Writing in Biology

DNA recombination -
- an example of gene translocation is the antigen receptor gene in the vertebrate immune system
- in B lymphocytes, DNA recombination (aka VDJ joining) leads to the expression of one particular variable (V) region gene for each
immunoglobin (Ig) light- or heavy-chain gene
- in the Ig k light-chain genes, there are >300 germline V segments and one constant (C) gene locus containing 4 joining (J) segments
and an enhancer region
- once the B cell has picked its AB, it proliferates many clones of the same antibody and we can fight off the immune attack
what are variable regions, it is random
- in the chromosome in the B cell, this is where its happening, a permanent excision of this part of the DNA
- the ones that aren’t good, die
- promoter sequence and enhancer (drives expression, in the intron, between variable and constant domain)
- DNA deletion brings a promoter carried by each V gene segment and the enhancer region b/w the J and C gene segments into
proximity, thus activating the translocated gene
Gene Conversion -
- this is another gene-translocation mechanism that activates one particular member of the multigene family (found in yeast mating-type choice and antigenic variation in African trypanosomes)
(- chicken Ig and T-cell receptor genes use gene conversion for their expression and diversification)
- the cell makes a copy of the gene and inserts it into an expression casette
- a copy of the gene to be activated is transferred into the expression cassette located remotely from the gene cluster

Monogamy: As previously mentioned, sexual selection is most intense in polygamous relationships as seen in leks and due to these intense pressures this is seen in less than 10% of all avian species. The alternative, monogamy, revolves around a bonded pairing of individuals that cooperate to copulate and raise their young as this is occasionally essential for the offspring to survive.. Males typically hunt, defend their territory and even assist with incubation in some scenarios and the females will determine the viability of their partner based on these efforts. Once formed, the duration of these bonds can vary with some relationships lasting only for the breeding season and other lasting for life. Despite the superficial appearance of monogamy, there are frequent episodes of “extra-pair copulation” by females who willingly accept advances from other males. On average, only 14% of the offspring in a nest are the offspring of the tending father. This is done by females to ensure variability and viability of their young and males participate in this behavior so as to pass on their genetics as frequently as possible.

HeLa cells were stolen from Henrietta Lacks without her knowledge or full consent, while she was in John Hopkins hospital seeking radium treatment for her cervical cancer, scientist George Gey sought the opportunity, while Henrietta was unconscious during surgery, to have a surgeon collect her cancerous tissue cells to be used for his research on growing a human immortal cell line. To Gey’s astonishment the cells grew perfectly and survived longer than any of the cells he had cultured before, and the rest is scientific history. Yet what science seems to forget is the woman behind the cells and how unethical scientific research was during the 1950’s to the early 1990’s. During that forty year time span many critical and obstructive research occurred all over the United States and possibly all over the world with no laws or pre-dispositions to help regulate the safety and prosperity of the subjects.

Lek Displays:  While many courtship displays occur in pairs, the most extreme cases of sexual dimorphism occur when courtship displays are done in large groups with multiple members of the same species. These large masses of courting displays are known as Leks and due to the extreme competition among the males in these groups there is additional emphasis on dominance and attractive morphology. Typically, a small number of males are selected for and sire the vast majority of the upcoming generation. As previously noted, natural selection favors those with the highest reproductive success so one must question why a subordinate male would continue to reside in these Leks if unsuccessful.  Studies have shown that females typically favor larger groups of males and subordinate males do have a minor chance to reproduce simply by being in the presence of a dominant figure. Of note, leks are typically more closely related to each other than other individuals in other leks and theories proposed by Paris Hamilton suggest that a subordinate role is tolerated more easily if the dominant male has similar genetics as this qualifies as reproductive success in a sense.

Good Gene Hypothesis: Courtship displays are ancient reproductive strategies that have been tightly associated with elaborate plumage. This elaboration is meant to convey superior fitness to females, however, the mechanism of this is unknown. The prevailing theory detailing this correlation is the “Good Gene Hypothesis”.  This theory suggests that exotic or more elaborate plumage serves as a handicap by making them less optimal for flight or running as well as more easily identifiable by predators. However, if a male is able to survive with these additional stressors then a female can infer that they are superior in terms of stamina or survival skills.  Furthermore, this theory suggests that plumage can reveal parasite load and hormonal levels as they have both been shown to affect brilliance or color scheme. Due to the high associated cost associated with developing, maintaining and surviving with such elaborate feather schemes, many species have developed post-breeding molting cycles to eliminate these handicaps during the non-breeding seasons.

