BIOL 1407 Lab Manual for Maxim & Speer
Student Laboratory Manual
Biology 1407 Austin Community College
Introduction
This manual is intended to be primarily an electronic document
available on-line. It should be viewed and printed as needed by
individual students. Its production has been supported by Austin
Community College and Texas Higher Education Coordinating Board.
Our approach in this manual is different from most traditional
manuals. We assume that students will work in small groups
(“teams”) rather than individually. We expect sharing and pooling of
data both within a group and among groups, not individual reports of
measurements. Tasks are not presented as techniques to be
demonstrated (like recipes to be followed) but rather as group
projects to be executed and communicated (like banquets to be
served and eaten).
Since Biology 1407 has an extremely challenging prerequisite
(Biology 1406), we want this course to reinforce, expand and practice
skills already present in students’ intellectual toolboxes. Students are
expected to “bring to the table” all these skills: basic use of light
microscope including quantitative measurements, micro-liter scale
volumetric measurements, preparation of chemical solutions and
quantitative dilution techniques, usage of electronic spreadsheets,
basic graphing and data analysis (including linear regression).
Various places in this manual refer students to their Biology 1406
laboratory manual for review. (That manual, like this one, is available
on-line.)
We also assume that (modest) modern computer-based tools
will be available in labs. These tools include: computers with word
processing and spreadsheet software, live internet connections at
high speed, microscopes with digital photo microscopy. Our students
should learn to think of these as fundamental tools in biological
research.
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Each exercise is presented in three parts. Part 1 is a very brief
introduction to the exercise. Part 2 is a series of things to complete
on line before class meeting, which includes taking a pre-lab quiz on
Blackboard. Part 3 presents a series of tasks to complete during the
lab period and cleanup instructions.
The instructions are generally not detailed because student
teams need to learn to direct their own work. Student teams should
learn to organize their work, execute it, and then communicate it.
Students are expected to develop intellectual independence of their
instructor and instructors are urged to wean students from “hand
holding” with regard to directions. Students should learn to “make it
happen”, not simply to follow step-by-step instructions. Of course,
procedures involved in "making it happen" must be subject to scrutiny
(preferably of colleagues) and reported accurately.
We have attempted to provide, when appropriate, local
relevance for these labs by choosing example organisms that occur
in Texas and that, in some cases, have economic importance in our
state.
One project will require multiple weeks to complete. In doing
this, students will be exposed to time frames for data acquisition that
are longer than a few hours and to illustrate biological phenomena
that unfold more slowly than typical lab exercises permit.
Another inclusion in this manual is phenomena of populations.
While traditional lab manuals for such courses focus on individuals,
we attempt here to direct students’ descriptions and examinations to
populations of individuals.
We hope that ACC students will use this biology class as a
vehicle for bringing multiple technological abilities (photography,
calculations, information acquisition, cell phone use, etc) to bear on
biological challenges. We want society’s convergence of technologies
to accelerate in our classroom and we expect our students to lead
society in this endeavor.
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Table of Contents
Lab 1
Safety Training and Equipment Orientation
4
Lab 2
The Art of Making Scientific Observations
Set up Tenebrio Experiments
6
Lab 3
Concepts of Relatedness
Preparation for Prokaryote Lab
10
Lab 4
Prokaryotes
15
Lab 5
Protists
19
Lab 6
Mosses, Ferns and Lycopods
21
Lab 7
Conifers and Flowering Plants
24
Lab 8
Flowering Plant Anatomy
28
Lab 9
Fungi
30
Lab 10
Sponges, Cnidarians and Platyhelminths
32
Lab 11
Mollusks and Annelids
36
Lab 12
Arthropods
40
Lab 13
Chordates
43
Lab 14
Chemical Signals
Conclude Experiments on Tenebrio
49
Lab 15
Electrical Signals and Nervous Systems
52
BIOL 1407 Appendices for Laboratory Projects
Appendix 1
Illustrating Biological Material
61
Appendix 2
Maintaining Laboratory Notebooks and Related Records
65
Appendix 3
Using “Prepared” Slides
66
Appendix 4
Reading a Vernier Scale
68
Appendix 5
Constructing Graphic Displays of Data
69
Appendix 6
Using ACC’s “Blackboard” Program
75
Appendix 7
Measuring an Area of Irregular Shape
76
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Lab 1: Safety Training and Equipment Orientation
I.
Brief Background
Modern biological research almost always requires teams of scientists to work
together while sharing both facilities and information. Without delay, you need to
form a lab “team”, learn our school’s standard practices (protocols) and establish
effective communications.
II.
1.
Pre-lab assignment
Review the following materials from Biol 1406 labs:
Use of light microscope
http://www.austincc.edu/biology/labmanuals/140612th/12th1406lab03.pdf
http://www.austincc.edu/biology/labmanuals/140612th/12th1406lab04.pdf
Keeping a lab notebook
http://www.austincc.edu/biology/labmanuals/140612th/12th1406labappA.pdf
2.
Review the following appendices to this lab manual:
Appendix 1
Appendix 2
Appendix 3
Appendix 4
Appendix 5
Appendix 6
Illustrating Biological Material
Maintaining Laboratory Notebooks and Related Records
Using “Prepared” Slides
Reading a Vernier Scale
Constructing Graphic Displays of Data
Using ACC’s “Blackboard” program
3.
After studying relevant material in your textbook and other information
sources, visit the “Blackboard” site for your class and complete this lab’s pre-lab
quiz according to your instructor’s directions.
III.
Student Tasks
1.
Participate in ACC safety training and sign official roster of persons
allowed to perform laboratory work in your lab room.
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2.
Get a "Student Skills Form" from your instructor. Fill it out. Mingle
with the other students until you have found a group of people that you think you
can work with and who have different skill groups. Assemble your lab “team”. In
general, it will be useful to have team members with differing sets of skills.
3.
Once your team is formed, come up with a team name. Tell your
instructor the names of all team members and the team name. Your instructor
will set up a group for you on Blackboard for file exchanges and intra-team
communication.
4.
All team members should demonstrate to their entire team that they
have competence in the techniques listed below. Most students will be more
comfortable with some techniques than others, but mutual instruction and
coaching is expected until all have competence in every technique.
Today’s exercise should be a review of most these materials, but some parts
are likely to be unfamiliar. Lab teams need to work together to establish
confidence in all team members’ competences. During today's lab, all students
are expected to use all the following equipment, techniques and software.
1.
General use of compound microscope. Get a prepared slide and
show your ability to properly focus, adjust lighting, use mechanical stage, change
magnification, and determine total magnification.
2.
General use of dissecting microscope. Get a prepared slide of a
fluke and a shell from your instructor. Demonstrate your ability to properly focus,
set lighting appropriate to the specimen, and determine total magnification.
3.
General use of digital camera to make photographs. Have all team
members take photographs of prepared slides using both compound and
dissecting microscopes. Take photographs of the shell and other large objects.
4.
Get an object from your instructor. Demonstrate that all team
members can use the Vernier scale to accurately measure the dimensions of the
object.
5.
Upload photographs to group file exchange in Blackboard
6.
General use of desktop computer with internet connection
7.
General use and access to Blackboard classroom software
8.
Cleanup your lab space.
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Lab 2: The Art of Making Scientific Observations
I.
Brief Background
Making observations is an essential part of a scientist's work. Some
branches of science rely heavily, if not exclusively, on observation. Just think
about astronomy, for example. For experiments and experimental work,
observations play a role in the background work that leads to research questions,
developing hypotheses, and designing experiments. Data collection relies on
good observations. The goal in this lab is to learn to how to make good
observations, to consider population characteristics instead of individual, and to
use simple descriptive statistics to summarize your observational data.
II.
Pre-lab assignment
1.
Review scientific inquiry in the textbook, Chapter 1, pages 18-24.
2.
Review the following materials from BIOL 1406 labs:
Collection and Analysis of Data
http://www.austincc.edu/biology/labmanuals/140612th/12th1406lab01.pdf
Use of Excel
http://www.austincc.edu/~emeyerth/exceltutor1.htm
http://www.austincc.edu/~emeyerth/exceltutor2a.htm
http://www.austincc.edu/~emeyerth/excel3.htm
Mean and Standard Deviation
http://www.austincc.edu/biology/labmanuals/140612th/12th1406labappB.pdf
Graphing Data
http://www.austincc.edu/biology/labmanuals/140612th/12th1406labappE.pdf
3.
Review the following appendices to this lab manual:
Appendix 1 Illustrating Biological Material
Appendix 2 Maintaining Laboratory Notebooks and Related Records
Appendix 4 Reading a Vernier Scale
Appendix 5 Constructing Graphic Displays of Data
Appendix 6 Using ACC’s “Blackboard” program
4.
After studying relevant material in your textbook and other information
sources, visit the “Blackboard” site for your class and complete this lab’s pre-lab
quiz according to your instructor’s directions.
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III.
Student Tasks
Task 1: Tenebrio Experiment
Your group needs to set up a Tenebrio experiment that you will be
following for several months. After today, you will need to collect data during
each lab for the rest of the semester.
You will need the following materials:
Habitat container
Oat or wheat bran
Cut up potatoes
8-10 Tenebrio larvae
Calipers
Balance
Weigh boats
Sketching materials
Digital camera and accessories
Your group needs to complete the following tasks.
1. Set up the habitats.
2. Collect your larvae from the master culture.
3. For each larva, collect the following data:
 length, using calipers gently
 weight, using the electronic balance and weigh boats
 written observations
4. Document with photographs.
5. Record the data in an Excel spreadsheet. Set up your spreadsheet so
you can continue to add data each week. Keep in mind that you will not be able
to keep track of each individual from week to week. Larva #1 from this week will
not be the same individual as Larva #1 next week.
You will need a separate data table for each week. You can either keep adding
sheets to your spreadsheet, using a different sheet for each week. Or, you can
construct a separate data table for each week within the same sheet.
By the end of the experiment, you will have descriptive statistics for each week.
At the end, you can put the descriptive statistics for each week into one data
table and graph changes in the variables over time.
6. You might want to start searching for information about Tenebrio on the
web or library. Some suggestions: life cycle, natural habitats, Youtube videos.
