Download Appendix 2: draft syllabus for BI 101, Fall 2011

Request for Designation as a Scientific Methodologies (SM) Course in Explorations
Name______Pete Van Zandt_______________________________________________
Course number and title_____ BI 101: Explorations in Biology____________
Departmental endorsement______________________________________________
Has this course been submitted for any other Explorations designation? ___No___
If so, which one? ______________
Please list which of your course assignments or activities addresses each of the guidelines, state
briefly how this is accomplished, and attach a syllabus or a preliminary redesign plan for the
course.
Criteria for a course in scientific methodologies include

Clearly defines a problem/question and states an appropriate rationale for
investigation
o An excerpt from the relevant laboratory exercises, wherein students learn about
investigating natural phenomena using experimentation, is in Appendix 1 below.
Briefly, students are required to examine either the behavior of termites (Lab 1)
or the genetic inheritance pattern in fruit flies (Labs 4 – 6).

Develops a testable hypothesis
o (see Appendix 1) For relevant labs, students generate hypotheses either on
their own (Lab 1), or are guided through this process from a limited number of
possibilities (Labs 4 – 6).

Tests the hypothesis using a suitable design, effectively analyzes resulting data, and
draws proper conclusions
o (see Appendix 1) For relevant labs, students evaluate these hypotheses either
by designing experiments (with the instructor’s help) to test the hypotheses they
develop (Lab 1), or through established experimentation and data analysis (Labs
4 – 6).

Communicates the findings in oral or written form
o For both exercises, the students prepare a laboratory report of their findings.
Return this form as one electronic file with a syllabus appended to [email protected] by 30 May 2011.
(See Appendix 2)
Appendix 1 – Selected laboratory exercises for BI 101
Lab 1: The Scientific Process with Termites
Work in groups of 3-4. On your desk, you should have a Petri dish with 4-5 termites in it. Take
out several different pens and draw circles (about 2-3 inches diameter) on the supplied paper.
Using the paintbrushes, gently brush the termites out of the Petri dish into the center of one of
the circles. Observe the termites for 5-10 minutes, and then answer the questions below:
1. Identify a behavior that you would like to investigate further
2. Develop a TESTABLE hypothesis to explain the behavior
3. Design a controlled experiment (using as many termites as you want) to test your hypothesis.
When doing this, be sure to discuss and identify the following terms for your experiment (this
will be based on your previous knowledge, so you’ll have to share ideas with each other).
Experimental Design:
• Null hypothesis
• Independent variables
• Dependent variables
• Experimental treatment
• Control treatment
• Sample size
4. Now the hard part…Choose an ecological phenomenon that interests you and your group.
How might you use the scientific method to investigate this phenomenon?
Labs 4-6: Investigating Mendelian Genetics Using Drosophila
Introduction
Genetics is the study of two main subjects, heredity and variation. Heredity determines the
similarities between individuals. Children resemble their parents, puppies resemble their
parents, and corn plants look like their parent plants. Variation is the cause of differences
observed between individuals. Siblings resemble one another but are not identical, they are
still unique individuals. Genetics attempts to explain the basis for the similarities and
differences observed in related individuals.
Humans have been curious about how characteristics are passed on from one generation to the
next for thousands of years and although they did not understand the basis of heredity they
quickly learned to apply genetic principles in the domestication of plants and animals. Initially,
the plants or animals having the most desirable characteristics were used to produce the next
generation. As the scientific basis of heredity became known, specific genetic principles were
applied to produce plants and animals for specific purposes and for particular environments.
From the earliest attempts by humans to explain inheritance of traits, the prevalent theories to
explain heredity centered on the concept of "blended inheritance." This concept held that
there was a blending or mixing of characteristics from the two parents, which led to the
production of offspring appearing intermediate between the parents. It is easy to understand
how this idea came into being and gained acceptance by the scientific community even into the
late 19th century. However, with critical, objective observation and reasoning you can readily
see why this is not an acceptable explanation for inheritance of traits. Consider your own
physical characteristics. Are they midway between those of your parents? Are there any traits
such as height, eye color, hair color, skin color, nose length, etc., for which you are exactly
midway between your parents? Are there any for which you are more extreme than your
parents? Are you perhaps taller than both of your parents? Any examples where the offspring
are more extreme than both parents should be impossible if blended inheritance is the correct
model for heredity.
The correct explanation of the mechanism of heredity came with the publishing of a paper by
an Austrian monk, Gregor Mendel, in 1866. Based on his results from hybridization
experiments with garden peas, Mendel proposed the idea of hereditary "factors" or units.
These factors later came to be called genes. Mendel proposed that these units were inherited
in equal numbers from each parent and these determined the observable characteristics of the
hybrid. The traits themselves are not inherited, but the factors, the units, or particles that
determine or control the observable characteristic are transmitted from parent to offspring.
The particular combination of factors inherited from the two parents determines the
characteristic(s) of the offspring.
Mendel's experiments led him to propose several laws or principles on which heredity is based.
These laws are the foundation of what is typically called Mendelian genetics. The term
"Mendelian genetics" refers to the subset of genetics concerned with the transmission of
characteristics from one generation to another. Its focus is on the organism. Molecular
genetics is concerned with the function of the gene. Its focus is below the level of the
organism.
Mendel's first law is called the "Law of segregation of alleles." This law states that when an
organism reproduces, the "factors" for a trait are segregated—i.e. they are separated into
different gametes. Mendel was not aware of chromosomes or the process of meiosis and so he
used the term "factor" for describing his concept of particulate inheritance. As we understand
it today each individual in a typical diploid eukaryotic population has two nonidentical copies of
each chromosome and each chromosome contains numerous genes. Therefore every
individual has two copies (alleles) of each gene or factor. These alleles may be the same, or
they may be different. When an individual forms gametes (sperm and eggs), each gamete
(which is haploid) carries only one allele for each trait. When two gametes combine
(fertilization) they produce a new individual (which is diploid) with two alleles for each trait.
