New Evolution Lab 7
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Dec 6, 2023
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Lab 7 Worksheet
Bacterial Evolution
Name:
TPS 1
: Are changes to colony morphology heritable? What do you think would happen if
you inoculated a new culture with a wrinkly colony, grew the culture overnight, and then
plated a sample of the bacteria?
Changes to colony morphology are heritable because morphological changes are due to
changes in bacterial DNA which is passed to offsprings. If we introduced a wrinkly colony
into the plate then we would see more individuals with this morphology because these
bacteria would reproduce overnight.
This worksheet is organized by how a research article is setup. It will ask
introductory questions, methods questions, results questions and discussion
questions.
In today’s lab, you will be doing a scientific exploration using bioinformatic tools
☺! Bioinformatics is an important growing field that does not require wet lab
work. Instead, you can answer scientific questions using publicly available data
and your very own computer.
As a newly appointed bioinformatic researcher, you have been tasked in
investigating what gene mutant causes the different phenotypic variations below.
Additionally, you will also be choosing your own mutant to look at.
Introduction:
Q1: What are some benefits and drawbacks of using bacterial genomes to study
evolution? (Name at least two benefits and one drawback)
If we are only using one genome to study evolution then it makes our study easier as it is
easy to interpret genetic variation which makes it easier to study complex traits. Another
benefit is that it can reduce the costs we need to study the evolution of target traits as we
can keep the genome in the lab. One drawback to this is that since we would only use
one genome, it can introduce biases which would make us believe that a complex trait is
mutated a certain way when in fact it occurs through a different mechanism in our
genome of study.
Methods:
Q2: Bowtie2 is called an “aligner” in bioinformatic tools. It “aligns” sequences to a
reference genome. Using google scholar (or another article finder), find another aligner
tool
[hint: you can use the key words “bioinformatics aligner”]
a.
What is the name of the aligner?
TM-Alinger
b.
What type of data does it use (DNA, RNA, single cell etc.)?
Transmembrane proteins
c.
Cite the aligner’s article (in correct format, points will be removed if cited incorrectly).
Example:
Langmead, B. and Salzberg, S.L., 2012. Fast gapped-read alignment with Bowtie 2.
Nature methods
,
9
(4),
p.357
.
Bhat, B., Ganai, N.A., Andrabi, S.M. 2017. TM-Alinger: Multiple sequence alignment tool
for transmembrane proteins with reduced time and improved accuracy.
Sci Rep,
7.
https://doi.org/10.1038/s41598-017-13083-y
Now it’s time to find out your mutants! Using the mutant 1, mutant 3, mutant 5 and
mutant 4 files, follow the slides starting from “downloading the all.var.tsv files” for
each mutant.
Results:
Q3: For each mutant below answer
ALL
questions: How many mutations did you find?
For each mutant: what is the “old” reference nucleotide and what base pair did it mutate
into? What “type” of mutation is this? What is the function of each mutant? Paste the
locus tag of each mutant (will be used later).
i.e. Number of mutations:
Base pair mutation:
Type of mutation:
Function of mutation:
Locus tag:
- If there is more than 1 mutation, fill this table out for each mutant.
a. Mutant 1?
Number of mutations: 2
Base pair mutations: C and T
Type of mutation: single nucleotide change, nonsynonymous
Function of protein: Sensory box/GGDEF domain/EAL domain protein
Locus tag: PFLU5329
Number of mutations: 2
Base pair mutations: G and T
Type of mutation: single nucleotide change, nonsynonymous
Function of protein: Chemotaxis response regulatory protein-glutamate methylesterase
CheB
Locus tag: PFLU1224
b. Mutant 3?
Number of mutations: 2
Base pair mutations: C to T
Type of mutation: single nucleotide change, nonsynonymous
Function of protein: methyl-accepting chemotaxis protein
Locus tag: PFLU1219
Number of mutations: 2
Base pair mutations: C to T
Type of mutation: single nucleotide change, nonsynonymous
Function of protein: Sensory box/GGDEF domain/EAL domain protein
Locus tag: PFLU5329
c. Mutant 5?
