Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
End of Summer Report
Rhodococcus Opacus
A tale of two phages: Is phage DNA sequence highly conserved
over time and space?
Phage Genome Evolution
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
The civil engineering lab (CVLB) conducts research related to how
microscopic organisms affect the environment.
Dr. Kung-Hui Chu work
studies biodegradation and bioremediation of priority pollutants and
emerging contaminants, molecular quantification of microbial risk in water,
optimization of bioenergy production, application of bioretention for
stormwater runoff management, and advancing knowledge on microbial
ecology of nitrogen and carbon cycles. She gets support from the Center of
Phage Technology (CPT) lab when the study of how phage (virus) affects
specific bacteria is necessary. Bacteriophages, or phage, are viruses that kill
bacteria. Coupled with moden DNA-based biotechnology, phage have
enormous potential as “green” anti-bacterial agents. The Center for Phage
Technology will position the Texas A&M University System as the world
leader in the application of phage to combat bacterial infections in humans,
animals, and plants, to promote food safety, to protect against potential
bacteriological weapons, and to prevent or mitigate the deleterious effects of
bacterial contamination, degradation, and corrosion in the petroleum
industrial.
The study of Rhodococcus opacus (R. opacus) has medical and
industrial applications that could affect humanity in the near future.
Some Rhodococcus opacus species are pathogens, and a better
understanding of phages specific to R. opacus can enhance the
development of phage therapy. Some R. opacus are foaming bacteria in
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
biological wastewater treatment processes, and phage treatment might
be possible to minimize common sludge bulking problems. Other
applications involve the generation of energy sources.
The scientific concepts specific to the study of how phage affects R.
opaccus are closely related to biology, and specifically to bacteriology.
These scientific studies have found that, although at one time it was
thought that the use of bacteriophage might be an effective way to treat
bacterial infections, it soon became apparent that phage are quickly
removed from the body, and thus, were of little clinical value. However,
bacteriophage are used in the diagnostic laboratory for the identification
of pathogenic bacteria (phage typing). Although phage typing is not used
in the routine clinical laboratory, it is used in reference laboratories for
epidemiological purposes. Of critical bacteriology importance, is the lytic
or lysogenic process. In either lytic or lysogenic process, the virus must
enter the cell. This involves two steps. (1) Attachment to the surface of
the cell. The type of cells a virus can infect is highly specific. A virus
protein binds specifically to a cell receptor, which generally has some
non-viral cell function. In some eukaryotic cells, virions are
nonspecifically carried in by endocytosis. This also accomplishes the
second stage of infection (2) penetration. In bacteriophage, the cell wall
and membrane are breached by enzymatic degradation and injection of
the genetic material into the cell. The mathematical concepts required to
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
understand the bacteriology behavior of phage and R. opaccus bacteria is
differential equations. This high level mathematical concepts cannot be
targeted at the high school level at the present time since the highest
level of math at my high school is Calculus 1.
The study of whether phage DNA sequence is highly conserved over
time and space, however, which is the specific project I am working on,
can target the concept of scatter plots and the generation of a
mathematical equation that can be used to compare the DNA sequence of
various phages. This level of mathematics can be applied in Algebra 1.
It may be possible to combine the Biology concepts of studying bacteria
and phages with the creation of math scatter plots and lines of fit to help
compare the DNA sequence of different phages. Specifically, it applies to
sections of the TAKS Objective 1 and Objective 2 related to functions.
Accordingly, the following TEKS and College & Career Readiness
standards are targeted:
1. TEKS
a. A.6 (A) – Develop the concept of slope and determine slopes
from graphs and tables.
b. A.6 (B) – Interpret the meaning of slope in situations using
data or graphs.
c. A.1(E) – Interpret and make decisions, predictions, and
critical judgment from functional relationships.
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
d. A.2 (D) – Collect and organize data, make and interpret
scatterplots.
2. EOC CRS (College Readiness Standards)
a. II.D.1 – Interpret and translate among multiple
representations of equations and relationships.
b. VI.C.3 – Analyze relationships between paired data using
graphing calculators.
3. ELPS (English Language Proficiency Standards)
a. 1.C – Use mapping, drawing, comparing, contrasting, and
reviewing to acquire basic and grade level vocabulary.
b. 2.E – Use visual, contextual, and linguistic support to enhance
and confirm understanding of increasingly complex and
elaborated spoken language.