The relationship between the two alleles for a trait helps explain why one does not always
observe a blending of traits in the offspring of a given mating. One allele may be dominant to
the other and in such a case will be expressed in the individual even if only one copy of that
allele is present. The other allele in such a case would be recessive and its expression is masked
by the dominant allele. If an individual has both of the dominant or recessive alleles for a given
trait then that individual is homozygous for that trait. If an individual has one dominant and
one recessive allele for a given trait then that individual is heterozygous for that trait. Two
parents may both express the dominant form of a trait but be heterozygotes. An individual's
appearance is referred to as its phenotype but the individual's genetic make up is referred to as
its genotype. Therefore, an individual who was heterozygous for albinism (albinism is inherited
as a recessive trait; normal skin pigmentation is dominant), would have a phenotype described
as normal pigmentation. Such an individual could be described as having a genotype of Aa,
where A represents the dominant allele for normal pigmentation and a represents the recessive
allele for albinism. If two such heterozygous individuals should marry and have offspring then
they could produce offspring having any of three possible genotypes, AA, Aa, or aa, and two
possible phenotypes, normal pigmentation or albinism. Either AA or Aa would produce a
phenotype of normal pigmentation. Heterozygous individuals are often referred to as carriers
because they have the recessive allele, but do not express it. Heredity is usually more
complicated than the above example, which shows a pattern of simple, dominant inheritance.
Some traits exhibit what is referred to as codominance, a pattern of inheritance in which both
alleles are expressed in the heterozygous individual. In addition, multiple alleles, polygenic
inheritance, gene interactions, pleiotropy, etc., all contribute to the complexity and difficulty of
understanding the genetics of an organism.
Mendel's second law is the "Law of independent assortment." This law states that genes for
different characteristics are inherited independently of one another. That is, the distribution of
the alleles controlling one characteristic to the gametes does not affect the distribution of the
alleles controlling a different characteristic to the gametes. This law holds only if the genes
controlling the traits are located on different chromosomes.
Procedures
This investigation of Mendelian genetics using Drosophila will require three weeks because of
the life cycle of the fruit fly. Specific tasks must be performed each week in order to complete
the study within this time frame. Drosophila was one of the first organisms to be used
extensively in genetic breeding experiments. It has continued to play an important role in
genetic studies, and today is certainly the best known and most widely used species for these
investigations. Its short life cycle (approximately 2 weeks), production of large numbers of
offspring, ease of growing in the laboratory, and the large variation in inherited characteristics,
all make Drosophila an excellent research organism and an ideal organism for beginning genetic
studies.
You will use the following timetable for completing your genetic studies using Drosophila:
First Lab Period
1. learn how to handle and anesthetize fruit flies
2. learn the life cycle of the fruit fly
3. observe and learn to distinguish between the different mutations that have been
used in the crosses you will be investigating
4. learn how to distinguish the sexes of fruit flies
5. prepare media in culture tubes for growth of your flies
Second Lab Period
1. remove adult fruit flies from the culture(s) you started in the first lab period
Third Lab Period
1. score (record) the results of the experimental fruit fly cross(es) you started in the
first lab period
2. analyze your results using a chi-square statistical test
First Laboratory Period
Before beginning genetic study of any organism it is useful to become familiar with its life cycle.
You should spend the first part of today's laboratory becoming acquainted with the life cycle of
Drosophila and learning to recognize specific mutant traits present in some of the stocks of
flies.
Drosophila is a holometabolous insect, i.e. it undergoes complete metamorphosis and thus
passes through four distinct stages during its life cycle—egg, larva (maggot), pupa and adult.
Obtain a culture tube containing wild type flies and you should be able to observe all 4 stages
inside the tube. Some ten hours after the female emerges from the pupa case she is ready for
mating. Following a brief courtship during which the male circles the female while vibrating his
wings, the female spreads her wings laterally and insemination takes place. Once sperm are
received from a male they are stored in seminal receptacles within the female and are then
used to fertilize all of the eggs laid by the female during the course of her lifetime. Some two
days after emergence the female begins oviposition. She will lay eggs for some 10 days and
produce some 400-500 eggs during this time.
EGG. The eggs are small (0.5 mm long), white and ovoid. They have thin filaments or stalks on
the anterior end that project from the egg case. These stalks serve to prevent the egg from
sinking and drowning in the softened medium and also aid the developing embryo in
respiration. This stage lasts about 1 day and ends when a small larva crawls out. They can be
observed with the use of a hand lens or dissecting microscope.
LARVA. The larvae are white, segmented and worm-like. There are black, hook-like mouth
parts in the narrow head. There are no eyes and no appendages. The larvae eat their way
through their environment. What is the natural environment of the fruit fly larvae and why are
these morphological specializations advantageous there? A larva passes through 3 larval stages
called instars. At the end of each instar they must shed their exoskeleton or molt. The larval
stages take about 4 days to complete. How do the larvae move without appendages?
PUPA. At the end of the last larval stage (3rd instar), the larvae move to a slightly drier location,
become immobile, and evert their anterior breathing spiracles. They form a pupal case or
puparium, which is analagous to the cocoon of a moth. It is within the puparium that
metamorphosis occurs. Metamorphosis involves reformation of almost all body structures.
The larval tissues are internally digested and the adult organs develop, all within a protective
case. Over the 4 days that this stage lasts, the puparium hardens and darkens to a brown color.