Number of mutations: 2
Base pair mutations: C to T
Type of mutation: single nucleotide change, nonsynonymous
Function of protein: Sensory box/GGDEF domain/EAL domain protein
Locus tag: PFLU5329
Number of mutations: 2
Base pair mutations: CCCTGGAGCGCC to CCC
Type of mutation: single nucleotide change, nonsynonymous
Function of protein: Sensory box/GGDEF domain/EAL domain protein
Locus tag: PFLU5329
d. Mutant 4?
Number of mutations: 1
Base pair mutations: A and C
Type of mutation: single nucleotide change, nonsynonymous
Function of protein: Uncharacterized protein YfiR
Locus tag: PFLU5211
Q4: What does the star at the end of Glu319* indicate?
The star at the end indicates that this is a stop codon so the mutant should have a stop
codon at the end.
Discussion:
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Related Questions
Could you please assist with correct number?
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PlZ asap
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Q24:
A 7 dilution is performed on a culture of bacteria in order to perform viable plate counts. From the dilution, *0.1 mL* of solution is plated on solid media, and 31 colonies of bacteria grow on the petri dish.
Assuming each colony came from a single bacterium, how many bacteria are in a single mL of the original culture? Express your answer to two decimal places using standard notation.
Since only 0.1 mL is put on the plate, this counts as an extra dilution!!!
Any time less than 1 mL is transfered, a dilution is being performed.
Any time more than 1 mL is transfered, a concentration is being performed.
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Clinical application: A 44-year-old man with HIV is receiving antibiotics through a intravenous
catheter. The antibiotics are to help treat a kidney infection. The patient develops a fever.
Subsequent cultures from the patient's blood, the needle tip, and from the insertion site all show
growth of an organism with large oval-shaped cells. The cells reproduce by budding.
(a) What is your guess about the identity of the pathogen?
(b) How do you think the antibiotics may have contributed to this outcome?
(c) What do you think the portal of entry was for this pathogen?
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3. Please help answer this question and please show all work on how you got the answers. Thank you so much!! :)
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7a. A petri plate is given to you with 80 colonies on it. I tell you that I did five 10x dilutions and then plated 0.1 ml from my last tube to get 80 colonies on a plate. How many living bacteria per ml were in that original sample? Draw out (or describe) all of the dilutions I would have done to get this number.
7b. Again, I have a plate with 80 colonies on it, but I tell you that I did one 100x dilution and two 10x dilutions before I plated that 0.1ml from my last tube. How many living bacteria per ml were in that original sample? Draw out (or describe) all of the dilutions I would have done to get this number.
please include drawings. thank you
arrow_forward
Naming and Classifying Microorganisms
1. Recognize the system of scientific
nomenclature that uses two names: a genus
and a specific epithet.
2. Differentiate the major characteristics of each
group of microorganisms.
3. List the three domains.
A Brief History of Microbiology
1. List at least four beneficial activities of
microorganisms.
2. Name two examples of biotechnology that use
recombinant DNA technology and two
examples that do not.
3. Explain the importance of observations made
by Hooke and van Leeuwenhoek.
4. Compare spontaneous generation and
biogenesis.
5. Identify the contributions to microbiology
made by Needham, Spallanzani, Virchow, and
Pasteur.
6. Define bacteriology, mycology, parasitology,
immunology, and virology.
7. Explain the importance of microbial genetics
and molecular biology.
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t Fall 2020 (page 2 of X
elearn.squ.edu.om/mod/quiz/attempt.php?attempt3D1335328&cmid%3D697149&page3D1
System (Academic)
The reason why Bacteria stain differently is mainly based on their:
Select one:
O a. Number and thickness of smear
O b. Cell wall structure
O c. Presence/absence of nucleus
O d. Size
O e. Origin
In the image provided, the basic unit of life is represented in the.....
