Perfect Paragraph

Submitted by bmoreau on Thu, 10/05/2017 - 13:12

Throughout the world there are hundreds, or even thousands of different cultures, rituals and religious beliefs. People, as they have been growing up have been enculturated and taught that what they do in their own culture is what is normal or right. It’s almost natural or an instinct to compare what we do in our cultures to what people do in others. When that happens an ethnocentric view on what other cultures do can come to light. It is best to study and see what cultures do from an emic perspective and try to understand why they do what they do, as if you were a part of their culture. The Aborigines in Australia partake in the practice of subincision, which could be seen as quite repulsive to some cultures, but there is a reason behind every practice, and the reasoning can be explained using the feminist theory.

Perfect Paragraph Week 5

Submitted by dwiley on Thu, 10/05/2017 - 12:55

Being a senior Biology student, I have heard about and studied the organisms in the Durfee Conservatory many times. So, I decided to start there for my methods project. On a Tuesday after classes I headed there with my iPhone to look around and find the most interesting plant to photograph. Upon entering, I was greeted with several fauna. It took me a few minutes, but I found a flower with spiky blue and purple petals shaped in a halo around several intricate green and yellow stomata, all sitting on top a lower halo of green oval leaves.  There was also a triad of white and purple spiracles in the direct center. Logging onto the Durfee Conservatory website, I deducted that the flower’s identity is the Passiflora caerulea, or the “Blue Sky”.

Mitosis Perfect paragraph

Submitted by briangriffin on Thu, 10/05/2017 - 11:53

              Every somatic cell in the human body has been created through a process called mitosis. Mitosis is a cellular process that results in two genetically identical daughter cells from a single mother cell. The cell lives most of its life in interphase and during this time it carries out a process called synthesis where the genetic material is duplicated. These sister chromatids then go into G2, another step in interphase, then the cell goes into mitosis. This consists of prophase, metaphase, anaphase, and telophase. In prophase, the sister chromosomes begin to condense and the nuclear envelope dissolves. In metaphase, the chromosomes line up along the metaphase plate and the microtubules attach to the kinectichore proteins which are bound to the centromeres. Then in anaphase the microtubules pull the sister chromatids apart and lastly in telophase, the chromosomes are on opposite poles of the nucleus. But at this stage the cell is still a single cell. The last process of this division is cytokinesis, where the rest of the cell divides resulting in two new daughter cells. This is how somatic cells are created and how an embryo goes from a single cell to a fully developed multicellular organism.

Physics- Law of Refraction and Reflection

Submitted by kmydosh on Thu, 10/05/2017 - 11:08

This lab examined how light is reflected and refracted through a D shaped lens, a converging, and diverging lens. Light travels in straight lines, as it enters a different medium the refraction index changes. Part of the light when is reflected and part of the light is refracted. This is the Law of Reflection. A protractor was used to measure the angle of incident, refraction, and reflection. Some error could have resulted from incorrect reading of the ray of light on the protractor. A thin lens was used to demonstrate how light rays diverge at a focal point for a converging lens to reveal an image. A lens combination was used to produce an image for a diverging lens, as a diverging lens alone does not produce an image. Error could have occurred here in the data because it was impossible to get the lenses perfectly close together. Snell’s law of Reflection was used to prove that when n1<n2 then theta 1>theta 2

Cell and Molec Practice

Submitted by samihaalam on Thu, 10/05/2017 - 09:32

Figure 9/19/17c:

Figure 1:

  • JD indistinguishable from normal receptor-negative and receptor-defective FH homozygote patients clinically 
  • add some labeled LDL, incubate at 37°C for 5hr, then TCA-soluble material measured (C), then wash, then hep. releasable and hep. resistant was measured 
  • circle = normal cells, triangle = JD cells

A:

  • binding
  • hep. releasable (how much LDL was bound to the cell surface receptors and then released by heparin, so how much NOT bound anymore) LDL concentration vs. LDL concentration added
  • curves look relatively similar
  • JD doesn't have a problem with his LDL binding to its receptors

B:

  • internalization
  • hep. resistant (how much was internalized, when heparin should have caused it to be released from its receptors and not internalized) LDL concentration vs. LDL concentration added 
  • JD's levels are a lot lower than normal cells levels
  • JD has a problem with internalizing his LDL! 