ADULT. The adult is the reproductive and dispersal stage of Drosophila. As the adult emerges
from the puparium it is soft, pale and wet. At first the fly is very long with unexpanded wings
which appear small and black. Within a short time the wings expand and the body takes on the
shape of the mature adult. Flies are light in color upon emergence but darken during the first
few hours. Recently emerged adults are difficult to sex and score for mutations that depend on
development of coloration. Mating of the newly emerged flies will begin some 8-10 hours after
leaving the puparium.
Note: See Appendix II, "Techniques for Working with Drosophila," for figures showing stages
in the life cycle of Drosophila and the parts of adult flies.
Differentiating Sexes and Mutants
Obtain some anesthetized adult flies from your instructor. Use a dissecting microscope and the
figures in Appendix II and in the laboratory to identify the following body parts:
Head, eyes, thorax, wings and their veins, halteres, abdomen,
six legs, bristles, and antennae.
Distinguish between males and females using the following characteristics:
Size – Females are usually larger than males.
Shape – The abdomen of males is rounded, blunt and cylindrical. Females have an abdomen
that curves to a point posteriorly.
Color – Males have the dark bands of the last few segments fused. Females have less black
pigment and have separate dark bands along the dorsal surface to very tip of the abdomen.
Sex Combs – Only males have a sex-comb. This is a darkly bristled structure located on the
anterior pair of legs of the male. It is in a position analogous to the lower leg and ankle region.
This is the most reliable method for positive sex identification.
Note that the wings of the wild type flies are longer and wider than the abdomen. Note also
that the eyes of wild type flies are red. The mutant traits that will be used in this investigation
are white eyes, sepia eyes (brown), vestigial wings (wings are shrunken and nonfunctional).
(Note: Flies that are newly emerged from the pupa case have unexpanded wings that are wet
and folded and may appear vestigial. However, these wings are still longer than the fly's
abdomen.) Examine flies that show each of the mutant traits listed above. You will not be told
the genotypes of the flies that you receive for your experimental cross(es).
Anesthesia – Flies will be anesthetized with triethylamine (FLYNAP). The goal is to inactivate
the flies but not kill them. Your instructor will demonstrate several techniques for
anesthetizing the flies. For written instructions on anesthetizing flies see Appendix II,
"Techniques for Working with Drosophila," in this lab manual.
Preparation of the Experimental Crosses
One normally begins with homozygous individuals when conducting an experimental cross.
One of the parents is homozygous for one allele while the other parent is homozygous for an
alternative allele at the same genetic locus. Usually one parent is wild type for the trait under
investigation while the other parent shows the mutant phenotype for the trait under study.
These pure breeding flies are referred to as the parental generation and are symbolized by
using P1. The offspring produced by the P1 cross are called the first filial generation and are
symbolized by using F1. If the F1 flies are allowed to interbreed they produce a second filial
generation and are symbolized by using F2. By analyzing the proportions of wild type and
mutated flies in the F2 generation you can determine the mode of inheritance of the mutation
under study and ascertain the genetic make-up of the flies in the F1 and P1 generations.
Before beginning your crosses be certain that you know where the incubator is located that will
house your flies while they are growing and reproducing. The incubator will keep the flies near
a constant temperature of 25o C. Higher temperatures increase the risk of mortality of the flies
and lower temperatures lengthen the time need to complete the life cycle.
Media Preparation – Obtain clean plastic culture vials, one for each cross you will be
conducting. Use the dehydrated media purchased from Carolina Biological Supply Company to
prepare the growth media for your flies. Following the example of your instructor add one
capful of dry medium (food flakes) to a clean tube. Add one capful of distilled water to the
culture tube containing the dry medium. Quickly swirl the contents to mix the media and
water. Set the tube on the counter to allow the medium to solidify. (This takes about 30
seconds). Add a few grains of yeast to each tube of medium you prepare; careful, not too
much. Immediately place a clean foam plug in the tube to prevent any flies from getting into
your culture tube. What is the function of the yeast and why is so little added?
Placing Flies in the Tube of Culture Medium – Place 10-20 flies in the tube of culture medium
you just prepared from the appropriate stock tube provided by your instructor. The flies you
will be adding to start your culture are F1 flies. The P1 cross was performed for you several
weeks earlier to provide you with enough time to complete your investigation. Use the
following protocol in transferring flies, or first anesthetize them, see Appendix II, "Techniques
for Working with Drosophila," and then transfer the flies to the culture tube.
1. Label your culture tube with your name and that of your lab partner. Indicate the
letter of the cross (this will be on the stock tube from which you obtain your flies), on
your label. Put the date and the lab section you are in on the label as well.
2. Remove the foam plug from the culture tube containing the freshly prepared medium
and invert the tube.
3. Tap the stock tube (containing the adult F1 flies) on the table top to knock the flies off
of the foam plug and toward the bottom of the tube.
4. Swiftly remove the foam plug from the stock tube and place your inverted new
culture tube over the stock tube.
5. Allow the flies in the stock tube to enter the new culture tube.
6. After about 10-20 flies have entered the new culture tube, remove it from the stock
tube and place foam plugs back into each of the culture tubes. Always plug the bottom
tube first and plug the inverted tube before turning it right side up. Mentally rehearse
the steps you are going to follow before you actually start the procedure. Get your lab
partner to assist you in this process.
7. If too many flies climb up into the inverted tube, tap both tubes as a unit to knock
most of the flies into the bottom culture tube and start over.
8. Check to make sure that your new tube is labeled correctly. Place it in the incubator
when you are finished.
If you decide to anesthetize the flies before placing them in your new culture tube then it is
crucial that you do not expose the flies to the FLYNAP too long since this may kill them or
reduce their fecundity. You must type (i.e. observe the phenotype) your F1 flies either before
or after you have started your cross. You start the cross of your F1 flies when you place them in
your new culture tube. To observe the phenotype of the flies it is necessary to anesthetize
them and observe them under a dissecting microscope. You know that both of their parents
were from different pure-breeding stocks (homozygotes). One of the parents in all of the P1
crosses was wild type while the other parent had a mutant phenotype. Therefore, what do you
know about the genotype of these F1 flies?
