Etch A Cell

by Justin Brown

The Zooniverse website is home to the Etch a Cell project. Zooniverse is a scientific platform where everyday citizens can help scientist do research without needing any scientific background at all. Etch a Cell is about the study of the nucleus, or center, of the cell in order to understand how it works. This is in an effort to study the changes in the structure of the nuclear envelope, the wall surrounding the nucleus, between healthy cells and diseased cell. Scientist need three dimensional models of the nuclear envelope in order to study them, and the Etch a Cell project allows for citizens to help create those models.

In this image the cell’s nucleus is “segmented”, with the annotation overlay toggling on and off for clarity (Etch a Cell)

Scientists can create the models using a process known as segmenting. An electron microscope is used to take pictures of multiple layers of the cell. These images are sent to the Zooniverse website where they can be viewed. The observer of these images can then draw a line where they think the nuclear envelope should be. After multiple citizens have viewed and recorded their analysis, the data is reviewed once more and the nuclear envelope is determined through consensus. This process repeats itself for the different layers of the cell until scientist can establish a full three dimensional view of the cell.

3D reconstruction of 2D segmented images of a nucleus (Etch a Cell)

Having a three dimensional look of the cell’s structure allows scientists to have an in depth analysis to study how the shape has changed and why. This research would take ages if the scientists were doing it alone. But thanks to those who participate in this scientific investigation and contribute some of their time and energy to help this study, scientists can work faster and develop computing software for this task.

The reason why this research is important is that it could help many people in the future. People with diseases, viruses, and cancer can truly benefit from this study. The end goal of the Etch a Cell project is to find treatments for people and to learn more about what happens to people with these illnesses on the cellular level. When a virus attacks a cell the nuclear envelope is broken down, exposing the nucleus and damaging the cell. This became known through research, but is only a small part of the importance of the nuclear envelope. The rest is yet to be determined, but the Etch a Cell project does greatly improve the quality and speed of the much needed cellular research.

Zooniverse. 2017, July 14.  Etch a Cell. Retrieved from https://www.zooniverse.org/projects/h-spiers/etch-a-cell/about/research

 

Etch a Cell

by Gabrielle Easterly

For decades, scientists have been trying to understand cells and how they work. The project that my group chose, Etch a Cell, will continue to assist scientists through a Zooniverse project. Zooniverse is a citizen science platform that allows  people to make an account and follow along with various projects to look at pictures and analyze them by either drawing something out, making marks, separating, or through other actions. For the Etch a Cell project we are instructed to look at a picture of a cell taken by an electron microscope and draw out the lining between the nucleus and the other chemicals that surround it called the nuclear envelope. While this project may not be the most fun to do, it can be very helpful for the development of cures for various diseases and cancers.

Our job is to segment the image taken by the electron microscope which allows for vision of smaller object such as cells. Segmenting is highlighting the topic of interest within an image, not just specifically identifying the nucleus and highlighting it. We are doing this because from this segmenting scientists can then create three-dimensional pictures that allow for better understanding of how the cell is formed. They are able to do this by segmenting together the different segments that we highlighted to create a model (The Francis Crick Institute). How cool?

The importance of this project by itself can not be stressed enough on the future development of health in the world! This project is extremely essential for cures to cell abnormalities caused by “cancer, infectious diseases (including HIV, tuberculosis, malaria), the immune system, the brain and nervous system, diabetes and several others” (Francis Crick Institute). The nuclear envelope forms in different ways based on what diseases or other cell irregularities that cause a negative or positive impact on the body. The nuclear envelope protects the nucleus and acts as a “gate,” and separates the chemicals outside of the nucleus from the nucleus itself (The Francis Crick Institute). With our couple of minutes to help these scientists we can help them understand cells better and make things more possible than they had been.

With what might seem like only a small amount of assistance, people like you and I can help change the dynamics of cell studies. Segmenting the photos by themselves makes the overall process of creating the three-dimensional models much easier for the scientists. From the creations of the three-dimensional models scientists will now be able to understand how different diseases affect the cell, specifically the nucleus and nuclear envelope. Eventually computers will learn to do both the segmentation and creation of models on their own but all it will take is the continuous help of citizen scientists. With enough help from citizen scientists we can help the scientists at the Francis Crick Institute be “able to train computers to segment automatically” which can further their understanding of biology and the ability “to work out how new treatments might be created” (The Francis Crick Institute).

From this project we, regular people or citizen scientists, will be able to help lead to ,eventually, further understandings of cells. The Zooniverse platform makes it simple for people to become scientists and you would not think that drawing a line around a nucleus would have as much of an impact as it potentially could. This process would have taken the scientists at The Francis Crick Institute much more time to complete by hand.

Remember you too can become a citizen scientist and help continue the study for treatments!

 

The Francis Crick Institute. (n.d.). Etch a Cell . Retrieved July 13, 2017, from https://www.zooniverse.org/projects/h-spiers/etch-a-cell/about/research

Count Flowers for Bees

by Alex Burr

Bees and other animals are pollinators, and pollinators are crucial to keeping plants, animals, and us alive. Without pollinators, we would be unable to grow 75% of the food grown in the US daily, including all the sweet fruits you love and all the bad vegetables your parents probably make you eat. For this reason, it is necessary to identify places pollinators can visit frequently in order to increase conservation efforts there.

Pollinators are broadly defined as any species that transfers pollen from one plant to another plant of the same species. Plants have both the pollen (analogous to sperm in males) and the stigma (analogous to an egg in females) needed to fertilize itself. While some plants are able to fertilize themselves without outside help, 80-90% of all flowering plant species cannot. They need another organism, a vector (like a bee), to transfer pollen to the stigma and fertilize the plant.