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Task 2: Making Observations
Your group will be looking at two different types of shells. You will need the
following materials:
A package of each type of shell
Calipers
Balance
Weigh boats
Sketching materials
Laptop computer
Digital camera and accessories
Your group needs to complete the following tasks:
1. For each shell type, make a sketch of a representative specimen and
make written observations. A sketch should have the name of the artist and the
date. Sketches should also include scale. Handwritten observations should also
include information on name and date.
2. Take a representative specimen of each shell and examine them with
the dissecting microscope. Make sketches and take photographs of each
through the microscope. (Note: be sure and record TM for all photographs and
sketches made with microscope.)
3. For each shell type, line up the shells and take a picture of the group.
4. Make written observations of the shells. Summarize the variation within
each type of shell. Compare the two species (shell types) by looking at
similarities and differences.
5. Set up an Excel spreadsheet for each shell type to record this data:
 shell length
 shell width
 shell weight
6. For each type of shell, take a photo of one shell and show with labels
how you measured length and width.
Note: you can use your own Photoshop software, the drawing tools in any
Microsoft Office product (such as Word or Powerpoint), Paint or any other
software that you have access to. However, check to make sure that your file will
open up in Microsoft Office 2003 when it is posted to Blackboard.
7. Collect all data for each shell in your two packages and record in data
tables.
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8. For each shell type, calculate descriptive statistics for each
measurement:
 average (mean)
 standard deviation
 range
9. For each shell type, make these graphs in Excel:
 scatter plot of length vs. width (Note: length is x axis)
 histogram of shell length (Note: continuous variables; bars touch)
 histogram of shell width
 histogram of shell weight
10. Upload your preliminary materials (observations, sketches,
photographs, data tables, spreadsheets, graphs) into Blackboard file exchange
for your group before lab is over. For sketches and handwritten observations,
you can either scan the material or take a photograph. Every member of your
group will then have access to the information to use in preparing their individual
electronic lab notebook entries.
Clean up procedures for this lab: Put the shells back into their respective
bags. Put all materials and equipment back where you found it.
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Lab 3: Concepts of Relatedness
Preparation for Lab 4
I.
Brief Background
To say that organisms or groups of organisms are “related” has meant
different things in the history of biology and still can mean different things in
different contexts today. In this exercise, students are to explore what “being
related” means in two different contexts: anatomical similarity and protein amino
acid sequence similarity. (What obvious potential point of comparison are we
ignoring here?)
II.
Pre-lab assignment
1. Students need to be aware of “FASTA” format for amino acid and
nucleotide sequences. Visit an online encyclopedia for a brief introduction.
2. Students need to be aware of the ExPASy (Expert Protein Analysis
System) proteomics server of the Swiss Institute of Bioinformatics (SIB). Visit
http://ca.expasy.org/ and note its search engine near the top of its homepage.
One can enter both protein names and generic epithets to search for a protein’s
report within a genus. Complete protein names and binomials sometimes score
a hit, too.
3. Students need to be aware of software that compares sequences of amino
acids and/or nucleotides. Visit http://align.genome.jp/ and notice the box that
accepts FASTA sequences for comparison. (Multiple sequences should be
entered at once, but all must be entirely in FASTA.) To actually execute the
comparison, scroll to bottom of the page and “Execute Multiple Alignment”.
4. After studying relevant material in your textbook and other information
sources, visit the “Blackboard” site for your class and complete this lab’s pre-lab
quiz according to your instructor’s general directions.
III.
Student Tasks
Task 1: Preparation for Lab 4 – Prokaryotes
We are going to study prokaryotes next week. Since agar plates need
time to incubate, we are going to start them this week and look at them next
week. There are two parts to this exercise:
 aerial samples to see the numbers and types of prokaryotes and other
microorganisms in the air
 habitat samples to see the numbers and types of microorganisms found
on surfaces and in the environment of the campus
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Your group needs the following materials:
4 petri dishes containing nutrient agar
Sharpie
Transparent tape
Sterile cotton swabs and/or plastic pipettes. Cotton swabs work best for
solid surfaces while pipettes work best for liquid samples.
Sterile water (for wetting cotton swabs before swabbing dry surfaces)
1. Prepare your aerial sample. Label the bottom of one petri dish with a
Sharpie. Write close to the edge and include the following information:
 Group name
 Date
 “Aerial sample”
Put the petri dish on a counter on the side of the room. Take the top of
the petri dish off. Leave it exposed to the air for one hour. Then, put the lid back
on the petri dish and tape it shut. Incubate the petri dish bottom side up (agar
side up) at room temperature for seven days.
2. Prepare your habitat samples. Choose three habitats within the room
or campus environment that you would like to sample. These habitats can be
parts of people’s bodies or cell phones or whatever. Use your imagination! Keep
track of the habitats you’ve chosen.
Label the bottom of each petri dish with a Sharpie. Write close to the
edge and include the following information:
 Group name
 Date
 "Habitat sample”
 Type of habitat (you should have one petri dish for each habitat).
Sample each habitat once, using separate swabs or pipettes for each
sample you take. When finished, tape the dishes shut and incubate bottom side
up (agar side up) at room temperature for seven days.
To sample with a swab:
Dampen the swab with sterile water. Lightly roll the swab over the surface
to be sampled. Open the petri dish slightly and lightly roll the swab over the
surface of the nutrient agar. Don’t jab the swab into the agar. Quickly put the lid
back on the petri dish.
To sample with a pipette
Collect a few drops of liquid with the sterile pipette. You don’t need a
whole pipette full, just a few drops. Remove the lid of a petri dish, quickly add
the drops of fluid to the petri dish, and put the lid back on. Swirl the dish to form a
thin film of the liquid on the surface of the agar. Keep the dishes top side up for
at least 30 minutes before turning them upside down to incubate them.
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Task 2: Vertebrate Forelimb Skeletal Anatomy
Use the vertebrate skeletons in lab to compare forelimb skeletal anatomy in:
● Frog (Rana)
● Rat (Rattus)
● Cat (Felis)
● Human (Homo)
● Pigeon (Columba)
● Bat
You need to identify these bones in each skeleton:
● Humerus
● Radius
● Ulna
● Carpals
● Metacarpals
● Phalanges
You will need your photo atlas to help you with this. Please note that
some bones may be fused or reduced in size. When fusion occurs, the name of
the fused bone usually reflects its parts, such as radioulna. In those cases, you
need to know the modified names.
Photograph and/or sketch forelimb skeletons for each animal. Make written
observations about similarities and differences among the forelimbs. Upload
your preliminary information into Blackboard file exchange for your group.
Task 3: Molecular-Based Phylogenetic Trees
We are going to use amino acid sequences to draw phylogenetic trees that
show possible evolutionary relationships among selected taxa. Keep in mind that
your phylogenetic tree will be based only on one protein sequence. We have
chosen to use "cytochrome c oxidase subunit 1". It has been sequenced for
many organisms and it is a good marker for phylum-level evolutionary
relationships because it is a conservative protein.
Use the ExPASy search engine to find protein amino acid sequences.
Search the top-listed data base; use the phrase “cytochrome c oxidase subunit 1”
followed by the generic epithet. Then, choose carefully from among the hits to
make sure you have a complete sequence. Use the checklist on the next page
to help you make sure you have collected the correct data.
After finding a complete sequence, get it in FASTA (scroll to bottom of page).
Save each sequence in a word processing document. Add each sequence to the
document as you acquire them. Do not add any extra information to the
document.
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Once you are finished with the document, enter all the sequences at once into
alignment software at http://align.genome.jp/ . Cut and paste to do this. After
alignment results are reported, scroll to the bottom of the results page. Have a
“Dendrogram with branch length” drawn for you. You will need to print your
dendrogram as well as your FASTA document in order to label your dendrogram
with confidence.
With your electronic lab notebook posting, you will need to include a
labeled dendrogram that shows the name of each branch. The original
dendogram will only show an abbreviation for the taxa. Write in the complete
genus or species name. Then, scan or photograph your dendrogram so it can be
uploaded.
Compare your dendrogram to the information in the textbook. Are there any
unexpected differences? If so, what are some plausible reasons for the
differences?
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Checklist of Organisms
Genus (common name)
Verify entry matches name
Verify protein name matches
Cytochrome c oxidase subunit 1
(Watch for and exclude subunit 2,
subunit II, fragment, etc.)
Verify this
is not a
report of a
fragment
# of amino acids
in protein
(unprocessed)
Anabaena
Anas (duck)
Arabidopsis
Artemia
Bos taurus (cow)
Brassica
Bufo (toad)
Canis familiaris (dog)
Canis latrans (coyote)
Crocodylus (crocodile)
Drosophila (fruit fly)
Euglena
Felis (cat)
Gallus (chicken)
Glycine (soybean)
Homo (human)
Leptotyphlops (Texas blind snake)
Macropus (Wallaroo)
Myotis (bat)
Nostoc
Ornithorhynchus (duckbilled platypus)
Oryza (rice)
Pantherophis (corn snake)
Paramecium
Penicillium
Phascolarctos (Koala)
Physarum
Pleurotus (oyster mushroom)
Rana (frog)
Rattus (rat)
Sceloporus (western fence lizard)
Solanum lycopersicon (tomato)
Triticum (wheat)
Xenopus (African frog)
Zea (corn)
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Lab 4: Prokaryotes
I.
Brief Background
The first living things were prokaryotes. Prokaryotes shaped our planet’s
chemistry. Prokaryotes served as the actual building blocks for eukaryotes.
Prokaryotes may be tough enough to survive blasts into space. Prokaryotes
exhibit dazzling variety in their nutritional patterns. A few prokaryotes generate
much human misery, but without prokaryotes humans would not exist to
experience misery (or other conditions).
Briefly consider some connections between these organisms and Texas.
http://www.utexas.edu/news/2008/04/23/biofuel_microbe/
http://repositories.tdl.org/tdl/handle/1969.1/2235
http://www.utmbhealthcare.org/Health/Content.asp?PageID=P02201
http://www.cdc.gov/mmwr/preview/mmwrhtml/mm56d730a1.htm
http://texashelp.tamu.edu/004-natural/disease-and-epidemic.php
Biologists are generally expected to recognize certain types of microbial life
under a microscope and students should acquire sight recognition ability of all
major groups covered in this lab manual.
II.
Pre-lab assignment
After studying relevant material in your textbook and other information
sources, visit the “Blackboard” site for your class and complete this lab’s pre-lab
quiz according to your instructor’s general directions.
