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carnivores teeth length VS. their skull length

Carnivorans include carnivores, omnivores, and even a few primarily herbivorous species, such as the Giant Panda. Important teeth for carnivorans are the large, slightly recurved canines, used to dispatch prey, and the carnassial complex, used to rend meat from bone and slice it into digestible pieces.

ferret

We compare the carnassial teeth of carnivores with their skull lengths to see if there is any correlation between these two characteristics.

We intended to do a pretty graph like everyone else. But we failed. Sorry, all we can provide is this ugly thing below.

e69caae591bde5908d1

Whales in Tubs

13360-happy-blue-whale-in-a-bath-tub-throwing-soap-up-into-the-air-clipart-illustration

Group:
Dylan Storey, Ayla Norris, Letitia Olson

Project:
We decided to compare the length of the whale to the length of their pectoral fin.  Using google image search we accessed a large variety of whale images.  We loaded these pictures into ImageJ and measured the length of the whale from the nose to the end of their body (not including their tail fin).  Then we measured the length of their pectoral fin from where it joins the body to the tip of the fin.  Taking into account the curve of body and fin using the freehand tool.
Using excel we created a bar graph showing the variation in the body length vs. fin.

We found that there is a large amount of variation between and within species of whale.  This could be due to the age and maturity, and position of whale in the pictures.  Since they are not all positioned the same direction some error occurs despite our use of the free style tool.

killer_whales-13564

finwhale

Relative Weight of Dogs and Their Owners by Jennifer and Dmitriy

Hypothesis: The ratio of owner to dog body width remains relatively constant and should produce a bell curve indicating that owners and dogs share a relative size ratio. (ie if the owner over-eats, then they tend to allow their dog to over-eat.)

We found that the dogs tended to mirror their owners in relation to relative weight gain. Bigger owners tended to have bigger dogs, smaller owners had smaller dogs. Although there were several cases where larger owners had smaller dogs and vice versa. The dog vs owner relative size centers around 1.5.

121

One photo used to determine the owner vs dog ratios.

Proportion of land area occupied by different things

picture-2 

knoxville

 

 

 

Knoxville

proportion of land occupied by various things

proportion of land occupied by various things

Oak Ridge

proportion of Oak Ridge occupied by various things

Our goal was to compare a larger city such as Knoxville with a smaller city such as Oak Ridge.  We wanted to focus on large structures and objects that would help us to compare the two cities in terms of population density and industrialization.  We measured the land area occupied by three types of things: buildings, parking lots, and everything else.  We created a pie chart to help describe what proportion of the land area is occupied by these things.  We hypothesized that Knoxville would have a higher proportion of its space occupied by buildings and parking lots because of its higher population density and industrialization.  Our hypothesis was largely supported by the data.  Knoxville did have a greater proportion of its land area occupied by buildings.  The difference in area occupied by parking lots was small.   Oak Ridge had much more of its land area occupied by other things.   We believe further that further observation and analysis may reveal that this other area is composed mostly of open undeveloped land.

Variation in Distance Between Buildings in Three Major Cities by Lenora and Keats

ParisWe measured 20 distances between buildings from arial views of New York City, Paris and Beijing found using Google Maps, and compared the average distance between buildings for each of these cities as well as the standard deviation of distances within a city. We hypothesized that Beijing would have the least distance between buildings while Paris would have the most. We also hypothesized that New York City would have the least variation in distance. Our data indicated that New York had the most distance between buildings while Beijing had the least. New York did have the lowest standard deviation of the three cities, however, none of the differences are statistically significant given that the variation among distances within the cities is larger than the variation among building distances between the cities.

 

building-distance

Starry Night: Brittany and Randy

Hypothesis: In a night sky, two bright stars will be on average farther apart from each other compared to two dim stars.

To test our hypothesis, we opened an image of a stary night sky, http://blogs.yogajournal.com/night%20sky.jpg, in ImageJ and measured the distances between stars in units of pixels. We imported our data into an excel spreadsheet to compare average distances. The average distance, in pixels, between two bright stars is 103.68, and the average between two dim stars is 14.89.

Conclusion: Based on the data collected, we fail to reject our hypothesis. Another direction that could be taken is the why behind the question. Is there a reason the brighter stars are further apart on average when compared to dim stars.

graph

Wnt protein

By Xiaomin and Jianzhuang

Introduction: Wnt proteins form a family of highly conserved secreted signaling molecules

that regulate cell-to-cell interactions during embryogenesis. Wnt proteins bind to

receptors of the Frizzled and LRP families on the cell surface. Mutations in Wnt genes or

Wnt pathway components lead to specific developmental defects, while various human

diseases, including cancer, are caused by abnormal Wnt signaling.

Bibliographic reference

The Wnt Homepage [http://www.stanford.edu/~rnusse/wntwindow.html]

Cohen ED, Tian Y, Morrisey EE. Wnt signaling: an essential regulator of cardiovascular

differentiation, morphogenesis and progenitor self-renewal.
Development. 2008 Mar;135(5):789-98.

