This method can help answer key questions in the space biology field about the generation of hypotheses to assist future research using publicly available all mix data. The main advantage of this technique is that it can be used as a tool for generating space biology data. The publicly available data on GeneLab allows researches to develop clinical theories about disease therapies or countermeasures for healthcare associated with spaceflight with relatively little cost.
Demonstrating the rodent habitats will be Yasaman Shirazi-Fard who is ISS mission scientist for rodent research. Following delivery, group the rodents within standard vivarium cages. And have the animals acclimate to NASA nutrient upgraded rodent food bars, lixits, and raised-wire floors until the animals are loaded into the transporter.
For travel between the earth and the International Space Station, place ten mice per side into each transporter for a total of 20 mice per transporter. Once on the International Space Station, attach the animal access unit to the transporter and use mouse transfer boxes to transfer five mice at a time to the habitats. To load the mice into the habitat, detach the animal access unit from the transporter and attach the unit to the rodent habitat.
Then, transfer the animals from the mouse transfer boxes to the rodent habitats where they will reside for the duration of the mission. Every day, video of the animals inside the habitats is examined by trained staff to monitor the health and well-being of the rodents. Guidance and oversight for all work involving animals is provided by an attending veterinarian.
Infrared imaging is used to see animals inside the habitats during the dark phase of the light-dark cycle, when mice are typically most active. This camera view shows food bars at the top of the frame, an access door and window on the left, and infrared lighting on the right. The water source is outside the camera view, behind the food bars in this view.
This is the ground control habitat on day two of the study, during the dark phase of the light-dark cycle. This habitat is oriented on earth with the waste tray at the bottom of the cage, the camera view is looking downwards along the gravity vector. The animal closest to the camera is sitting on top of the food bars, eating.
There are five mice in this habitat although only a few are usually observed at one time. Mice tend to prefer enclosed nest-like places such as the recessed space between the food bars and the cage wall where they are seen congregating in this view. This is also the location of the water source.
The mice are ambulating, grooming, and showing social interactions that are typical behaviors for mice on earth. Mice use all six walls of the habitat to freely move around and are observed frequently climbing up and down the walls. This is the flight habitat on day two of the study during the dark phase of the light-dark cycle when mice are typically most active.
During space flight, as on earth, the mice move around the habitat using all six sides of the cage. The mice actively explore and ambulate throughout the habitat and exhibit the same behaviors as mice on earth including eating, drinking, grooming, and social interactions. Mice use different methods to propel themselves about the compartment.
Early during the flight the mice were typically seen using their forelimbs to pull themselves along the wire mesh, later during the flight, the mice tended to use all four limbs to run across the wire grid lining the habitat. The mice also moved by floating from one location to another. As the mice acclimated to the habitat during the Rodent Research One Study, they not only became adept at moving about the compartment but also learned to anchor themselves to the walls using their tails, and/or paws.
Demonstrating the data analysis, metadata axis, and study description will be Sam Gebre, a data coordinator on the GeneLab team. To find data sets for analysis on GeneLab, open the GeneLab webpage and click on data repository. Enter the keywords into the search data box to search for specific areas of interest and select any other data bases of interest as desired.
Then, click the magnifying glass icon to begin a search. When all of the key words have been searched and you've reviewed the data sets, click tools, then collaborative workspace, and log in or register for a new account as appropriate. After logging in, click help and user manual, to access detailed instructions on how to use the workspace.
For each user, select public gene lab to access all of the data sets in the gene lab repository and open the folder with the data of interest. To copy the data sets of interest to a local directory workspace, right click on an individual file, select copy/move in the menu that appears, select the folder to copy the file into and click copy. Then find the data sets related to the previous publications just located in the data sets search, and copy the metadata files over to the local workspace.
To access the metadata files for each data set of interest, open the public gene lab data set sub folder, and access one or more metadata files contained in a metadata sub folder of each data set to locate the metadata information for the data set of interest. Ensure that every data set has a single zipped file that provides metadata according to the investigation, study, assay tab specification. Open an appropriate text editor to visualize and access the investigation, study, assay tab metadata containing the text description for the study and the assay metadata for each data set.
Then, check for the presence of the output assay data files that are located within each data set sub folder by type of assay. To analyze the transcriptomic data, click tools in the to menu, and click galaxy. Use the genome space importer tool to import data from the gene lab, genome space.
The data will appear in the history of the analysis section. After confirming the appearance and the imported data sets and the current history, use a GeneLab galaxy tool to populate a form in the center panel with options for analysis and the specification of data inputs. Complete the form and click execute to create jobs for executing the analysis and check for jobs submitted that are represented in the history and color coded to indicate the status of the execution, then link the tools into the complex workflow, managing the workflows with the workflows tool, and use the shared data menu to share the data sets workflows and histories with other investigators.
As illustrated in this representative graph, using principle component analysis plots to group the biological replicates, the leading edge genes from the gene set enrichment analysis gene sets can be determined. Using the genes with 1.2 fold change, the genes involved with predictions for upstream regulators, canonical pathways, and bio functions can be predicted, allowing the common overlapping genes involved for all the genes to be grouped. Then network representation of how these key genes driving the response between the rodents and the rodents habitats and the vivarium controls displays the central hubs for each data set being analyzed.
For example, map kinase one is the central hub for space shuttle mission STS108 skeletal muscle tissues from mice and can be interpreted as the gene that is driving the key genes and most likely the central player for causing biological differences for mice housed in rodent habitats versus vivarium cages. Taking a systems biology approach, the gene from all the data sets that is the most connected when constructing a network from all the key genes was then determined, revealing that map kinase one is indeed the most connected gene and central hub from all of the key genes. While attempting the procedure, it's important to remember that researchers conducting space biology rodent research experiments will work closely with NASA's rodent research mission scientists, set up and perform the experiments.
In addition, all space biology related all mix data is available on NASA GenesLab platform and using this procedure is the most efficient method for developing new hypotheses related to space biology. This technique can also be applied to any other all mix data sets related to biological systems such as cancer biology, Alzheimer's and cardiovascular disease. After its development, this technique paved the way for researchers in the field of space biology to begin considering research on the effects of carbon dioxide for astronauts in the International Space Station.
