Making Figures with Inkscape

Submitted by sbrewer on Fri, 09/22/2017 - 11:37

Screencasts for making multipanel scientific figures using Inkscape

Creating Figures: Part 1. Compositing
Creating Figures: Part 2. Labels and Arrows
Creating Figures: Part 3. Document Properties and Exporting

Hints

  • Think ahead of time. What is your figure going to look like? Should you crop imagery ahead of time? Do you need to adjust image or exposure? (Note: Some journals don't allow digital manipulation of imagery). Do this in a bitmap editing program (e.g. GIMP or Photoshop).
  • Do all your work in a folder. Put your image files in there. Save your SVG file in there. Save early and often.

Workflow

  1. Import all your images: Either Link or Embed. Note things can be “above” or “below” others. Click or drag over to select. Hold the “shift” key to select multiple objects.
  2. Composite your images to make your design: Lock proportions to avoid stretching. Turn “snapping” on or off. Set height and width directly to resize. Use Align and Distribute (switch to "relative to first selected").
  3. Construct one label: Make a square box, make both stroke and fill the same (black or white). Put a text field in and add a letter. Use sans font. Use align and distribute to center letter.
  4. Duplicate label to make more: Select both, duplicate object, move. Repeat as necessary.
  5. Finish each label: Replace each letter as necessary. Use Align and Distribute to center. Select both and group. Use align and distribute to put labels at corners of each panel.
  6. Create arrows: Use the Line Tool to draw a straight line segment (click, click-click). Then use Fill and Stroke tool to set the line width and add arrow head to start (or end).
  7. Set the Page Size: Open Document Properties. Resize Page to Drawing. Set background to not be transparent (increase alpha channel to 255).
  8. Export Finished Figure: Export PAGE. Set width to 1200pixels. Save with name “Lastname-Original.png” The resultant PNG file is your finished figure.

Note: Do not share your finished figure or include in your METHODS manuscript until your methods have been followed!

Monkeys in zoos have human gut bacteria

Submitted by tterrasi on Sun, 09/24/2017 - 21:06

            Billions of bacteria are part of the primate gastrointestinal tract, contributing to metabolic, autoimmune, and pathogen resistance. These bacteria are correlated to metabolic and autoimmune human diseases that are shown in western societies. Factors such as poor environment, stress, or antibiotic use can lead to dysbiosis, which is a microbial imbalance. This can cause the movement of bacteria, expansion of pathogens, and harmful bacteria to move into and out of the gastrointestinal tract. Overall microbial diversity can be lost due to dysbiosis. Understanding how diet and lifestyle can affect the composition of the gut microbiome is an important health issue to focus research towards.

            A study of nonhuman primates in captivity was conducted to show the relationship between lifestyle and diet on gut microbial diversity to better understand primate conservation and human dysbiosis. The red-shanked douc and the howling monkey were the two species studied with a sample of different individuals from captive and wild environments. Both these species are folivorous, meaning a diet that is nutritionally poor and hard to digest. These species are hard to maintain in a captive environment due to the challenge of providing a wild-like diet. It was found that in captivity, the nonhuman primates have a loss in fiber, which in turn, a loss of native gut bacteria. Also, being in captivity, with the loss of native bacteria, they become colonized with two distinct bacteria, Prevoltella and Bacteroides. These are largely found in the human gut microbiome. The researchers confirmed this phenomenon in eight other captive environments that showed the same convergence pattern. By studying the most prevalent animal model to humans, other primates, can show environmental and diet behaviors that lead to a host of gastrointestinal diseases.

Methods (part 1)

Submitted by vthong on Sun, 09/24/2017 - 20:50

I walked along the path connecting Herter to ILC, with Du Bois to my left during the walk. I stopped at the __th tree on the left, which is a Norway Maple labeled with a plaque. I took the picture of the Norway Maple from a lamp post that is to the right of the path. It is the second to last lamp post at the fork of the sidewalk, closest to the Norway Maple. The picture is taken correctly if Du Bois is not in the back of the photo, but should to out of the frame to the left. Still facing the Norway Maple on the side with the plaque, I looked down and noticed an interestingly shaped root. If you look down at the roots, it is slightly to the right relative to the plaque. The root sort of takes shape of a human with arms and legs. I crouched down and took a picture of the human-shaped root. In my photo, the root is overcast by the shadow of the leaves of the Norway Maple. These photos were taken on Saturday morning at 9:15Am.

Types of ion pumps notes

Submitted by daniellam on Sun, 09/24/2017 - 18:06

There are many types of ion pumps but the most common types are the sodium potassium pumps, the calcium pumps, and the potassium leak channels. The sodium potassium pump cleaves a huge amount of ATP as energy and the percentage of ATP consumed in the brain is 70%. These pumps are critical to set membrane potentials and functions by pumping 3 sodium ions out of the membrane and 2 potassium ions into the membrane. The body always has a very small concentration of calcium on the inside due to calcium ions’ property to be a signaling molecule. This pump actively pumps calcium ions out of the cytosol. The potassium leak channels provide a major role in generating membrane potentials as well. These randomly open but don’t allow other ions to pass beside potassium ions. These channels allow potassium to migrate down its concentration gradient to bring the membrane toward equilibrium. These three types of ion pumps provide are essential component to our body’s daily function.

