Genealogical Experiment of Fish Types

Genealogical Experiment of Fish typecastsDavid HessAbstractTo introduce us to proteins, which truly make one organism different from another in terms of phenotype, our instructor challenged us to study the visible and proteomic traits of salmon, cat tilt, turbot, hali scarce, and yellow-fin tuna and estimate how each fish is related on the evolutionary tree. To do so, our lab assort first accessed online research websites to compargon the phenotypes of the different Ichthyoids. We specifically researched sizes, swim types, biological features, habitat preferences, and taxonomic names that derive from the evolutionary tree. After this, we then obtained samples of the musculus tissue in each fish, which were provided by the instructor, and then extracted the proteins from each sample. By treating the samples with sodium dodecyl sulfate and applying heat. We were able to denature theD1 tertiary and quaternary structures of the proteins, which left-hand(a) the proteins long, stringy , and negatively charged. Next, we were able to separate the proteins by length a la gel electrophoresis, and comp be the different proteins in the fish as we observed the different exclude that appeared on the gel. After comparison both the physical traits and the proteins in each fish, we were to predict which species preceded the next according to evolution.PurposeThe purpose of this lab is to study the physical attributes and proteomics of different species of fish to determine the potential genealogical tree connecting these speciesInstructor/BackgroundProteins often bind together, forming polypeptide chains. Some atoms on these chains are hydrophilic, tour others are hydrophobic. This is due to the fact that the different r- crowds (the only part of an amino acids that distinguishes it from another), may or may not form hydrogen bonds with the water molecules that they are summered in. When a hydrophobic group enters the body of water, the hydrogen bonds in the water break apart, yet fagnot bind to the r group on the amino acids, so the water forms bonds with itself again around the r-group, thus pushing the r-group away due to the magnetic forces that push similarly charged atoms away from eachother. However, if a hydrophilic group is exposed to water, hydrogen bonds are formed with the r-group, pulling the r-group out of the remaining protein structure due to magnetic forces pulling the two bodies together as they are oppositely charged. These two interactions cause the protein to bundle up, making it hard to perform accurate gel electrophoresis on. It becomes especially difficult when these proteins bind together with disulfide bonds. light up and sodium dodecyl sulfate break apart the disulfide and hydrogen bonds. This allows us to separate the proteins in electrophoresis, which can then be compared. AData/Organization D2of RecordsThe following data results from reseach using the Fishbase website to compare phenotypes between the studied fish v ernacular NameSalmonscientific FishOncorhynchus Ketataxonomic courseificationFamilySalmonidae (Salmonids)OrderSalmoniforms (Salmons)ClassActinopterygii (Ray-Finned Fish)Size gook Published Weight 15.9kgEnvironmentMarine Freshwater brackish Benthopelagic AnadromousDepth compass 0-250mBiologyInhabits Ocean and Coastal streams. Adults complete eating in freshwater. Die After Spawning. Migrating fry forms instills in estuaries, remain close to shore for a few months, and disperse and enter into the sea. Epilegic.Swim TypeAnguilliform (Moves Body and Caudal Fin) additional FactorsDefinitions of unknown TermsEpilogic-Living in the upper zone of the ocean from just below the surface to about 100m in perspicacityCommon NameHalibutScientific FishHippoglossus HippoglossusTaxonomic ClassificationFamilyPleuronectidae (Right-Eye Flounders)OrderPleuronectiformes (Flatfish)ClassActinopterygii (Ray-finned Fish)SizeMax enter Length 470.0cmMax Recorded Weight 320.0kgEnvironmentMarine DemersalD epth 50-2000mBiologyAdults are Benthic, but occasionally Pelagic. Feeds mainly one other fishes, but also eats cephalopods, large crustaceans, and other bottom-living animals. Seriously affected by overfishingSwim TypeAnguilliform Body and Caudal FinAdditional FactorsDorsal SpinesDefinitions of Unfamiliar TermsBenthic stick ups one the bottom of a body of waterPelagic Lives far away from landCommon NameCatfishScientific FishNeoprius GraeffeiTaxonomic ClassificationFamilyArildae (Sea Catfishes)OrderSiluriformes (Catfish)ClassActinopterygii (Ray-Finned Fishes)SizeMax Length 60.0cmEnvironmentMarine Freshwater Brackish DemersalPH Range 7.5-8.2AnadromousBiologyInhibit freshwater rivers and lagoons, Brackish estuaries, coastal marine waters. Feeds on arthropods, insects, aquatic plants, mollusks, prawns, crayfish, fishes, and bottom detritusSwim TypeAnguilliform (moves body