Enter your observations on the F1 phenotypes on the data sheets provided in this exercise. In
addition, fill in the other information requested on this sheet and retain it. You will need this
information as you complete your investigation and collect your data for analysis.
Second Laboratory Period
Removing F1 Adult Flies – During the past week the F1 generation of flies have been actively
laying eggs in the culture tubes you started last week. If you look carefully in the culture vials
you will note the presence of eggs, larvae and pupae which represent the F2 generation of flies.
If you do not see evidence of living larvae or pupae in your culture vial, or if there is evidence of
a fungal infection, then show the culture vial to your instructor to obtain advice on how to
proceed. In order to prevent confusion of the F1 adults with the F2 flies that will begin to
emerge in a few days it is important that ALL of the F1 adults be removed in today's lab.
Following the procedures outlined last week, (see Appendix II to refresh your memory),
anesthetize the flies in your culture vial and place them in one of the fly morgues present in the
laboratory. The morgue contains a detergent solution, which will cause the flies to sink to the
bottom of the fluid and drown. Try to prevent any of your flies from escaping into the
laboratory. After you have removed all of your adult F1 flies return your culture vials to the
incubator to permit the continued growth and development of the F2 generation.
Third Laboratory Period
Making Hypotheses and Predictions – This week you will determine if the alleles for the
mutations you are studying are inherited as dominants, codominants or recessives, and if they
are X-linked or autosomal. Use the space provided on the next page to write out your
hypotheses and the predictions of the ratios you would expect among the F 2 offspring for
each of your crosses. (Note: Make preliminary observations of your F2 flies to determine if you
are dealing with a monohybrid, dihybrid, or sex-linked cross, and if the mutation is inherited as
a dominant or recessive before proceeding to generate appropriate hypotheses and predictions
for each of the crosses.) For example, if you find that Cross #1 has only two phenotypes and
the mutant allele is recessive to the wild type allele, and they are distributed among both sexes
in approximately equal numbers then your hypothesis might look like the following:
Data Collection—Counting F2 Offspring – Obtain your culture vials that contain the genetic
crosses you started two weeks ago from the incubator. These vials hold the F 2 generation of
flies for each of the crosses you started at that time. Anesthetize the flies in one of these vials
with FLYNAP, following the procedures you have used previously. At this point in time it is not
necessary to be concerned about anesthetizing them for too long a period, since these flies will
all be placed in the morgue after you finish your counts. It is important to first determine how
many phenotypes are present among the F2 flies and if there are any differences between
males and females with regard to the presence of a particular phenotype. None of your crosses
will have more than four different phenotypes present.
Separate the different phenotypes into groups. You need to count a minimum of 100 total flies,
so if you have less than this number you will have to return in a few days and repeat this
procedure of anesthetizing and counting the adult flies. Record your counts in Table 1 on the
data sheets provided. Be careful to record your data on the proper sheet (i.e, cross 1 goes on
the sheet for cross 1). Determine an approximate ratio of the phenotypes you observed. For
each of your crosses, compare your observed approximate ratio with your hypotheses and
predictions and determine which hypothesis most closely fits the data collected.
Testing Data Against Predictions – Analyze your results statistically using the Chi-square Test
(see below). This procedure allows you to compare your observed numbers of offspring with
your predicted numbers to determine if they are statistically different from one another. Can
you accept your hypothesis or must you reject it? If you must reject your hypothesis, it may be
useful to test a different hypothesis using the Chi-square analysis. Once you have accepted one
of your hypotheses, deduce what the genotypes and phenotypes of the parental (P 1), and F1
generations must have been and complete the information on your Drosophila Data Sheets.
After finishing analysis of your fly crosses turn in your completed data sheets and the Chisquare analyses that you performed on your data. Use the sheet entitled "Chi-Square
Calculations" to show your Chi-square analysis.
Each group should complete a total of 4 Chi square analyses, including one for their own data
and one for the pooled lab data for both Cross 1 and Cross 2.
DROSOPHILA RESULTS
CROSS # 1
As you determine the phenotypes and genotypes, fill in the blanks:
P1 Phenotype: (female)__________________
X
(male)_____________________
P1 Genotype: (female)__________________
X
(male)_____________________
F1 Phenotype: (female)__________________
X
(male)_____________________
F1 Genotype: (female)__________________
X
(male)_____________________
Date F1 cross started ___________
Date F1 flies removed ___________
Date F2 flies counted ___________
Table 1. The Phenotypes and Numbers of F2 Progeny
Phenotypes
Your observed
Your observed
Lab observed
Lab observed
totals
ratio
totals
ratio
Males (white eyes)
Males (wild type)
Females (white eyes)
Females (wild type)
TOTALS
-------------------
------------------
DISCUSSION QUESTIONS FOR CROSS 1
The possible inheritance patterns for Cross 1 are:
(1)
(2)
(3)
(4)
Autosomal recessive (normal Mendelian inheritance)
Autosomal dominant
Sex-linked recessive
Sex-linked dominant
1. The allele for white eyes in flies is recessive. Is it possible to tell that based on your observed
ratios? Why or why not?