Count Flowers for Bees is a collection of photos of Ireland’s countryside, where there are many flowering plants that need vectors (aka cross-pollinating plants). The research team that took these photographs needs your help in counting the total number of each kind of flower in each picture. When you count these flowers, the research team is able to identify the areas most populated with cross-pollinating flowers that therefore need conservation efforts the most. Without these conservation efforts, humankind could lose many of the flowering plants and/or the vectors they need to create food. This project is important because it concerns the very pollinators we all need to create the majority of our food, and without food humankind cannot survive (we think).  

Endangered Species

by Kristian Marinez

  Mouse lemur contemplating its existence.

Who global warming affects.

When most people think of endangered mammals threatened by global warming they think of polar bears on melting glaciers. That’s not the most serious case. Most endangered mammals are actually tropical animals in warm climates. Instead of a polar bear being endangered from global warming it can most likely be a mouse lemur in Madagascar. I am interested in the endangerment of mammals simply because they are breathtaking creatures. They think and feel just like us humans do and it’s a shame that a whole lot of them are endangered. It’s interesting to find out the reason for their endangerment instead of just knowing that they’re endangered.

 

Where mammals are endangered and how many are endangered.

The data to support the reasons for mammals endangerment come from the World Bank and informs us with how many mammals are endangered and in which regions endangered mammals can be found. The graph below shows the highest numbers of endangered mammal species (organized from greatest to least) and their region. The  two regions with the most endangered mammal species are East Asia & the Pacific and Sub-Saharan Africa. These regions have a staggering 891 endangered mammals each. The third highest region, Latin America & Central Asia, has 640 endangered mammals. The fourth highest region with the amount of endangered mammals is Europe & Central Asia, with 307 endangered mammals. The three regions with the least amount of endangered mammals have less than 300 mammals each. South Asia has 249 mammals, Arab world has 217 mammals, and Middle East & North Africa have 203 mammals.

 

How global warming affects endangered mammals.

From this data, there is a noticeable pattern of a high number of mammals endangered in hot/tropical regions, like Mexico, Madagascar, and Asia, as compared to cooler regions like the Middle East & North Africa. We notice this trend because an increase in temperature (like that caused by global warming) by even a small amount can affect mammals in tropical climates since they are less resilient to heat change. This is because these species are accustomed to living in a certain temperature range, and once this range is surpassed, these animals have a hard time living. For example, global warming cause mouse lemurs to shift habitats and find a different way to obtain food than before.

 

Sources:

http://www.bbc.com/earth/story/20150226-what-hope-is-there-for-madagascars-threatened-lemurs

http://www.dailygalaxy.com/my_weblog/2009/03/global-warmings.html

http://data.worldbank.org/indicator/EN.MAM.THRD.NO

http://a-z-animals.com/animals/grey-mouse-lemur/pictures/4167/

Jungle Rhythms!

 by Ronnie Ovando (a 2016 Adler Astro-Journalist)

When stepping through the Zooniverse citizen science project “Jungle Rhythms,” it feels as if one is playing a Nancy Drew or Sherlock video game. The project contains a bunch of old documents relating to tree life cycles between the 1930’s – 1950’s. The goal is to be able to interpret the hand written documents that have lost their color due to old age. The documents are designed to be like calendars, to be labeled according to what happened that particular year to the tree. The video game-like challenge comes from having to be detail-oriented in order to understand and catch the little markings with the documents.

The African rainforest is said to “store up to 66 Pg (Picograms) of carbon,” according to the project’s home page. Scientists at Jungle Rhythms are concerned for how this will affect or effect climate change, and how exactly weather conditions can alter the forest. For example, droughts can severely affect structure and function. By using the documents and knowledge of the rainforest’s weather history, the participants can possibly figure out how trees react to weather.

How did the Jungle Rhythms scientists collect this documented history of tree cycles? Between 1937 and 1958, researchers at Yangambi research station studied over 2000 trees. They all recorded data that dealt with life cycles (also known as phenology) such as fruit development, leaf growing, etc. The data was organized in calendar-like tables, which have sections that are separated into years. The original copies were made digital in order to translate without ruining the hand written documents.

Transcribing the documents seems like a job only for scientists, but the skills needed for this task are common. The home page states “The human eye and brain is finely tuned to finding patterns and picking up these slight nuances in shading.” Essentially, our brains are wired to do this! In order be a successful citizen scientist, one also must have a good base in knowledge of the trees in the African rainforest in order to understand the context of the data.

“A Summary Table” – Jungle Rhythms

 

The picture above is an example of how the documents look and are organized. It’s almost calendar-like, expect with listing years instead of just months. Each section listed is divided by 6 months, and at the far left are the names of the trees being recorded. Within those sections, data is represented by lines, crosses, or other types of marks. Very few words are used.

“Tombe Writing – Jungle Rhythms”

Here’s a good example of writing within one of the tables. The writing above reads “Tombe,” which according to Google Translate, means “falls” in French. It can be concluded then that the tree fell sometimes this year. The time when is hard to interpret. For me, I assume that the fact that no month is emphasized in the picture, that the scientists did not know the exact month the tree fell, but concluded that it fell between March – August.

For people who are interested in both science and history, this Zooniverse project does a great job and attending to those two fields. Jungle Rhythms is hoping to discover new data concerning African trees, and the interpretation of the documents.