Writing in Biology - Section 1

In cancer studies, the changes of gene expression is what is concerning to scientists.  As a result, RNA is necessary to study changes in gene expression.  RNA is an extremly unstable molecule and it needs to be to ensure regulations of gene expression.  In order to study RNA effienctly, reverese transcription is used via reverse transcripase to create cDNA from the RNA template.  When the RNA is being studied, the introns have already been spliced out allowing for a precise understanding of the exact DNA sequence causing the regulation without introns interferring with it.  PCR can then be used to replicate the cDNA and allow for several copies of DNA to be used.  In PCR, there a phase where the reaction platues.  Therefore, there needs to be flourences and a window to see the levels of all the DNA to determine which sequences are amplyfying fastest.  Before the platue, the levels can be compared to see what gene is expressed most in the cancer cells.

PCR, polymerase chain reation, is used to create replications of DNA in the lab.  Temperatures of a bath are raised and cooled to ge the double strands to separate, primers to be inserted and tac polymerase will extend the stand.  The process is left with short stands of target sequences which have been replicated as they were defined by primers.  This started as a labor intensive process which required hours of manual labor and a large quanitites of enzymes until a bath was invented which allowed for the thermoregulation of the temperature.  

Due to the increased use of capsaicinoid and tolerance of capsicums in the human diet, other health benefits emerged as a consequence.  In Tsuchiya’s study of the effects of capsaicinoids on membrane fluidity, bacterial growth and platelet aggregation were the two subjects (2001).  The lipid form of capsaicinoids were able to interact with the membrane in bacterial cells, inhibiting their growth (Tsuchiya, 2001). This effect on bacteria could result in capsaicinoids being essential in maintaining a healthy gut biome for an individual who was raised in an environment with a high spicy food tolerance.  Gastrointestinal disease has been reported to be decreased with capsaicin consumption (Deng et. al., 2016). In platelets of humans, rabbits, and rats, capsaicinoids were shown to decrease their aggregation (Truchiya, 2001). Capsaicin has already been proven in other studies to decrease cardiovascular disease (Deng et. al., 2016).  The effects of membrane fluidity could be one of the physiological changes within the body which decreased cardiovascular disease. In China, a study was conducted to determine if chili intake and capsaicin had any effect on the obesity of the population (Shi, Riley, Taylor, & Page, 2017). Although this was one of the first conclusive studies done involving obesity, there was conclusive evidence that chili intake had an inverse effect on obesity and might provide a low cost solution to obesity problems in China (Shi, Riley, Taylor, & Page, 2017).  Through the decrease of obesity, there is a multitude of other health complications that can be relieved. One of the flaws with the studies on the health benefits of capsaicinoid consumption is the lack of physiological understanding within the body of how it alters the health of the individual. Until these pathways are fully understood, there will be a slew of health benefits that are not maximized.   

In the study, the limited sample size decreases the accuracy of the study.  Based on the information given, Ulmus americana are the most susceptible to leaf miner infection and have the greatest chance of the leaf miner surviving within the leaf.   From the phylogeny of Ulmus, it is expected that Ulmus americana would have the greatest deviation from the other two species.  While the Ulmus parvifolia and Ulmus carpinifolia had a varying leaf miner presence, they had a relatively similar crude death rate indicating a similarity between the trees which could be explained by their phylogenetic relationship.

Ulmus or elm species and leaf miners.  Leaf miners are relatively harmless to trees but they can have an esthetic effect on trees if they are part of the landscape.  We selected three elm tree where vary along the phylogenetic tree of Elms, the Japanese, smooth and American, with the American being the outlier.  From there two trees from each species had 25 leaves collected from it and the number of leaf mines were counted as well as the number of aborted leaf mines, meaning the leaf miner died.  For our results, we looked at the total number of leaf mines as well as the proportion of those were aborted, the average leaf mine per leaf of each species and the crude death rate per a 1,000 population.  These results showed the highest rate of infestation in the American.  There were similarities in the data of Smooth and Japanese Elm.  Our sample size was very small to have a meaningful statistical analysis done therefore any results of the lab cannot fully support any theory but there are indications that phylogeny can affect the infestation of leaf miners in Elm species as well the their probability of aborting.  For future studies, we would like to expand the sample size of leaves collected as well see if the mortality of leaf miners is seasonal. 