Species used in the alignment:
CLUSTAL W (1.81) multiple sequence alignment

Q8VEJ3 ——KGQEGESCLRTSDCGPGLCCARHFWTKICKPVLREGQVCSRRGHKDTAQAPEIF
Q9UBT3 ——KGQEGESCLRTFDCGPGLCCARHFWTKICKPVLLEGQVCSRRGHKDTAQAPEIF
Q9UBU2 –MSHIKGHEGDPCLRSSDCIEGFCCARHFWTKICKPVLHQGEVCTKQ-RKKGSHGLEIF
2jtk_A GSMPHIKGHEGDPCLRSSDCIDGFCCARHFWTKICKPVLHQGEVCTKQ-RKKGSHGLEIF
Q9QYZ8 –MPHIKGHEGDPCLRSSDCIDGFCCARHFWTKICKPVLHQGEVCTKQ-RKKGSHGLEIF
O94907 –MYHTKGQEGSVCLRSSDCASGLCCARHFWSKICKPVLKEGQVCTKH-RRKGSHGLEIF
O54908 —-HTKGQEGSVCLRSSDCAAGLCCARHFWSKICKPVLKEGQVCTKH-KRKGSHGLEIF
**:**. ***: ** *:*******:******* :*:**:.. … ::. ***

Q8VEJ3 QRCDCGPGLTCRSQVTSNRQH–SRLRVCQRI
Q9UBT3 QRCDCGPGLLCRSQLTSNRQH–ARLRVCQKI
Q9UBU2 QRCDCAKGLSCKVWKDATYSSK-ARLHVCQKI
2jtk_A QRCDCAKGLSCKVWKDATYSSK-ARLHVCQKI
Q9QYZ8 QRCDCAKGLSCKVWKDATYSSK-ARLHVCQKI
O94907 QRCYCGEGLSCRIQKDHHQASNSSRLHTCQR-
O54908 QRCYCGEGLACRIQKDHHQASNSSRLHTCQR-
*** *. ** *. . :**..**.

image

interpretation of the results

The highly conserved domain are almost in the surface of three-dimension structure, which

are in purple color. The inner part of the protein are variable.

questions you are still working on

We can see large part of yellow color in the image. That means there are still some

insufficient data about the conservation of this protein. We need further research on the

yellow part.2jtk

Consurf Activity Cytochrome C

Goup:
Ben Ernest, Joel Bucci, Letitia Olson

Intro:
Cytochrome C oxidase is an enzyme in the electron transport chain that catalyzes electron transfer to reduce oxygen to water.  This reaction produces protons, which are then used to power the ATP synthases

Reference:
Axel Harrenga and Hartmut Michel. The Cytochrome c Oxidase from Paracoccus denitrificans Does Not Change the Metal Center Ligation upon Reduction. J Biol Chem, Vol. 274, Issue 47, 33296-33299, November 19, 1999

Species:
Paracoccus Denitrificans

Aligned against:
Rhodobacter sphaeroides
Rhizobium leguminosarum
Rickettsia felis
Rickettsia bellii
Rickettsia prowazekii
Rickettsia conorii
Marchantia polymorpha
Beta vulgaris
Bradyrhizobium japonicum
Zea mays
Aegilops columnaris
Arabidopsis thaliana
Prototheca wickerhamii
Glycine max
Cyanidium caldarium
Pisum sativum
Chondrus crispus
Oenothera bertiana
Acanthamoeba castellanii
Ustilago maydis
Phytophthora megasperma
Metridium senile
Emericella nidulans
Neurospora crassa
Etc…

Image:

cytochrome-c-oxidase1

Results:
Degree of conservation is high in the interior of the protein and more variable on the surface.   More specifically, the copper-binding site (indicated by the arrow), which is essential for protein function, due to its role in accepting electrons, is very highly conserved.

Questions:
Is the copper binding site the active site?
How does protein structure change when copper is reduced?

Protein Luciferase: Lenora & Elizabeth

Intro:

This particular enzyme is an oxidative enzyme that imparts bioluminescence to the firefly Photinus pyralis. In research, the enzyme is used to study anesthetic-protein interactions.

Ref:

Structural basis for the inhibition of firefly luciferase by a general anesthetic.
Franks, N.P.,  Jenkins, A.,  Conti, E.,  Lieb, W.R.,  Brick, P. Biophys.J. v75 pp. 2205-11, 1998

Image:

Interpretation: Most of the enzyme is variable except for a small site we believe to be the oxidation site for luciferin.

Questions:

Biological: Why is most of the protein  variable? What does this mean about the structure of the protein?

Technical:  How do we get the rotating space filled model into this blog.

Gyrase: Brittany and Randy

Intro: Gyrase is a protein involved in maintaining the negative supercoiled structure of DNA. It is a two subunit protein and its function in DNA is ATP dependent. Because of its function gyrase is involved in many DNA associated processes including replication, transcription and repair.

DNA Gyrase: Structure and Function
Reece, R.J.; Maxwell, A
Crit Rev Biochem Mol Biol. 1991;26(3-4):335-75.

 

1ab4_bio_r_500.jpg

When viewing the space filled model, the outer region of the protein appeared to be variable while the inner region was more conserved. A link showing the space filled model is below

http://consurfdb.tau.ac.il/fgij/fg.htm?mol=/temp/1AB4A_ConSurf_DB_pipe.pdb

 

We had difficulty copying the space filled model into the blog. How can this be done?