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If there is only enough vaccine to save one pregnant mother and her puppies, the German Shephard dog breed should be saved. These dogs are confident, courageous, smart and are highly ranked due to their loyalty. These large muscular dogs are a preferred breed for many types of work including disability assistance and many police distinguished roles (Greenberg, Aurora). These dogs are dog kind’s finest all-purpose worker as their trainability exceeds that of many other breeds of dogs. German Shepherds require lots of movement and exercise, but the breed is very easy to maintain “usually requiring just a quick brushing every few days or so” making them simple to groom and manage (Greenberg, Aurora). Every family deserves to experience life with a loving and protecting dog. What was once a mutual service contract between two very distinct species became something much more like love. Being able to save this breed, will allow people to become more joyful and live the life they enjoy with this outstanding breed of dogs. 

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 occurring 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.  One database includes expressed sequence tags (ESTs), which are sequences derived from cDNA clones.  A set of ESTs can be joined together to form a consensus “contig” sequence, which can then be used to find an mRNA for the gene.  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.  Both programs output predicted intron-exon boundaries as well as a predicted protein sequence.  We compare the two predictions and finalize our working map with intron-exon boundaries and a predicted protein sequence, keeping in mind the differences between ab initio and homology-based searched.  We then proceed to research our gene of interest and provide an assessment of function of our gene. 

The combination of our target corridors and habitats, total to a cost of 5 million dollars which is directly in line with our budget. All of our financial resources will be used to their fullest potential as the impact of the protected habitats and corridors will allow for the continued gene flow and safe passage from one jaguar population to another. There will be $2,650,000 allotted to the conservation of certain corridors while the remaining $2,350,000 will be used to protect valuable populations throughout South and Central America.Affected by habitat loss, fragmentation, human wildlife conflicts and illegal wildlife trade, jaguars are a species that face the risk of extinction as a direct result of human actions. Although countless populations continue to decline through poaching, ecosystem degeneration, and human intolerance, there is hope. Through our efforts in preserving jaguar habitat patches and corridors, jaguars are able to disperse, bringing new genetic material to new areas to increase genetic variability which helps to preserve populations. Choosing to conserve habitat patches of decreasing species allows them the ability and space to grow, while conserving areas of stable populations provides healthy populations. Preserving the corridors which connect these two permits jaguar populations to expand their gene pool which in turn promotes the best traits to be selected which will allow the species to better adapt and survive.

If there was a new retrovrius killing domestic dogs, but we could save one pregnant mother, the breed of dog we should save is the Poodle. This becuase Poodles are both family friendly and highly intelegent - the most intelligent of all dog breeds. These dogs not only make great family pets, but they can be trained for special and specific purposes. 

Poodles make great pets because they are loyal, alert, and trainable. Poodles are hypoallergenic, which would allow people with allergies to dog hair to also be able to have a dog as a pet. They are also highly intelligent which means they could be trained easily and could be used as service dogs and support animals. They were originally bred to be hunters, which could be useful if there were ever times of food shortages.  The dogs are good swimmers and known to have soft mouths which allowed them to gently recover hunters prey. All in all, because Poodles are good family pets and could be useful to society, they are the breed of dog that should be saved if there was ever a retrovirus. 

We have chosen habitats 11 and 12 because their populations are below 50 and steadily decreasing; it is essential that we protect these areas so that the two populations do not go extinct. Similarly, habitats 13 and 14 hold decreasing  populations. As a result. we must conserve corridors W, U, V, and T. Since U and V connect 11 and 12 to 13 and 14 , W connects these populations to habitats 15, 16, and 17, all holding stable populations. We will conserve these steady populations because it is important that the depleted and decreasing populations have access to healthy ones in order to increase genetic variability. We have also chosen to protect habitat 20 because although it is further from our other chosen areas, the location itself holds minimal data on jaguar population status. This area is critical for further research to determine if it is in danger or not. Likewise to corridor W, we will protect corridor T because this connects the decreasing populations to habitat 2 which is a large, stable population. It will be preserved like habitats 15, 16, and 17 to increase the jaguar population gene pool which allows for better adaptation and survival rates. Next to habitat 2, we will also conserve corridor A connecting to habitat 1 because although habitat 1 is currently stable, if this population were to become cut off from habitat 2 it would fall at risk to inbred populations. Additionally because it is located further north, this will allow for further jaguar migration and dispersal to different areas in the north. Next to habitat 2, we will protect habitats 3 and 4 due to decreasing population and by connecting them we hope to stabilize habitat 2 with more migration. Along these lines, corridor E will be conserved so that it may bridge together habitats 3 and 4 with 6, 7, and 8 to allow for dispersal of varied populations. Habitats 6 and 7 both contain populations that are below 50 animals and steadily decreasing, so conserving and connecting these to neighboring populations should preserve these populations from total extinction and allow them to grow. Finally, we will protect habitat 8 because it is the only piece of land connected to the decreasing populations in habitats 6 and 7, therefore allowing these populations to intermingle. This  will help them to maintain a diverse gene pool and increase overall population size.