III.
Student Tasks
Safety Notes:
1. Use gloves when handling petri dishes after they have been inoculated with
microorganisms.
2. Do not open petri dishes after they have been inoculated.
3. Dispose of petri dishes and any gloves that are accidentally exposed to
microorganisms in the biohazard bag when you are finished recording data.
4. Disinfect tables after disposing of petri dishes.
Task 1: Aerial and Habitat Samples
Last week, you started agar plates. Today, your group is going to look at
the plates. The plates have been incubated for seven days at room temperature.
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1. On the aerial and habitat samples, observe the microorganism colonies
that have grown on the agar. DO NOT OPEN THE DISHES. Since we do not
know what these microorganisms are, you should not expose everyone in the
room to them! Use gloves when handling the dishes.
2. Sketch or photograph your samples. Describe the colonies, using
general terms such as color of the colony, relative size (tiny, small, huge, etc.),
texture (rough, smooth, shiny, wrinkled).
3. Dispose of petri dishes and contaminated gloves in the biohazard bag.
Principles of Bacterial Colony Morphology
When a single bacterial cell is deposited on the surface of a nutritive medium, it begins to
divide exponentially. After thousands (up to billions) of cells are formed, a visible mass
appears. This mass of cells is called a colony. Each species of bacterial or fungal organism
will exhibit characteristic colonies.
This info is taken from the Microbugz web site at: http://www.austincc.edu/microbugz/
Task 2: Living Prokaryotes in Yogurt
An easy way to see living bacteria is to look in yogurt containing live
bacterial cultures. This is also a good opportunity to see different bacterial
shapes and arrangements. The three most common bacterial cell shapes are
coccus (round little balls; pl. cocci), bacillus (rod-shaped cells; pl. bacilli) and
spirillum (cells twisted into S-shapes; pl. spirilla). Some common arrangements
are chains (strepto-) and irregular clusters (staphylo-). The names for these
shapes are often part of the scientific names of bacteria, such as Staphylococcus
aureus and Bacillus anthracis.
Caution: When looking at the yogurt culture, if you see spirilla, you are not
paying attention or you need to check your focus or lighting.
Your group will need the following materials:
Clean microscope slide and cover slip
Toothpick
Yogurt culture
Dropper bottle of water
Compound microscope
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Take a very small (tiny) yogurt sample by dipping the tip of the toothpick
into the yogurt. Transfer the yogurt to your microscope slide. Add a drop of water.
Mix the yogurt and water with the toothpick. Put a cover slip over the yogurt
smear. Observe the bacteria by looking at the thinnest portion of the smear with
the microscope. (You’ll have to go to high power to see the bacteria.) If you
have trouble seeing the bacteria, adjust the light with the iris diaphragm.
Document the bacteria you see with either sketches or photographs.
Identify the shape for each type that you see. Make written observations.
Task 3: Cyanobacteria
Cyanobacteria are an important group of common bacteria. They carry
out oxygenic photosynthesis in basically the same way plants do. Most can fix
nitrogen (convert atmospheric nitrogen to ammonia), which means they can
make their own fertilizer if they have to. Consequently, cyanobacteria have some
of the simplest environmental needs of any organism. Give them light and air
(which contains carbon dioxide and atmospheric nitrogen) and they can live
pretty well without almost anything else. Cyanobacteria were the first organisms
to evolve oxygenic photosynthesis, so they can take credit for changing the
atmosphere from one relatively free of oxygen to one with enough oxygen for you
and the rest of us aerobic organisms to survive.
You’ll be looking at a couple of cyanobacteria genera: Oscillatoria and Nostoc.
Oscillatoria is a freshwater cyanobacterium, a typical pond-scum inhabitant. Its
basic form is a filament (a thread) of individual cells attached to one another.
When you observe it, keep an eye out in case it moves.
Nostoc is a terrestrial cyanobacterium. To stay active and continue carrying out
photosynthesis, Nostoc secretes huge quantities of a gelatinous carbohydrate
around its filaments. The carbohydrates absorb water and keep the cells moist.
This makes Nostoc the jolly green jelly ball organism! Unlike Oscillatoria, Nostoc
filaments often contain more than one type of cell. Most are normal, contain the
blue-green photosynthetic pigments, and carry out photosynthesis. Others are
larger, paler and have very thick cell walls. These cells are called heterocysts
and they carry out nitrogen fixation. So Nostoc is capable of some cellular
division of labor, which means that Nostoc can be considered a very simple
multicellular organism.
Your group will need the following materials:
Oscillatoria and Nostoc cultures
Clean microscope slides and cover slips
Pipette
Balance and weigh boats
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Remove a few strands of Oscillatoria from the culture. Make a wet mount.
Observe the Oscillatoria under low and high power. Document with sketches or
photos. Make written observations.
Observe the dried Nostoc culture. Document with sketches or photos and
make written observations.
Weigh a piece of dried Nostoc in a weigh boat. Keep it in the weigh boat
and add water to hydrate it. After 20 minutes, pour off any water that has not
soaked in and reweigh the Nostoc. Make sure you record your data and
document any changes in appearance.
At this point, we are not going to keep telling you to document with
photographs or sketches and take written observations. You will be continuing to
do this throughout the rest of the semester, so get in the habit of doing so now.
Use forceps or probes to pull off a small piece of the rehydrated Nostoc.
Make a wet mount and examine under low and high power. You will probably
have to flatten the slide. If so, put a paper towel over the cover slip and pressing
firmly with your thumb. Don’t press so hard you break the slide or cover slip!
You may have to add a little more water afterward; do so at the edge of the cover
slip while it is still on the slide.
Clean up procedures for this lab:
Dispose of all slides and glass coverslips in the glass sharps container. If
coverslips are plastic, they may be thrown away in the regular trash.
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Lab 5: Protists
I.
Brief Background
“Protista” is falling from use as a kingdom name; nonetheless, it is a useful
term for a very large group of organisms. This polyphyletic assemblage can be
divided (for beginners) into autotrophs and heterotrophs. This lab introduces
students to some famous autotrophic and heterotrophic “Protists”.
Briefly examine these links to some of Texas’ autotrophic “Protists”.
http://www.tpwd.state.tx.us/landwater/water/environconcerns/hab/redtide/
http://www.tpwd.state.tx.us/landwater/water/environconcerns/hab/otherhab/
http://www.physorg.com/news100350969.html (note wavelengths)
http://www.baysfoundation.org/archives_07_10_Sargassum.php
http://www.dshs.state.tx.us/idcu/disease/amebiasis/faqs/
http://www.dshs.state.tx.us/idcu/disease/malaria/faqs/
http://www.cdc.gov/mmwr/preview/mmwrhtml/00036836.htm
http://www.dnr.state.mn.us/volunteer/janfeb03/slimemolds.html
http://handsontheland.org/monitoring/projects/slimemolds/slimemolds.cfm
II.
Pre-lab assignment
After studying relevant material in your textbook and other information
sources, visit the “Blackboard” site for your class and complete this lab’s pre-lab
quiz according to your instructor’s general directions..
III.
Student Tasks
Task 1: Autotrophic Protists
Document these autotrophic protists and label indicated structures.
Phylum Bacillariophyta
Mixed diatoms (freshwater or marine)
Phylum Dinoflagellata
Ceratium
Phylum Euglenida
Euglena
eyespot
chloroplasts
flagellum
Trypanosoma
flagellum
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Phylum Chlorophyta
Volvox
vegetative cells
daughter colonies
Phylum Phaeophyta
Sargassum or Fucus or Laminaria
blade
stipe
holdfast (if present)
air bladders (if present)
Task 2: Heterotrophic Protists
Document these heterotrophic protists and label indicated structures.
Phylum Ciliophora
Paramecium
cilia
oral groove
contractile vacuole
food vacuole
Stentor
macronucleus
cilia
Phylum Apicomplexa
Plasmodium
red blood cells: infected and uninfected
merozoites
Phylum Rhizopoda
Amoeba
pseudopodia
nucleus (if visible)
Phylum Myxomycota
Physarum
plasmodium
look for cytoplasmic streaming
Clean up procedures for this lab:
Dispose of all slides and glass coverslips in the glass sharps container. If
coverslips are plastic, they may be thrown away in the regular trash.
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Lab 6: Mosses, Ferns and Lycopods
I.
Brief Background
Polytrichum (or Mnium) is used here as a representative of the phylum
Bryophyta. Students should know general characteristics of this phylum and
additional examples of organisms in it.
Common garden ferns or specific genera (such as Cyrtomium, Polypodium,
Thelypteris or Ceratopteris) are used here as representatives of the phylum
Pteridophyta. Students should know general characteristics of this phylum and
additional examples of organisms in it.
Selaginella is used here as a representative of the phylum Lycophyta.
Students should know general characteristics of this phylum and additional
examples of organisms in it.
Students should understand plants’ “alternation of generations” and
understand how it varies among these phyla. Which tissues are haploid? Which
are diploid? What roles are played by mitosis, meiosis, syngamy (union of
gametes)?
Students are cautioned that true plant stems sometimes occur
underground (rhizomes) and true plant roots sometimes occur above ground.
“Rhizomes” sometimes are confused with “rhizoids”; rhizoids are single cells;
rhizomes are stems and therefore quite complex in structure.
Furthermore, leaves can be compound and portions of a compound leaf
can be mistaken for stem. A beginning student should look for a good definition
of “leaf”, “stem”, and “root”.
Use this search engine to locate natural occurrences of these organisms in
Texas (positive search results usually include a link to distribution maps):
http://plants.usda.gov/checklist.html
II.
Pre-lab assignment
After studying relevant material in your textbook and other information
sources, visit the “Blackboard” site for your class and complete this lab’s pre-lab
quiz according to your instructor’s general directions..
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III.
Student Tasks
Task 1: Mosses
Examine the different mosses that are available in lab. Locate and label
indicated structures and generations. Document your observations.
Gametophyte generation
Spore
Protonema
Phyllids (leaf-like structure)
Caulid (stem-like structure)
Rhizoids
Gametangium (gametangia)
Antheridium (antheridia)
Archegonium (archegonia)
Calyptra (old archegonium)
Sporophyte generation
Embryo
Stalk (seta)
Capsule (sporangium)
Peristome
Task 2: Ferns
Examine the different ferns that are available in lab. Locate and label
indicated structures and generations. Document your observations.