C:

  • degradation
  • TCA-soluble material vs. LDL concentration added 
  • JD's levels are a lot lower than normal
  • seems like he has a problem degrading, but could it just be because he has a problem internalizing, so thath's why his numbers look so low? need more data on rate of internalization I think...
    • I think it actually is showing the rate (units = ng/(mg * 5hr)) 
    • SO, his rate of internalization is low too
  • normal FH patients - if receptor negative, they have no receptors, so their binding levels would be very low
    • if receptor-defecient, they're LDL has trouble with the LDL-LDL receptor interactions, and so their binding levels would also be rather low
    • BUT, JD shows that his binding levels are relatively normal, while he has a problem with internalizing and then degrading LDL
    • so, he's phenotypically similar to normal FH patients, but molecularly unique from them 

 

Results of Methods

Submitted by jgcahoon on Wed, 10/04/2017 - 23:06

Figure 1 and Figure 2 shown above have many differences. The first noticeable difference is the presence of shadows in the replicate. Another big difference was the labeling of each square. Figure 1 contains large, red letters while the replicate has smaller black letters. The location of these labels was also different for every picture except A. The dimensions of each picture are not the same, as Figure 1 appears more vertical, while Figure 2 is more horizontal. The arrows are red in both, but pictures B and D in both figures have arrows facing in different directions. Looking at picture B, the distance to the tree is not the same in the figures, as the replicate is zoomed in on the bark more. The angle of the picture taken is different in picture C when comparing the two as well. Lastly, the distance to the tree is different when comparing picture D.

Achromatopsia draft

Submitted by msgordon on Wed, 10/04/2017 - 22:56

 While acquired Achromatopsia is associated with damage to either the thalamus or the fourth visual association area (V4) of the cerebral cortex, the majority of cases are congenital and the condition is passed down through an autosomal recessive inheritance pattern.  It is generally accepted that there are six genes associated with the disease; CNGA3, CNGB3, GNAT2, ATF6, PDE6C, and PDE6H. Of those five, the most commonly seen mutations occurs in the CNGB3 and CNGA3 genes. The findings of one study found that the CNGB3 variants are primarily responsible for Achromatopsia in people of European and Middle Eastern descent while the CNGA3 variants are mainly responsible for the condition in people of Chinese descent.Like all autosomal recessive conditions, the condition is seen more frequently among people with a high degree of consanguinity. However, the most common pathogenic variant across all probands is c.1148delC in the CNGB3 gene, which results in a nonsense mutation in the protein (p.Thr383IlefsTer13). This particular mutation was found by whole exome sequencing — the sequencing of all the genes expressed in the body through the sequencing of exons. The placement of this early stop codon renders the resulting protein nonfunctional. Consequently, patients with this particular mutation will display complete loss of cone function and cone degeneration. Thus, they will also display a complete loss of color vision. 

Methods Project 1st Draft

Submitted by hamacdonald on Wed, 10/04/2017 - 22:20

Abstract:

    The purpose of this project was in gain insight into how to write a manuscript. The importance of writing thorough methods that are able to be reproduced. Also to separate observations and inferences from one's writing.

    In this project one student had to create a method section that was to be followed by another peer. The first student was to create an original multi-paneled scientific figure and the second student was to follow these instruction and create a replicate solely based off the written methods.

    In this project, I took three pictures of the Labrador Violet using my Iphone 5. I then created my figure by using the software Inkscape in the BCRC.

    The resulting Figures had differences that were able to be identified as observations without drawing inferences on what causes these differences. What did cause these differences were referred to as factors that could be controlled.

    In conclusion, one has to be extremely meticulous when describing how to replicate something if they are expecting the same result as the original. It is hard to state observations without wanting to explain what causes these observations, but is critical to remaining unbiased. It would take many drafts to perfect any research paper and peer editing to enable unbiased reviews/ editing.

Introduction:

    In Biology 312 taught by Professor Brewer the “Method’s Project” is done to instill the importance of correctly writing scientific papers.When writing in the scientific forum, it is important to produce replicable work.  It is critical to be meticulous in one’s writing so the methods can be performed again and produce a replicable product. It is also crucial to be able to appropriately note the differences between observation and inference in terms of one's own writing, and to avoid making any inferences.

    This methods project entails taking three pictures of a living organism to create a multi-panel scientific figure, and to write a method section that is copied by a peer with the goal of producing the same exact figure.  This will highlight the factors that are and are not controlled by the creator of the original figure when writing their methods.