In a 25 mL Erlenmeyer flask benzoin (0.503 g) and ethanol (4.0 mL) was added and swirled until dissolved. Sodium borohydride (0.1 g) was added with a microspatula over five minutes. Mixture was gently swirled for 20 minutes. Mixture was cooled in ice-water bath. Water (5.0 mL) and 6 M HCl (0.3 mL) was added. Water (2.5 mL) was added 15 minutes later. Product was collected via vacuum filtration. Solid was washed with ice-cold water and dried on filter for 15 min. Crude yield and MP determined. Crude material (1.5 mg) was reserved for TLC. Crude solid was recrystallized from acetone with 25 mL Erlenmeyer flask. Melting point and percent yield was determined. Benzoin, recrystallized product, and crude product was dissolved in ethyl acetate in three vials. TLC plates was spotted and run in 9:1 CH2Cl2:ethanol in capped chamber until 1 cm from top. Spots viewed under UV light and marked.

After modeling two reserves after the example C, I wanted to increase the heterozygosity while increasing the number of runs without a lost of alleles. The best way to do this was to increase the size of the individual populations. I went from four to three habitats to achieve this and was successful. As you can see in the table above, the heterozygosity went up from 0.18 to 0.23, and there was one run more than the Reserve C that did not lose an allele. Out of 20 runs, these are very impressive results. This makes Reserve 1 the “best” fit reserve for the population of ferrets and will promote the success of more and more generations. In comparison to reserves A and B, Reserve 1 is much more successful. It is clear that the best reserve uses parts of each example to achieve a better grouping of habitats. In Reserve A, the size of the population was a successful way to promote the movement of genes through a population, however it reached fixation many times. In Reserve B, the generation of ferrets was represented in 4 separate habitats. This was not very successful as the habitats heterozygosity was minimized and fixation was reached very fast with such small populations. However, the idea to promote different alleles by separating the generation gave inspiration for genetic drift in Reserve C. As explained before, this reserve gave inspiration to both custom reserves, but itself was not successful enough because the distribution of populations was still too small. To avoid sampling error from small populations, and to still achieve the flow of diversity throughout the populations, Reserve 1 was the best model to save the ferrets with successful genetic drift.

After modeling two reserves after the example C, I wanted to increase the heterozygosity, while increasing the number of runs without a lost of alleles. The best way to do that was to increase the size of the individual populations. I went from four to three habitats to achieve this and was successful in my goal. As you can see in the table above, the heterozygosity went up from 0.18 to 0.23, and there was one run more than the Reserve C that did not lose an allele. Out of 20 runs, this is very impressive. This makes Reserve 1 the “best” fit reserve for the population of ferrets and will promote the success of more and more generations. In comparison to reserves A and B, Reserve 1 is much more successful. It is clear that the best reserve uses parts of each example to achieve a better grouping of habitats. In Reserve A, the size of the population was a successful way to promote the movement of genes through a population, however it reached fixation many times. In Reserve B, the generation of ferrets was represented in 4 separate habitats. This was not very successful as the habitats heterozygosity was minimized and fixation was reached very fast with such small populations. However, the idea to promote different alleles by separating the generation gave inspiration for genetic drift in Reserve C. As explained before, this reserve gave inspiration to both custom reserves, but itself was not successful enough because the distribution of populations was still too small. To avoid sampling error from small populations, and to still achieve the flow of diversity throughout the populations, Reserve 1 was the best model to save the ferrets with successful genetic drift.

To start the lab, we labeled five test tubes from zero to 40 minutes, and one with the label of Tet+Ink. Next, 500 microliters of Tetrahymena solution was and another 500 microliters of India Ink was added to the tube labeled Tet+Ink. We had to add seven microliters of serotonin to the same tube to assess how the serotonin would affect the rate of phagocytosis in the tetrahymena cells. In the five other tubes labeled from zero to 40 minutes, we added 20 microliters of glutaraldehyde solution (WE DID NOT add glutaraldehyde to the Tet+Ink tube). After starting a timer we immediately added 100 microliters of the solution in the Tet+Ink tube to the first tube, labeled zero minutes. At ten minute intervals, 100 microliters of the Tet+Ink solution was added to the next tubes. We were careful to mix the solution and glutaraldehyde within the tubes. After 40 minutes passed, we put 15 microliters of the solution in each tube onto separate microscope slides. We then observed and counted the number of dark colored vacuoles in ten different cells for each slide. Finally, we recorded the number of vacuoles found into a table and calculated the average and standard deviation for each tube.