Download deadinburgh

An unknown pathogen ravages Scotland’s capital, turning the
unlucky souls into bloodthirsty ambling beasts.
You are one of the last uninfected citizens in a city under martial
law, cut off from the rest of the UK.
Now, with help from real scientists, you have only hours to decide
how to save Edinburgh, and perhaps the world.
DEADINBURGH
Route of Infection
What we need to do
It is important that we quickly identify the route of infection
of a new disease outbreak, that scientists are calling
Lazarus, so we can take measures to prevent
transmission of the infection. We have received
information about cases reported around the country but
the scientists have not had time to analyse the reports. In
order to help the scientists in the safe zone interpret the
data that has been collected we need to present them in a
way that is easy to understand. You will need to put the
case reports into a table and draw a pie chart to show the
likely route of infection.
You should be able to:
Keywords
Virus, bacteria, route of infection, • Present data in tables and pie
charts
symptomatic, percentage, mode,
• Choose the correct way to present
pie chart
•
•
data
Calculate the mode
Calculate percentages
Recent scientific research
New technology and laboratory breakthroughs, such as
the discovery of a gene in flu that causes severe
infections and the ‘barcoding’ of viral diseases to rapidly
test new outbreaks for potentially lethal mutations, are
changing the potential for us to understand the
progress of illness and identify new threats.
Scientists have gained fresh insights into how the
bacteria Salmonella is able to change key cells that line
the intestine and how Campylobacter survive in the acid
conditions of our stomach, enabling the bugs to thrive.
By changing the make-up of intestinal cells, Salmonella
bacteria are able to cross the gut wall and infect vital
organs such as the kidneys and the liver. When
exposed to the highly acidic conditions of our stomach
Campylobacter change their behaviour and focus on
movement, making them better at invading our tissues.
These findings may help explain how eating infected
meat enables bacteria to infect us and causes changes
in healthy bodies leading to more severe illness.
Activity 1:
We have received case reports from nine infected individuals.
Information on how they were possibly infected is provided below, but the scientists have not had time
to process the data.
You will need to decide how the disease was transmitted in each case!
Possible routes of transmission are:
Contact – direct physical contact such as touching an infected individual
Saliva – saliva from an infected individual comes into contact with the victim such as being bitten
Blood – blood from an infected individual comes into contact with a victim such as through a cut in the
skin
Cases
1.
2.
3.
4.
5.
6.
7.
8.
9.
Bite on the forearm by symptomatic individual that drew blood
Scratched on the face by a panicking injured man leading to bleeding
Fingers chewed off by symptomatic individual
Coughed on by an individual who went on to develop symptoms
Cut themselves on a rusty nail in a plank of wood that had been used to
fight off symptomatic individuals
Got spit in the eye when surrounded by a horde of slobbering
symptomatic individuals
Got blood in the mouth in an attack on a group of symptomatic
individuals
Policeman who was in close contact with a crowd of infected people
trying to break out of a quarantined area, no obvious injuries.
Suffered a needle stick injury after trying to sedate a symptomatic
individual
Contact
·
Saliva
· Blood
Question 1: How many were infected by each of
the following routes?
• Contact
• Saliva
• Blood
Draw a table to show your results.
Question 2: Plot the data in a pie chart.
Question 3: Which is the most common route of
infection (mode)?
Question 4: What percentage of the cases was
transmitted by saliva?
Answers
Activity 1, Question 1: How many were infected by each of the following routes?
Route of transmission
Contact
Saliva
Blood
Question 2: Plot the data in a pie chart.
Number of cases
1
3
5
Route of infection
Contact
Blood
Saliva
Question 3: Which is the most common route of infection (mode)?
Blood
Question 4: What percentage of the cases was transmitted by saliva?
33.3%
Glossary
Bacteria – A very large group of single celled organisms that lack organelles or a nucleus,
some of which can cause disease.
Campylobacter – A group of bacteria that are spiral in shape and have a flagella at one or
both ends. They are one of the main causes of bacterial foodborne disease.
Culture – A method of multiplying microorganisms by growing them in a liquid or gel under
laboratory conditions so they can be studied.
Intestinal – In the region of the digestive tract after the stomach.
Route of transmission – The passing of a disease from an infected individual or group to a
previously uninfected individual.
