rmmcdonald's blog

As a result of following the methods stated above, Sinclair Emans created a figure that matched and contrasted the original. Overall the two figures contained distinct differences in terms of compositing, size, and labeling. When comparing each of the panels similarities and differences could also be noted. 

Comparing overall figures: compositing, size, labeling

    Overall, each of the figures followed the same formatting style, with one large photo on the left and two smaller photos on top of each other to the left. However besides that similarity, most of the other characteristics of the complete figure are contrasting. The overall resolution and lighting of each of the photos were significantly different. The resolution of Figure 1 seemed blurrier and the lighting appeared overexposed compared to the sharp resolution of Figure 2. Figure 1 contained even, white spacing between each of the panels while Figure 2 had a more significant gap between panel B and C. This links to the sizing of B and C, where the panels in Figure 1 were horizontal in contrast to Figure 2 where they were vertical. The letters that marked each panel in Figure 1 were black letters with no background. In comparison, the letters that marked each panel in Figure 2 were black letters with a white square background and a black border. The overall ordering of the panels were switched, therefore A from Figure 1 matches with B from Figure 2. 

From the inception of Rome as city, military and violence was ingrained in Roman culture. A society made primarily of men, most Romans had to have military experience in order to survive in the city. As the city grew and the government expanded, not everyone was capable nor had the means to gain a military background. Therefore, people who came from wealthy backgrounds that were able to afford the expsenive equipment and time away from home stepped up as the Roman military. Since Rome had no official organized army, these group of men who led these military expeditions to expand personal wealth as well as Roman wealth had to be honored by the government in order to encourage more of this action. This was evident by the establishment of the concilium centuria where the calvary was the class with the greatest number of votes, eventhough they had the smallest population in Rome. Honor and glory in Roman politics therefore became intrinsically tied to military success. If one wanted to be a successful Roman politicain, he had to build his own army and bring back a triumph to Rome. This would eventually escalate to the point that politicains would make up wars in order to gain more glory. 

The title of the poster my lab partner and I created was, "Qualifying the Effect of Microscope Properties and Techniques". In a series of experiments we learned how to properly use a research quality light microscope. The experments were geared towards the technical ascepts of the microscope. This involoves the use of filters, shutters, and adjsuting numerical aperature when capturing images. There were also a variety of methods we practiced in order to capture a high quality image. These methods included setting up Kohler illumination, use of fluoroescent microscopy, and properly using an oil immersion lense. All these various experiments came together to encapsultate our main objective of qualifying the effect of microscope properties and techniques in order to create a high quality image.

Capturing evidence of phytophagy on the UMass campus offered a process to learn about how to create a perfect figure and follow others’ methods. The focus of my figure was a leaf found on a large bush in the rooftop garden of the John W. Olver Design Building. I chose this specimen due to its convenient location and obvious signs of phytophagy. In addition factors were more easily controlled since this is a privately maintained garden therefore the bush would not be destroyed. I also considered controlling the time of day, zoom, perspective, and quality of photos taken of this example of phytophagy so that it can be replicated accurately.

The title of the poster my lab partner and I created was, "Qualifying the Effect of Microscope Properties and Techniques". In a series of experiments we learned how to properly use a research quality light microscope. The experments were geared toward practicing the use of technical ascepts of the microscope. So this involoves the use of filters, shutters, and adjsuting numerical aperature. There were also a variety of methods we practice in order to capture a high quality image. These methods include setting up Kohler illumination, use of fluoroescent microscopy, and setting up an oil immersion lense. All these various experiments came together to encapsultate our main objective of qualifying the effect of microscope properties and techniques in order to create a high quality image.

A major part of our experiments was adjusting numerical aperature under a variety of different conditions in order to see its effect on the visualization of a sample. The following figure shows a change in numerical aperature when the magnification is kept constant  x100 and visualized with fluorescense. The fluorescent beads are figure A-C. The numerical aperature increases left to right: starting with 0.5, increasing to 0.875, and finally ending at 1.25. This is similar for the photos of the DAPI stained nuclei. Visually, we can conclude that both the DAPI stained nuclei and the fluorescent beads increase in image intensity as numerical aperature increases because we can see it gets brighter. This observation is quantified in the table because we mapped the fluorescent intensity of the five nuclei over the three different numerical aperature settings. The intensity of 1.25 is much greater than 0.5 proving that intensity increases as numerical aperature increases. It can also be argued that resolution increases too because the minimal loss of image light. 