Sporophyte generation
Embryo
Vascular tissue
Stem
Roots
Leaves (simple or compound? Vascular tissue present?)
Fiddlehead
Sporophylls and vegetative leaves
Sorus (sori)
Sporangium (sporangia) with stalk and annulus
Gametophyte generation
Spores
Young prothallus (prothallia)
Mature prothallus
Gametangium (gametangia)
Antheridium (antheridia)
Archegonium (archegonia)
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Task 3: Lycopods
Examine the different lycopods that are available in lab. Locate and label
indicated structures and generations. Document your observations.
Sporophyte generation
Vascular tissue
Stem
Roots
Leaves (simple or compound? Vascular tissue present?)
Strobilus (strobili) (= cones)
Sporophylls
Microsporophylls
Megasporophylls
Vegetative leaves
Sporangia
Microsporangia
Megasporangia
Gametophyte generation
Spores
Microspores
Megaspores
Male gametophyte (= microgametophyte) may not be
available
Female gametophyte (= megagametophyte) may not be
available
Clean up procedures for this lab:
Put everything back in its proper place. If you made wet mounts, dispose
of the slides and glass coverslips in the broken glass container. Plastic coverslips
may be discarded in the trash.
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Lab 7: Conifers and Flowering Plants
I.
Brief Background
Pinus is used here as a representative of the phylum Pinophyta
(Coniferophyta). Students should know general characteristics of this phylum and
additional examples of organisms in it.
Lillium (or Brassica or Glycine) is used here as a representative of the
phylum Magnoliophyta (Anthophyta). Students should know general
characteristics of this phylum and additional examples of organisms in it.
Students should understand plants’ “alternation of generations” and
understand how it varies among these phyla. Which tissues are haploid? Which
are diploid? What roles are played by mitosis, meiosis, syngamy (union of
gametes)?
Use this search engine to locate natural occurrences of this organism in
Texas (positive search results usually include a link to distribution maps):
http://plants.usda.gov/checklist.html
http://www.fs.fed.us/pnw/pubs/pnw_rp389.pdf
II.
Pre-lab assignment
After studying relevant material in your textbook and other information
sources, visit the “Blackboard” site for your class and complete this lab’s pre-lab
quiz according to your instructor’s general directions.
III.
Student Tasks
Task 1: Conifers
Examine the different conifers that are available in lab. Locate and label
indicated structures and generations. Document your observations.
Sporophyte generation
Stem
Roots
Leaves
Strobili (= cones)
Microspore-producing cone (= pollen cone)
Megaspore-producing cone (= ovulate cone = seed cone)
Sporophylls
Microsporophylls
Megasporophylls
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Sporangia
Microsporangia
Megasporangia (= ovules ≠ eggs)
Integuments
Micropyle
Gametophyte generation
Spores
Microspores
Megaspores)
Male gametophyte (= pollen = microgametophyte)
Female gametophyte (= megagametophyte) inside ovule
Archegonium
Seed structures
Note genetic status of each:
Old sporophyte, female gametophyte, new sporophyte
Megagametophyte
Embryo
Cotyledons (how many?)
Hypocotyl
Radicle
Seed coat
Task 2: Flowering Plants
Examine the different flowering plants that are available in lab. Locate
and label indicated structures and generations. Document your observations.
Sporophyte generation
Stem
Roots
Leaves
Strobili (flowers) – see section below
Sporophylls
Microsporophylls (= stamens)
Megasporophylls (= carpels)
Sporangia
Microsporangia (= anthers)
Megasporangia (= ovules)
Integuments
Micropyle
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Gametophyte generation
Spores
Microspores
Megaspores)
Male gametophyte (= microgametophyte = pollen)
Female gametophyte (= megagametophyte) inside ovule
7 cells
8 nuclei including egg and endosperm mother cell
Flower parts (all sporophytic)
Sepals
Petals
Microsporophylls = stamens (collectively, the androecium)
Anther (= microsporangium)
Filament
Megasporophylls = carpels
Stigma
Style
Ovary
Ovules (= megasporangia ≠ eggs) with integuments
and micropyle
Dissect a flower and identify each part.
Fruit
Ovary wall
Seeds
Dissect all fruits available and identify each part.
Bean Seed, soaked
Note genetic composition of all tissues
Embryo
Hypocotyl
Radicle
Seed coat
Put on gloves and safety eyewear. Dissect a bean seed into two
parts. Soak bean seed half with iodine. Look for the cotyledons
(how many?). Where's the endosperm?
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Corn Seed, soaked
Note genetic composition of all tissues
Embryo
Hypocotyl
Radicle
Seed coat
Put on gloves and safety eyewear. Dissect a corn seed into two
parts. Soak corn seed half with iodine. Look for the cotyledons
(how many?). Where's the endosperm?
General dissecting equipment includes: sharp probe, dull probe, sharp blade,
forceps, scissors, water with dropper, paper towels, blank microscope slides,
cover slips, dishes to hold organisms and materials under dissecting microscope,
ruler, pins.
Biologists sometimes use stains on material being examined. Sometimes
stains are highly specific for substrate and other stains are broad in the kinds of
substances to which they attach. Stains often are hazardous and biologists
should wear gloves when handling them. Slides and materials containing
hazardous stains need to be treated as hazardous waste; the volume of this
material is generally quite small.
Clean up procedures for this lab:
Dispose of dissected seeds, fruits, flower parts, and gloves in the general
trash. Put excess iodine used to stain seeds in chemical waste disposal. Return
all equipment and specimens to their proper places.
All dissecting equipment, including pins, must be washed and dried
before stowing. Clean off your desks with Lysol or appropriate cleaning
solution.
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Lab 8: Flowering Plant Structures
I.
Brief Background
Several flowering plants, such as Ranunculus, are used here as
representatives of the phylum Magnoliophyta (Anthophyta). The structures
examined in this lab are from a major clade of flowering plants, the eudicots.
II.
Pre-lab assignment
After studying relevant material in your textbook and other information
sources, visit the “Blackboard” site for your class and complete this lab’s pre-lab
quiz according to your instructor’s general directions..
III.
Student Tasks
Task 1: Roots
Examine the specimens and slides. Identify the structures.
Radish roots
Root hairs
Tap root
Root apical meristem
Root cap
Apical meristem
Zone of cell division
Zone of elongation
Zone of maturation (if visible)
Eudicot root cross section
Epidermis
Root hairs
Cortex
Endodermis
Pericycle
Vascular bundle
Xylem
Phloem)
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Task 2: Shoots
Examine the specimens and slides. Identify the structures.
Basil Plants (or other plant)
Shoot system
Stem
Internode
Node
Terminal buds
Axillary buds
Leaves
Petiole
Blade
Shoot apical meristem
Leaf primordia
Axillary buds
Apical meristem
Eudicot stem cross section:
Epidermis
Cortex
Pith
Vascular bundle
Xylem
Phloem
Eudicot leaf cross section
Cuticle
Upper epidermis
Palisade parenchyma
Spongy parenchyma
Mesophyll
Air spaces
Vascular bundle
Xylem
Phloem
Lower epidermis
Stomata
Guard cells
Clean up procedures for this lab:
Put everything back in its proper place. If you made wet mounts, dispose
of the slides and glass coverslips in the broken glass container. Plastic coverslips
may be discarded in the trash.
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Lab 9: Fungi
I.
Brief Background
Fungi are an ancient monophyletic group of enormous ecological and
social importance. All good biologists are keenly aware of them. Fungi have
vastly different life styles from animals and plants.
Some Texas connections:
http://www.texasmushroomfestival.com/
http://cahe.nmsu.edu/news/1997/052997_sorghum_ergot.html
You can also search Wikipedia for ergotism.
II.
Pre-lab assignment
After studying relevant material in your textbook and other information
sources, visit the “Blackboard” site for your class and complete this lab’s pre-lab
quiz according to your instructor’s general directions..
III.
Student Tasks
Task 1: Fungi
Examine the specimens and slides. Identify the structures.
Phylum Zygomycota: Rhizopus
Hypha (hyphae)
Sporangiophore
Sporangium (sporangia)
Asexual spores
Gametangia
Zygosporangium (= zygospore)
Suspensor cells
Phylum Ascomycota: Peziza
Hypha (hyphae)
Ascus
Ascocarp
Ascospores
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Phylum Basidiomycota: Coprinus and Agaricus
Hypha (hyphae)
Basidiocarp (= tertiary mycelium)
Pileus
Stipe
Gills
Basidium (basidia)
Basidiospores
Secondary mycelium
Task 2: Lichens
Examine the specimens and slides. Identify the structures.
Lichens
Growth forms: crustose, foliose, fruticose
Ascocarps
Lichen Thallus slide
Fungal hyphae
Algal cells
Task 3: Endomycorrhizae (Phylum Glomerulomycota)
Examine the slides. Identify the structures.
Endotrophic mycorrhizae slide
Hyphae
Plant root cells with fungus
Plant root cells without fungus
Clean up procedures for this lab:
Put everything back in its proper place. If you made wet mounts, dispose
of the slides and glass coverslips in the broken glass container. Plastic coverslips
may be discarded in the trash. If you dissect anything in this lab, clean up the
tools and dissecting tray. Dissected parts can be thrown away in the regular
trash.
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Lab 10: Sponges, Cnidarians and Platyhelminths
I.
Brief Background
Scypha (also known as Grantia) is used here as a representative of the
sponges. There are also a variety of sponge specimens available to show the
gross anatomy of sponges. Students should know general characteristics of this
phylum and additional examples of organisms in it. There are a few freshwater
sponges but most are marine. Sponges are sessile animals. As adults they filter
feed, pulling water in through numerous small holes (pores or ostia) on their
surface and filtering out microscopic organisms before shooting the water out of
larger holes (oscula) on top of their bodies.
More information about sponges, especially weird carnivorous sponges,
can be found at:
http://www.ucmp.berkeley.edu/porifera/poriferalh.html
Hydra and Obelia are used here as representatives of the phylum
Cnidaria. Students should know general characteristics of this phylum and
additional examples of organisms in it. Hydra lives in fresh water while most
cnidarians are marine. Obelia is a marine cnidarian that is often used to
demonstrate the typical life cycle of cnidarians and the two basic body forms
found in this phylum. It alternates between sexual medusae and asexual polyps
during its life cycle.