and caudally fin)Additional Factors1 Dorsal spine, 7 dorsal soft rays, and 15-19 soft anal spinesDefinitions of Un familiar TermsAnadromous Migrates from freshwater to spawn in salt-waterCommon NameYellowfin TunaScientific FishThunaus AlbacararesTaxonomic ClassificationFamilyScombridae (Mackerels, Tunas, Bonitos)OrderPerciformes (Perch-Likes)ClassActinopterygii (Ray-Finned Fishes)SizeMax Weight 200.0kgMax Length 230.0cmEnvironmentMarine Brackish Pelagic-Oceanic OceandromousDepth Range 1-250mBiologyLives above and below thermoclines, Pelagic in open water, rarely seen around reefs, school by size, large fish school with porpoise, sensitive to low concentrations of oxygen, resides near ocean debrisSwim TypeAnguilliform (Movements of body and/or Caudal fin)Additional Factors11-14 Dorsal Rays, 12-16 Dorsal soft rays,11-16 Anal Soft Rays, 39 VertebraeDefinitions of Unfamiliar TermsCommon NameTurbotScientific FishScophthalmus MaximusTaxonomic ClassificationFamilyActinopterygii (Ray-Finned Fish)OrderPleuronectiformes (Flatfish)ClassActinopterygii (Ray-Finned Fish)SizeMax Published Weight 25.0kgEnvironm entMarine Brackish Demersal Oceandromous TemperateDepth Range 20-70mBiologyLive one sand, rock, or mixed bottom. Almost Circular Bottom. Eye side without scales, but instead bony tubercles. Feeds one bottom-living fishes (sand eels, gobies, etc.) and larger crustaceans and bivalves. Lives especially in Brackish WatersSwim TypeAnguilliform Movements of body and/or caudal finAdditional FactorsLarvae are initially systematic, but after 40-50 days, the right eye moves to its left side.Definitions of Unfamiliar TermsOceandromous migratory one salt-waterUpon the conclusion of our lab, we obtained a gel with protein bands that looked like this The following graph shows a standard curve based on the distance that the bars travelled and the angle of said barsThe following accede describes the distances various bands of proteins moved down their wells. We would use this information to calculate the weight of these bands by comparing them to our standard curveD3By using the band distances an d the standard curves that we made, we were able to calculate the weight of these protein bands in Kilo DaltonsBy comparing the bands on the gel, our lab group made the following tables showing which fish had certain proteins in their muscles tissue.*Each, X represents the presence of the mentioned protein on the left-hand side of the table in the fishThis table compares the proteins located in the chart above, and shows the similarities of proteins between the species.ResultsUpon the completion of the analysis of our results, we obtained the following CelptogramD4. We knew that Species E only shared a joint protein with species B, so it undeniable to be on one of the ends of the CleptogramD5. We also noted that species C and D shared multiple common proteins in common, so they needed to be close together on the tree. During our analysis of the proteins, our teacher identified which letter represented each fish (it had remained a blind experiment up till this point) as the followi ngFish A-SalmonFish B-Yellow fin TunaFish C-HalibutFish D-TurbotFish E-CatfishWith this extra information, we were able to analyze both our results and the evolutionary tree to create the cleptogram. For example, we noticed that species C and D both had a similarity with D, so we looked at the evolutionary tree to measure whether Tuna or Halibut were closer to Salmon evolutionarily to finish our prediction.DiscussionWhen reviewing the data once more, we noticed some discrepancies in our cladogram compared to the evolutionary tree. For example, our Yellow-fin Tuna found its way onto the set about of the tree, when it should have landed near the end according to the evolution tree in our packet. Otherwise, we believe this experiment D6was a success, as we learned about how proteins can be used to supplement genetics and give us another creature in understanding our history. This could possibly be result of contamination in the fish muscle samples, due to touching the muscles with th e same pair of gloves when transferring them into the tunes for protein extraction. If we were ever to do this experiment again, we would be sure to use tweezers of another similar tool to handle the muscles.Work citedHydrophobic_Interactionshttp//chemwiki.ucdavis.edu/Physical_Chemistry/Physical_Properties_of_Matter/Atomic_and_Molecular_Properties/Intermolecular_Forces/Hydrophobic_interactionsD1Include secondary here as well.Get this publishedhttp//www.journys.org/content/proceduresD2Could this have been organized into a data table which contains all the fish and is still able to describe these different features of the bioinformatics?Thank you for getting the bioinformatics in hereD3Good connection between data sets.D4cladeogramD5?D6Great work This experiment went swimmingly Hah