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Phylogenetics Activity Result Worksheet
BIO 2060L Section: 5
Your Name: Emmanuel Lujano
ACTIVITY: HOW TO BUILD A PHYLOGENETIC TREE
Learning Objective: Explain how to prepare and read a phylogenetic tree.
1.
Paste your phylogenetic tree with the highlights indicating the branches that are di±erent from
the ²ow chart in the Lab Instruction Appendix.
2.
Describe the major di±erences between the phylogenetic tree and the ²ow chart.
On the Gram-Positive side, a few di±erences were the ²ow chart’s grouping of Bacillus and
Lactobacillus on the basis that they are both rod-shaped, hence bacillus. The phylogeny tree prepared
shows that this criterion is not enough to warrant their place as sister taxa. The phylogeny tree also
posits that the staphylococcus and streptococcus are not close enough to be sister taxa as well, even
though the ²ow chart makes the assumption because of the de³ning cocci characteristic. On the
Gram-Negative side, the ²ow chart places Citrobacter and Enterobacter as sister taxa on the basis of
being Lactose +, while the phylogeny tree posits that the relationship between the two is far more
complex.
3.
In your opinion, which would be a better tree to represent the evolutionary relationship of
microorganisms, the phylogenetic tree OR the ²ow chart (tree). Explain why?
I believe that the ²ow chart depicts a much more intuitive interpretation, making it easier to
understand the groupings and certain de³ning characteristics. However, for in-depth accuracy based
on genetic similarities and di±erences, the tree is able to show the relations between di±erent species on
a deeper level that might be more useful to applications and research.
4.
Answer the following questions about your phylogenetic tree. Please use the terminology
de³ned in the PowerPoint slides. All species names must be written in the binomial
nomenclature format.
a)
Give an example of two species located on proximal branches (sister taxa).
i)
Bacillus cereus and Staphylococcus capitis
b)
Is there a single outgroup branch (species)? If yes, provide the species name.
i)
Yes, Neisseria gonorrhoeae
c)
Nodes are points of species divergence. A resolved node should have only two
branches. In your tree, how many resolved nodes do you see?
i)
3
d)
Polytomies are nodes that are not resolved/unclear. Is there a polytomy in the tree? If
yes, provide the names of the species on a polytomy.
i)
No
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Grades for Arysta Visser: 23 x M Uh-oh! There's a problem w X b The restriction EcoRI cleaves X + Untitled spreadsheet - Goog X
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18. The restriction EcoRI cleaves double-stranded DNA at the sequence 5'-GAATTC-3', the
restriction enzyme HindIII cleaves at the sequence 5'-AAGCTT-3', and the restriction enzyme
BamHI cleaves at 5'GGATCC-3. An 805 bp circular plasmid is digested with each enzyme
individually and then in combination, and the resulting fragment sizes are determined by
means of electrophoresis. The results are as follows:
1
Restriction Enzyme(s)
EcoRI
BamHI
HindIII
EcoRI and BamHI
EcoRI and HindIII
BamHI and HindIII
3
Practice
====•=•€ EX
Fragment lengths (base pairs)
430 bp, 375 bp
470 bp, 335 bp
Lab Report 6…
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2. Calculate the effective dilution. You were given a sample which contained 5.5mL of
bacterial culture. You added 10uL of phage solution to the culture. What was the
effective dilution produced by the addition of the phage solution?
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Gmail .ll LTE
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40%
#3 Mol Bio Gene o...
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•..
Complete the following tasks.
You discovered that a species of bacteria can break down Styrofoam™ (polystyrene) products due to an
enzyme it produces, polystyrenase. You wish to study the gene that codes for this enzyme.
Task 1: DNA Extraction
To begin work on the bacterium, you begin by extracting its genomic DNA (gDNA). What is the purpose of
the following procedures? Answer briefly but completely.
Using sodium dodecyl sulfate, a detergent
Answer:
а.
b. Adding RNase A and Proteinase K during extraction
Answer:
Adding ethanol before recovering the DNA extract
с.
Answer:
Task 2: Polymerase Chain Reaction
After purifying the gDNA extract, you want to isolate and amplify the polystyrenase gene. You perform PCR
using the appropriate gene-targeted primers. What is the purpose of the following PCR components? Answer
briefly but completely.
DNA polymerase isolated from Thermus aquaticus
a.
Answer:
b. Deoxynucleotide triphosphates (DNTPS)…
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BIOTECHNOLGY
Date:
Name:
Instructor:
Section/Group:.
POST-LAB QUESTIONS
1. In one or two sentences, summarize the technique of gel electrophoresis.
2. How does the process of gel electrophoresis separate DNA fragments?
3. Why is the fact that DNA has a negative charge so important in the gel electrophoresis process?
Biotechnology 165
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Helping tags: Biology, bacterial count, dilution, serial dilution
WILL UPVOTE, just pls help me answer the following questions and explain them clearly. Pls
show complete solutions also for the computation part. Thank you.