    The organism I chose to display in my multi- panel scientific figure is the Labrador Violet. The Labrador Violet is a perennial native to The United States, Canada, and Greenland. They grow in terrestrial habitats such as Alpine or subalpine zones, cliffs, forests, meadows/ fields, mountain summits, and swamps, and anthropogenic, man-made habitats. Two distinguishing traits of this organism are the purple flowers and the violet hues of the leaves. It is nicknamed, “American dog violet” and has edible leaves.

    When choosing this organism I had to keep in mind several factors for replication. First off, I wanted to use a plant to allow for less movement of the organism when compared to that of an animal. I chose an accessible area, the Franklin Permaculture Garden. The time of day is controlled. This plant is low to the ground and less likely to be affected by wind.

    When producing the actual figure after pictures were taken, I controlled factors by using inkscape to produce my image. I gave exact dimensions of the pictures and explicit orientation of the pictures in respect to each other.

Methods:

    Last week I took pictures of the specimen known as Labrador Violet. I found the Labrador Violet in Franklin dining hall Gardens. I went at 4:00 PM on Friday the 22nd of September. It was a partly cloudy day in the high 70’s.

    I approached the garden facing the dining Hall with the Morrill buildings at my back. I walked into the Garden and passed the sign in the center that states, “FRANKLIN PERMACULTURE GARDEN, sponsored by Umass Dining”. At the sign I went right and walked up the far right side of the garden until I saw a sign that said, “Labrador Violet, Viola labradorica, Family: Violaceae, edible leaves; dynamic accumulator; ground cover”. Here is where the specimen is located on the ground.  

    I used the Iphone 5 to take pictures of the plant. All pictures were taken with the camera screen facing vertically not tilting the phone in anyway. First I took a picture that captured the entirety of the plant. This included the sign labeling the plant. The sign is located in the right hand side of the picture, about 1.5 cm down the phone screen and on as far right to the edge of the camera that allowed me to include the whole sign. In order to get this picture I had to squat down and get as low as possible to have mainly just the Labrador Violet in the picture.

After I took a picture of the majority of the plant, I took pictures highlighting some of the distinguishing traits of the Labrador Violet. I took pictures of the purple flowers. There were only around four of these flowers fully developed. I picked one of them that was close to the sign that labeled the plant. It was to the left of the sign roughly one foot and away. I put my camera as close up to the flower as the Iphone 5 allowed in focus. This flower was roughly one and a half centimeters tall and wide. The flower has a white center with darker purple lines protruding up one of the petals.

After I took pictures of one of the flowers, I took a picture focusing on the leafs that show the violet colored hue’s that the plant is named after. I selected a leaf that had a darker violet color than the surrounding leaves. The surrounding leaves were more green than violet. For this picture the plant was centered. It had a stigma that came out of the center of the leaves, it went up to the left, and  followed  the center of the large left leaf.

 

After I took the picture,I went onto inkscape in the BCRC computer lab in order to create my scientific figure. I started out by emailing myself the three pictures of the Labrador Violet. Once I received these emails, I saved each picture onto the desktop and exported them all to “png”. From there I created a folder titled, “Figure- Hailey” and saved all three pictures in here.

I opened up inkscape and titled my project. To do this, I went to “File”, “Save As”, and wrote into the header at the top, “Hailey- Original”. I then imported in all of my images by clicking “File” and then “Import”. Then I selected “to desktop” on the left panel of options which lead me to the folder I created. I clicked onto the folder “Figure-Hailey” and held down the command button as I highlighted the three pictures.

Once all pictures were imported into Inkscape, I formatted the pictures. In order to do this, I clicked on the blank backspace (not any of the three pictures), and then clicked the lock button on the top of the screen. This button looked like an open lock and when clicked turns into a closed lock. It was located to the right of the “W:” (width) selection. I then selected my first image, the image including the sign of the Labrador Violet, and set the “H:” (height) to 1000.000 mm. This was repeated for the next two pictures, but instead changed the heights of both to 500.000 mm.

I then formatted the pictures together so the picture including the whole plant and the sign labeling the plant were to the left of the other two pictures. The picture containing the purple flower was put below the picture with the purple hue of the leaves. All three of the images were connected corner to corner with no space in between.

