Title that reflects the lesson activities
Bacterial Identification Virtual Lab
Purpose Statement
The purpose of this lab is to highlight inquiry and comes at a critical point in our two part unit. In
part 1 of our unit the key concepts Form, Function and Structure and how they relate to DNA
were introduced. Understanding of these concepts focused on factual content, related concepts,
processes and skills. The summative assessment in part 1 consisted of an exam covering the
major topics in genetics. Going forward we are transitioning to an idea centred approach to the
content with a focus on knowledge’s application and the transfer of conceptual understanding to
inform ethical decision making. This approach is best summed up in the following concept
statement which expands our key concepts to include Perspectives and Relationships; “There are
a variety of perspectives regarding the relationship between scientific knowledge and
understanding and its application.” Students have just finished presenting on the various
applications of genetics i.e. forensics, GMO’s and genetic testing. Now through this inquiry
based virtual lab students will familiarize themselves with a powerful technology (PCR) central
to many of the applications of genetics they have just presented on. This inquiry highlights our
AOI/Global Context which is Human Ingenuity/Scientific & Technical Innovation. Due to
budget constraints I cannot provide a hands-on opportunity which allows students to sequence
genes. However through this virtual lab students will deepen their understanding of genetics by
applying it in a virtual environment which parallels an actual DNA lab. The purpose of the lab
has an inquiry focus and asks students to use modern gene sequencing techniques to identify an
unknown pathogen causing an illness in a sick individual using a cultured sample. The virtual lab
will help students answer two of our inquiry questions: “What are the positive and negative
aspects of various biotechnologies?” and “How has biotech changed our world and what is the
future of biotech?”. Upon successful completion of the lab students will feel empowered
(Knowledge and Understanding are Powerful!) because they will have applied their
understanding in a real life context. Finally, building on the personal connection to the
application of genetics students gain from this experience, we will begin to discuss the
implications which arise as a result of the use and application of genetics. This sets us up for the
final part of unit two which relates to ethical reasoning and decision making in regards to the
application of genetics.
The essential question(s) targeted
Unit Question- How should we use Life’s Blueprint (DNA)?
Inquiry Question- What are the positive and negative aspects of various biotechnologies?
Inquiry Question- How has biotech changed our world and what is the future of biotech?
Time for teaching the lesson and time for teacher preparation to teach the lesson
Teaching Time- 2-3 Days
Prep Time- 1 prep period
Materials needed to teach the lesson
Internet and a PC (laptop, desktop or tablet size mobile device)
Projector or Promethean Board
Supported Desktop Web Browsers: The following browsers are supported and recommended.
For the virtual lab to work properly be sure that JavaScript and cookies are enabled and your
pop-up blocker is disabled. Adobe Flash is required to view the animations in the desktop web
browsers listed below.
Microsoft Internet Explorer version 8 or greater (IE 9 is recommended).
Mozilla Firefox version 9 or greater.
Google Chrome version 9 or greater.
Apple Safari version 5 or greater.
Brief background content information for the teacher (i.e., explanations of the concepts to
be taught and/or new vocabulary introduced with definitions of this vocabulary)
Background:
Virtual Bacterial Identification Introduction
The purpose of the lab is to familiarize students with the science and techniques used to identify
different types of bacteria based on their DNA sequence. Not long ago, DNA sequencing was a
time-consuming, tedious process. Now using modern techniques it is routine. The techniques
used in this lab are applicable in a wide variety of settings, including scientific research and
forensic labs.
Basic Steps
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Prepare a sample from a patient and isolate whole bacterial DNA.
Make many copies of the desired piece of DNA.
Sequence the DNA.
Analyze the sequence and identify the bacteria.
The piece of DNA used for identifying bacteria is the region that codes for a small subunit of the
ribosomal RNA (16S rRNA). We will refer to this piece as 16S rDNA. Different bacterial
species have unique 16S rDNA sequences. The identification relies on matching the sequence
from the students sample against a database of all known 16S rDNA sequences.
Learning Objectives
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What kinds of patient samples are used for the purpose of identifying possible pathogens?
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What does PCR do, how does it work, and why is it useful?
How do you separate the desired DNA from all others?
How does an automatic DNA sequencer work?
Why is it possible to use a DNA sequence to identify bacteria?
Vocabulary:
16S rRNA, Ribosomes This is covered in more detail in the lab. Ribosomes are cellular
organelles that are the site of protein synthesis. They comprise various protein molecules
as well as associated RNA molecules (known as ribosomal RNA or rRNA). 16S rRNA is
one of the three RNA molecules associated with the ribosomes of procaryotes. 16S
signifies its size.
Anneal, Melt, Extend These are the three status indicators that appear during PCR. In
the context of PCR, annealing refers to the cooling phase following a melting phase.