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
The outline below shows the conceptual design of my proposed
classroom lesson:
Rhodococcus Opacus
A tale of two phages: Is phage DNA sequence highly conserved
over time and space?
Phage Genome Evolution
I.
Lesson Description (TEKS A.1.D and E, A.2.D. and A.6.D., CCRS II.D.1 and
VI.C.3)
a. The student will create 4 quadrant poster that will include an
interpretation of the data, an equation, a table of values, and a
graph.
b. Use DNA sequence base pairs RopaN4 and RopaN1 phages, and
other Ropa-X phages.
c. Evaluate differences and similarities by analyzing the slope of the
line created by the base pair counts.
d. Explore if this represents a new area of study of phage genome
evolution.
II.
Key vocabulary terms
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
a. Scatter plot, positive correlation, negative correlation, line of fit,
line of best fit, slope, bacteria, phage, Rhodococcus opacus, DNA
sequence, lyse process.
III.
Lesson Materials
a. Powerpoint presentation of teacher work in the E3 program.
b. Description of how engineering can affect our lives do through the
Video: YouTube - a day made of glass
c. Video : YouTube - T4 Virus infecting a bacteria.
d. DNA sequence base pairs data of phages.
e. 35 Poster boards, 6 sets of color sharpies, crayons, package of blue
permanent markers, package of red permanent markers, 12 Rulers,
6 yard sticks, 20 Avery color coding labes ¼” diameter
f. Sample picture of DNA sequence of a phage similar to the one
shown below. Retrieved from:
http://www.jbc.org/content/275/38/29672.full
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
g. Samples of DNA sequence base pairs scatter plots of the actual
phages studied during the E3 program laboratory work.
h. Poster created during E3 program.
i. Calculators, TI Nspire CX CAS color calculator with software package,
j. Digital Overhead projector
IV.
Room Preparation
a. Write TEKS and Lesson Objectives on board.
b. Arrange students to work in groups of 4.
c. Place markers, poster boards, yard sticks, rulers, colored dots,
glue, graph paper, and calculators at center of desks for each team.
d. Place E3 Poster on front board to allow for easy viewing by the
students.
e. Upload powerpoint presentation and video.
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
V.
Procedures: This lesson is an enrichment project right after students
would have studied and solved problems on functions and scatter plots
normally covered in Chapter 3 and 4 in Algebra 1 Glencoe Math book
during the 2nd 6 weeks. This normally occurs in October.
a. Engage
i. Ask students to write on a piece a paper a list of activities
engineers do.
ii. Show the Video: YouTube - a day made of glass
iii. Coordinate the lesson on bacteria and phages with the
Biology teacher. Explain the connection between their study
of bacteria and phages in their biology class to studies in
environmental engineering.
iv. Ask students to describe what they think environmental
engineers do.
b. Explore
i. Provide students with copies of DNA sequence base pairs
scatter plots of phages different from the study done during
the E3 program and ask them to find at least 4 similarities.
ii. Ask students to decide the correlation of the scatter plot they
are working with (positive, negative, no correlation).
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
iii.
Use random selection by placing numbers in a bowl and
taking out the numbers to see who would answer first.
Groups may not repeat the same answer.
c. Explain
i. Review the vocabulary terms.
ii. Present the Powerpoint of the work done by the teacher in E3
program,
iii. Show Video : YouTube - T4 Virus infecting a bacteria.
iv. Describe the impact of finding whether phages conserve their
DNA structure through time and space (phage genome
evolution)
v. Describe application of phage to combat bacterial infections in
humans, animals, and plants, to promote food safety, to
protect against potential bacteriological weapons, and to
prevent or mitigate the deleterious effects of bacterial
contamination, degradation, and corrosion in the petroleum
industrial.
vi. Refer to the DNA base pairs scatter plots provided to help
them understand how to interpret similarities by finding the
slope of the best fit line.
d. Elaborate
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
i. Provide students with data points in ordered pairs related to
the actual phages studied during the E3 program. Each group
will get a different set of data points from a different phage.
