BioIT S1 08-09: Assignment for 30 July 2008

The following groups will demonstrate the following projects on Aug 6, 2008.

All of them involve research, checking out Internet sites and biology books.

They also involve some trial and error, practice, and planning. You will be making mistakes. I therefore suggest you start immediately.

I am available the whole week to provide assistance.

I. Group 6
4 Gatorade bottles containing the following:
1. Fruitflies, all female.
2. Fruitflies, all male.
3. Fruitfly larvae only
4. Fruitfly pupae only

Discuss how you went about your project.
Describe the life cycle and anatomy of the fruitfly.
Briefly present a simple research article on fruitflies that demonstrates their usefulness to man.
Note: Your main problem is that it takes up to 10 days to get larvae and pupae; so start immediately.

II. Group 2
Construct an ant farm.
Describe how you went about your project.
Describe the life cycle, anatomy, and social structure and behavior of ants.
Briefly present a simple research article on ants that demonstrates their usefulness to man.
Note: the farm itself is easy to construct. The trick is finding the ants.

III. Group 3
Construct a Warburg apparatus and demonstrate that it works for insects.
Describe how you went about your project, from construction to calculation.
Briefly present a simple research article that used a Warburg apparatus or something similar.
Note: Any insect will do, but larger ones give better readings. The difficult part is the construction of the apparatus itself. Though most components are simple materials, the capillary tubes are very fragile, and it is a challenge to seal the connections without breaking them. The apparatus is also very sensitive--even the temperature from your fingers will cause you problems. You'll get the hang of it, though.

IV. Group 1
Determine the wavelengths of light to which Euglena are most phototaxically attracted.
Describe how you went about your project.
Describe Euglena and phototaxis in Euglena.
Briefly present a simple research article that involves Euglena and/or phototaxis.
Note: The challenge here is to construct two mini dark rooms that allows you to split light and expose parts of the culture to only one color of light. The first dark room will use multi-colored cellophane; a second darkroom will use a prism. Differences in results are expected.

V. Group 4
(Warning: Some amoeba are potentially deadly, and their cysts or eggs can remain undetected in the water sample. Thus, the project entails some risk, particulary when isolating pure amoeba. Do not touch any part of your face when working with amoeba. Wear gloves and always wash your hands before and after working.)

Isolate amoeba using agar plates and pond water.
Describe amoeba and their anatomy.
Briefly present a simple research article on amoeba, demonstrating their importance to man.
Note: Although amoeba are very common in the wild, it is not guaranteed that you will be able to isolate them. Knowing where to look and how to collect ups your chances. And since they are transparent, they will not be easy to detect. That's what the agar is for: we will detect them because they eat the agar and will form visible canals.

VI. Group 5
Produce zebrafish embryos, and present a slide show of photographs you took in the course of observing their development.
Describe how you went about the project.
Describe zebrafish, their anatomy and life cycle, and their embryonic development.
Briefly present a simple research article on zebrafish, demonstrating their importance to man.
Note: The big challenge here is how to separate the females from the males. Getting the embryos is easy after that.

BioIT Sem 1 08-09: Protists

Microscopic animals and their parts

1. Paramecium
a. Cytoplasmic streaming: moving cytoplasm around the edges of the animal
b. Contractile vacuole: located centrally; circular; tends to shrink and expand; there may be two of them
c. Nucleus: dark-colored central body; usually circular
d. Peristome: median location; the funnel-shaped opening that leads to the esophagus
e. Esophagus: constriction that leads from the peristome to the food vacuole
f. Food vacuole: end of the esophagus; dark-colored if it contains food

2. Rotifer (multicellular)
a. Corona: the anterior ring lined with ciliated cells
b. Eyespot: small dark-colored spot located immediately posterior to the corona
c. Stomach: large, central, dark-colored chamber (if it contains food)
d. Vitellarium: the outer transparent skin
e. Foot: the long posterior organ that serves for attachment
f. Toe: the end of the foot

3. Planaria (multicellular)
a. Ocelli: the two eyespots
b. Mouth: the opening of the gastrointestinal tract, located ventral and medial
c. Pharynx: passage from the mouth to the two lateral branches of the gastrointestinal tract