Briefly visit these sites for some Texas cnidarians.
http://www.tmc.edu/health_briefs/05_01_98-sting.html
http://en.wikipedia.org/wiki/Craspedacusta_sowerbyi (Craspedacusta occurs in
Travis County.)
http://flowergarden.noaa.gov/image_library/images_maps_figures/gulf_map.jpg
http://www.gulfbase.org/reef/view.php?rid=fgb1
http://www.tpwd.state.tx.us/learning/webcasts/gulf/jellyfish.phtml
Dugesia is used here as a representative of phylum Platyhelminthes.
Students should know general characteristics of this phylum and additional
examples of organisms in it. Many free-living members of Platyhelminthes are
known by the common name “planarians”. Many other Platyhelminthes are
parasitic, tapeworms and flukes for example, and have significant impact on
humans and our agricultural animals. Most platyhelminths are aquatic, but a few
are terrestrial.
Briefly consider these “Texas connections” for platyhelminths:
http://creatures.ifas.ufl.edu/misc/land_planarians.htm (Bipalium is fairly common
in Austin) and http://www.dshs.state.tx.us/idcu/disease/taeniasis/faqs/.
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II.
Pre-lab assignment
After studying relevant material in your textbook and other information
sources, visit the “Blackboard” site for your class and complete this lab’s pre-lab
quiz according to your instructor’s general directions.
III.
Student Tasks
Task 1: Sponges
Examine the sponge specimens and slides of Scypha (Grantia). Identify
the structures.
Entire sponges:
Ostium (ostia)
Osculum
Slides:
ostium (ostia)
incurrent canal
radial canal
spongocoel
choanocytes
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Task 2: Cnidarians – Hydra
Examine living specimens and slides of Hydra. Identify the structures.
Type of symmetry
Gastrovascular cavity
Mouth
Hypostome
Tentacles
Cnidocytes
Basal disc (“pedal disc”)
Bud
Gonads
Epidermis
Gastrodermis
Mesoglea
Feeding Hydra: Place a healthy Hydra in a watch glass or depression
slide with some food (Daphnia). Choose a small live Daphnia or you may see a
defensive response, not a feeding response. Feeding response can be slow—
so patience is required.
Task 3: Cnidarians – Obelia, a colonial hydroid
Examine prepared slides of Obelia: hydroid colony and medusae. Locate
the structures.
Feeding polyps
Tentacles
Reproductive polyps
Medusa buds
Mature medusa
Tentacles
Mouth
Task 3: Platyhelminths
Examine living specimens of Dugesia in watch glasses and observe their
behavior. Examine slides (whole mounts, x-sec). Identify the structures.
Type of symmetry
Dorsal surface
Ventral surface
Anterior end
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Posterior end
Left side
Right side
Cephalization
Head
Auricles
Eyespots (eyecups)
Mouth
Pharynx
Epidermis
Gastrodermis
Mesenchyme
Gastrovascular cavity
Clean up procedures for lab:
Return the living specimens to their appropriate culture jars. Return
prepared slides to the correct boxes.
Watch glasses and depression slides are not disposable. They
should be cleaned, dried and saved for future use.
If you made wet mounts on a regular slide, dispose of the slides and glass
coverslips in the broken glass container. Plastic coverslips may be discarded in
the trash.
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Lab 11: Mollusks and Annelids
I.
Brief Background
Loligo is used here as a representative of the phylum Mollusca. The
mollusks are a varied and successful group of invertebrates. Most mollusks are
marine, but there are also lots of freshwater and terrestrial species. While most
mollusks have external shells, most cephalopods do not. Cephalopods are
cephalopods are predatory and their external features reflect this lifestyle. You
can find more information about squid mating displays (including color changes
and behavior) at: http://www.nhm.ac.uk/hosted_sites/tcp/Ssepioidea.html
Lumbricus is used here as a representative of the phylum Annelida. Students
should know general characteristics of this phylum and additional examples of
organisms in it. It is a well-known annelid, familiar to gardeners and fishermen; it
is inexpensive and easily reared or procured at bait stores. It is atypical of its
phylum in that it is terrestrial --most annelids are aquatic. Earthworms provide a
good introduction to metamerism.
Briefly consider this “Texas connections” for annelids.
http://digital.library.unt.edu/permalink/meta-dc-5476 (proteomics)
http://www.sbs.utexas.edu/shankland/default.htm
http://flowergarden.noaa.gov/image_library/video/christmastreespawning.mov
(Aquatic annelids off Texas' coast)
II.
Pre-lab assignment
After studying relevant material in your textbook and other information
sources, visit the “Blackboard” site for your class and complete this lab’s pre-lab
quiz according to your instructor’s general directions..
III.
Student Tasks
Safety Notes:
1. Use nitrile gloves and wear safety eyewear while dissecting specimens.
2. Dispose of gloves and all preserved specimen scraps in the scrap bucket.
3. Fresh specimens (not preserved) should be put into a bag and placed in the
regular trash.
4. Fluids from preserved specimens should go into the appropriate container.
5. Disinfect tables after completing the dissection.
6. Wash your hands before you leave the room.
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Task 1: Mollusks – Squid Anatomy
Examine the external anatomy of a squid and identify the structures.
Head
Body
Mantle
Fins
Eyes
Arms
Tentacles with tentacular clubs
Funnel
Mouth
Beaks
Remove the beaks with forceps. Notice how the ventral beak overlaps the
dorsal beak, just opposite to a parrot's beak. Make small cuts in the edge of the
mouth, so you can open it to extract the radula. Remove the radula with forceps.
Put the radula and beaks into a small dish with water and examine with the
dissecting microscope.
Put the squid on its back and open the mantle along the midline. Locate
the gills and the pen. The pen is what remains of the shell.
Task 2: Annelids – Earthworm Dissection
Obtain a living earthworm and observe its external anatomy.
Type of symmetry
Anterior end
Posterior end
Dorsal surface
Ventral surface
Annulus (Annuli)
Clitellum
Prostomium
Mouth
Anus
Brush a fingertip along the side of the worm from back to front to feel the
setae. Observe the behavior of the earthworm.
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Place your earthworm into the 50% ethanol solution. (Check with your
instructor before you do this.) This solution will anesthetize it quickly. Wait until
the earthworm stops squirming, about 10-15 minutes.
Pin the earthworm to the dissecting tray bottom, dorsal side up and 5-7 cm
from the side of the tray. One pin goes through the prostomium. Another pin
goes 7-10 cm posterior to the clitellum.
Use a scalpel to make an initial cut through the dorsal body wall, posterior
to the clitellum. Then use fine scissors to cut forward to the prostomium along
the dorsal midline. Be careful to cut only through the body wall. Do not cut
into internal organs underneath. It helps to keep the blades of the scissors
parallel to the bottom of the dissecting tray.
Spread out the body wall and pin it to the dissecting tray so you can see
internal organs. Use a dissecting probe to break the septa as you do this. Add
water to prevent the organs from drying out while you observe the critter's
innards. You'll need a dissecting microscope to find the small stuff, like the brain.
Identify the structures:
Septum (Septa)
Segment
Coelomic cavity (coelom)
Pharynx
Esophagus
Crop
Gizzard
Intestine
Seminal vesicles
Seminal receptacles
Dorsal blood vessel
Ventral blood vessel
Aortic arches (hearts)
Metanephridia
Remove part of the intestine and locate the ventral nerve cord.
To see the cerebral ganglia (brain), open the dorsal wall through the
prostomium. Look for two white structures.
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Obtain an earthworm cross-section slide. Locate these structures.
Lumen of intestine
Typhlosole
Coelomic cavity (coelom)
Metanephridia
Setae (if visible)
Clean up procedures for this lab:
Put everything back in its proper place. Dispose of gloves and preserved
specimen scraps in the scrap bucket. Fresh specimens (not preserved) should
be put into a bag and placed in the regular trash. Fluids from preserved
specimens should go into the appropriate container.
All dissecting equipment, including pins, must be washed and dried
before stowing. Clean off your desks with Lysol or appropriate cleaning
solution. Wash your hands before you leave the lab room.
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Lab 12: Arthropods
I.
Brief Background
Homarus is used here as a representative of the phylum Arthropoda.
Students should know general characteristics of this phylum and additional
examples of organisms in it. Homarus is a well-known arthropod, famous as a
food for humans. It is useful as a representative of Arthropoda for beginners
because it is large and easy to examine. (Crayfish can be substituted, but are
much smaller.) This is also an excellent example for illustrating biological
homology (lobster appendages are mutually homologous) and metamerism.
Briefly consider these sites for lobster relatives in Texas.
http://www.tpwd.state.tx.us/publications/annual/fish/crabreg/
http://www.tpwd.state.tx.us/learning/webcasts/gulf/coastal_bays.phtml
II.
Pre-lab assignment
After studying relevant material in your textbook and other information
sources, visit the “Blackboard” site for your class and complete this lab’s pre-lab
quiz according to your instructor’s general directions..
III.
Student Tasks
Safety Notes:
1. Use nitrile gloves and wear safety eyewear while dissecting specimens.
2. Dispose of gloves and all preserved specimen scraps in the scrap bucket.
3. Fresh specimens (not preserved) should be put into a bag and placed in the
regular trash.
4. Fluids from preserved specimens should go into the appropriate container.
5. Disinfect tables after completing the dissection.
6. Wash your hands before you leave the room.
Task 1: External Anatomy of Lobsters
Examine the external anatomy of the lobster. Determine whether your
specimen is a male or a female. Identify the structures.
Frozen lobsters should be submerged in warm water in lab sink
immediately prior to dissection.
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Verify the general body regions and surface features.
Type of symmetry
Cephalothorax
Abdomen
Rostrum
Compound Eye
Carapace
Telson
Anus
Examination of the appendages should begin at the posterior end from a
ventral view. From ONE SIDE ONLY, remove appendages one at a time (be
sure to take entire appendage), discuss their functions, set them aside for
photography and sketching. When you reach the rear-most walking leg a fresh
challenge arises; important portions of appendages are hidden under the
carapace. These hidden structures (are they internal or external?) need to be
removed along with the “leg” to which they are attached.
When you reach the large pincers you are only a little more than half
finished with appendages. Continue careful appendage removal until you reveal
the mouth (surprisingly difficult to perceive, although it is quite visible). You will
return to the mouth when you are engaged in internal anatomy examination.