Salmonella – A group of rod shaped bacteria that cause infections in humans and animals.
Symptomatic – Displaying symptoms
Virus – A small infectious agent made of nucleic acid and a protein coat that can only replicate
inside cells.
You should be able to:
• Present data in tables and pie
charts
• Choose the correct way to present
data
• Calculate the mode
• Calculate percentages
DEADINBURGH
Progress of disease
What we need to do
Scientists are working on how the infection gets into the
body and spreads. They need to find out what the
infectious agent is doing when it gets in to the body and
how it spreads around. Research on the evolution of
viruses suggests they kill the cells they infect faster if they
are competing with another infection in the body. You will
need to carry out calculations to see if a bacteria
suspected to be involved in the disease survives in the
acidic conditions found in our stomach.
You should be able to:
Keywords
Bacteria, pH, route of
transmission, symptomatic, ratio,
percentage, mean, histogram
•
•
•
•
Present data in tables and bar
charts
Choose the correct way to present
data
Calculate fractions and
percentages
Use percentages to calculate ratios
Scientists have discovered new evidence
about the evolution of viruses showing that
when they infect a host they cooperate with
other similar viruses to kill cells slowly but
speed up the rate at which they kill the cells
if there is an unrelated infection in the cells.
This discovery will help scientists
understand how an illness progresses.
Scientists have gained fresh insights into
how the Salmonella bacteria are able to
change key cells that line the intestine and
how Campylobacter survive in the acid
conditions of our stomach, enabling the
bugs to thrive. When exposed to the highly
acidic conditions of our stomach
Campylobacter change their behaviour and
focus on movement, making them better at
invading our tissues.
Activity 1
Question 1:
Bacteria were grown in the following concentrations
of Nitrogen (N2), Oxygen (O2) and Carbon dioxide
(CO2):
85 % N2
5 % O2
10 % CO2
Express the percentages as a ratio in simplest form?
Activity 2
Question 1: One ml (1000 µl) of bacterial culture were grown in varying pH.
Complete the table by calculating the missing values.
pH
Bacterial
colonies
Portion
(aliquot) µl
7.0 (control)
6.0
5.0
4.0
3.75
3.5
3.25
3.0
21
17
23
6
2
1
1
0
20
20
200
200
400
400
600
600
Fraction of
1ml bacteria
sample
1/50
1/50
1/5
Colonies per ml
% survival
21 ÷ 0.02 = 1050
100
81.0
6 ÷ 0.2 = 30
0.5
2/5
3/5
1 ÷ 0.6 = 1.67
0 ÷ 0.6 = 0
0.16
0
Question 2: Plot the results in a graph or a chart. Think about the best
way to present your data.
Question 3: Human stomach acid can be as high as pH 7 if you have eaten
a large meal or as low as pH 2 if you are producing a lot of stomach acid on
an empty stomach. Scientists are worried that if even 0.5% of these bacteria
can survive you may become infected.
What would your stomach pH have to be to kill more than 99.5% of the
bacteria?
Answers Activity 1
Question 1:
Bacteria were grown in the following ratios of Nitrogen
(N2), Oxygen (O2) and Carbon dioxide (CO2):
17:1:2
What were the percentage concentrations of the three
gases?
85% N2
5% O2
10% CO2
Answers Activity 2
Question 1: One ml (1000 µl) of bacterial culture were grown in varying pH.
Complete the table by calculating the missing values.
pH
Control (7.0)
6.0
5.0
4.0
3.75
3.5
3.25
3.0
Bacterial
colonies
21
17
23
6
2
1
1
0
Aliquot
(µl)
20
20
200
200
400
400
600
600
Fraction of
culture
1/50
1/50
1/5
1/5
2/5
2/5
3/5
3/5
Colonies
per ml
1050
850
126
30
5
2.5
1.7
0
% survival
100
80.95
10.95
2.86
0.47
0.24
0.16
0
Question 2: Plot the results in a graph or a chart. Think about the best
100
way to present your data.
90
% survival
80
70
60
50
40
30
20
10
0
7
6
5
4
3.75
pH
3.5
3.25
3
2
Answers Activity 2
Question 3: Human stomach acid can be as high as pH 7 if you have eaten
a large meal or as low as pH 2 if you are producing a lot of stomach acid on
an empty stomach. Scientists are worried that if even 0.5% of these bacteria
can survive you may become infected.