2. What patterns do you see among the different phenotypes?
3. What ratios of F2 flies do you expect if a trait is autosomal recessive? Below, use punnett
squares to determine generate hypotheses about expected ratios of F2 flies, starting with the P
generation. Assume individuals in the P-generation are homozygous. Hint: use R = allele for
red eyes, r = allele for white eyes
Hypothesis 1: Autosomal Recessive
P generation and F1 progeny
F1 generation and F2 progeny
Parental cross_________x__________
F1 cross_________x__________
 F1 progeny genotype
__________
EXPECTED RATIO OF F2 GENERATION:
Red-eyed flies: White-eyed flies
____________:____________
4. What ratios of F2 flies do you expect if a trait is sex-linked recessive? Hint: use punnett
squares as before (in this case, you will have two possible crosses, with the P generation either
a cross between red-eyed females x white-eyed males or between white-eyed females x redeyed males- Do punnett squares for each). Assume individuals in the P-generation are
homozygous.
Hint: for sex linked traits, you must use XX for females and XY for males (attach appropriate
alleles, R and r, to appropriate chromosomes)
Hypothesis 2: Sex-linked Recessive (P = red-eyed females x white-eyed males)
P generation and F1 progeny
F1 generation and F2 progeny
Parental cross_________x__________
F1 cross_________x__________
 F1 progeny genotype
__________
EXPECTED RATIO OF F2 GENERATION:
Male white eye: male wild type: female white eye: female wild type
____________:____________:_______________:_____________
Hypothesis 3: Sex-linked Recessive (P = white-eyed females x red-eyed males)
P generation and F1 progeny
F1 generation and F2 progeny
Parental cross_________x__________
F1 cross_________x__________
 F1 progeny genotype
__________
EXPECTED RATIO OF F2 GENERATION:
Male white eye: male wild type: female white eye: female wild type
____________:____________:_______________:_____________
5. Before running your Chi-Square test, what do you think is the inheritance pattern for Cross
1?
6. Conduct Chi-square tests of the hypothesis that you think is the most likely of these choices
(your answer to question 5). Show your calculations below and use the attached Chi-Square
calculation pages.
6a. Based on the expected ratios of your hypothesis, what are the expected numbers of
flies per phenotypic category (USE THE SAME EXPECTED RATIOS for your group data,
and for the total lab data)?
Group
Lab
6b. Conduct Chi-Square tests for your group data and for the totals for the lab on
attached calculation sheets.
7. Chi-Square Results:
Group:
2 = _____________________
___________________
df = ___________
P-value =
Are your observed results (from your group) consistent with expected values based on
your hypothesis?
Lab:
2 = _____________________
___________________
df = ___________
P-value =
Are the observed results from the entire lab consistent with expected values based on
your hypothesis?
8. If there is a difference between the overall results from your group and the entire lab, what
might be the reason for the difference?
DROSOPHILA RESULTS
CROSS # 2
As you determine the phenotypes and genotypes, fill in the blanks:
P1 Phenotype: (female)__________________
X
(male)_____________________
P1 Genotype: (female)__________________
X
(male)_____________________
F1 Phenotype: (female)__________________
X
(male)_____________________
F1 Genotype: (female)__________________
X
(male)_____________________
Date F1 cross started ___________
Date F1 flies removed ___________
Date F2 flies counted ___________
Table 2. The Phenotypes and Numbers of F2 Progeny (ignore sex)
Phenotypes
Your observed
totals
Your observed
ratio
Lab observed
totals
Lab observed
ratio
wild type eyes, wild
type wings
sepia eyes, wild type
wings
wild type eyes,
vestigial wings
sepia eyes, vestigial
wings
TOTALS
-------------------
------------------
DISCUSSION QUESTIONS FOR CROSS 2
1. Based on your observed ratios, are the traits for sepia eyes and vestigial wings recessive or
dominant? Explain.
2. What patterns do you see among the different phenotypes?
3. What ratios of F2 flies do you expect if the traits are autosomal recessive? Hint: use punnett
squares or probability calculations to determine the expected ratios of F2 flies, starting with
the P generation. Assume individuals in the P-generation are homozygous.
Hint: Use R = allele for red eyes, r = allele for sepia eyes, W = allele for normal wings, w = allele
for vestigial wings, remember that individuals have two alleles for each trait, and that gametes
have one allele for each trait
Both Traits Autosomal Recessive
P generation and F1 progeny
progeny
Cross ____________x______________
____________x______________
F1 generation and F2
Cross
RATIO OF F2 GENERATION:
(red eye, norm wing):(se eye, norm wing):(red eye, vg wing):(se eye, vg wing)
_________________:________________:______________:______________
4. Conduct Chi-square tests of the hypothesis that the traits are both autosomal recessive. Show
your calculations below and on the attached Chi-Square calculation pages.
4a. Based on the expected ratios of your hypothesis, what are the expected numbers of
flies per phenotypic category (USE THE SAME EXPECTED RATIOS for your group data,
and for the total lab data)?
Group
Lab
4b. Conduct Chi-Square tests for your group data and for the totals for the lab on
attached calculation sheets.
7. Chi-Square Results:
Group:
2 = _____________________
___________________
df = ___________
P-value =
Are your observed results (from your group) consistent with expected values based on
your hypothesis?
Lab:
2 = _____________________
___________________
df = ___________
P-value =
Are the observed results from the entire lab consistent with expected values based on
your hypothesis?
8. If there is a difference between the overall results from your group and the entire lab, what
might be the reason for the difference?
Conducting a Chi-square Test
To test whether your observed ratios match a particular expected ratio, you will use a statistical
procedure called a Chi-square test.. This procedure will help you determine which hypotheses
about the inheritance pattern is correct.
In science, it is not sufficient to say that something "looks close enough for me," or "that seem
reasonable." In most experiments, data will not be clear-cut and you will need to conduct some
type of statistical analysis to compare your results with your predictions in an objective way.
The best statistical test to use for analysis of genetic inheritance patterns is the Chi-square test.
