By Dr. Tyler Moore
I had the wonderful opportunity to spend two weeks studying in the Gene Regulatory Networks in Development course at the Marine Biology Laboratory (MBL) at Woods Hole, Massachusetts. The course was led by Dr. Scott Barolo (U Michigan Medical School) and Dr. Isabelle Peter (Cal Tech) with contributions from many additional faculty.
The course focused on ways to experimentally and computationally analyze and visually represent the regulatory networks that control gene expression (“Gene Regulatory Networks”). Integrated networks of gene expression control developmental processes ranging from sea urchin endoderm and mesoderm specification, arthropod body segment patterning, development of limbs, determination of organ size, and more.
In addition to hearing from faculty about their research into gene regulatory networks, I also had the opportunity to do some hands-on learning of computational tools for analyzing and representing gene regulatory networks. Here is a regulatory network my group put together on sonic hedgehog (Shh) signaling in patterning the posterior versus anterior hand during limb development. The arrows represent inducers of a gene and the blocks represent inhibitors of a gene. The colored lines are signals that are present in a particular region and the grey lines are signals that are absent from a particular region.
Although the class was rather high paced, we did have some down time. We had the opportunity to tour the MBL rare books collection, which included early editions of Antonie van Leeuwenhoek’s drawings, Newton’s publication describing his new telescope design, early Ernst Haeckel work, and hand-painted illustrations from the Captain Cook voyages. I even had the opportunity to hold Thomas Hunt Morgan’s Nobel Prize (awarded for his uncovering the role of chromosomes in inheritance).
I was in awe to be surrounded by so many people with vast and diverse experiences, both the faculty and the students. I’m very grateful to have been a part of this class. I received more advice and instruction than I can describe in this post, and I am excited to put it to use in our classes and research.
On Friday a very enthusiastic and bright group of students from the King Science Health Career Academy visited Bellevue University and toured a variety of STEM related programs. The main purpose of the tour was to give the middle school students a better perspective on what possible careers they can go into in STEM.
We entertained them with an overview of what we do on a daily basis in our biology, chemistry and A&P labs. Seeing live tropical cockroaches, human brains and touching anatomical models is always a recipe for fun and excitement. Of course we couldn’t resist offering them a variety of (controlled) explosions, volcanoes and electrical blasts! To be honest, we (especially Johnny) like blowing things up as much as the students.
With the help of Oliver, Prof. Kim Brehm inspired the students by illustrating how educational technology can be used to make math fun and accessible. She provided a great overview of the necessity for math in every area of study, and amazed the visitors with the fact that her online students could do their course work in their pyjamas.
Prof. Dough Rausch opened up the visitors’ minds about the opportunities in the growing field of cybersecurity. Students were surprised by the fact that there is more to it than hackers with hoodies and that there are potential applications of cybersecurity in pretty much any aspect of our modern day lives. I’m sure he had at least a couple of them fantasizing about a job at the CIA or NASA (which would be awesome!).
We always enjoy having visitors interested in learning and we hope we inspired them to stay curious, keep asking questions and continue to learn more about science, technology and math!
This week the World Wildlife Fund reported their studies on the Living Planet Index, which found that the population sizes of more than 4,000 animal species have declined by 60 % between 1970 and 2014. The Living Planet Index tracks the population abundance of thousands of mammals, birds, fish, reptiles and amphibians around the globe, and is an indicator of the global diversity and the overall health of our planet.
The full report can be downloaded here. The main conclusion is a dramatic decrease of biodiversity that is ongoing and showing no real sign of slowing down.
(Just for clarity, these results do not mean a loss of 60 % of total animals, but depends on the relative size of each of the population.) The report does not only discuss the species diversity loss, but also provides a comprehensive overview of how the planet and human activity are connected. As the report indicates, “the main drivers of biodiversity decline continue to be the overexploitation of species, agriculture and land conversion – all driven by runaway human consumption.” Read More
Join us on Tuesday evening Oct 23, at 5:30 pm for a chemistry voyage to Mars!
Together with ACS (American Chemical Society), the Bellevue Science labs are hosting a live webinar on the chemistry of Mars. There will be pizza, drinks and raffle prizes. More information is in the flyer below. Hope to see you there!
During last weeks Lunch and Learn Seminar, Dr. Tyler Moore took us on a journey through time and animal evolution. In his talk on ‘Creating and Controlling Dinosaurs: The Science of Jurassic Park’, or ‘Making Dino’s for big kids’ as he called it, Dr. Moore explained what defines a dinosaur and what would be the most scientific way to approach reverse engineering a real dinosaur.
In his talk, he answered intriguing questions about where to find potential ‘dinosaur DNA’ as a template. (spoiler: No, it is not from an amber enclosed mosquito that he is using as a cane…). We also learned about how to make a chicken with dinosaur teeth and why the lysine contingency from the Jurassic Park movies would never work in real life (and neither did it in the movie). The more science inclined people in the audience also learned more about specific gene regulation and protein expression patterns that are important in developmental biology. Read More
Last Friday several of our biology students visited the Methodist Hospital Microbiology and Pathology lab in Omaha. The Methodist Pathology Center provides clinical and anatomic pathology services to medical facilities, physicians and other health care providers throughout Nebraska, Iowa and Missouri.