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Escherichia
coli
Mycobacterium
phlei
Bacillus
Micrococcus
subtilis
luteus
A
B
Figure 1: Agar Slant Cultures of Bacteria
(Gary E. Kaiser, Ph.D.- Professor of Microbiology)
. Observe and describe the colour of the slant cultures (A-D) in fig 1. (
. Define the following terms: pure culture, sterile medium, inoculum, aseptic
technique, and colony.
What is the name of the cultures that you used
. Where they gram negative or positive
Define the following terms: psychrophile, mesophile, thermophile, and
hyperthermophile.
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Question:-
Define the bacterial categories that each type of bacteria belongs to. You only have to name the categoriesNOT the actual species of bacteria Note: there will be more than one category . A bacterial species that grows best at 37 degrees Cand when a small amount of oxygen is present
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Which cultures would be suitable for the transduction experiment and why?
Which cultures would not be suitable for the transduction experiment and why?
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1) both streak plating and pour plating produce isoluated colonies. What is the underlying explanation for why both methods work; that is, what are both methods doing with repect to the bacterial cells?
2) If streak plates failed to produce isolated colonies, describe two things that you could do to improve your chance of generating isolated colonies.
3) Why do we care so much about producing isolated colonies? what is an isolated colony composed of? What can you do with an isolated colony?
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ISOLATE #2
Isolation of Gram-positive Bacteria from the Nose and Skin – Part III –
Use the results from your Gram stain (morphology and Gram stain result), along with the results you record
in the table below to determine the genus of "Isolate #1" and "Isolate #2". Refer to Table 1 in “Isolation
of Gram-positive Bacteria from the Nose and Skin – Part III.
Additional Information to HELP Below!
1. MSA:
Record the results for "Isolate #2 below:
Results of Tests to determine the genera of "Isolate #2:
a. Isolate #2: Cell Morphology (shape)
Results & Interpretation
(not just positive or negative, what
do the results tell you about the
unknown bacteria?)
Appear to be rounded ball like, Bacteria is coccus shaped .
Possible genera (genus)
(there may be more than one)
Test
b. Isolate #2: Gram stain result
Gram Postive. (The color I see on my screen is purple.)
c. List at least two genera (not species) of bacteria that are consistent with the Gram reaction
and morphology you observed.
Morphology…
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Use the data below to calculate the colony forming units per mL (CFU/mL) from a
sample of bacteria after growing the sample in an incubator for 2 hours.
Culture density (CFU/mL) =
Time
1 hour
2 hours
1x 10-¹
1 x 10-²
1x 10-³
1x 104
number of colonies
(dilution) x (volume plated, in mL)
Dilution (before plating) Volume spread on plate (replicate plates)
1x 10-1
1x 10-²
1x 10-³
1 x 104
0.1 mL
0.1 mL
0.1 mL
0.1 mL
Number of colonies observed
0.1 mL
0.1 mL
0.1 mL
0.1 mL
TNTC
660
101
8
TNTC
220
15
3
TNTC
783
115
7
TNTC
180
9
7
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Im 100
4. You have a culture of yeast that is at a density of 8x10' cells/mL. You dilute the sample 1:10, then
1:1,000 again, and finally you dilute the sample an additional 1:5. You add 0.1 mL of the final dilution
to a spread plate. Assuming that most of the cells in the original culture were living, how many colony-
forming units do you expect to count on your pour plate the next day?
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Identify the shapes and arrangements of the following bacteria observed under the microscope. Recall: look for the arrangement seen with most cells; you may see another arrangement that is less common.
option: diplo, bacillus, negative, coccus, positive, staphylo, strepto.
Gram stain
Cell arrangement
Cell Shape
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Q10) What genera produce endospores?
- What culture would have more endospores? A bacterium in broth culture for 24 hour or 72 hours?