Then I labeled the three images. I first labeled the picture of the close up of the plant without the fully developed flower “A”. I clicked on the text button on the left panel of icon and created a box in which I typed a capital letter A. The font size was then changed to 144 and color changed to white. In order to change the color I clicked on the letter and went to the button of the screen and selected the white box option of the spectrum of colors shown. I repeated this process to create labels “B” and “C”.  Label “B” was for the purple flower, and label “C” was for the picture on the right displaying the entire plant. I placed “A” in the top left hand corner of picture described as A. I placed “B” in the lower left hand corner of picture described as picture B. And I placed “C” in the lower left hand corner of picture described as C.

After the three pictures were labeled “A”, “B”, and “C” I created two arrows. The first arrow pointed at the stigma in picture “A”. I used the straight line tool which is eleven icons up from the bottom on the left hand side of Inkscape. I clicked on the tool, dragged the line to the right, and then double clicked to create my line. Next I clicked on “Object” on the very top of the computer screen, then clicked on “Fill and stroke…”, and set the width to 5.000 mm. I added an arrow by going under the “Stroke Style” tab and went under “markers”. I clicked on the third drop down to the right of “markers” and selected the second arrow option down. Then I changed the coloring of the marker to white by going to “Stroke paint” and clicking on the far right of the color spectrum.  Next I dragged the arrow to picture “A” and had the arrow pointing at the stigma coming out of the leaves. I made sure the arrow was not hanging off the edge of the figure. Then I left clicked on this arrow and hit “copy” and clicked “paste” in order to make a second arrow that pointed at the purple flower in picture “B”.

After I created the figure I set document properties. I went under “file” then “Document Properties”. Under the “Orientation:” section I clicked on “resize page to content…”. Then clicked “Resize page to drawing or selection”. Next adjusted the background color by clicking on “background color” located at the bottom of the “Document Properties” box. Then another box popped up and I clicked on the checkerboard style bar at the bottom and dragged the line all the way from the left side to the far right side.

To save my figure, I went to “File” and then “Export PNG image…”. The width was corrected to 1200 pixels. I made sure the file type was saved under “MacDonald-original.png” then clicked “Eport”. I then went under the finder tab on the computer desktop and found my figure saved onto the desktop.

Figures

Figure 1. Labrador Violet Original. Photographs taken on Iphone5, Section “A” the white arrow is pointing at the stigma of the plant. These leafs show the violet hues that give the plant its name. Section “B” the arrowing is directing toward the purple flower of the Labrador Violet.

 

Figure 2.

Results

Figure 1, the original figure, contains many differences when compared to Figure 2, the replicated figure. Starting out with the varying sizes of the two figures. Figure 2 is much smaller than Figure 1. The sizes of the individual sections, “A”, “B”, and “C” also vary from Figure 1 to Figure 2. All three pictures in Figure 1 were taken vertically. In Figure 2 all but “C” were taken vertically. Along with the font size of the letters labeling these sections. The orientation of these three figures in relation to one another is different as well. In Figure 1, “A” is located in the top right corner with “B” directly below it. In Figure 2, “A” has no other section below it.

The content of the three sections, “A”, “B”, and “C” vary. In Figure 1 “A” is the picture showing the close up of the leaves. Whereas, in Figure 2, “A” is a picture of the entirety of the plant including the sign with its name. In both Figures 1 and 2, the largest picture is the one showing the whole plant with the sign. In both Figures, the section labeled “B” is showing the purple flower of the Labrador Violet.

In Figure 1, all of the edges match up leaving no white space in between the three pictures. In Figure 2, section “B” and “C” shows white above “B” and below “C”. Also the edges of these two sections do not touch in the corner. They have varying widths in Figure 2, but share the same width in Figure 1.

Figure 2 contains two smaller boxes, one colored white and the other color black, sitting outside the confines of the three pictures. Figure 1 does not contain anything outside of the three pictures.

The two white arrows in Figure 1 and 2 do appear to be the same size, width, and color. However they share a different orientation. In Figure 1 they are pointing to the right. Whereas in Figure 2 they are both pointing to the left. The first arrow in Figure 1 picture “A” is pointing at the stigma on the violet colored leaves. In Figure 1, the first white arrow is on the picture of the whole plant. The second arrow is pointing at the purple flower in Figure 1 but is pointing at the stem in Figure 2.