Final Draft Ecology Assignment

Submitted by hamacdonald on Sat, 09/23/2017 - 19:40

The species, monito del monte, Dromiciops gliroides native to the South Western part of Argentina and Chile. Due to its location south of the equator  it would most likely shift downward, away from the equator. The reason for this being is global warming is slowly warming the earths surface temperatures making this location no longer suitable for the monito del monte. Although this shift is relatively slow, maybe only a few degrees higher this makes a substantial difference to the specie. This is proven in the graph, "Change in population size of Dromiciops gliroides in the study area" as the number of monito del monte drastically declines from around 1600 in 2002 to 600 in 2016. This once suitable location for the species has warmed gradually to a temperature that does not support the needs of the species. Therefore, it has caused them to slowly shift downward away from the equator and find a new location with a more suitable to their temperature needs.

   It would be expected that this red star is the northernmost part of its range. Based on both the graph and the patterns of global warming heating the earths surface. The graph shows a steady decrease in the monito del monte in this area starting at around 1600 individuals in 2000-2002 and decreasing to as little as 600 in 2014-2016. This suggests that they are migrating out of this area. Given the center of a distribution range should be the highest population, would prove that this decreasing population is not the center of the range. Due to global warmings trends of heating up the earths surface, the monito del monte would logically go downward away from the equator to cooler regions. Their old location is no longer suitable to their lifestyle, proven by the Change in population size of Dromiciops gliroides in the study area” graph.

Yeast media notes

Submitted by daniellam on Sat, 09/23/2017 - 18:12

There are three types of media that are used for yeast. These three types are used for different purposes. The first kind is YED which contains all the nutrients needed for growth. This type has HA2 strains can survive. This media also causes the yeast to accumulate a red pigment due to the accumulation of P-ribosylamino imidazole that is exposed to oxygen. The second type is MV which has a minimal amount of pure chemicals needed for growth; this type lacks adenine so neither HA2 nor HB1 can grow. YEKAC is the third type and is nutritionally unbalanced. This type is used as a starvation media so that it triggers yeast to form their haploid forms as asci from their diploid state. Each type has a different function for lab use when looking at yeast.

Perfect Paragraph 2 (Week of 9/18-9/24)

Submitted by jmazzola on Sat, 09/23/2017 - 15:00

     Recently, a feldspar mineral by the name of Labradorite has become popular as more have discovered the stone’s beautiful “flashing” color when shown under light. This unique iridescent phenomena is called “labradoresence”, named especially for the stone. The mechanism of this color play is the result of light shining through the rock, striking what’s called a “twinning surface” and then reflecting off and thus producing the iridescent colors. These colors, which are often compared to those of aurora borealis, are comprised of brilliant blue, green, golden yellow or purple shades, while the primary color of the rock is usually gray with black lines running through it. Labradorite species that show all of these colors mostly covering the whole surface of the piece are known as “spectrolite”, which is considered to be the highest quality of the stone, primarily found in Finland or Madagascar, but sometimes can also be found at it’s original discovery site in Labrador, Canada. The beauty of this stone did not go completely unnoticed in the past however, as some religious groups in the northern hemisphere called the stone “frozen fire”. It was said back then that pieces of it had fallen down from the Northern lights, or that the stone originated on Earth primarily but trapped the “fragments” from the spectacle within. So clearly, given it’s unique properties and past, it is no surprise that this stone has gained much popularity in the jewelry industry in recent years.

Methods Project Draft 2

Submitted by samihaalam on Fri, 09/22/2017 - 17:21

On September 21, 2017 at around 4:00PM Durfee Conservatory was approached coming from the stairs in between Morrill N and Morrill S. The temperature was about 25°C and the atmosphere was cloudy, humid, and slightly windy. At the circular courtyard, facing the Durfee Conservatory, there were two paths to take into the garden and the left path was taken. At about halfway down the path, there were observed to be a patch of plants with variegated leaves, with green leaves and pink patches on the leaves. They were located in between a patch of flowers with very bright pink petals and a patch of flowers with small purple flowers. Standing on the sidewalk facing the plants, a picture was taken, holding the camera high above the flowers to capture as many of the target plants as possible.

Staying in the relatively the same spot, another picture was taken closer to the plants, holding the camera on the iphone about one foot away horizontally and on the same level vertically as the plants. An up-close photo was also taken of one plant specifically. The iphone was held about 10cm away from the plant, facing the petals so that inside of them could be seen.

A picture was also taken of the card describing of the plant. The card was approached, and the picture was taken holding the iphone camera about a foot away and directly across from the card. The picture was taken so that the description appeared on the far left of the picture, and the rest of the picture contained the target flowers. 

Starting Methods Project

Submitted by hamacdonald on Fri, 09/22/2017 - 12:53

When looking through the garden outside of Frank dining hall, I came across a funny plant, Hypericum perforatum, more commonly known as, “St John’s Wort”. Having never heard of it before, I think it would be perfect for this project and for me to learn about something new. The description on the plant in the garden says, “Tea Herb, Medicinal”. This triggered my attention, what is this plant used for?

St Johns Wort falls under the Hypericaceae family. It is known for its medicinal traits in treating depression. The name St John’s Wort comes from the traditional harvesting on June 24th, St John’s Day.  The genus name Hypericum is created from the Greek words hyper and eikon meaning above picture. This is why some people believe if they hang these plants over religious photos on St John’s day it will ward off evil spirits.

Replicating the picture I took of these the plant shouldn’t be too hard. I went to Frank around 6 PM. One factor that will have to be controlled is waiting for no bees to be on the flowers. I personally waited for a bee to fly away because this would be easier to replicate no bee present on the flower. Some factors out of my control are if someone comes and picks these flowers or if any weather factors effect the plant in anyway.

Pages

Subscribe to Writing in Biology RSS