Thusly, only group 1 males showed changes in minimum frequency and bandwidth in response to noise. Neither group 1 nor group 2 males changed their trill rates, which negatively affected their vocal performance. Only the group 1 males showed an increase in minimum frequency because they, unlike the group 2 males, were at risk of having their songs masked by the background noise. Unexpectedly, group 2 males decreased minimum frequency with increasing vegetation, and group 1 males showed higher minimum frequency with increasing urban structure. As noise was not correlated with either urban or vegetative structure, the latter outcome is likely not due to the fact that more structured habitats are noisier. These results suggest that, based on individual variations in their songs, males generate novel spectral adjustments in response to anthropogenic noise. Additionally, peak frequency decreased with increasing urban structure for both groups, likely because lower frequency sounds don’t suffer as much from the effects of reverberation as high frequency sounds. Neither group adjusted their trill rates in response to urban structure, despite the fact that an increase in reflective surfaces causes trill notes to slur. Also, males didn’t shorten their trills in order to minimise accumulation of reverberation over the song. Thus, since group 1 males in an urban setting narrowed their bandwidth but didn’t increase trill rate, they had poorer vocal performance. Similarly, group 2 males in an urban setting suffered poorer vocal performance because they didn’t lower their trill rates,. As such, both groups of males could experience reduced mating success. However, it is possible that males cannot adjust trill rate or song length because of constraints imposed by female preference. Alternatively, males may benefit from sound reflections by picking perches which cause their signals to experience constructive rather than destructive interference. That is, instead of reverberations causing the signals to become slurred and to cancel out, they would add up to increase in amplitude, thereby propagating the signal even further. In sum, it is possible that chipping sparrows in structured environments choose their perches based on how well their song is amplified rather than by how little their song is degraded.

Thusly, only group 1 males showed changes in minimum frequency and bandwidth in response to noise, and neither group 1 nor group 2 males changed their trill rates, which negatively affected their vocal performance. Only the group 1 males showed an increase in minimum frequency because they were at risk of having their songs masked by the background noise unlike the group 2 males who already had minimum frequency above background noise. Unexpectedly, group 2 males decreased minimum frequency with increasing vegetation, and group 1 males showed higher minimum frequency with increasing urban structure. As noise was not correlated with either urban or vegetative structure, the latter outcome is likely not due to the fact that more structured habitats are noisier. These results suggest that, based on individual variations in their songs, males generate novel spectral adjustments in response to anthropogenic noise. Additionally, peak frequency decreased with increasing urban structure for both groups, likely because lower frequency sounds don’t suffer as much from the effects of reverberation as high frequency sounds. Neither group adjusted their trill rates in response to urban structure, despite the fact that an increase in reflective surfaces causes trill notes to be slurred with one another, especially at high trill rates. Males also didn’t shorten their trills in order to minimise accumulation of reverberation over the song. Thus, since group 1 males in an urban setting narrowed their bandwidth but didn’t increase trill rate, they had poorer vocal performance. Similarly, since group 2 males in an urban setting didn’t lower their trill rates, they also suffered poorer vocal performance. As such, both groups of males, and especially group 2 males, could experience reduced mating success. It is possible that males cannot adjust trill rate or song length because of constraints imposed by female preference. Alternatively, males may benefit from sound reflections by picking perches which cause their signals to undergo constructive interference rather than destructive interference. That is, instead of reverberations causing the signals to become slurred and to cancel out, they would add up to increase in amplitude, thereby propagating the signal even further. In sum, it may be the case that chipping sparrows in structured environments choose their perches based on how well their song is amplified rather than by how little their song is degraded. 

Hi, 
My name is Ziwei, and this is my poster on how the removal of the seed coat affects the seed germination rate. So, what is the seed coat? The seed coat is a protective covering that surrounds the seed and protects the seed from the environment that the adult plant may not be able to survive in. In addition to the protective role that the seed coat plays, the seed coat also plays a role in controlling germination and produces some compounds that are beneficial to the seed. This indicates that while it may seem like the seed coat is not doing anything, the seed coat is actually biologically active. One of the things that have been suggested recently is that the seed coat actually impedes seed growth.  The reason why the timing of germination is important is if the seed starts germinating, there is no going back. There is no way for a germinated seed to become ungerminated. However, there are situations where a faster germination rate would be an advantage. To see if the removal of the seed coat increased the germination rate, we removed the seed coat of the seed, and allowed it to germinate, and measured the rate. Our result indicates that the seed germination is somewhat faster in certain types of seeds, however, we were not able to get a definite answer of whether removing the seed coat caused the seed to germinate faster. Due to the small sample size. My personal theory is that because there are so many compounds that seed coat produces, there may be some compounds that are produced by the seed coat that is needed for germination. Because of this, my next experiment would be to remove half of the seed coat and see if that would make the seed germinate faster because if only half of the coat was removed, there would be a beneficial compound without the physical barrier of a seed coat. That's basically what this project is about. Do you have any questions?

This paper was focused on the effects of anthropogenic noise, urban structure, and vegetation on the trills of chipping sparrows. Chipping sparrows evolved in an open habitat, thus an urban environment generates neoteric selection pressures on their song. The researchers aimed to answer three major questions: (1) whether individuals with different song variants generated novel solutions to noise and reverberation; (2) how the opposing forces of background noise and highly reflective structures affect song; and (3) the effects of noise and structures on trills and subsequently, vocal performance. Their predictions hinged on splitting males into two groups. Group 1 was composed of males that had lower minimum frequencies, higher maximum frequencies, broader bandwidths, and lower trill rates than group 2 males. They predicted that group 1 males would sing at a higher and narrower frequency band but would not change their trill rate. Whereas they predicted that group 2 males would decrease trill rate, but wouldn’t change their trill frequency. Lastly, they predicted that noise would have a greater affect on frequency, that structure would have greater affect on song timing, and that vocal performance would decrease with increasing noise and structure.