Drafts

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. 

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.

 In the second experiment that was done for the paper, whole mounted retinas from control and P23H rats were labeled with Cx43 and GFAP.  The results indicated that the density of Cx43 IR puncta in GCL was greater in the P23H rats. Cx43 levels were increased 2 fold in the P23H rat retinas compared to the control. The results suggest that there is a role of Cx43 in the pathogenesis of degeneration. The expression observed in P23H rats correlated with astrocyte hypertrophy suggests an increment of Cx43 expression per astrocyte. Retinal immunofluorescence was done using the marker GFAP and vimentin. Immunofluorescence of GFAP protein was done. P23H rats showed intense GFAP immunoreactivity and revealed colocalization between intermediate filament proteins. The vimentin/GFAP positive Muller cells extended into the subretinal space and expanded, filling areas left by degenerated photoreceptors. There was a 7.8-5.3 fold increase in GFAp expression in the P23H rats compared to the control. This data suggest that the GFAP expression increased in retinal degeneration. The increased GFAP expression is also thought to stabilize newly formed terminal processes of Muller cells and provide resistance to the stress and is essential for the formation of glial scars neurite growth infiltration of monocytes neovascularization, and integration of cells in retinal transplants. GFAP immunoreactivity was analyzed in the ONL of whole mounted retinas from control and P23H rats.  In P23H rats, there was more loss of photoreceptors in the ONL which was linked to the appearance of hypertrophied side branches of muller cells into the outermost photo layer. Most of the cone cells also expressed a short morphology. The loss of rod cells also altered the cone mosaic in the ONL there is a correlation between the ring-like area of cone degeneration and the muller cell apical processes. The results suggest that the orientation of the cone cells are disrupted by cone degeneration with muller cell apical processes forming clusters.  This also indicates that the loss of photoreceptors induces changes in vascular tissue that activates muller cells. The overall research shows that the disease in the photoreceptor cells also affects the cells that are around those cells, and as a result, there is a need to take into account when discovering future research.

 To do the experiments  P23H-1 line rat is often used. To a certain extent. It presents a similar phenotype but not the genotype since the mutated rhodopsin protein gene sequence is inserted into the rats and the preexisting normal rhodopsin was not mutated. In addition, the rats that were used in the studies had 18 copies of the mutated gene, whereas in a human there would be one or two at most.  It added to the understanding of the disease by creating a model of the disease that can be studied, even though the model is an imperfect one.

To understand just how devastating an increase in greenhouse gases could be for our planet we must first understand how greenhouse gases work. Energy reaches our planet from the sun in the form of solar radiation. When it touchs the surface it is either reflected away or is absorbed and released as infrared radiation. This radiation would normally leave the atmosphere however gases in the atmosphere act as a one way mirror and trap some of it. Without any gases we could not survive, however with too much we will also run into problems. Our atmosphere is made of 78% N2, 21% O2, 1% Ar, 0.4% H2O and <0.1% of other gases with carbon dioxide at 0.041%. If carbon dioxide levels are 'low' compared to the rest of the gases in the air, why is it always talked about? The gas is rising in airborne concentrations steadily since data was first taken in 1960. A longitudinal study by the NOAA Earth System Research Laboratory has shown that from 1960 to today carbon dioxide levels have risen by 90 ppm (parts per million). This seemingly small increase could have devastating affects on our enviornment. Global temperatures have been rising from the increase in efficient green house gases such as carbon dioxide, but also notably methane and nitrous oxide. According to a 2018 study of temperature increases and it's affect on organsim ranges predict that at a 3.2 C change in average temperature will result in  geographic range loss greater than 50% for 49% of insects, 44% of plants, and 26% of vertabrates. This temperature is what most countries have accepted in emissions talks. With everything we know about greenhouse gases and their affect on our planet this is an unnexcusable reality we are facing in the near future.

 In the third experiment that was done for the paper, FTIR spectra of reconstituted and eluted rhodopsin protein were measured. The experiment indicated that there is a decrease in alpha-helix and an increase in beta-pleated sheets in both mutations but the differences were stronger in P23H. The N15S mutation protein is more folded compared to P23H mutation. This indicates that there is a decreased amount of alpha-helix in misfolded fraction compared to wt. Circular dichroism spectra were recorded with samples of rhodopsin and clathrin e 6.  There is a loss of alpha-helix structure from wt to the mutants with a further loss in P23H. Clathrin e6 stabilizes the alpha helix of the wt and the P23H but not N15S.  This indicates that clathrin e6 causes stability in the alpha helix of the P23H mutated proteins. The whole paper impacts the disease by indicating why the mutation of P23H has a more impact compared to patients with a mutation in S15N, and suggest a possible therapy for the mutation P23H.  
The mutation affects the stability of the cone structure causing the protein to aggregate and to be instable. This, in turn, causes degeneration of cone cells, which directly leads to a decrease in vision. There are phenotypic differences between individuals with the same genotype; however, this is not well studied since many different genes cause retinitis pigmentosa, and P23H mutation in RHO gene is relatively rare in an already rare disease. The variability is due to the different mutation types that are present as over 40 different mutations can result in retinitis pigmentosa. It is also possible that there are modifiers. However, this is not studied very well.