What would your stomach pH have to be to kill more than 99.5% of the
bacteria?
pH 3.75
Glossary
Bacteria – A very large group of single celled organisms that lack organelles or a nucleus,
some of which can cause disease.
Campylobacter – A group of bacteria that are spiral in shape and have a flagella at one or
both ends. They are one of the main causes of bacterial foodborne disease.
Culture – A method of multiplying microorganisms by growing them in a liquid or gel under
laboratory conditions so they can be studied.
Intestinal – In the region of the digestive tract after the stomach.
Route of transmission – The passing of a disease from an infected individual or group to a
previously uninfected individual.
Salmonella – A group of rod shaped bacteria that cause infections in humans and animals.
Symptomatic – Displaying symptoms
Virus – A small infectious agent made of nucleic acid and a protein coat that can only replicate
inside cells.
You should be able to:
• Present data in tables and bar
charts
• Choose the correct way to present
data
• Calculate fractions and percentages
• Use percentages to calculate ratios
DEADINBURGH
Infectious or not
What we need to do
Scientists have been monitoring the movements of groups
of people since the start of the outbreak hoping to predict
and identify infected individuals. We have received data
on the movement of groups of individuals.
The scientists need you to calculate how fast the
individuals are moving and how far they can travel in a
day. You will also need to analyse the results of observers
to determine if you can tell the difference between infected
and uninfected individuals. You must then decide if we
should fit monitoring devices to healthy people so we can
get early warning of potentially infected individuals?
You should be able to:
Keywords
Symptomatic, percentage,
probability
•
•
Convert percentages to decimals
Multiply probabilities
New technology and laboratory
breakthroughs, such as the monitoring of
healthy cows with electronic tags are
changing the potential for us to detect and
understand the progress of illness.
Researchers are using mathematical
techniques and statistical analysis alongside
wireless tracking sensors to monitor the
health of a herd of dairy cows in new
research aimed at helping farmers spot that
cows are unwell before symptoms appear. It
is hoped that such early detection of
illnesses such as lameness and mastitis
would result in less suffering for the cows as
well as ensuring milk yields.
Activity 1
Complete the table to work out how fast each individual is moving.
Individual
1
2
3
4
5
6
7
8
9
10
Distance (miles)
0.4
3.2
2.1
4.5
2.1
4.3
0.7
Time (mins)
48
76
237
65
335
71
26
Speed (miles/hr)
0.56
0.08
2.37
7.38
1.77
231
Speed = Distance ÷ Time
Question 1: The group is 45 miles away. If they do not stop moving how
long will it take for the first individual to reach our position?
Activity 2
Activity
Shuffling aimlessly (SA)
Walking in circles (WC)
Walking in a straight line (WS)
Walking backwards (WB)
Lying down (LD)
Running (R)
Proportion of time spent
doing activity for healthy
(uninfected) human
10%
10%
30%
20%
10%
20%
Proportion of time
spent doing activity
for infected person
30%
20%
10%
10%
20%
10%
Time
(mins)
Individual
30
60
90
120
150
180
210
240
270
300
1
2
3
4
5
SA
WS
LD
WS
SA
WC
WS
SA
WC
WS
SA
R
SA
WC
WS
WB
R
LD
R
SA
WS
R
WS
WC
WS
WS
WB
WS
SA
WS
LD
R
LD
WC
R
SA
R
LD
WS
R
LD
R
SA
WS
R
LD
R
SA
SA
R
Question 1: For each of the 5 individuals calculate the probability of the
given sequence of behaviours being carried out:
a) assuming that they are normal (uninfected)
b) assuming that they are infected
Activity 2
Question 2: Should all of the individuals that were observed who reach
the quarantine zone be treated as if they have succumbed to infection? If
not which of the individuals should be protected from the rest of the horde
heading towards our position?
Question 3: Is the monitoring of the behaviour of individuals able to
distinguish between those that are infected and those that are not? Would
you recommend that everyone wears a monitoring sensor and would it be
ethical to require everyone to wear one at all times?