Trimyristin was isolated from ground nutmeg seed using t-butyl methyl ether to yield 29% crude product.  The crude trimyristin was recrystallized once to yield 40% of product and recrystallized a second time to yield 10% of pure product.  The starting material, ground nutmeg seed, contains many more compounds than just trimyristin, which would explain why the yields appear to be of small value.  As the purity of the product increased through successive recrystallizations, the amount of product obtained decreased as the mass of the impurities or other compounds were lost.  Excessive heating could have caused some reactant to evaporate out of the distillation column, and the cotton fiber may have absorbed some of the solution when performing pressure filtration.  The purity is represented in the melting points of the products.  The first recrystallized product had a melting point of 48-50 °C, and the second recrystallized product had a melting point of 50-52 °C.  Both of these ranges suggest that impurities were present because they are lower than the literature value melting point of trimyristin is 56-57 °C.  However, after each successive recrystallization the melting point became closer to the accepted value for trimyristin indicating the removal of most impurities.  The product is still assumed to be trimyristin.

Although quantitative analysis was not possible for fixed NIH 3T3 cells treated with TMR-dextran and lysotracker. This could have occurred due to possible insufficient exposure time and binning combinations when capturing images, or insufficient incubation time and conditions for the lysotracker and TMR-dextran. However, based on previous studies and common science knowledge, we are able to infer what visual and quantitative data of this investigation should resemble. After 15 min. of incubation time, the average total intensity of the TMR-dextran should be high at the surface of the cell relative to the interior. This is due to the relative brevity of the incubation time, where has not been sufficient time for many of the dextran molecules to be invaginated into the cell’s luminal space. The interior images should also display a relative high intensity of lysotracker at this point. After 75 min. of incubation time, the average total intensity of the TMR-dextran should be high at the interior of the cell relative to the surface. This is because the cell has had sufficient time to invaginate a majority of the dextran molecules and form endosomes and protonate, bringing them into the cell’s luminal space and closer to lysosomes. At this point, the interior images should display high lysotracker total intensities and high dextran total intensities, which would confirm that the dextran migrated to the inner most part of the luminal space.  

At t=0 min., the average total fluorescence intensity of NIH 3T3 cells at the surface of the cell was relatively high due to the lack of time that the endosomes had to migrate to the interior of the cell. At t= 0, transferrin had just been introduced to the cellular environment, and were only able to quickly to bind to the receptors of the cell, which rest on the cell surface. After 30 min. of incubation, cells exhibited relatively similar average total fluorescence intensities on the surface and interior, demonstrating moderate amounts of migration of endosomes to the interior of the cell. This added time allowed for the ligand bound transferrin to be internalized via clathrin coated pits to coated vesicles and migrate deeper into the cell. After 90 min. of incubation, the interior of the cell exhibits a relative higher average total intensity compared to the surface. This again is due to the added incubation time, which has allowed the previously early endosomes to acidify, releasing iron, which then brings the transferring molecules closer to the interior where sorting endosomes are found. 

Live LLC-Pk1 cells with GFP tagged tubulin were treated with TMR-dextran. Control group cells were incubated with solely TMR-dextran, while treatment group cells were incubated with TMR-dextran, and subsequently incubated in nocodazole. Both groups were time-lapse imaged at 40X magnification for 300 s (1 frame every 10 s). Vesicle movement was then quantitatively analyzed using ImageJ’s “TrackMate” plugin to measure total displacement of vesicles (Figure 5). Cells treated with nocodazole demonstrated a lower average displacement of vesicles compared to control group cells (0.164µm, 0.716µm, respectively) (Table 1). Composite image frames of start, middle, and end of the time-lapse image series visually display the differences in movement of the vesicles over time across groups (Figure 4).

Each of the eight teams will be assigned a location at different spots around the UMass campus. These spots are: next to the stream behind Sylvan dorms, in the woods across the street from Sylvan dorms, near the pond next to lot 44, next to the campus pond, near the water tower by the top of Orchard Hill, next to Mill River in a wooded area, next to Mill River close to the road, and in the garden outside of Franklin Dining Hall. Each team will use “Google Maps” to get the latitude and longitude of the specific spot they choose.