Chi-square Analysis – The Chi-square test is useful for comparing observed numbers in different
categories with predicted values. The Chi-square test tells you the probability that the
difference in the results you observed in an experiment versus what you would expect or
predict could be due to chance events alone. Observed numbers that are close to predicted
values will give you a high probability that the slight difference was due to random events and
you can have confidence that2your hypothesis that led to those predictions is a reasonable one.
 =
The Chi-square formula is shown below:
(O-E)2
E
O = number observed
E = number expected
= summation of all categories
Example
Suppose that you count the number of F2 fruit flies and find a total of 80 flies. Of these 80 flies,
55 are red-eyed (wild type) and 25 are white-eyed. You might be expecting a 3:1 ratio if red is
dominant to white and these genes have a straight-forward inheritance pattern. Your expected
frequencies for 80 flies would then be 60 red-eyed and 20 white-eyed.
How close are the observed values to the expected values? Use the Chi-square test to
determine if the difference you observed has a reasonable probability of being due to chance
alone or if the hypothesis should be rejected as unreasonable to account for the results
obtained. Using the numbers given the calculations would look like the following:
2 = 
(25 – 20)2 +
20
(55 – 60)2
60
The reason there are two sets of numbers above is that there are two classes of offspring
observed, white and red. The χ2 value is obtained by adding the results from these two
calculations together, i.e. you obtain the summation. The results of the calculations:
χ2 =
1.25 + 0.42
χ 2 = 1.67
Each Chi-square value has a certain probability of occurrence, depending on the number of
categories or classes. This is quantified as the degrees of freedom, which is equal to the
number of classes or categories – 1. The above example has the smallest possible number of
degrees of freedom, 2 – 1 = 1. Statisticians have developed probability tables that permit you
to determine the probability of obtaining a χ 2 value like yours using the appropriate degree of
freedom. Use one of the Chi-square probability tables provided for you in the laboratory to
determine the p value (probability value) for the above χ 2. If the χ 2 value has a probability of
less than 0.05 (for one degree of freedom the p value at 0.05 is 3.84) then it indicates that the
results obtained are not likely the result of chance events. This means that if the hypothesis is
correct and if the experiment was repeated 100 times you would obtain a value greater than
3.84 only 5 times or 5% of the time. Since the χ 2 value of 1.67 for the above example is less
than the χ 2 value at the p = 0.05 level you would say that the difference between the observed
and expected values is not significant at the 0.05 level and you would accept the hypothesis
that gave you the predicted (expected) values. Because you do not know the exact p-value that
corresponds to your χ 2 value, you can present p as (0.25>p>0.10). If the p-value corresponding
to your χ 2 value was less than 0.05, then your expected values and observed values are
significantly different, suggesting that your hypothesis about the inheritance pattern should be
rejected.
CHI-SQUARE TABLE
Degrees of
freedom
Probability of committing a Type I error
0.90
0.50
0.25
0.10
0.05
0.01
1
0.016
0.46
1.32
2.71
3.84
6.64
2
0.21
1.39
2.77
4.61
5.99
9.21
3
0.58
2.37
4.11
6.25
7.82
11.35
4
1.06
3.36
5.39
7.78
9.49
13.28
5
1.61
4.35
6.63
9.24
11.07
15.09
CHI-SQUARE CALCULATIONS
Cross 1 group data:
Phenotype
category
O
E
(observed #
flies)
(expected #
flies)
O-E
(O-E)2
(O-E)2
E
χ 2 = Sum:
P-value
Cross 1 lab data:
Phenotype
category
O
E
(observed #
flies)
(expected #
flies)
O-E
(O-E)2
(O-E)2
E
χ 2 = Sum:
P-value
CHI-SQUARE CALCULATIONS
Cross 2 group data:
Phenotype
category
O
E
(observed #
flies)
(expected #
flies)
O-E
(O-E)2
(O-E)2
E
χ 2 = Sum:
P-value
Cross 2 lab data:
Phenotype
category
O
E
(observed #
flies)
(expected #
flies)
O-E
(O-E)2
(O-E)2
E
χ 2 = Sum:
P-value
TECHNIQUES FOR WORKING WITH DROSOPHILA
Anesthetizing Fruit Flies with Flynap
The following procedures describe how to effectively anesthetize your fruit flies without killing
them. In anesthetizing your flies care should be used to avoid releasing them into the room
and to minimize their exposure to FlyNap. Keep the bottles of FlyNap tightly closed, keep the
lid on your anesthetizer, and clean up spills.
Method 1
1. Remove the large cap from the bottom of an anesthetizer. Place 3-4 drops of FlyNap on the
foam plug. Do not add any if you can already smell FlyNap on the foam. Replace the large cap.
Remove the small plug in the top of the anesthetizer.
2. Transfer flies from the culture vial containing food to the anesthetizer as follows:
a. Tap the flies off the foam plug, quickly remove the foam plug and invert the bottle
onto the small end of the anesthetizer.
b. Hold the bottles together firmly to prevent escape of any of the flies. Holding the pair
together as a unit, tap the flies into the anesthetizer. [Do not pound too hard which
can cause food to go into the anesthetizer along with the flies]
c. Quickly stopper the anesthetizer, remove the culture vial, stopper it and set it aside.
All of the flies do not have to be cleared from a culture vial at once.
3. Watch the flies closely and open the anesthetizer when the flies are quiet. Place the
anesthetized flies on a white card for examination.
4. If the flies do not stop moving then add additional FlyNap to the anesthetizer.
5. If you continue to have problems getting your flies anesthetized then ask your instructor for
assistance.
Method 2
1. Obtain a clean plastic culture vial and foam plug marked for FlyNap use. Remove the foam
plug but keep it close at hand. Obtain some FlyNap and a black anesthetizing "wand."