4. Hydra (multicellular)
a. Mouth: located at the base of the tentacles
b. Tentacles: arms
c. Ectoderm: the outer layer of the skin
d. Gastroderm: the lining of the digestive cavity
e. Digestive cavity: hollow cavity where digestion takes place
f. Mesoglea: layer of cells between the ectoderm and the gastroderm

5. Euglena
a. Flagellum: whip-like motor organelle located posteriorly
b. Nucleus: large, round, central, dark-colored body; distinguished from the smaller eyespot
c. Eyespot: small, red-colored photoreceptor located anteriorly
d. Chloroplasts: green-colored organelles generally distributed throughout the body

6. Vorticella
a. Three rows of cilia: motile organelles located anteriorly forming three rows
b. Buccal funnel: or mouth; at the base of the rows of cilia
c. Superficial pellicle: the outer covering of the animal
d. Vacuole: contractile organelle located inside the animal
e. Macronucleus: central, dark body containing DNA; in the form of a horse-shoe
f. Peduncle: coiled spring-like appendage that attaches the animal to the substrate

REPORT ON

1. Taxonomy, anatomy, habitat, and food requirements.

2. Significance to humans. Summarize a recent research article to illustrate. For example: Upadhyaya A et al. Power limited contraction dynamics of Vorticella convallaria: an ultrafast biological spring. Biophys J. 2008, 94(1):265-272. “Vorticella convallaria is one of the fastest and most powerful cellular machines. The cell body is attached to a substrate by a slender stalk containing a polymeric structure---the spasmoneme. Helical coiling of the stalk results from rapid contraction of the spasmoneme, an event mediated by calcium binding to a negatively charged polymeric backbone. We use high-speed imaging to measure the contraction velocity as a function of the viscosity of the external environment and find that the maximum velocity scales inversely with the square root of the velocity. This can be explained if the rate of contraction is ultimately limited by the power delivered by the actively contracting spasmoneme…etc.”. Explain this to us in layman’s terms, especially the significance to humans. You may use illustrations and other strategies to make the presentation good. Suggested sources: PUBMED (a search engine that will give mostly summaries); Scientific American.

BioIT Sem 1 2008-2009: Assignment for the next 3 wks

We are going to have a free cut on the 16th of July as I will be out of town. To ensure you have a productive time, here is an assignment that I hope will challenge and entertain you.

It's called ARTIFICIAL LIFE.

Instructions (per group)

1. Search the Internet for simple simulation freeware. There are many; these include Framsticks, PhyloStrat, Simulistics, Boppers, Game of Life, etc. I recently found a good one (demonstrations.wolfram.com) which features thousands of simulations. For example, the Predator-Prey demo, a rather good model for rabbits and foxes, and viruses. You'll need to install the free Mathematica Player for this. These programs were designed as research tools to experiment on various aspects of life such as metabolism, ecological interaction, and evolution. SimCity and other such "games" are not allowed.

2. Study the documentation and examples. Play around a little. This playing part should take up more than half your time!

Then design and carry out an experiment in that virtual world.

a) What is/are the questions you would like to answer? Typical questions include "what if" (e.g. what would happen if I adjust the growth rates of predator and prey just so?); "what model explains" (e.g., the algae experiment); "compare and contrast" (e.g., which is better, grass tea or wheat tea for growing paramecium); and "classification and patterns" (e.g., how many kinds of general growth curves are there).
b) What is your tentative answer?
c) What experiment can you do to prove your answer is wrong? What data will prove you wrong?
d) In case your experiment proves your answer wrong, test other answers.
e) Right or wrong, prove everything with data.

3. Have me approve your problem first. Give me also a short description of the program and your approach. You may submit this as a comment on this blog.

3. Groups may use the same software, but they can not answer the same problems.

4. Each group will make a presentation on the 23rd July that will cover:

a) Introduction. Background and significance (yes, your problem should have significance) of the problem. Background of the software. Summary of the experiment and its results.
b) Methods and Materials
c) Data
d) Discussion. Includes possible weak points about your approach.
e) Conclusion and proposals for future work.

4. Not everyone has to speak; but everyone has to work.