- How specifically does a flagella stain let us see the flagella? (they’re too thin to be seen with 1000X magnification)
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Performing a bacterial isolation by streaking, using sterile (aseptic) technique, consider
the expected outcome on the streak plate after the following:
Two organisms were in the original sample. Organism G was present at twice the
abundance of Organism H (so 2/3 of the original sample).
The streak plate was generated using 4 areas (quadrants)- A, B, C & D. Area A was
inoculated with a loop containìng 3 mìllion organisms from the original culture, which
was mixed very well and considered to be homogeneous. Areas B, C & D were streaked
from the previous area with a sterilized loop, with each streak transferring 2% of the
organisms from the previous area (assume the relative abundance of the two organisms
was maintained).
What is the expected outcome in Area
on this streak plate? 2d
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Question:-
Name ten examples of bacteria and give their colony morphology. ( indicate the media used for each)
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There are two cultures of yeast cells in the pictures, one has been incubated for 6 hours and one has been incubated for 24 hours. After a 10x dilution by taking 100µl of each culture and adding it to 900 µl water in a microcentrifuge tube and 100µl sample from the tube was taken to view in the counting chamber.
a) Count the total number of yeast cells for each culture respectively
b) Calculate the concentration and density of yeast cells for each culture respectively
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6a. A sample is given to you that contains 6 million cells per ml. You must make a series of serial dilutions in order to get a countable number on a plate to prove that there are indeed 6 million cells per ml. The plate that you eventually put a sample of bacteria on must have between 10 and 100 colonies for ease of counting. What dilutions do you make to get this many colonies on a plate? How many colonies do you have on that plate? Show what dilutions you make (Write exactly how much liquid you move into each test tube and how much liquid was in the test tube, ex. Move 1 ml of culture into 9 ml of water – 10x dilution). Don’t forget to tell me how much liquid you eventually put on your plate. (If you want to draw something out, you could draw then take a picture of it with your phone and submit the image along with the worksheet).
6b. Do the same problem as in 6a, but now you have to do it in 3 test tubes or less. What dilutions do you do now?
please use drawings to help…
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Someone can please help me to fill in the blanks by compare and contrast domain bacteria and domain arches using the chart below
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Below are the results of streak for isolations of Bacterium 1 and Bacterium 2 before and after they were cryopreserved using glycerol stock. Identify if the culture is pure or not
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Sample Station 2
• This is micrograph of a Gram
stained bacterium. Look at the
cells indicated by arrows, answer
the following:
A. What is the cell morphology?
B. What is the cell arrangement?
C. What is the Gram reaction of
this organism?
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Plaque assay (Bacteriophage Titer) Answer questions 2 & 3
2. Why don't bacteriophages continue spreading over the entire plate until all of the E. coli cells on the plate are lysed?
3. Why is it important that bacterial cells should be in the exponential growth phase for this experiment?
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In the experiment by Bernard Davis, bacterial F+cells and F- cells were growing while separated by a filter. Filter pores allowed the passage of the liquid medium but not the bacteria cells. As a result:
1) prototype colonies grew well on minimal medium
2) F+ cells were converted to F- cells despite the physical separation
3)F- cells were converted F+ cells despite the physical separation
4)F+ cells were not converted to F- cells because of the physical separation
5) F- cells were not converted to F+ cells because of the physical separation
6)there was no growth of prototypes on minimal medium
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Please answer fast
Dilution Problem. A culture of Staphylococcus is diluted as follows:
(1) 20mL are added to 80mL of water.
(2) 10uL from (1) are then added to 9.99mL of water.
(3) A 10-2 dilution is made from tube # (2).
(4) 100uL from (3) are plated for a pour plate and incubated.
Growth Problem.A culture with approximately 2x103 cells/mL were incubated. After 3 hours, the number of cells had increased to 3x105.
a) How long was the generation time in minutes?b) How many generations have occurred
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