Antennules (= First Antennae)
Antenna (Antennae)
Maxilla (Maxillae)
Maxillipeds
Chelipeds (chela, chelae)
Walking legs
Gills
Swimmerets
Uropods
Task 2: Internal Anatomy of Lobsters
For internal anatomy, turn your animal with its dorsal side up and work to
remove one side of its carapace (same side as appendages were removed).
This should be sort of like shelling a hard-boiled egg—there is a distinct
membrane below exoskeleton. Leave it intact if you can—it will need to be
removed, but if it remains intact while removing half the carapace, you will be
assured that the delicate heart will be intact. The heart, like the mouth, can be
difficult to perceive, even though it is large. Look for its ostia as a visual cue.
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Students often confuse the following structures: gonads, digestive gland,
antennal gland (green gland). Here are some pointers:
 Digestive gland is usually largest, most conspicuous internal
structure and is usually a yellowish green.
 Antennal gland (green gland) is entirely different—it is at base
of antenna and it is a dark green;
 Gonads, both ovaries and testes, also are often green (ranging
from blackish to yellowish) green—they are highly variable in
appearance depending upon reproductive status of animal—but
generally parallel the intestine for much of its length.
While examining digestive system, be sure to put a dull probe into the
mouth and discern the mouth’s relationship to the stomach. Open the stomach
and carefully examine its interior; you will likely see its last “meal” but you also
should see some complex structures comprising the stomach’s walls. What can
you hypothesize about their function? Of what material do they appear to be
composed?
Abdominal segments are largely muscle, but be sure to examine the easily
visible intestine (locating anus will help) and nerve (visible through exoskeleton).
Make special note of spatial relationship between nerve and intestine.
Heart
Ostia
Stomach
Gastic mill
Ovaries, testes
Antennal gland (= green gland)
Nerve cord
Brain
Clean up procedures for this lab:
Put everything back in its proper place. Dispose of gloves and preserved
specimen scraps in the scrap bucket. Fresh specimens (not preserved) should
be put into a bag and placed in the regular trash. Fluids from preserved
specimens should go into the appropriate container.
All dissecting equipment, including pins, must be washed and dried
before stowing. Clean off your desks with Lysol or appropriate cleaning
solution. Wash your hands before you leave the lab room.
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Lab 13: Chordates
I.
Brief Background
Perca (perch), Rana catesbeiana (bullfrog) and Rattus norvegicus (domestic
rat) are used here as representatives of the phylum Chordata. Students should
know general characteristics of this phylum and additional examples of
organisms in it. Furthermore, biologists working in research areas associated
with human health care (including pharmacy) can expect extensive use of rats in
professional research.
Wild rats are traditionally viewed as a nuisance. For example:
http://www.plano.gov/Departments/Health/rat_control.htm
There is good reason:
http://www.cdc.gov/mmwr/preview/mmwrhtml/00001270.htm
Bullfrogs in Texas:
http://www.zo.utexas.edu/research/txherps/frogs/rana.catesbeiana.html
II.
Pre-lab assignment
After studying relevant material in your textbook and other information
sources, visit the “Blackboard” site for your class and complete this lab’s pre-lab
quiz according to your instructor’s general directions..
III.
Student Tasks
Safety Notes:
1. Use nitrile gloves and wear safety eyewear while dissecting specimens.
2. Dispose of gloves and all preserved specimen scraps in the scrap bucket.
3. Fresh specimens (not preserved) should be put into a bag and placed in the
regular trash.
4. Fluids from preserved specimens should go into the appropriate container.
5. Disinfect tables after completing the dissection.
6. Wash your hands before you leave the room.
Task 1: Rat Dissection
Examine the external anatomy of a preserved rat and identify the general
body regions:
Head: pinna (external ears), eyes, whiskers, mouth,
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Body
Thoracic region
Abdominal Region
Tail
Forelimbs
Hindlimbs
Claws
Hair
Nipples of mammary glands
Working from a ventral view, open a window in the integumentary system
with a mid-ventral cut from lower abdomen to upper thoracic region. Follow with
three cuts at right angles to the first—one cut in lower abdomen another cut in at
bottom of rib cage and another above the heart region. Skin should lie away
from intact musculature below.
Open abdominal cavity and examine it thoroughly. Early on, identify the
caecum and avoid opening it. Identify the large liver. Later in abdominal
examination, it will be necessary to remove the liver in order to examine
structures behind it.
Examine diaphragm and esophagus’ connection to stomach before
opening thorax. Cutting through ribs will now open the thoracic cavity. Examine
it thoroughly. Observe the heart and lungs.
Proceed to neck and head. It will be necessary to make a difficult cut
through the hinge of jaw in order to lay open the pharynx.
Use the rat skeleton to observe the skull and other parts of the skeletal
system.
Integumentary system
Skeletal system (observe on rat skeleton)
Axial division
Appendicular division
Muscular system
Diaphragm
Digestive system
Mouth
Hard palate
Soft palate
Salivary glands
Pharynx
Esophagus
Stomach
Small intestine (duodenum), mesentery
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Caecum
Large intestine
Rectum
Anus
Liver
Pancreas
Circulatory system
Heart
Spleen
Gas exchange (“respiratory”) system
Pharynx
Lungs
Trachea
Larynx
Urinary system
Kidney
Ureter
Urinary bladder
Urethra
Nervous system
Eye
Endocrine system
Adrenal gland
Thymus
Pancreas
Reproductive system
Testes
Scrotum
Vas deferens
Ovaries
Uterus
Oviduct (cp. Fallopian tube)
Task 2: Perch or Frog Dissection
Half of the lab groups will dissect perches. The other half will dissect
bullfrogs. Your instructor will decide which vertebrate your group will dissect.
When your group is through with this dissection, you will be responsible
for demonstrating your animal to a group that dissected the other animal. Be
sure and do a good job, so you can effectively teach the parts of your animal to
other groups. The other group will teach you about their animal. Quid pro quo.
At the end of this lab, compare the body parts of the rat, the bullfrog and
the perch. Include these comparisons in your posting for the week
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Perch Dissection
Identify surface features.
Tongue
Mouth
Jaws (mandible, maxilla)
Eyes
External nares (nostril)
Operculum
Dorsal fins
Fin rays
Caudal fin
Anal fin
Pectoral fins
Pelvic fins
Lateral line
Anus
Scales
To examine the internal structures, open the body cavity by making a midventral cut from the anus to just behind the operculum. Lay the fish on its right
side, so its head points towards your left. Cut around the back of the gill
chamber to the dorsal surface. Go back to where you started the midline incision
and make another cut upward to the dorsal surface until you reach the backbone.
Connect the cuts by cutting along the top of the body cavity and remove the
whole side of the body wall.
To reveal the gills, remove the operculum. Identify the internal organs. If
you pop the swim bladder, you will probably just find the space where it used to
be. Move the organs around, but don't take them out unless it is absolutely
necessary. That way, the other groups will see the organs in the animal in a
manner as close to natural as possible.
Digestive system
Stomach
Pyloric caeca
Liver
Gall bladder
Intestine
Circulatory system
Heart
Spleen
Respiratory System
Gills
Swim bladder (air bladder)
Urinary system
Kidneys
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Urinary bladder
Reproductive system
Male: Testes
Female: Ovaries
Bullfrog Dissection:
Identify surface features.
Mouth
External nares (nostril)
Eyes
Tympanic membrane
Forelimbs
Hindlimbs
Cloaca (opening)
Smooth skin
To examine the internal structures, open the body cavity by making a
midline incision from its pelvic girdle to its pectoral girdle. Use scissors to make
the incision. (Hint: pick up the loose skin in the abdomen area and make a slit
there first.) Keep the blades of the scissors parallel to the surface of the body to
avoid damaging internal organs as you make the incision. Once you have
finished the midline incision, make flaps by cutting across the body at the
pectoral girdle and the pelvic girdle. Continue the cuts until they are halfway up
the body wall.Pin open the flaps with T pins.
Identify the internal organs. Move the organs around, but don't take them
out unless it is absolutely necessary. That way, the other groups will see the
organs in the animal in a manner as close to natural as possible. You may have
to remove the ovaries if your frog is a reproductive female.
Circulatory System
Heart
Spleen
Digestive system:
Tongue
Esophagus
Liver
Gall bladder
Stomach
Pancreas
Small intestine
Large intestine
Respiratory system
Vocal sac opening (if male)
Lungs
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Urinary system
Kidneys
Urinary Bladder
Reproductive System
Male:
Testis (testes)
Fat bodies
Females:
Ovary (ovaries)
Oviducts
Uterus
Fat bodies
Clean up procedures for this lab:
Put everything back in its proper place. Dispose of gloves and preserved
specimen scraps in the scrap bucket. Fresh specimens (not preserved) should
be put into a bag and placed in the regular trash. Fluids from preserved
specimens should go into the appropriate container.
All dissecting equipment, including pins, must be washed and dried
before stowing. Clean off your desks with Lysol or appropriate cleaning
solution. Wash your hands before you leave the lab room.
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Lab 14: Chemical Signals and
Conclude Tenebrio Experiments
I.
Brief Background
Seed germination generally requires imbibing large amounts of water. It is
reasonable to expect that concentration of available water would impact
germination. Brassica is a well-known, fast germinating member of the mustard
family.
Artemia embryos (often referred to as “eggs”) withstand long, extreme
desiccation and resume development when water is available. It is reasonable to
expect that water concentration impacts dormancy break.
Euglena is a frequent inhabitant of aquatic environments and it is
reasonable to expect it has limits of osmotic tolerance.
Students should have already located some information sources relevant
to these organisms during their “Meet Some Organisms” laboratory exercise.
Briefly consider these “Texas connections” for these organisms.
http://www.pubmedcentral.nih.gov/articlerender.fcgi?blobtype=html&artid=1280988
http://aggie-horticulture.tamu.edu/extension/Texascrops/brassicacolecrops/index.html
http://www.tpwd.state.tx.us/landwater/water/environconcerns/hab/otherhab/
II.
Pre lab assignment
After studying relevant material in your textbook and other information
sources, visit the “Blackboard” site for your class and complete this lab’s pre-lab
quiz according to your instructor’s general directions..
III.
