1. MICROBIAL GENETICS &
MICROBIAL INTERACTIONS
Last Lecture Sets for Examination 3
Thursday, September 15, 2011
2. 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)
Thursday, September 15, 2011
4. 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
Thursday, September 15, 2011
8. 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
Thursday, September 15, 2011
12. 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.
Thursday, September 15, 2011
13. 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.
Thursday, September 15, 2011
16. 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
Thursday, September 15, 2011
21. 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
Thursday, September 15, 2011
22. 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
Thursday, September 15, 2011
23. 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.
Thursday, September 15, 2011
26. BENEFITS FROM
BIOTECHNOLOGY
Thursday, September 15, 2011
27. BENEFITS FROM
BIOTECHNOLOGY
Thursday, September 15, 2011
28. BENEFITS FROM
BIOTECHNOLOGY
Thursday, September 15, 2011
29. 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”
Thursday, September 15, 2011
30. PRINCIPLES OF DISEASE AND
EPIDEMIOLOGY
onlinecourses.science.psu.edu
Thursday, September 15, 2011
31. MECHANISMS OF
PATHOGENICITY
Thursday, September 15, 2011
33. TRANSMISSION & SOURCES
OF INFECTION
Reservoirs of infection: Humans, Animals and Non-living e.g.
soil
Contact: Direct, Indirect, Droplets
Thursday, September 15, 2011
34. TRANSMISSION & SOURCES
OF INFECTION
Vehicles (inanimate)
Vectors (ticks, mosquitoes, fleas)
Mechanical (flies)
Thursday, September 15, 2011
36. REPORTING DISEASES &
SURVEILLANCE
MORBIDITY (The rate of incidence of a notifiable disease) = How many got
sick?
MORTALITY (deaths from notifiable diseases) = How many died?
Thursday, September 15, 2011
37. REPORTING DISEASES &
SURVEILLANCE
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
Thursday, September 15, 2011
38. REPORTING DISEASES &
SURVEILLANCE
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)
Thursday, September 15, 2011
39. IMMUNOLOGY & Q: Why do you
think your
ITS APPLICATIONS lymph nodes
swell when
there is
infection?
Thursday, September 15, 2011
40. MIAN FUNCTION OF IMMUNE
SYSTEM = DISCRIMINATION
Thursday, September 15, 2011
41. MIAN FUNCTION OF IMMUNE
SYSTEM = DISCRIMINATION
Thursday, September 15, 2011
42. MIAN FUNCTION OF IMMUNE
SYSTEM = DISCRIMINATION
Thursday, September 15, 2011
50. 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
Thursday, September 15, 2011
51. VACCINES : GLOBAL CHALLENGES
Parungao-Balolong 2011
Thursday, September 15, 2011
52. PASSIVE AND ACTIVE IMMUNIZATION
Parungao-Balolong 2011
Thursday, September 15, 2011
70. MICROBES AND THE
BIOGEOCHEMICAL CYCLES
Thursday, September 15, 2011
71. MICROBES AND THE
BIOGEOCHEMICAL CYCLES
Thursday, September 15, 2011
72. Microbial decomposition
Proteins and waste products Amino acids
Microbial ammonification
Amino acids (–NH2) Ammonia (NH3)
Nitrosomonas
Ammonium ion (NH4 +) Nitrite ion (NO2- )
Nitrobacter
Nitrite ion (NO2 -) Nitrate ion (NO3- )
Pseudmonas
Nitrate ion (NO3 -) N2
Nitrogen - fixation
N2 Ammonia (NH3)
Thursday, September 15, 2011
73. MICROBES AND THE
BIOGEOCHEMICAL CYCLES
Thursday, September 15, 2011
74. Microbial decomposition
Proteins and waste products Amino acids
Microbial dissimilation
Amino acids (–SH) H 2S
Thiobacillus
H 2S SO42– (for energy)
Microbial & plant assimilation
SO4 2– Amino acids
Thursday, September 15, 2011
75. 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
Thursday, September 15, 2011
78. Water Quality
Microbes 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
Thursday, September 15, 2011
80. Algal Blooms
Pollutants (nutrients) may cause algal blooms.
Algal blooms lead to eutrophication.
Thursday, September 15, 2011
81. Coliforms
Aerobic or facultatively anaerobic, gram-negative, non–
endospore forming rods that ferment lactose to acid +
gas within 48 hr, at 35°C
Indicator organisms
Used to detect fecal contamination
MPN
Most probable number/100 ml of water
Thursday, September 15, 2011
93. SPECIAL TOPICS IN
MICROBIOLOGY
BIOTERRORISM &
DUAL RESEARCH
Thursday, September 15, 2011
94. OUTLINE
❖ Overview: Dual-Use Research
❖ Overview: Risks
❖ Biotechnology and
Bioterrorism
❖ Case Studies
Thursday, September 15, 2011
95. 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
Thursday, September 15, 2011
96. “Legitimate scientific work that could be misused to
threaten public health or national security”
What is
Dual-Use
Research?
Thursday, September 15, 2011
98. 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
Thursday, September 15, 2011
99. “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)
Thursday, September 15, 2011
100. “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)
Thursday, September 15, 2011
102. ❖ 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.”
Thursday, September 15, 2011
103. ❖ 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.”
Thursday, September 15, 2011
107. ❖ 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.
Thursday, September 15, 2011
109. ❖ 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.”
Thursday, September 15, 2011
112. ❖ 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
Thursday, September 15, 2011
113. VIDEO ON
SCIENTISTS’ VIEWS
Thursday, September 15, 2011
114. “are there potential benefits
to public health and safety
from application or utilization
of this information?”
We must PREVENT
such MISUSE
without IMPEDING
research
PROGRESS!
Thursday, September 15, 2011