2. Transfer flies from the culture vial containing food to the anesthetizing vial as follows:
a. Tap the flies off the foam plug, quickly remove the foam plug and invert the empty
anesthetizer onto the culture vial.
b. Invert the entire assembly, so the culture vial is now on top.
c. Hold the bottles together firmly and tap them as a unit to force the flies into the
anesthetizer. [AVOID POUNDING]
d. Quickly stopper the anesthetizer, remove the culture vial, stopper it and set it aside.
All of the flies do not have to be cleared from a culture vial at once.
3. Dip the wand into the FlyNap and squeeze out the excess on the side of the bottle. Tap the
flies down to the bottom of the anesthetizer, push the foam plug to one side with your finger,
and insert the wand into the anesthetizing vial. The foam plug will keep the wand in place.
4. Watch the flies closely and open the anesthetizer when the flies are quiet. Place the
anesthetized flies on a white card for examination.
5. IMPORTANT! The foam plug of the anesthetizer will get FlyNap on it. Do not use this plug in
one of your culture vials since it may have sufficient FlyNap on it to kill your culture.
Figures Showing Drosophila Eggs and Larvae
Figures Showing External Structures of Drosophila
Appendix 2: draft syllabus for BI 101, Fall 2011
BI 101: Explorations in Biology-Fall 2011
Birmingham-Southern College
Course Syllabus
Class: TTh 8:00-9:20 am in SSC 134
Class Instructor:
Office Hours:
Peter Van Zandt, Ph.D. ([email protected])
SSC 246 - Monday & Thursday 1:00 – 3:00, and by appointment
Lab sections and instructors (all labs meet in SSC 101)
Lab 1 (T 12:30 – 3:20 pm): Van Zandt
Lab 2 (W 2:00PM - 4:50 pm): Shew
Lab 3 (Th 12:30 – 3:20 pm): Shew
Required materials:
1. Biology (Volume 3 – Evolution and Ecology). 2008. P.H. Raven et al. McGraw Hill:Boston, MA.
2. Lab manual. 2007. M. Gibbons, S. Duncan, H.W. Shew, and P. Van Zandt, available from the BSC
bookstore.
3. EcoBeaker manuals for a) Islands & Natural Selection, and b) Sickle-cell Alleles, both available from
the BSC bookstore.
Course Web Page: You should already have access to the Moodle page for this class. Look here daily
for lecture outlines, reading guides, figures, important announcements, extra credit opportunities, lab
assignments, data sets, etc.
Course Description:
A course for non-science majors designed to provide an understanding of selected fundamental
biological principles and processes. This course does not count towards the biology or biologypsychology major.
The class will consist of four modules, ranging from the more traditional organismal biology fields of
Ecology and Evolution to the more applied areas of Ethnobotany and Forensic Science.
Course Goals: The goals of this course are for you to:


Understand and implement the scientific method
Gain proficiency with interpreting graphs and figures





Work with classmates to better understand course concepts
Develop writing skills
Participate in class discussions
Develop critical thinking and problem solving skills
Become better informed citizens
Expectations: To achieve the goals described above, each student is expected to



abide by the Birmingham-Southern College Honor Code (see below) and all other college policies
read in advance, prepare for and actively participate in class activities
be an active participant in your education – ask lots of questions

complete the exams, quizzes, assignments, and in-class activities

respect all peers and instructors involved with this course.
Course Policies:
1. The Birmingham-Southern College Honor Code: All students in this course are expected to
maintain academic integrity and uphold the Honor Code at all times. Specifically in this course,
the following are considered violations of the Honor Code: collaborating on work assigned for
individual completion; consulting or possessing work (except exams) of those who have
previously completed this course; overstating your level of participation in a group
assignment; using unauthorized resources in the completion of exams, quizzes, and
assignments; plagiarism; turning in work that is not your own; lying, stealing, and lack of
adherence to the instructions on any examination, quiz, assignment, or course policies listed
below. You are expected sign an honor pledge on all work done for credit. Any violation of the
honor code will be reported to the Honor Council and will result in a zero on that assignment.
Penalties imposed by the Honor Council may be in addition to this academic penalty, and often
include academic probation, suspension, or expulsion.
2. Attendance & Participation: Successful completion of this course requires active participation.
Therefore, attendance in the classroom is strongly encouraged. You are expected to be on time
and to stay for the duration of the class meetings.
3. Learning Accommodations: Under the directives and guidance of the Americans with
Disabilities Act (ADA) and Rehabilitation Act of 1973, we are committed to providing appropriate
accommodations to meet the learning needs of disabled students. If you believe that you
qualify for learning accommodations based official documentation, please contact me, and
appropriate learning accommodations in accordance with the recommendations can be
arranged. It is critical that you contact me within the first week of the course so that I can make
the appropriate arrangements. If you believe that you have a learning disability, but have not
self-identified please contact the BSC Counseling and Health Services by calling x4717.
4. Communication: Office hours are Monday and Thursday 1-3 pm, but please feel free to set up
an appointment if you have class during those hours. I will check and respond to student email
and phone messages as soon as possible. An email class list will be created and used often to
communicate important information about the class, so you are expected to check your BSC
email frequently.
5. Cancellations & Time/Location Changes: If class or lab are cancelled or if there is a change in
time or location of class for any reason, an email announcement will be sent and posted on
Moodle and a sign posted on the classroom or lab door as soon as possible. In the event that
class is cancelled, you will be expected to complete the scheduled reading. You will also be
expected to complete assignments due for the cancelled class. Labs will be rescheduled if
possible.
6. Course Work & Evaluation: Letter grades, as defined by the BSC 2006-2007 Catalog, will be
assigned at the end of the course based on the number of possible points that you can earn
where 93-100% = A, 90-92% = A-, 87-89% = B+, 83-86% = B, 80-82% = B-, 77-79% = C+, 73-76% =
C, 70-72% = C-, 67-69% = D+, 60-66% = D, and <60% = F.