Student Tasks
Task 1: Alcon Blue Butterfly Video
Watch the Attenborough video about Alcon Blue butterflies, gentian plants,
ants and ichneumon wasps. The video will be shown by the instructor. Here is
the web site: http://www.youtube.com/watch?v=Mb3OQPT3qbU
Discuss the video with your group and answer the following questions.
1. Flow chart the life cycle of the Alcon Blue butterfly.
2. Flow chart the life cycle of the ichneumon wasp.
3. Discuss the roles of chemical signals seen in this video.
4. Discuss the four types of intra- and interspecific interactions seen in this video.
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Task 2: Termite Tracking
Obtain the following materials:
Petri dish
White paper
Pens of different colors and types
Pencils of different colors
Scissors
Termites
1. Cut a piece of paper to fit the inside of your petri dish.
2. Draw a large figure eight on the paper with a ballpoint pen. Go over
the figure 8 carefully several times with the pen. Place the paper in
the petri dish.
Note: the ink needs to be fresh. Do not try to be efficient and make all
of your figure eights in advance.
3. Coax a termite onto a scrap piece of paper which can be used then to
place the termite onto the paper in your petri dish. Observe its behavior when it
encounters the figure 8.
4. Record your data in a data chart. Use the following symbols:
Tracking response)
+
No response)
–
5. Repeat steps 1-4 using all of the different writing utensils. You will have
to change termites after a few minutes, as they get dehydrated and tired.
6. Pool your data with the other groups. Analyze the data and present
your conclusions in your posting.
Task 3: Conclude Tenebrio Experiment
Take your final data measurements and make sure that everybody has a
copy of all data and photographs.
Your group should discuss how to analyze the data. You should be
thinking about how to summarize the changes you have seen over the semester
and how to present your data in both tables and graphs to illustrate these
changes.
Your group should also discuss the life cycle of Tenebrio and determine
the sequence of life cycle stages in this insect. As part of your report, you should
include a description of the hormones involved in each transformation.
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Determine the format of your final report. Each team member will be
writing a separate report but your group can work together to develop data tables
and graphs. Develop your data tables and graphs today during lab.
Clean up procedures for this lab:
Put everything back in its proper place. Put all termites back into their
original containers. Paper can be discarded in the trash. Check with your
instructor about how to cleanup the Tenebrio experiments.
Clean off your desks with Lysol or appropriate cleaning solution.
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Lab 15: Electrical Signals and Nervous Systems
I.
Brief Background
Although the complexity of different parts of the nervous system varies
among vertebrates, the components and organization are essentially the same.
The basic functional unit is the neuron, which is supported by a variety of
different glial cells. Neurons are linked together to form pathways, which vary in
complexity. This lab will focus on examining neurons, a simple pathway, and the
basic structure and organization of the vertebrate central nervous system.
II.
Pre lab assignment
Examine the diagram on page 1066 of your textbook, which shows the
vertebrate nervous system. Identify the brain, spinal cord, and nerves on the
shark nervous system diagram (dorsal view). Which components belong to the
central nervous system? Which components belong to the peripheral nervous
system?
After studying relevant material in your textbook and other information
sources, visit the “Blackboard” site for your class and complete this lab’s pre-lab
quiz according to your instructor’s general directions..
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III.
Student Tasks
Task 1: Neurons and Supporting Cells
Examine a motor neuron slide using low power of your compound
microscope.
Identify these structures:
 Neurons
Nuclei
Projections (axon and dendrites)
 Supporting cells
Task 2: Spinal Cord Model
Examine a human spinal cord model that shows the spinal cord in crosssection.
Identify these structures:
 Ventral median fissure
 Dorsal median sulcus
 Gray matter
 White matter
 Gray commissure
 Central canal
 Ventral horn
 Lateral horn
 Dorsal horn
 Ventral white columns
 Lateral white columns
 Dorsal white columns
 Dorsal root
 Dorsal root ganglion
 Ventral root.
Note the position of the spinal cord with reference to the vertebra.
Note how the nerves attach to the spinal cord.
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Task 3: Spinal Cord Slide
Examine a cross section of a spinal cord slide, using scanning or low power.
Identify these structures:
 Ventral median fissure
 Dorsal median sulcus
 Gray commissure
 Ventral gray horn
 Lateral gray horn
 Dorsal gray horn
 Ventral white columns
 Lateral white columns
 Dorsal white columns
Task 4: Spinal Reflex – The Patellar Reflex
Check the knee-jerk or patellar reflex of your lab partner. Record the
responses of both participants and include in your posting.
1. The subject should sit on the lab table or tall lab chairs with legs hanging
over the edge but not touching the floor.
2. Find the patellar tendon of the subject. It is the tendon directly below the
patella or knee cap.
3. Strike the patellar tendon with the small end of the reflex hammer and
note the response in your lab report. WARNING: Stand to one side or you may
be sorry!
4. Divert the subject's attention by having him or her lock hands together
and push them together hard while you strike the patellar tendon again. Note the
response.
5. Change places and have your lab partner test your patellar reflexes.
6. Compare the results with your class mates.
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Task 5: Comparative Brains
Examine the brain models of various vertebrates:
Lamprey larva
Dogfish shark
Trout
Frog
Alligator
Pigeon
Rabbit
Dog or Human
Locate these structures:
 Cerebrum
 Cerebellum
 Brain stem (medulla + pons + midbrain)
 Optic lobes (except human) = superior colliculi of midbrain
 Olfactory bulbs
 Pituitary gland
 Spinal cord
Color Coding on the Models:
Yellow =
cerebrum, olfactory lobes
Blue
=
optic lobes
Gold
=
hypothalamus and pituitary
Salmon =
cerebellum
White
=
brain stem and spinal cord
Observe the differences between the various brains, especially the relative
size of the various parts and how much folding is visible on the surface.
Estimate the relative percentages of each structure.
Fill in the tables on the next page.
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For each vertebrate, estimate the percentage of total brain mass taken
up by these brain regions:
(Note: will not add to 100%)
Vertebrate
Lamprey larva
Dogfish Shark
Trout
Frog
Alligator
Pigeon
Rabbit
Dog
Cerebrum Cerebellum
Brain Stem
Rate the level of folding of the surfaces of the cerebrum and cerebellum in each
vertebrate brain. Use descriptive terms such as: high, low, none
Vertebrate
Cerebrum
Cerebellum
Lamprey larva
Dogfish shark
Trout
Frog
Alligator
Pigeon
Rabbit
Dog
Note: Lobes are not folds.
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Task 6: Sheep Brain Dissection
Safety Notes:
1. Use nitrile gloves and wear safety eyewear while dissecting specimens.
2. Dispose of gloves and all preserved specimen scraps in the scrap bucket.
3. Fresh specimens (not preserved) should be put into a bag and placed in the
regular trash.
4. Fluids from preserved specimens should go into the appropriate container.
5. Disinfect tables after completing the dissection.
6. Wash your hands before you leave the room.
Obtain a sheep brain specimen in a dissecting tray.
1. Note the meninges, or protective coverings of the brain, if present.
2. Remove the meninges with scissors.
3. Identify these external features:
 Cerebrum
 Right and left cerebral hemispheres
 Longitudinal fissure (separates right & left cerebral hemispheres)
 Cerebellum
 Optic chiasma
 Hypothalamus
 Midbrain
 Pons
 Medulla oblongata
 Olfactory bulb
 Spinal cord
4. Use a scalpel to section the brain through the longitudinal fissure.
5. Identify these internal features:
 Corpus callosum
 Thalamus
 Pineal body
 Hypothalamus
 Midbrain
 Pons
 Medulla oblongata
 Cerebellum
 Cerebrum.
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Clean up procedures for this lab:
Put everything back in its proper place. Dispose of gloves and preserved
specimen scraps in the scrap bucket. Fresh specimens (not preserved) should
be put into a bag and placed in the regular trash. Fluids from preserved
specimens should go into the appropriate container.
All dissecting equipment, including pins, must be washed and dried
before stowing. Clean off your desks with Lysol or appropriate cleaning
solution. Wash your hands before you leave the lab room.
Check Your Understanding
Identify the structures on the neuron diagrams below. Color each part.
8
1
2
3
7
9
6
4
5
1. ___________________________
6. __________________________
2. ___________________________
7. __________________________
3. ___________________________
8. __________________________
4. ___________________________
9. __________________________
5. ___________________________
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Label the diagram of a spinal reflex arc.
4
1
2
3
5
1.
___________________________
2.
___________________________
3.
___________________________
4.
___________________________
5.
___________________________
6.
Add colored arrows to the diagram above showing the direction of
information flow during a spinal reflex.
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Identify these structures on the diagram of a patellar reflex:
sensory neuron
motor neuron
sensory receptor (stretch receptor)
effector (muscle)
Add colored arrows to show the direction of signals.
3
1
4
2
1.
___________________________
2.
___________________________
3.
___________________________
4.
___________________________
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Appendix 1 Illustrating Biological Material
Biologists make frequent use of both sketches and photographs. In this
course, you should develop competence at both.
Sketches have the following advantages: They show features that photos
do not show—for example, structures’ three dimensional features revealed by
repeatedly using fine focus, or subtle differences in color. They can reflect
examination of multiple individuals and thus be a sort of composite. They force
biologists to look carefully at material, deciding what is important and what is
trivial-- thus they document what the biologist perceives at the time of the
observation.
Photographs have the following advantages: They are quickly and easily
made. They accurately portray shapes, sizes and positions of photographable
structures (although only in two dimensions). They record information that is
present in the view but not considered important at the time of photo.
All illustrations in this course must include all the following information:
identity of material as best it is known, source of material, date illustration was
made, person responsible for making illustration, indication of size of material
and conditions under which it was viewed.
Sketches are usually made in pencil and are the one place in laboratory
records where erasures are not viewed as attempts to hide information. General
appearance of sketches is improved if they are enclosed in a circle (for material
viewed through a microscope) or a rectangle (for material viewed with naked eye
or simple magnifying glass). Leader lines for labels should be at ninety or 45degree angles and labels should be outside illustration and square with page.
Here is a highly recommended discussion of an unfortunate side of
biological illustrations:
http://www.nature.com/ncb/journal/v8/n2/full/ncb0206-101.html.