Explain to them that this is actual data that was provided
during the Teacher’s work at Texas A&M College Station.
ii. Students are to create a table of values using the data and
paste in on their 3rd quadrant of their poster.
iii. Students may choose to graph the values using Excel, graph
paper, or draw graph on poster board. The graph will be
pasted on the 4th quadrant of their poster.
iv. Students will use the STAT function of their TI-84 calculators
to enter the data points, do a line of fit and a best fit line.
v. Using the data entered, students will generate an equation in
slope-intercept form and write the equation on the 2nd
quadrant of their poster.
e. Evaluate
i. Students will determine the type of scatter plot created.
ii. Students will evaluate the slope and y-intercept generated
from the slope-intercept equation.
iii. Students will write their interpretation of the data on the 1st
quadrant.
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
iv. Students will place their posters right next to each other on
one of the walls of the classroom. Students will compare and
contrast the slopes of each other posters to evaluate if there
are similarities in the DNA sequence base pairs.
v.
Students will write a simple paragraph describing the
differences and similarities they see in the data and predict
whether the phages have a high degree of similarity.
f. Concluding activity
i. Explain the similarities and differences of the phages using
the posters created by the students.
ii. Help students understand that if the similarities are high, it
means that phages can actually conserve their DNA through
time and space, and that this is a brand new phenomena that
is yet to be explored.
iii. Encourage students to view science, math, and engineering
as possible areas of interests that will help them study new
concepts such as phage genome evolution when they go to
college.
iv. Review the work done at the Center for Phage Technology at
Texas A&M.
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
In terms of resources available, Brownsville Independent School
District provides computers to teachers and calculators for every student. I
understand from conversing from other science teachers in the E3 program
that phages are studied in the Biology class. I will need to investigate if any
lab work is done that allows students to study samples of bacteria. The
supplies that I will need are 35 Poster boards, 6 sets of color sharpies,
crayons, package of blue permanent markers, package of red permanent
markers, 12 Rulers, 6 yard sticks, 20 Avery color coding labes ¼” diameter,
and TI Nspire CX CAS color calculator with software package. The TI Nspire CX
calculator along with the software package allows for visual comparison of scatter plots
simultaneously and in color. This feature is a significant enhancement that will help
student see in real time the effect of changing points in the scatter plots.
In terms of time constraints, I believe that if I cover the concept of
scatter plots and spend 2 to 3 days on this enrichment activity, it will be an
acceptable activity that will increase the depth and rigor of the concept. The
EOC exam will require less objectives than TAKS, but the depth and rigor
must be increased significantly, and I believe this enrichment lesson falls
perfectly in line with the rigor and depth required by the EOC exam. I do
not believe at this point that there other logistical or technology constraints
associated with this particular lesson.
The student outcomes I expect is a deep understanding of the
concepts of slopes and scatterplots at the rigor required the CCRS of the End
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
of Course Exam. Students will be able to correlate biology lessons with
Algebra lessons as fundamental tools to understand our world around us,
and the impact of the study of micro-organisms in the future. I expect to
spark the students’ interest in STEM careers and provide with a substantial
answer to the question: How will I ever use the Algebra skills I am learning?
ALGEBRA 1 – DATA ANALYSIS PRETEST
1. Which of these graphs shows a negative SLOPE?
a.
c.
b.
d.
2. Find the slope of the line that passes through the pair of points
(–3, –2), (5, 4). Graph the line.
m = ____
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
3. Which equation describes a line having a slope of 2 and
a y-intercept of 7?
a.
y =–2x –7
b.
y = –2x + 7
c.
y = 2x+7
d. y = 7x – 2
4. Which equation fits the data in the table?
a. y
.. = 4 –
b. y = 4x +
x
c. y = x + 6
d. y =
x+4
5. What is the slope of the line in the graph below?
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
m=
6. What is the equation of the line for the following graph?
a.
y = 3x - 2
c.
y = - 3x - 2
b.
y = - 2s + 3
d.
y = - 3x – 1
7) Write an equation of the line when given a point and the slope.
Show both the calculation method and the graphical method.
(-3,-2)
m = _4_
3
y=
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
8) The table below shows the number of student absences for
the school year in Mr. Cruz’s math classes.
Which of the following best represents the data shown in the
table?
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
9) The graph below shows the amount of time that Dennis
spent studying for his Algebra 1 class.
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
10. Which of the following is a possible equation for a trend line
of this scatterplot?
A.
B.
C.
D.
f(x)
f(x)
f(x)
f(x)
=
=
=
=
1/2x + 11
1/2x – 11
–1/2x + 11
–1/2x – 11
11) Determine the trend of each graph shown.
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days
Armando Vital, Rivera High School, Brownsville ISD, Algebra 1, Grade 9, 4 instructional days