Point distribution
Exams
Final Exam
Quizzes
Lab assignments
Paper
Title, summary, outline
First draft
Final draft
Participation
TOTAL
1170
400 (4 x 100 ea)
200
100 (20 x 5 ea)
220 (11 x 20 ea)
25
50
125
50
Exams:
 There will be four regular exams worth 100 pts each and one cumulative final exam worth 200
pts. Each of the 4 regular exams will be designed to emphasize the material in one module, but
material may be integrated across the modules.
 Exams will include a combination of multiple choice, short answer, and essay questions relating
to your reading or information that we covered in class. You may also be asked to recall and
interpret figures from the text or from presentations, but much of the focus will be on critical
thinking rather than just memorization. You must understand the concepts in order to apply them to
new situations.
 If you know in advance that you’ll be absent during an exam I will arrange for an alternate test
that will be entirely essay based. Missed exams cannot be made up. If an exam is missed due to
extenuating circumstances, i.e., documented and Provost office-approved medical or family
emergency, the points from that exam will be assigned equally to the other exams.
Quizzes:
There will be 20 unannounced quizzes in class or lab throughout the semester, to ensure that you show
up on time, are completing your reading assignments, and are prepared for class. The quizzes should
not be difficult, provided you have done the reading. The total quiz grade will be equivalent to one test
grade. Missed quizzes cannot be made up.
Lab assignments:
See the lab manual for information on lab policies and assignments.
Paper:
Briefly, you will be required to submit a term paper on a topic from one of the four modules of this class.
The paper topic need not correspond with one of our class topics, but you will have to have your topic
approved by your lab instructor. There is more complete information in the lab manual.
Class participation:
Participation in every class meeting is important. To earn full credit, you should ask questions and
contribute your background, understanding, and opinions to class discussions.
Turnitin.com:
You will be turning in your assignments through turnitin.com, which also has tips on avoiding plagiarism.
We have begun to use the website Turnitin.com as a tool to educate our students about what plagiarism
is and how to avoid it by citing sources correctly. Talk with me if you have any problems, questions, or
concerns.
TurnItIn information on plagiarism: http://www.turnitin.com/research_site/e_home.html.
Study skills:
I strongly encourage you to visit the Study Skills web site from BSC’s Counseling and Heath Services
Website:http://www.bsc.edu/campus/counseling/index.htm. Another good resource at BSC is the
Academic Resource Center (ARC - http://www.bsc.edu/academics/arc/index.htm), which provides you
help with paper writing, study skills, and can even put you in touch with a peer tutor for your classes.
Late Assignments: Late work will always be accepted and awarded some points. Work is considered
late if not turned in when the assignment was due. If an acceptable excuse is provided, there will be
no late penalty for late work. Otherwise, late work will lose 5% of its total possible point value every
24 hours starting at the time the assignment was due. However, the maximum penalty is 50% of the
point value of the assignment to encourage you to turn in late assignments, no matter how late they
may be.
Class and Lab Schedule:
Date
Day
Week
Topic
Readings/Assignments
Labs
30-Aug
Th
1
Course introduction
none
No labs this week
4-Sep
T
2
Community ecology I
Raven et al., Ch. 56
Lab 1: Library tour / Termites
6-Sep
Th
2
Community ecology II
Raven et al., Ch. 56
11-Sep
T
3
Population Dynamics
Raven et al., Ch. 55
13-Sep
Th
3
Human Population
growth & Impacts
Raven et al., pp. 11611166; pp. 1227 -1234
18-Sep
T
4
Conservation Biology
Raven et al., Ch. 59
Lab 3: Stream Sampling
20-Sep
Th
4
Exam I
25-Sep
T
5
Darwin and Evolution
Raven et al., Ch. 21
Lab 4: Fruit fly I
27-Sep
Th
5
Genetics
Raven et al., pp. 395403
2-Oct
T
6
Natural Selection
Raven et al., pp. 404412
4-Oct
Th
6
Sexual Selection
Raven et al., pp. 11331137
9- Oct
T
7
Coevolution
Raven et al., pp. 11751178
11- Oct
Th
7
Speciation and
macroevolution
Raven et al., pp. 433452
16-Oct
T
8
Exam II
No labs this week
18-Oct
Th
8
NO CLASS
Fall Break
23-Oct
T
9
Basic Botany
Raven et al., pp. 581584; 594-602
25-Oct
Th
9
Useful plant parts
h.o. available on BB
30-Oct
T
10
Agriculture
h.o. available on BB
Lab 2: Tree Diversity
Lab 5: Fruit fly II/EcoBeaker on
Islands & Natural Selection (due
in next week’s lab)
Lab 6: Fruit fly III/EcoBeaker
Sickle-Cell Alleles (due in next
week’s lab)
Lab 7: Supermarket botany
Lab 8: Ethnobotany hike at
Ruffner Mtn. Nature Center
1-Nov
Th
10
Medicinal plants
h.o. available on BB
6-Nov
T
11
Stimulants & Drugs
h.o. available on BB
Lab 9: Worms on Drugs
8-Nov
Th
11
Exam III
13-Nov
T
12
Crime Scene
Investigation
h.o. available on BB
Lab 10: Forensic Palynology
15-Nov
Th
12
DNA
h.o. available on BB
20-Nov
T
13
Fingerprints
h.o. available on BB
22-Nov
Th
13
NO CLASS
27-Nov
T
14
Forensic Anthropology
h.o. available on BB
29-Nov
Th
14
Forensic Entomology
h.o. available on BB
4-Dec
T
15
Exam IV
12-Dec
W
FINAL EXAM (9-12)
No labs this week
Thanksgiving Break
Lab 11: Fingerprinting
No labs this week