The mutation in the gene affects the physiology of the cell in the tissue by causing degeneration of the rod photoreceptors, which in turn causes changes in the surrounding cell tissue. Without rod cells in the retina is unable to process vision completely. In this experiment, the researchers investigate the evolution of microglial changes during retinal degeneration in P23H rats. The cell density and morphology of the retinal degeneration were studied at different ages in normal and diseased retinas through immunocytochemical localization of GFAP. Astrocyte quantification showed that astrocyte density increased astrocyte density was lower in adults there was a significant increase in astrocyte numbers in P23H rat at P120 in all regions examined. In P23H rats the retina also showed a progressive disruption of blood vessels and there were tangles of blood vessels. There was also astrocyte hyperplasia and hypertrophy accompanied by increased GFAP activity. When the retina is undergoing a dramatic remodeling due to retinal degeneration, there is a major change in the astrocyte number the numbers change less when the degeneration process slows down.

One main feature of music is that it can elicit a host of different emotions. Autobiographical memory is the long term memory that allows recovery of experiences and knowledge. One autobiographical component is emotion which is basically what helps remember certain memories than when emotions are not involved. Thus this current study tried to find a link between emotions and music-evoked autobiographical memories in AD. They asked the subjects to choose their favorite music as they hypothesized that favorite music hold high emotion valence. When asked about their favorite music, some were unable to name them and so their family helped out by naming it. After going through the conditions, they were asked for any details they remembered. They were rated using a TEMPau that measures autobiographical memory – zero for absence of memory and ranging up to a four for feelings, emotions, thoughts and perceptions. The emotions were categorized as positive or negative and rated accordingly. The results showed amazing results for the chosen condition: the controls scored an average of 4 as expected, but the AD patients had scored 3.33. Furthermore, they produced more positive words than negative, and hence the autobiographical memory relevant to it. 

Our project focused on the germination rates of various species of plants. We were interested in how the seed coat affected the dormancy of a seed and would nicking the seed coat decrease the amount of time a seed needed to germinate. To do this we germinated seeds in petri dishes. Our control was a dish with 10 seeds that did not have their seed coat altered. We chose to use 6 different species so we had 6 dishes each with ten seeds. We then took 10 seeds of each species and nicked their seed coat where the cotyledon should first start to emerge. We checked in the seeds every 12 hours for 3 days to see how quickly each type of seed germinated. We recorded the initial sign of germination, fully germinated seeds, and growth of the cotyledon up to 2cm in length. We then ran a t-test looking at how many seeds germinated on days 1.5-3 days amongst all species comparing the nicked seeds with the control group. None of our p-values showed statistical significance with 5% significance levels. This told us that the nicked seeds did not germinate any faster than the control.

Mutation of RP4 mostly affects the rhodopsin protein. The structure of the protein is a protein made of an n tail, c tail, 8 alpha-helix, and 5 turns and the protein is embedded in a membrane. The normal function of the protein is to activate the G protein to start a phototransduction cascade. When the light hits Rhodopsin, retinal that is attached to the protein isomerizes and causes rhodopsin to activate the G-protein, which in turn starts the phototransduction cascade.
 An experiment that aimed at testing changes that leads to more instability in rhodopsin structure causes severe disease in patients. Specifically, the experiment aimed at testing the function of the protein that has the P23H mutation and the N15S mutation. In the first experiment, A purified protein of the mutant and wt rhodopsin were recorded using a UV spectrometer, and a thermal denaturation experiment was done on the proteins. The result showed that P23H had a lower yield of correctly folded protein compared to N15S, and the thermal stability of P23H was75% less compared to the wild type protein. This indicates that the P23H is a less stable protein compared to N15S and wt. The mutation is a more serious mutation compared to N15S indicating that people with the P23H will have serious symptoms compared to people who have an N15S mutation. In the second experiment that was done, Meta II fluorescence was measured, and the data were analyzed using a sigma plot. The result showed that Total fluorescence after light activation was lower than wt for both P23H and N15S due to aggregation. The results imply that both of the mutations were more prone to aggregation compared to the wt. In the third experiment that was done, the protein was reacted with n-glycosidase F. An immunoblot was run and used for densitometric analysis linear regression was performed on the result of the immunoblot. The result showed that the proportion of unglycosylated species was much higher in P23H than in N15S and WT and lower intensity at lower molecular weight bands indicating that there is some degradation of P23H. P23H and N15S both have a higher intensity of Dimer and higher molecular weight which indicates that there was a higher rate of aggregation. The degree of aggregation and glycosylation was higher in P23H compared to N15S which was in turn higher what wt. This shows the differences in aggregation and glycosylation explains why the severity of the phenotype differs between the two mutations.

Our group focused our research on lichen abundance and air pollution. It turns out that lichens can be used as bioindicators of air pollution as their abundance of both species and individuals is correlated with pollution rates. Using this knowledge we compared lichen in two spots around campus, the campus pond and the woods behind sylvan residences, and compared the data. Our results yielded no significant difference in lichen abundance between the two spots. Thus we conclude either there is no difference in air pollution between these areas on campus or because we used trees near the outskirts of the sylvan woods they may not have been representative of the area.