During the melting phase, DNA's double strands separate. During the annealing phase,
single strands that are complementary come together to reform double strands (this
process is called hybridizing). During PCR, instead of the two original strands coming
together, a primer molecule, which is present in a much higher concentration than the
DNA, will bind to the single strand DNA. Then, during the extend phase, DNA
polymerase extends the 3' end of the primer molecule, making a copy of the DNA.
BLAST BLAST (Basic Local Alignment Search Tool) is a set of tools for comparing
sequence information in proteins or DNA by using all available public sequence
databases. It is designed to find matches in sequence information by looking for close
matches of a small portion of DNA or protein within a larger whole sequence. The tool is
available publically from the National Library of Medicine.
DNA Polymerases Enzymes that accurately copy a DNA template by polymerizing
nucleotides to form a DNA that is complementary to the template. Different DNA
polymerases are responsible for replication and repair of DNA. Polymerases extend the
chain by adding nucleotides to the 3' end of the growing DNA.
Oligonucleotide A short chain of a small number of nucleotides.
Pathogenic agent A disease-causing organism. It could be anything from a virus,
bacteria, to a multicellular organism such as a parasitic worm.
Phylogenetic Relating to the evolutionary relationships of organisms. A phylogenetic
tree, for example, refers to a graphic representation of the evolutionary history of
organisms described in a branching pattern. Such trees are made with a variety of
information, but for bacteria, a powerful technique is to use the similarity of DNA
sequences to deduce relatedness. An assumption is that close relatives share more DNA
similarity than distant ones. However, there are complications with this method, which is
described in detail in the last part of the lab.
Polymerase Chain Reaction (PCR) A method for creating a large number of copies of a
specific piece of DNA. It uses a version of DNA polymerase that can function at high
temperatures together with an automated temperature-controlled device known as a
thermocycler. See the PCR section of the lab for details.
Primers Oligonucleotides that have been designed and manufactured to bind to a specific
part of a known segment of DNA. DNA polymerase can then extend the oligonucleotide
and replicate the DNA. The process allows replication of the specific known segment of
DNA, particularly in conjunction with PCR.
Supernatant Floating on the surface, or relates to the clear fluid over a sediment or
precipitate. In this lab, used to describe the layer of fluid that is over the centrifuged
particulate matter.
Thermocycler A device with an incubation well whose temperature can be programmed
to change very rapidly, accurately, and in repetitive cycles. An incubation well is a metal
block into which special sample tubes fit perfectly.
Lab Tools:
Automatic DNA Sequencer
Automatic DNA sequencers are basically elaborate gel
electrophoresis machines mated to fluorescent marker detectors.
Earlier models used flat traditional gels with the sample replicated
into four different lanes. That way, each lane could be dedicated to
detecting one specific fluorescent marker (corresponding to one
nucleotide species). More modern machines can read all four different markers in the
same lane. The model we use in the lab is even more advanced, using a capillary tube
instead of a flat gel to run the electrophoresis; thus, the quantity of required sample is
smaller.
Digestion Buffer
Readily available in kits, this is a generalized buffered solution of proteolytic
enzymes designed to eat the bacterial cell wall and release the cellular content into
the solution. Other proteins are also digested.
Microconcentrator Column
This small piece of equipment essentially acts as a sophisticated microfilter.
Microconcentrator columns separate macromolecules based on size. The model
used in this lab retains large DNA molecules while smaller molecules such as
nucleotides, primers, and DNA polymerases pass through. The trapped DNA
molecules can be released by centrifuging the column upside down.
PCR Machine
Automatic PCR machines have become sophisticated, easy to use, and widely
available. It can be argued that this is one piece of equipment that has
revolutionized the study of genetics in recent years. Standard predescribed settings
can give perfectly good results (as we do in this lab), but the researchers can always
customize the cycling program (i.e., number, temperature, duration, etc.) in case of
difficulties.
PCR Master Mix
The "brew" that contains everything necessary to carry out the polymerase chain
reaction to amplify the 16S rRNA gene. Consists of water; a buffer to keep the mix at
the correct pH for the PCR reaction; large quantities of the four nucleotides adenine,
cytosine, guanine, and thymine; large quantities of oligonucleotide DNA primers that
bind the 16S rDNA region to initiate the replication process; and a heat-stable DNA
polymerase that extends the copy DNA strand.
Strip Tube
These are conveniently joined and color-coded microcentrifuge tubes. Each
tube is designed to contain a different primer, and the different colors
correspond to forward or reverse replication direction. (See part 4 for
details.)
Pipettes
Standard micropipette that has become the workhorse of modern biology labs.
Clearly explained activity directions including supporting materials such as any
worksheets, tables, or written materials that accompany the lesson. Be careful to clearly
explain what students and teacher will be doing
Directions- A detailed explanation and instructions are included for each step of the lab.
Students will follow the step by step procedure as they complete each part of the lab.
