Drafts

Overall, I enjoyed the methods project. Before beginning the project, I thought it may be too much work, and I was a little annoyed about how much out-of-class time was required. After beginning,however, I started to see just how valuable the project actually was. I also was surprised at how smoothely it went, and I dd not have to put extreme aounts of effort into it, especially following the methods of my peer. I found it useful to see someone else's writing and use it to format methods sections in other classes. Overall, this project taught me how to write clearly and concisely, how to put just the right amount of detail into something, and how to put myself into anoher scientist's shoes. I imagined being a person outside of this class, and how my thought process would be if I was seeing these methods for the first time. It also helped me remove myself from the writing, even when using "I" statements, when we went over differences vs. assumptions and writing without judgement. I used what I learned from the methods project to help me write my midterm report for another lab, and I am sure it will help me again in the future.

            Our project’s goal was to observe the effects that manipulating the seed coat had on germination rates. The seed coat is important for protecting the seed in the ground, but we were wondering if it is completely necessary. To test this, we used soybean species and had some serve as a control group, some where the coat was nicked with a needle, and some where the seed coat was completely removed. Over the course of 3.5 days, the seeds were placed in petri dishes with wet paper towels, and we periodically checked all the seeds and recorded how many of each treatment had germinated. Because another group completed this project with us, we focused mostly on the control group vs. the nicked group. Our results show a trend in faster germination among the nicked seed coats, but after statistical analysis we cannot conclude that nicking of the seed coat leads to faster germination, and we must say that the differences observed most likely occurred by chance.

Th cell cycle is the series of events that occurs within the cell that let it grow and divide. G1 is the first phase, where the cell is growing and building up nutrients to prepare for DNA replication. This occurs next, in the S phase. After DNA replication is G2 phase, which is another growth hase. The cell is growing to help it be big and full of enough nutrients for when it divides. Cell division occurs during M phase after G2, and this includes, prophase, metaphase, anaphase, and telophase. After cytokinesis occurs, the cell cycle is finished. Throughout the cell cycle, there are certain checkpoints to make sure everything is a-ok before proceeding. These checkpoints include checking for DNA damage, incomplete DNA replication, and inproper spindle attachment. 

BORIS is a program used in the life sciences for coding and observation of videos. In my lab, we use BORIS to code for teh behavior of slugs in obervational experiments. I am currently using this program to score the behavior of baby slugs after exposing them to conpressin for an hour. I record them for an hour in untreated conditions, and then for an hour in water with a 10^-6 concentration of conopressin. The behaviors I am scoring for are explore, turn (either right or left and 180/360 degrees), top-surf, sie-surf, escape, contract, and rear. Top-surfing is described as floating, where only the foot is attached to the top surface of the water. Side-surfin is described as the foot being attached to the wall of the well. Rearing is the lifting of only the head and looking up while the rest of the body stays attached to the floor. 

To determine whether different habitats have different sized trees, we measured the diameter at breast height (dbh) of adult trees in three sites at the Holyoke Range in Amherst Massachusetts. The sites included a north slope, south slope and flat area at an area called  “The Notch” on the Holyoke range. The dbh of these trees was used to find basal area of the adult trees present in eight replicates. After analyzing the basal area of adult trees it was determined that the average basal area was not that different between the slopes. The species Quercus rubra/velutina was also specifically looked at because of its high density at each site compared to other species. It was predicted that the basal area of this species would be larger on the flat than on either north or south slopes. It was actually found that the north slope have higher average basal area than either the flat of the south slopes. Ultimately, the results did not support the hypothesis that steeper slopes have small trees due to higher mortality rates of of larger trees.

They used ELISA kits (used to detect and quantify proteins) to measure the beta-amyloid and tau, along with the TH. After processing, they injected the sample into the HPLC for analysis. T₄, T₃, rT₃ were detected in the HPLC. For the most part, there was no difference observed between AD and control groups. However, there was a lower correlation coefficient between CSF T₃ and blood T₃in AD patients as opposed to control. CSF TH and CSF beta-amyloid had no significant correlation. The absence of correlations showed the complex distribution of TH between blood and the CSF. . The same could be said for CSF T₄, T₃or rT₃between patients and controls. This was probably due to the fact that it was difficult to find controls who would want to opt for a lumbar puncture. They found significant negative correlations between rT₃, or rT₃/T₃ratio and MMSE only in AD patients. 

Behavioral experiments have shown that the principal and secondary eyes work together to precisely target moving stimuli. For example, Dr. Beth Jakob and colleagues investigated how the secondary anterior lateral eyes direct the principal eyes of Phidippus audaxwhen tracking moving objects. Phidippus audaxwere tethered in front of an eye-tracker that recorded the movement of the principal eye retinas. When spiders with their anterior lateral eyes unmasked were shown a moving disk, the principal eye retinas moved close together and were able to track it. Meanwhile, masked spiders were unable to track moving disks with their principal eye retinas. This indicated that principal eyes can precisely target moving stimuli only with the guidance of the secondary eyes (Jakob et al., 2018). Furthermore, Cupiennius salei, a wandering spider from the family Ctenidae, has also been shown to have closely cooperating principal and secondary eyes. Cupiennius saleihave moveable principal eyes that are controlled by four muscles (Kaps, 1996) (Land, 1969). Masking the Cupiennius saleisecondary eyes reduced their principal eye movement (Neuhofer et al., 2009). 

All spider families for which data exist have movable principal eyes. However, the size and motility of the principal eyes vary greatly. Jumping spiders can move their retinas in all directions, whereas other families are capable only of very small lateral movements. In addition, the amount of overlap in the field of view between the principal and secondary eyes varies across families. Small principal eyes with a wide range of motion, such as in jumping spiders, depend on information gathered by the secondary eyes to be directed to a target. I predict that these families will invest more in visual pathway neuropils and in the number of optical glomeruli. In families with larger principal eye retinas with wider fields of view and less motility, information from the secondary eyes may be less important. This may lead to less investment in visual pathway neuropils and a decrease in the number of optical glomeruli.                      

The secondary eye pathway of jumping spiders is complex compared to other spiders (Long 2019). Of interest for me are the optical glomeruli of the secondary eye medulla. Information from the secondary eyes is sent to the lamina, followed by the medulla. From the medulla, nerves project and combine in the mushroom body (Strausfeld et al. 1993). Unlike the mushroom body in insects, it is likely that the mushroom body in spiders is completely given over to vision. In insects, information from the lamina is passed to the medulla via a complete chiasma and this retains a panoramic field of view. In spiders, information from the lamina is chunked in the medulla before being passed to the mushroom body (Strausfeld, 2012). This prevents a panoramic view but may increase the spider's ability to quickly process motion information in discrete regions of the visual field. This may be particularly important for targeting the movement of the principal eyes. Retinotopic information from the lamina is passed to the protocerebrum simultaneously via a separate tract (Strausfeld, 2012). 

The visual systems of different spider families can be correlated to their life histories and behaviors. Many diurnal cursorial spiders like salticids have enlarged principal eyes and small secondary eyes with a wide field of view for detecting prey. Nocturnal hunters like wolf spiders (Family Lycosidae) and net-casting spiders (Family Deinopidae) have small principal eyes and enlarged secondary eyes. Meanwhile, some ambush predators like crab spiders (Family Thomisidae) and web-building spiders like long-jawed orb weavers (Family Tetragnathidae) tend to have small, evenly spaced principal and secondary eyes. Furthermore, the visual processing pathway is separate for the principal and secondary eyes. And the principal and secondary eyes each have their own neural pathway within the spider brain (Strausfeld and Barth, 1993).