Writing in Biology

For our project proposal my group had two different ideas. The first idea that we had was to monitor the behavior of ducks and geese on the campus pond. We would monitor many different things in order to create nine separate research projects that every group could complete. One thing that we would test is the correlation between the weather and how many geese or ducks would be on the pond. Another thing that we would try and measure is how many ducks and geese are on the pond at a specific time of the day. To do this a group would need to take measurements at multiple time periods throughout the day. Another thing we would try and measure is how the ducks and geese reacted when people were nearby. Did they leave the land to go in the pond during class transitions? Did they leave the pond all together? Were they inclined to come up to the people? Questions along those lines. Another key aspects of this question that we would try and test is the ratio between ducks and geese on the pond at any given moment and if anything changes to affect the ratio of them. To better understand this last aspect we must first find any correlations within the previously mentioned questions.

When a geneticist is given an unknown DNA sequence and is tasked with finding out its function, there are two approaches.  Ab initio, or “from the beginning” involves using programs that analyze the sequence for known trends in gene expression. These trends include translation initiation occuring at ATG, and intron boundaries being defined by GT at the beginning and AG at the end.  Stop codons include TAG, TAA, and TGA. Using these in combination with more complex trends of gene expression, ab initio programs can make a prediction about the coding sequence and protein sequence of a gene. The other method is homology based searches. These include comparing a query sequence to sequences of nucleic acids of a known origin. In this lab, we begin by building two predictions of the protein our gene encodes: one using ab initio methods and another using homology based methods.  For the ab initio method, we use the program FGENESH. For the homology based searches, we use Phytozome and NCBI BLAST. We compare the two predictions and proceed to research our gene of interest.  We then provide an assessment of function of our gene.  

The Swainson hawk is a type of buteo that is a long distance migrant that breeds along the west of the United States. This large predator has an average length of 19-22 inches, and a wingspan of 46-54 inches. It prefers to hunt in open areas, in habitats such as plains, farmlands, or dry grassland. Although the bird is large in size, it primarily feeds on small birds, small mammals, reptiles, and catching insects midair. In contrast, another type of buteo is called the Broadwing hawk, located in the east of the United States. The Broadwing hawk is among the smallest of buteos, with length of 13-18 inches, and a wingspan of 32-38 inches. It has a broader diet than the Swainson hawk, but it is comprised of similar items. This bird prefers to hunt from a perch, waiting for prey along woodland/forest edges and near water. Broadwings seems to prefer forests to wait for insects while the swainson will catch insects midair in the clearings. Broadwings don’t prefer to hunt on the wing, and have smaller more rounded wings. I would guess that because they do not hunt on the wing as frequently, they do not need to have large wings like the Swainson, which primarily hunts while soaring.

Birds use visual landmarks to help them travel and migrate long distances. Pigeons, for example, use railways, highways, and rivers even if routes are not direct. Some waterfowl follow watercourses to help them migrate but often they are scared to cross open bodies of water unless it is windy. They also use the sun as a compass. Homing pigeons and common starlings follow the sun to lead them home and will not travel until they can see the sun.

When fear strikes your body, you react almost instantaneously. What happens is first, the amygdala activates right before you consciously process the problem and begins the fight-or0flight response. The hippocampus and frontal cortex then kick in which are the rational center of our brain and help analyze whether the input is a true danger. The cardiovascular system increases the breathing rate and heartbeat while dilating and allows more oxygen to reach your muscles. The signals then reach the endocrine glands where a surge of adrenaline and cortisol are the result. The endocrine signals push glucose and other molecules out of reserve and into the blood which rushes into the muscles and you respond with a fight or flight.

Tympanoctomys aureus, also known as Golden Vizcacha Rat, is a species that is classified as critically endangered from the South American country of Argentina. Its habitat includes the wetlands and the population of the species has been decreasing. The major threat to this species has to do with the loss of its habitat which is due to agricultural expansion that is occuring in Argentina. All of the indiviuals of this species live in a single location that is less than ten kilometers squared large. The threats are not solely argicultural they also have to do with annual and perennial non-timber crops, small farming, and agro farming. There is no solid information available on the population status of this species. There is no known conservation actions taking place to ensure that this species begins to thrive. 

There are multiple methods to identify the protein coding portions of a gene. Ab initio, meaning “from the beginning,” methods use general rules about coding versus non-coding regions to predict the structure of new genome sequences with no given information. On the other hand, homology-based methods give a more reliable interpretation of an unknown gene, matching the gene to known sequences to predict its structure. The unknown gene is matched to expressed sequence tags (ESTs), sequences derived from cDNA clones; however, the cDNA is already shorter than the mRNA it is a copy of, and the EST contains errors when sequenced from its cDNA. ESTs that perfectly or almost perfectly match the unknown can then be combined based on overlapping regions to create a consensus sequence called a “contig.” Contigs can then be compared to the full-length cDNA of the gene to determine which consensus sequence matches closely.

The function of an unknown gene can also be predicted through thorough research. Because there is such an extensive library of sequenced genomes, there is almost always a close sequence match when comparing an unknown gene; however, the function of these genes are still a mystery. Predicting the function of an unknown gene usually starts with bioinformatics, where computer software is used to access genomics data and match similar DNA and protein sequences to the unknown. Information on these related proteins can then be further researched through online and physical libraries to predict the function of the unknown.

Cetaceans are split into two main Suborders: S.Mysticeti and S.Odontoceti. Suborder Odontoceti contains all the toothed whales, and there are features common to all families in the suborder. These include the presence of teeth, an asymmetrical skull (likely used in echolocation), a single external nares, and a melon. The melon is an oil-filled structure most evident in sperm whales that is thought to be used to focus sound during echolocation. Odontocetes also have an ear bone (petrosal) that is surrounded by sinuses and entirely disconnected from the skull, which serves to reduce the vibrations passing into the bones of the skull. In Mammalogy lab we looked at four of the families of Odontocetes: F. Delphinidae (dolphins), F. Phocoenidae (porpoises), F. Monodontidae (belugas and narwhals), and F. Physeteridae (sperm whales and pygmy sperm whales). F. Delphinidae have a beak-like snout, conical teeth, a skull that is concave from the tip of the premaxillary bone to the nasals, and flippers that are shaped like sickles. F. Phocoenidae on the other hand have spade-like teeth, a blunt rostrum, and flippers that are paddle-shaped. F. Monodontidae have skulls that in profile look flat or convex, forward-pointing conical teeth, and do not have a dorsal fin. F. Physeteridae have the most asymmetrical skull of all the Odontocetes and do not have teeth in their upper jaw.