Answers Activity 1
Individual
1
2
3
4
5
6
7
8
9
10
Distance (miles)
0.4
3.2
0.1
2.1
4.5
2.1
2.8
3.2
4.3
0.7
Time (mins)
48
342
76
237
65
335
71
26
146
231
Speed (miles/hr)
0.6
0.56
0.08
0.53
4.15
0.38
2.37
7.38
1.77
0.18
Question 1: The group is 45 miles away. If they do not stop moving how long
will it take for the first individual to reach our position?
10 hours 51 minutes
Answers Activity 2
Question 1:
Time
(mins)
Individual
30
60
90
120
150
180
210
240
270
300
Overall probability
of being uninfected
1
0.1
0.1
0.1
0.2
0.3
0.3
0.1
0.1
0.1
0.1
1.8 x 10-9
2
0.3
0.3
0.2
0.2
0.2
0.2
0.2
0.2
0.2
0.2
2.3 x 10-7
3
0.1
0.1
0.1
0.1
0.3
0.3
0.1
0.1
0.1
0.1
0.9 x 10-9
4
0.3
0.1
0.1
0.2
0.1
0.1
0.1
0.3
0.3
0.1
5.4 x 10-9
5
0.1
0.3
0.3
0.1
0.3
0.3
0.2
0.2
0.2
0.2
1.3 x 10-7
Overall probability
of being infected
1
0.3
0.2
0.3
0.1
0.1
0.1
0.2
0.3
0.2
0.2
4.3 x 10-8
2
0.1
0.1
0.1
0.1
0.1
0.1
0.1
0.1
0.1
0.1
0.1 x 10-9
3
0.2
0.3
0.3
0.2
0.1
0.1
0.2
0.2
0.3
0.3
1.3 x 10-7
4
0.1
0.2
0.2
0.1
0.2
0.3
0.2
0.1
0.1
0.3
1.4 x 10-8
5
0.3
0.1
0.1
0.3
0.1
0.1
0.1
0.1
0.1
0.1
0.9 x 10-9
Answers Activity 2
Question 2: Should all of the individuals that were observed who reach the
quarantine zone be treated as if they have succumbed to infection? If not which
of the individuals should be protected from the rest of the horde heading towards
our position?
Individuals 2 and 5 seem have a low probability of carrying out the sequence of
behaviours recorded if they were infected. They are probably not infected and
instead trying to escape the horde of infected without drawing too much attention
to themselves.
Question 3: Is the monitoring of the behaviour of individuals able to distinguish
between those that are infected and those that are not?
In this case the monitoring seems to have identified a clear difference in the
probability of individuals being infected. However, there are other factors to
consider such as the individuals being carriers of the disease, because they are
not susceptible to the infection but can still pass it on to others.
You should be able to:
• Convert percentages to decimals
• Multiply probabilities
DEADINBURGH
Viral replication
What we need to do
Scientists from the Roslin Institute have collected samples
of infected cells from members of the public. In order to
determine the concentration of the virus and establish how
much virus is enough to infect someone, the scientists
infect human cells grown in culture with dilutions of the
virus.
The scientists need your help to work out the
concentrations of the samples and the infectivity.
You will then need to present your results to the scientist
using the appropriate graphs and tables.
You should be able to:
Keywords
Agar, assay, bacteria,
concentration, culture, dilution,
DNA, growth media, pathogen,
plaque, PFU, RNA, symptomatic,
virus
•
•
•
•
Write numbers in standard form
Choose appropriate results to draw
conclusions
Present data in a line graph
Solve simultaneous equations using
substitution
Viruses evolve to cause disease. The
immune system and medicines ‘evolve’
to kill viruses.
There are many types of viruses and
some are more harmful than others. For
example, the common cold and winter
flu are quite common and for most
people they are not especially
dangerous. Other viruses, like SARS or
rabies, can be very dangerous.
Viral diagnostics could become far
quicker with the development of
'barcodes' of viral diseases to identify
potentially lethal mutations. There is
even the potential for diagnosing viral
infections without having to use cultures
of cells to grow the virus or carrying out
sequencing to identify the genes
Activity 1: Dilution calculations
Question 1: Calculate how much of the original sample is in each tube and show
your answer in decimals.
Write the volumes in standard form for each tube e.g. 1 x 10-1.
Calculate the dilution factor for each tube.