The legacy of Cicero that I knew about before reading his quick biography was that he was an excellent orator. That still seems true, but he was certainly more than that. It appears his oratory skills are what elevated him to the next level of his political career. I doubt he had any remarkable military experience because "he was spare and lean, and owing to a weakness of the stomach" (Plutarch, III). Therefore he must have relied strongly on his oratory and debating skills in order to prove himself to the people of Rome. I think it was especially interesting that he was a son of a knight, not a nobleman, which was rather unique for a consul. This must reflect how highly Rome though of Cicero because they did not care about his lineage when they chose him to run against Catiline. I also find it interesting that despite his drastic ruling to execute traitors, the Roman people still seemed to support him. In fact they "voted him the greatest honours ever conferred and called him the father of his country" (Plutarch, XXIII). I wonder if the Romans actually approved of the executions or just so vehemently supported Catiline that they bestowed him these honors regardless. 

Through out the past few decade various ways to sequence the genome had been invented. Originally the genome could only be sequenced in small portions and required mostly human oversight/work to set up the sequencing. This method of sequencing was time consuming and expensive. Today, next generation sequencing has revolutionized the way genomes are sequenced. Mass Parallel squencing is acomplished by sonicating a genome and ligating short, universal primers into the cut DNA strands. That is then poured over a "Chip" where individual fragments of DNA bind to unique positions by the primer that was just ligated on. Then synthesis begins on all the segments. A fluorescent ddNTP base pairs and is captured by a special camera. Next the ddNTP is altered so that the 3' end has an OH group where a new ddNTP molecule can bind. This process is repeated over and over again until all the strands are sequenced. Next, a program will run to match all the overlapping segments into one strand. It is convention to have atleast 30 overlapping sequences in one position to maintain accuracy of the sequencing. 30 overlapping segments would be known as having a depth of 30. 

Figure 26:

The lighting of the figures seem significantly different. The figure on the left might have only used the flash for picture A while the figure on the right used the flash for photo A. However both figures used the flash for picture B. As for picture C, it is hard to tell what might have caused the difference in lighting. It might be caused by a difference in focus. As for the picture, the picture meant to establish the setting, the figure on the left has the flower to the side while the picture on the right has the flower focused in the middle. As for picture B, the one on the left is more zoomed in than the one on the right. This same difference occured in picture C as well. The flower appears to have changed as well. It seems to have wilted in the time between when the photos were taken.
 

Possible Categories:

Lighting:

Figure on the left had better lighting than the figre on the right. The right seemed to used the flash more which distorted the imade.

Sizing:

The images altogether are the same physical size. However the zoom on the images differ since the figure on the left has photos that are generally more close up.

Coloring:

The flash impacted the coloring diference between the two figures. The figure on the right had more grey in it because of the flash.

Set up of Figure:

The set up of the figures are exactly the same except for the font of the letters that mark what the images are.

Chromatin Immunoprecipitation is an important molecular tool used to discover all parts of the genome that a transcription factor can bind to. Chromatin Immunoprecipitation, or CHip-Seq, involves the use of antibodies that bind to the transcription factor of choice in order to withdraw all the genetic material from the cells. The first step requires the crosslinking of proteins and DNA together. Once the Transcription factor has been attached to the DNA, the DNA is sheared into 300 base pair segments. Next beads with antibodies that recognize a specific transcription factor are added so that the DNA-transcription factor complex binds to it. The immunoprecipitation part of this experiment involves centrifuging the substance so that a pellet is formed containing only the beads that are attached to the DNA-transcription factor complex. The protein is then uncrosslinked from the DNA and the short strands now get sequenced. The sequenced DNA portions are then mapped on the genome to see where the transcription factors bind. This experiment can reveal valuable information when combined with RNA-Seq. RNA-Seq will give all the genes that are acitive so overlapping the results of a CHip-Seq test will tell you what genes are activated by a specific transcription factor.

Chromatin Immunoprecipitation is an important molecular tool used to discover all parts of the genome that a transcription factor can bind to. Chromatin Immunoprecipitation, or CHip-Seq, involves the use of antibodies to bind to the transcription factor of choice in order to withdraw all the genetic material from the cells. The first step requires the crosslinking of proteins and DNA together. Once the Transcription factor has been attached to the DNA, the DNA is sheared into 300 base pair segments. Next beads with antibodies that recognize a specific transcription factor are added so that the DNA-transcription factor complex binds to it. The immunoprecipitation part of this experiment involves centrifuging the substance so that a pellet is formed containing only the beads that are attached to the DNA-transcription factor complex. The protein is then uncrosslinked from the DNA and the short strands now get sequenced. The sequenced DNA portions are then mapped on the genome to see where the transcription factors bind.