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Here is an example of a mediocre sketch and a mediocre photograph of the
same material. Sketches reveal what a biologist deems important at the time of
drawing (notice red-stained structures are ignored in sketch) and include
interpretations of material (note indications of haploid and diploid and reference
to missing structure). Photos, on the other hand, show everything equally—
crucial cells are equal to dust on the slide as far as a photo is concerned.
Drawings and photographs are data, not works in progress. Changes made later
(label change, inversion of photo, etc) should be treated as corrections to data—
as you would treat a correction in a table of quantitative data.
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Note here that changes have been made and notated in lower left corner.
Carefully prepared biological drawings (as for publications) often contain
large amounts of implied information. They illustrate the way things are
“supposed” to look—and thus the way we are “supposed” to perceive them; they
often imply relationships among juxtaposed drawings; they often summarize, in
visual terms, theoretical predispositions of the artist. This famous illustration by
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Ernst Haeckel shows some hard-to-see bones as they are supposed to look and
implies homology among them.
(Haeckel is famous for contributing to our notion of biological homology.
Students might be interested in investigating “Haeckel’s Law”. One site for it:
http://www.bookrags.com/research/haeckels-law-of-recapitulation-ansc-03/)
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Appendix 2 Maintaining Laboratory Notebooks and Related Records
Doing science, like performing art, is often a self-conscious activity
drawing on personal discipline and cultivated practice. Consciously “doing
science” requires an important habitual discipline of creating records. This habit
usually must be learned (rarely does it come naturally), but scientists value it
greatly; it is a large component of our intellectual strength and one of civilization’s
greatest benefits.
Our records include, foremost, our observations—“facts” that are not much
subject to argument. But our records also include a sort of window on our
thoughts—calculations and predictions and labels—that often are subject to
reconsideration. All these things are recorded in expectation that they will be
examined again in the future, at a time when the immediacy of the present is
forgotten or unknown.
How much information should be recorded? Well certainly one should
record everything that seems pertinent, but one never knows what seemingly
trivial fact will be important in future considerations. While filtering, it might seem
completely adequate to say “solution was filtered” but some day it might be
useful to know what brand of filter paper was used. When scientists are
repeatedly using equipment, microscopes for example, they should record
equipment particulars in a separate place in their notebooks (near front or near
back).
Biologists have long established practices of “vouchers”—actual
specimens of living things—that are preserved as records. These can be
pressed and dried plants, frozen samples of blood, pelts of animals, etc. This
practice (dating from at least the 18th century) has served us well especially now
that protein and DNA analysis can add new dimensions to our observations. As
much as is practical, students should retain actual samples of their studied
organisms. Obvious exceptions exist: items that are likely to decay and stink,
items that are large, items that are hazardous, etc.
Our current age of electronic records and communication gives scientists
new opportunities for collection, manipulation, dispersal and examination of
records. In this course, students are expected to utilize both traditional writtenon-paper records and electronic ones.
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Appendix 3: Using “Prepared” Slides
Take one slide at a time; they must be shared and we don’t have one for
each student. Share these slides.
Slides are not equally good. Have some idea about what you need to
see before grabbing the first available slide; read the label on the slide (not just
the label on the box); boxes often have several different subjects housed inside;
often slides are filed in a wrong box. Some companies produce consistently
better slides than others. With your illustration, name the company that produced
the slide. Generally you should seek slides that show typical features of your
subject. It usually is a waste of time to concentrate on aspects of a slide that are
accidents of its preparation (artifacts, we call them) or that are not illustrating the
purpose of the slide.
Take care to replace slides in their correct box when you finish. Never
leave slides on the microscope.
Slides get very dirty. Wipe with lens paper or chem wipe.
Here are some standard abbreviations:
cs = cross section
ls = longitudinal (long) section
wm = whole mount
Preparation of “prepared” slides can be quite complex. Often materials
have been fixed, dehydrated, embedded, sectioned, stained, and mounted.
Fixation of tissue is rapid killing and preserving against change. Fixatives
are often extremely hazardous and are among the greatest hazards faced by
beginning laboratory workers.
Dehydration of tissue is gradual replacement of water in tissue by
alcohol—this is needed in order to accomplish the next typical step.
Embedding of tissue is replacement of alcohol (which replaced water) with
paraffin (or substitute) which, when hardened, will allow for very thin slicing or
sectioning.
Sectioning of tissue is cutting into suitable thin slices (thin enough to
transmit light). It usually involves a specialized machine called a microtome.
Staining of tissue usually involves adding coloring agents with some
specificity for components of the tissue. Sometimes multiple stains are
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employed. Almost all color in prepared slides results from these stains—prior
processing removes most natural color.
Mounting of sections involves careful placement of sections on slides and
“gluing” cover slips.
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Appendix 4: Reading a Vernier Scale
(See also http://physicspmb.ukzn.ac.za/OnlineExercises/IntroVernier/intro2.html )
Main scale--here reading between 6.2 and 6.3, but closer to 6.2.
Main scale-here reading
between 10
and 11, about
halfway
between them.
Vernier
scale--here
its 6 mark is
most closely
aligned with
a mark on
the main
scale. This
scale is
reading 10.6
units.
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Appendix 5: Constructing Graphical Displays of Data
Students should already be aware that numerical data often are presented
graphically. They should cultivate skills at graphic presentation (especially using
excel) but they should also develop discernment regarding appropriate and
inappropriate graphic display.
Graph Example 1: Data (these are not real data) presented in a table—at almost
every hour, on the hour, the number of birds at a bird feeder was recorded. A
few hours were missed.
Hour of
Day
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
Number of
birds at Station
0
0
No count made
No count made
0
3
6
11
21
1
1
0
0
2
0
0
0
3
5
4
1
0
0
0
A data table is almost always a good first presentation of data. It is the starting
point for almost all other graphic presentations. Sometimes it is enough.
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Graph Example 2: Same (fake) data presented in a simple scatter plot—a
scatter plot usually contains no information other than that in its table, but may
suggest patterns.
Scales must, of course be appropriate to the subject and regular in their
intervals. ( For example, here we have “number of birds” not “log number of
birds” and “Hour of Day” not “Year of Century”; also every marked interval on the
y-axis is 5 birds and every marked interval on the x-axis is 2 hours.)
Scientific data often have a distinct independent (x) variable and a distinct
dependent (y) variable. If time is one of the axes, it usually is the independent
variable.
A good graph title says something other than re-stating the axes. Axes
must always be labeled and usually have units indicated.
A scatter plot is almost always a good second presentation of data.
Daily Feeding Record
number of birds at station
25
20
15
10
5
0
1
3
5
7
9
11
13
15
17
19
21
23
Hour of Day (July 4, 2008)
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Graph Example 3: Same (fake) Data presented in an appropriate bar graph
Bar graphs contain no more information than scatter plots and are subject
to the same requirements.
Daily Feeding Record
number of birds at station
25
20
15
10
5
0
1
3
5
7
9
11
13
15
17
19
21
23
Hour of Day (July 4, 2008)
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Graph Example 4: Same (fake) data presented in an inappropriate bar graph
This graph is an example of a practice that students should AVOID. It is
displaying three dimensions of “data” when only two exist. That third dimension
(easily added by graph drawing programs) should be used only if there is a third
dimension of data to show—for example if temperature had been recorded at
each hour, we might have an interesting and valid third dimension to graph. But
we don’t; this “fluff” is distasteful and actually impedes good interpretation of
data.
Daily Feeding Record
25
20
number of birds at
station
15
10
5
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23
21
19
17
Hour of Day (July 4, 2008)
15
13
11
9
7
5
3
1
0
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Graph Example 5: Same (fake) data with an inappropriate line drawn
Inserting a line into a set of data points should be done thoughtfully. To
insert a line implies continuity of variables—here it implies that at hour 7.25, there
were (or could have been) 11.3 birds present. This is not reasonable since
“number of birds” is a discrete variable—it only exists in whole numbers. (Time,
by contrast is a continuous variable—there is such a thing as hour 7.25.)
Furthermore, it is not reasonable to expect this relationship to be linear,
even though parts of it may be extremely linear (linear regression can be used to
determine what line most nearly is described by a set of points).
Some biological relationships are regular, but not linear. For example, this
data set suggests (but does not directly address) a hypothesis that this feeding
station experiences two episodes of feeding per day.
Daily Feeding Record
number of birds at station
25
20
15
10
5
0
1
3
5
7
9
11
13
15
17
19
21
23
Hour of Day (July 4, 2008)
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Graph Example 6: Same (fake) data with many inappropriate lines drawn
This graph has the same problems as the previous, except that there are
several lines instead of only one.
Daily Feeding Record
number of birds at station
25
20
15
10
5
0
1
2
3
4
5
6
7
8
9
10 11 12 13 14 15 16 17 18 19 20 21 22 23 24
Hour of Day (July 4, 2008)
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Appendix 6: Using “Blackboard”
BIOL 1407 students at Austin Community College are required to utilize
“Blackboard” to access most materials for this course.
Students must establish their electronic identification with ACC. This is
called an “ACCeID”
From ACC’s homepage (http://www.austincc.edu/) go to lower right corner
and select “Blackboard Login”.
Select student guide and login. Explore and see how much you can figure
out.
Blackboard is complex and only a few of its features will be utilized in
BIOL 1407, so don’t try to comprehend it all at once. Your familiarity will increase
with usage.
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Appendix 7: Measuring Area of an Irregular Shape
Biologists frequently need to know an irregular shape’s area. Some
variation of the following method often will suffice.
If the object is sufficiently flat, the object or its photograph or a tracing of
its outline, is placed under a transparent grid (often graph paper). The number of
squares within the outline is then counted or, better, the number of line
intersections is counted. This provides a direct measurement of the number of
grid units2 that comprise the area of the image. If object is a photograph, grid
units2 are then converted to “real world” units2; thus, the real world area of the
object is measured.
Smaller spaces on grid result in more accurate measurements of area.
Example: this shape on the left is placed under a grid and the number of
intersections counted (for an intersection that falls on the line, count it as a half).
In this example, the area of the shape is 209 square grid units.
If we have determined that, in this situation: 9 linear grid units = 25 mm,
then (9 linear grid units) 2 = (25 mm) 2 or 81 grid units2 = 625 mm2
The real world area of our shape is: 209 grid unit2 x (625 mm2 / 81 grid
units2) = 1613 mm2
Software now exists that does this automatically, if images are digital.
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