Record your results in the table below
Tube
1
2
3
4
5
6
7
Volume of original
sample per ml (ml)
Standard form (ml)
Dilution factor
Activity 2: Calculating the level of infectivity
Question 1:
Calculate the number of PFU’s in the original sample by multiplying the
number of plaques on your chosen petri dish with the dilution factor of the tube
the sample was taken from.
PFUs = plaques x dilution factor
Convert to standard form.
Activity 3: Testing the effectiveness of treatments
Question 1:
Data has been received for some other anti-viral drugs. The data we received
from the experiments show that:
17 PFUs and 33 doses of Moroxydine = 14 plaques
22 PFUs and 40 doses of Metisazone = 20 plaques
15 PFUs and 20 doses of Peramivir = 15 plaques
45 PFUs and 15 doses of Zanamivir = 42 plaques
How many plaque forming units does each dose of anti-viral drug prevent? Is
it better or worse than Cidofovir? By how much?
Activity 3: Testing the effectiveness of treatments
Question 2: Plotting data and interpretation of results
The scientists have collected data on different doses of Arbidol.
25 PFUs and 0 doses of Arbidol results in 25 plaques
25 PFUs and 5 doses of Arbidol results in 15 plaques
Assuming that people who are exposed to 25 PFUs of virus have symptoms, plot
a graph of doses of Arbidol versus number of plaques formed.
Treatment
Doses
Plaques
Arbidol
0
25
Arbidol
5
15
Arbidol
10
5
How many doses of Arbidol should a person take to make sure that the virus is
stopped?
Answers
Activity 1: Dilution calculations
Question 1:
Tube
1
2
3
4
5
6
7
Volume of original
sample per ml
0.1
0.01
0.001
0.0001
0.00001
0.000001
0.0000001
Standard form
1x10-1
1x10-2
1x10-3
1x10-4
1x10-5
1x10-6
1x10-7
Activity 2: Calculating level of infectivity
Question 1:
1.16 x 108 PFUs
Dilution factor
10
100
1000
10000
100000
1000000
10000000
Answers
Activity 3: Testing the effectiveness of treatments
Question 1: How many doses of anti-viral drug are required to prevent each
plaque? Is it better or worse than Cidofovir? By how much?
11 doses of Moroxydine prevents 1 plaque
20 doses of Metisazone prevents 1 plaque
20 doses of Peramivir did not prevent any plaques
5 doses of Zanamivir prevents 1 plaque
Arbidol doses vs. Plaques observed
Question 2:
30
Extrapolating from the
graph 12.5 doses of
Arbidol would be required
to prevent the infection.
Plaques observed
25
20
y = -2x + 25
15
10
5
0
0
2
4
6
8
Doses of anti-viral drug
10
12
Glossary
Assay - a procedure for measuring the biochemical or immunological activity of a sample.
Agar – A gelatinous material derived from certain marine algae. It is used as a base for bacterial culture media that can
be poured when heated up and which sets solid at body temperature.
Bacteria – A very large group of single celled organisms that lack organelles or a nucleus, some of which can cause
disease.
Culture – A method of multiplying microorganisms by growing them in a liquid or gel under laboratory conditions so
they can be studied.
Dilution - The process of making weaker or less concentrated.
DNA – Deoxyribonucleic acid. A self-replicating material made of a double-stranded nucleic acid which is present in
nearly all living organisms. It is the carrier of genetic information for cell growth, division, and function.
Growth media - a liquid or gel designed to support the growth of microorganisms or cells.
Pathogen – a broad term for a replicating agent such as an organism or infectious particle which causes disease in
another organism, typically a virus or bacterium.
Plaque – a visible region of dead cells formed within a cell culture, such as bacterial cultures within a growth media.
PFU - Plaque forming unit. A measure of the number of particles capable of forming plaques per unit volume is a
measure of viral concentration. The PFU of a solution is the concentration of viruses in a solution which are capable of
lysing host cells and forming a plaque in a culture.
RNA – The genetic material of many viruses, that code for the proteins and enzymes needed by the virus to replicate
and survive.
Symptomatic – Displaying symptoms.
Virus – A small infectious agent made of nucleic acid and a protein coat that can only replicate inside cells.
You should be able to:
• Write numbers in standard form
• Choose appropriate results to
draw conclusions
• Present data in a line graph
• Solve simultaneous equations
using substitution