Support Materials- Student Handout on PCR and DNA Replication, Online Note Book
detailing each step; Online Reference which includes a glossary, list of tools (both of these are
listed above) and a encyclopedia of bacteria; Students Science Notebooks are needed to complete
the Cornell Notes, Procedure and Essays; Students must print the page once they have
successfully completed the Lab
Teacher Will
Describe and explain the overall
objectives/process of each step in the lab.
Student Will
Complete the lab with their partners and will
take Cornell notes on the overall
objectives/process of each step in the lab.
Explain the importance of detailed procedures
to science. Give an example of how to create a
detailed step by step procedure covering the
first step in the lab.
Circulate the room, answering questions and
give help and support as students complete the
lab.
Describe and Explain criteria E.
Describe and Explain criteria A and its
associated command terms. Give detailed
instructions and examples of how to use the
strands in the criteria as prompts and respond
to them in essay format.
Record the simple step by step procedure that
they follow during each step in the lab.
Complete the Lab.
Successfully Complete the lab by correctly
identifying the unknown pathogen. (criteria E)
Use the strands in the criteria A as prompts and
respond to them in essay form.
How students’ prior understandings are elicited/assessed and utilized
The students will perform this lab after learning about various applications of genetic science.
The technology used in this lab will be discussed in class. Also students will informally present
on the various applications of genetics of which PCR plays a central role in many of these
applications; i.e. PCR technology is used in DNA fingerprinting in forensic investigations.
Students will have just completed part 1 of the unit and the summative assessment on DNA and
genetics so their understanding of DNA’s structure and the central dogma, especially replication
will be utilized and expanded upon.
How new understandings and skills will be assessed with criteria specified
I will be assessing students’ understandings and skills in a variety of ways aside from successful
completion of the lab.
Skills- Students will complete the lab with their partners and will take Cornell notes on the
overall objectives/process of each step in the lab.
Students will also record the step by step procedure that they followed during each step in the
Lab.
Understandings- After successful completion of the lab students will be asked to demonstrate
the following understanding(s) regarding the application of genetic science utilizing the PCR
technique. Understanding will be assessed using the following strands in criteria A** and E.
Students will demonstrate their understandings using criteria A by responding to the command
terms in a short essay format.
Criteria E will be used to judge successful completion of the Lab.
Criteria A
The student explains how PCR is applied and how it may be used to address a specific problem
or issue in a local or global context.
The student describes the effectiveness of PCR and its application in solving the problem or
issue.
** The use of these particular strands will serve as a formative assessment which aims to prepare
students to write the One World essay which is the summative assessment for part two of our
unit.
Criteria E
Draw conclusions consistent with the data and supported by scientific reasoning.
Descriptions of specific teaching methods that will be used including how students will be
“hooked” into the lesson activities
The “Hook”- Students will have the opportunity to immerse themselves in a state of the art
DNA lab experience. They will be learning a process that is not only an effective tool in
diagnosing diseases caused by pathogens but also has applications in sequencing genes, forensic
science, cloning, identifying mutations ETC..,. This virtual lab is a technology based activity
which also uses the National Center for Biotechnology Information’s BLAST tool, which is a
gene library that matches unknown sequences of DNA against their catalogue.
Teaching Methods- Inquiry Based Learning, Application of Concepts, PBL/Problem Solving,
Cooperative Learning, ATL’s (Social/Collaboration; Thinking/Critical Thinking), Command
Terms (State, Describe & Explain), AOI/Global Context- Human Ingenuity/ Scientific &
Technical Innovation, Direct Teaching-Discussion, Guided & Independent Practice, Tech-Online
Activity, Performance Based
The aspect(s) of the learner profile that is/are developed and possibly assessed
Inquirers- As this is the main theme of the lesson inquiry is the primary focus. Students will
play the role of a scientist identifying an unknown pathogen. They will use a virtual lab
environment which utilizes all of the modern techniques to take a sample from an ill person and
sequence and match the DNA of the pathogen against a library of all known pathogenic DNA
sequences. This lab is fun, engaging and will give students the confidence that they could apply
their knowledge and understanding in a real life context. Successful inquiry will be assessed
through identification of the unknown pathogen.
Other Learner Profile ConnectionsKnowledgeable- They explore concepts that have local and global significance. In so doing, they
acquire in-depth knowledge and develop understanding.
Thinkers- They exercise initiative in applying thinking skills critically to approach complex
problems.
Communicators- They understand and express information confidently. They work effectively
and willingly in collaboration with others.
Connections to more than one subject area
Technology Teacher- This lesson is a virtual online lab activity which requires tech support.
Students will be completing the majority of this lesson in our computer lab. I will be working
closely with our technology teacher to assist students in navigating the lab.
APA references for the lesson including web resources for teacher and students
Howard Hughes Medical Institute, B. (2000-2013). Virtual bacterial id lab. Retrieved from
http://www.hhmi.org/biointeractive/bacterial-identification-virtual-lab