUMINESCENCE


Water QualityMicrobes are filtered from water that percolates into groundwater.

Some pathogens are transmitted to human in drinking and recreational water.

Resistant chemicals may be concentrated in the aquatic food chain.

Mercury is metabolized by certain bacteria into a soluble compound, concentrated in animals


Algal BloomsPollutants (nutrients) may cause algal blooms.

Algal blooms lead to eutrophication.


ColiformsAerobic or facultatively anaerobic, gram-negative, non–endospore forming rods that ferment lactose to acid + gas within 48 hr, at 35°C

Indicator organismsUsed to detect fecal contamination

MPNMost probable number/100 ml of water


Figure 6.18b


MUG fluorescent compoundβ- galactosidase


WATER TREATMENT PROCESS


FOOD PRESERVATION : CANNING


Food Preservation Pre-sterilized materials assembled into packages and aseptically filled (Aseptic packaging)

Gamma radiation kills bacteria, insects, and parasitic worms

High-energy electrons


FERMENTATION

Sugar Ethyl alcohol + CO2Saccharomyces cerevisiae

Malic acid Lactic acidLactic acid bacteria

Ethyl alcohol Acetic acidAcetobacter or Gluconobacter


FERMENTATION


Yeast Fermentations


END OF LECTURESThursday, September 15, 2011

SPECIAL TOPICS IN MICROBIOLOGY

BIOTERRORISM & DUAL RESEARCH


OUTLINE

❖ Overview: Dual-Use Research

❖ Overview: Risks

❖ Biotechnology and Bioterrorism

❖ Case Studies


Biological Research has led to the development of new drugs, treatments, and medical

advancements that have profoundly impacted our health and way of life

The General Public holds scientists and their work in high regard and trusts that they will act in the best interest of society


What is Dual-Use Research?

“Legitimate scientific work that could be misused to threaten public health or national security”


THUS: any medical advance that improves the ease of engineering,

handling, or delivering treatment has the potential to be applied by those wishing to do harm and can be considered "dual-

use


“advances in biotechnology … have the potential to create a much more dangerous biological warfare threat … engineered biological agents could be worse than any disease

known to man.” (CIA, 2003)


Case Studies


❖ Dr. Wimmer, Distinguished Professor in the Department of Molecular Genetics and Microbiology at the State University of New York (SUNY) at Stony Brook

❖ 1991: Published the chemical formula of the polio virus

❖ 2001:biochemically synthesized (deliberately) poliovirus according to its genomic sequence in the absence of a template without a DNA or RNA template, or the help of living cells

❖ 2002 published in Science

❖ DUAL USE Implications: unnecessarily demonstrating how bioterrorists could use modern scientific techniques to create dangerous pathogens

❖ POLICY: “prior to attempting synthesis of a microbial chromosome we commissioned an independent bioethical review of our proposed scientific plan.”


❖ Dr. Stuart Levy of the Tufts University School of Medicine (Antimicrobial Agents and Chemotherapy, 2006) identified a gene in Yersinia pestis similar to an Escherichia coli gene known to cause multiple antibiotic resistance

❖ Yesinia pestis causes plague, famously known as the “Black Death” after it caused an estimated 50 million deaths throughout Europe, Africa, and Asia in the 1300’s.

❖ confers resistance to a variety of drugs, oxidative stress agents, and organic solvents

❖ transcriptional regulators of a multidrug efflux pump

❖ MarR protein represses transcription of the efflux pump, whereas the MarA protein increases its expression, thereby activating antibiotic resistance.


❖ In his 1945 Nobel Prize lecture, Fleming ended with a cautionary remark saying; “but I would like to sound one note of warning… it is not difficult to make microbes resistant to penicillin in the laboratory by exposing them to concentrations not sufficient to kill them, and the same thing has occasionally happened in the body.”


❖ PROS: experiments could uncover the reasons why the Spanish flu pandemic was so deadly and could offer insight into avian flu pathology and how it might become transmissible in humans.

❖ CONS:

❖ publication of the viral sequence, conditions under which the virus was handled and the threat of its escape into the environment;

❖ recreate deadly and transmissible though extinct or eradicated viruses;

❖ can be used for the design of a weapon of mass destruction; there is a risk verging on inevitability of accidental… or deliberate release of the virus.

❖ IMPACT TO PUBLIC HEALTH: advancement in tools to sequence genomes and synthesize DNA; BUT could be used to engineer biological weapons


VIDEO ON SCIENTISTS’ VIEWS


We must PREVENT such MISUSE

without IMPEDING research

PROGRESS!

“are there potential benefits to public health and safety from application or utilization of this information?”


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