1. A bacterial culture was grown for 9 hours. At 3-hour interval, the culture was sampled to
determine the population of the culture, by transferring 25 ml of the suspension to 225
ml 0.85% NaCl. Three consecutive dilutions were further made by using 1 ml aliquot in 9
ml of 0.85% NaCI. One ml from each dilution was plated in each of duplicate plates. The
following table shows the results of the plating method.
Sampling
COUNTS
2nd dilution
3rd dilution
4th dilution
0,0
30: 35
250;245
1st dilution
1st
2nd
3rd
0; 0
240; 235
TNTC
55; 60
5; 6
TNTC
TNCT
TNTC
TNTC
a) Illustrate the dilution series used and label the final dilution of each dilution.
b) Determine the bacterial count (CFU/ml) every 3 hours of incubation for 9 hours.
Show all computations.
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3. Recombinant protein is produced by a genetically engineered strain of Escherichia coli during cell
growth. The recombinant protein can be considered a product of cell culture even though it is not
secreted from the cells; it is synthesized in addition to normal E. coli biomass. Ammonia is used as
the nitrogen source for aerobic respiration of glucose.
The recombinant protein has an overall formula of CH1.5500.31N..25. The yield of biomass (excluding
recombinant protein) from glucose is measured as o.48 g/g; the yield of recombinant protein from
glucose is about 20% of that for cells.
How much ammonia is required?
What is the oxygen demand?
If the biomass yield remains at 0.48 g /g, how much different are the ammonia and oxygen
requirements for wild-type E. coli that is unable to synthesize recombinant protein?
а.
b.
с.
24°C
08:39
Berawan
27/04/2022
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helping tags: biochemistry, agarose gel electrophoresis, genomic DNA isolation, gel electrophoresis
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Guide Questions:
Illustrate the different forms of bacteria.
1) Spherical - coccus
diplococcus
streptococcus
staphylococcus
mono coccus
2) Rod-shaped bacillus
club-shaped bacilli
rodswith square ends
fusiform bacilli
rods with rounded ends
3) Curved rod - spir illa
a. rigid form
Spirillum
vibrio
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Article:
Biomimetic Engineering of Nanodelivery Systems: Artificial Viruses in the Making
In an effort to engineer the next generation of nanoscale vectors, scientists have moved from using inorganic components aimed at obtaining inert structures to utilizing biological building blocks that are able to convey additional functionalities to the resulting construct. To cope with the complexity of the body and to evade the multiple layers of defense that tissues and organs have, it is critical to rely on the ability of certain materials to interact with, rather than to eschew, the biology of our body. Every NP system conceived to date faces one common fate: whether injected,…
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a) inoculum is from an old culture
b) shifting cells from rich culture medium to a poorer one
c) exponentially growing culture is transferred into the same medium under the
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Lesson 2
Focus Questions
1. What chemicals and molecules are needed for PCR, and what is the function of each
component?
2. Examine the 150 base promoter sequence below.
Kaylee Kauff
5'TAGAAAAGGA AGGTGGCTCC TACAAATGCC ATCATTGCGA TAAAGGAAAG
GTATCATTC AAGATGCCTC TGCCGACAGT GGTCCCAAAG ATGGACCCCC
ACCCACGAGG AGC ATCGTGG AAAAAGAAGA CGTTCCAACC ACGTCTTCAA3'
Write in the sequence of the complementary strand and mark the 3' and 5' ends of the
complementary strand.
43
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Module 10 DNA & Protein - 20
O Module 9 Genetics - 2021SP/B X
B Take Test: Heredity 2 Homewor X
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* Question Completion Status:
QUESTION 1
Some dogs bark while following a scent trail; others are silent. The barker allele is dominant (B) to the silent recessive allele (b). The allele for straight tails
is dominant (S) over the allele for curly tails (s). If two dogs are heterozygous for both traits, which of these correctly identifies the genotypes of the
parents?
O a. BbSs x BbSs
O b. BbSs x bbss
O c. BbSs x bbSs
O d. Bbss x bbSs
QUESTION 2
Some dogs bark while following a scent trail; others are silent. The barker allele is dominant (B) to the silent recessive allele (b). The allele for straight tails
is dominant (S) over the allele for curly tails (s). If two dogs are heterozygous for both traits, when we "FOIL" to see what allele combinations they can give
to…
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6. If the y-intercept of a Lineweaver-Burk plot = 1.91 (sec/millimole) and the
slope = 75.3 L/sec, KM equals:
a 0.0254 millimolar (mM).
b. 0.523 millimolar (mM).
c. 5.23 millimolar (mM).
d. 39.4 millimolar (mM).
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