The picture showcasing the close up of the leafs shows a different leaf in Figure 1 than in Figure 2. There are six centered violet colored leaves in Figure 1 and only two in Figure 2. The orientation of the leaves is different as well. The picture showing the entire plant is different in Figure 1 there are no woodchips shown like in Figure 2. There is also sky seen in Figure 2 in the picture of the whole plant. The flower in section “B” of both figures is orientated in different directions. In Figure 1, the flower is opened up toward the camera, whereas in Figure 2 it is facing downward toward the ground.

 

Discussion

Factors need to be controlled in order to produce an exact replicate. Starting in order as mentioned in the results, the size of the entirety of the figure is controlled. At the end of the methods it was stated to correct the pixel width to 1200 but this was not followed. Next the size of each individual picture has to be controlled by selecting the lock icon in inkscape and altering just the heights of the pictures. Because Figure 2 took picture “C” horizontally, the pictures did not align as the way instructed in the methods, in which all pictures were taken vertically. The orientation of the three, “A”, “B”, and “C” need to be controlled. In the methods, it was described as, “I then formatted the pictures together so the picture including the whole plant and the sign labeling the plant were to the left of the other two pictures”. But the original figure shows the picture of the whole plant to the right of the other two pictures.

Which picture was to be labeled “A”, “B”, or “C” was controlled in the methods. However, due to the difference in location of the larger picture with the whole plant in both Figures, the labeling of pictures switched. In the methods it describes “C” as the whole plant on the right. Because a different picture is on the right side in either Figure, the labels are also different.

The pictures “A”, “B” and “C” do not match up in Figure 2 due to the picture taken horizontally. This should be stated more clearly in the methods and describe the difference between the two styles, vertical and horizontal.

The two boxes seen outside of the pictures in Figure 2 do not exist in Figure 1. The factor that was not controlled for this is the methods should state that nothing should exist outside the confines of the three pictures taken on the Iphone. These pictures should fill the entirety of the page.

The arrows required more description in the methods regarding the process on inkscape. The orientation was not controlled by using the exact locations using X and Y that the software allows. This feature would of controlled this factor.

The actual leaves/ flowers that were taken pictures of required more control. Using a ruler or measuring device to give exact locations from a known landmark would prevent the varying leaves and flowers from Figure 1 to Figure 2. Also stating no sky and no wood chips in the picture would control the varying angles for the picture of the entire plant in both Figures.

This project produced two varying Figures for the results. The goal of the project was not just to create a perfect method sections, but to later address all of the factors that were not controlled, and learn from this for the future.

 

CAM Photosynthesis

Submitted by tterrasi on Wed, 10/04/2017 - 21:07

              CAM photosynthesis is a similar process to C4 photosynthesis, in that PEP carboxylase fixes carbon dioxide to produce OAA. Instead of forming malate, OAA is converted to malic acid. Malic acid is shuttled to the vacuole of the cell, not moved out of the cell to bundle sheaths cells as shown in the C4 pathway. At night, stomata are open, PEP carboxylase is active, and malic acid accumulates in the cell’s vacuole. During the day, stomata are closed. Malic acid is shuttled out of the vacuole and converted back into OAA, releasing carbon dioxide in the cytosol. The carbon dioxide is now fixed by rubisco, and the Calvin Cycle begins. The advantage of CAM is that photosynthesis can occur during the day while stomata are closed, greatly reducing water loss. This is why CAM plants are found in environments that are hot, and dry environments, but has cool nights, such as deserts.

Methods Project Results (part 1)

Submitted by samihaalam on Wed, 10/04/2017 - 18:21

Differences:

in general:

  • different arrow heads used
  • original is 1200 x 1050, replicate 1200 x 1600

A:

  • replicate head-on features the plaque in the section
  • different angle than I used
  • replicate appears sunnier, original seems more in shadow
  • replicate also features plaque for the next species over in upper right hand corner 

B:

  • replicate's ruler is in mm, original was in cm
  • leaf pointing down 
  • ruler underneath leaf, original ruler on top of leaf
  • shadows are different 
  • original arrows probably longer
  • thumb/fingers in different directions 

C:

  • different leaf used
  • original more zoomed in
  • original arrows probably longer

D:

  • different leaf used 
  • replicate has arrow more in middle of leaf, original has arrow pointing more towards corner of photo
  • original more zoomed in
  • shadows different
  • original arrows probably longer

Factors:

  • I forgot to mention certain things 
  • different leaves were used 
  • weather/time - probably affected sunlight levels/shadows

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