The tour is an optional, yearly activity that is open to all of our science students, however it is typically part of our Microbiology or Anatomy and Physiology classes, because those cover many of the techniques and topics that students get to experience on the tour. Even though our students are trained well in these techniques and have learned the concepts, once they see these being applied on real patient samples in a real hospital setting, they start to see things at a different level. As a result you can see the excitement in the student’s eyes and that alone makes these trips worth the extra effort.
Buvaneshwari Seshadri, Sydney Robertson, Julie Richards, and Samantha Fitch at Methodist Hospital Lab
The tour was guided by Julie Richards who is the Program Director of the Medical Laboratory Science Program (see below). Some of the things the students were able to see was how blood samples are sorted and analyzed, how routine chemical tests are performed in an automated manner, how various microbial infections are identified, and how tissue samples are screened for potential tumors after surgery.
Some students spend their summer traveling exotic locations or working boring summer jobs. Sydney Robertson, a senior Biology student, decided to spend her summer in the lab solving the genome of Rhodopseudomonas rutila (and seven other bacterial genomes). Besides gaining valuable technical and research skills, this also resulted in a recent publication in the journal Microbiology Resource Announcements, entitled: Draft Whole-Genome Sequence of the purple nonsulfur photosynthetic bacterium Rhodospeudomonas rutila R1.
These bacterial genomes were never sequenced before and unraveling these has environmental and evolutionary implications. Specifically, these efforts contribute to the suggestion that there is a need for a re-classification of the Rhodopseudomas bacterial species. Read More
There are many ways to do a lab notebook. Here is how mine is put together and some suggestions for improving your lab notebook game.
My top priorities for a lab notebook:
1. Easy to enter information
-If making lab notebook entries is cumbersome, you won’t keep up
2. Easy to find information
-If you want to repeat an experiment with the same doses or see if your calculations from a previous experiment were correct, you need to be able to easily find your entries
3. Includes any information you may want later
-Write everything down. You never know what might be useful later.
Below is a guide through my [Dr. Tyler Moore’s] notebook showing how I accomplish these three priorities.
My Lab Notebook is a 3-Ring Binder
My lab notebook evolved from my experience with various mentors. I like to use a 3 ring binder for my lab notebook. It is easy to organize and it is easy to add pages later, so you don’t run out of space. You can also easily add in extra pages of graphs/tables for your results.
Dividers Break Up Different Projects
The dividers in my lab notebook are used to divide up different projects. The projects have a name that is meaningful to those of us working in the lab, such as “ERK IRF3 Lucia.” Each experiment within a project is named with the name and a sequence number: “ERK IRF3 Lucia #1” “… #2”, etc. Experiments with the same name but a different number are often repeats or repeats with variations. All of our data are cataloged into folders on the computer with the names of the experiments, making it easy to link data and electronic files to the lab notebook entries.
The Layout of a Notebook Entry
All of my notebook entries have at least the following 3 categories: purpose, overview, and methods.
Purpose: The purpose section is a quick statement for why I am doing the experiment. This section may seem unnecessary, but it can be very valuable when trying to make sense of results when a lot of time has passed.
Overview: The overview section is a diagram of how I am going to set up the experiment and what measurements or analyses I will use for a readout.
Methods: The methods section is probably the most important. This section is the detailed step-by-step notes written as I do the experiment. The methods section is dated (and often has a time as well). I like to number each of the steps. It is very important to include all of your calculations and dilutions in your methods section. You never know when math errors can help explain peculiar results of an experiment. You should also include the vendor information and stock concentrations of all media and reagents when you use them for the first time.
Results/Discussion/Other Comments: I don’t always include my results in my lab notebook, because my results are often digital files in folders that correspond to the experiment name in my notebook. For the experiment above, “B16 ERK SEAP #1”, all the data were in an Excel Spreadsheet and a graph. These were all compiled in the “B16 ERK SEAP #1” folder on my computer.
If certain things happened that could impact the interpretation of the results, it is important to add them in. If one of the calculations was incorrect, if one of the wells was contaminated with a fungus, etc., it is important to make a very visible note to aid in the interpretation of the results.
Having a well-organized and thorough lab notebook will make it easier to compile your notes into your senior thesis. It will also make it more likely for your experiments to contribute to the larger project. I hope this information was of some help. I would be happy to hear any comments regarding your ideal lab notebooks.
Bellevue University does not have traditional classes on Fridays, but the Science Center of Excellence is open from 8AM until 4PM each Friday during the term! This Open Lab format allows students and researchers full access to all facilities, faculty and staff, and equipment to learn laboratory operations, conduct research, study and just hang out with our resident scientists.
Free Lab Fridays are a great way for students, faculty, lab staff and collaborators to take full advantage of the BUNSCE facility in a fun learning environment. As Johnny Farnen the lab manager jokes, “We blow something up at least once a week around here…sometimes even on purpose!” From conducting live demonstrations for tour groups to collecting specimens in the field, interested students gain invaluable experience in addition to the high tech education they earn at BU.
Often, movies from BU’s “Science of Science Fiction” Course start at noon, making for an entertaining lunch break. There is nothing quite like viewing hard science fiction with actual experts and PhDs providing commentary!
Forget the Oscars, if you are in scientific research, the Golden Goose awards where it’s at. Did you ever think basic research on chicken eggs or goose glands or on the imperfections of the human brain could lead to anything more than feeding scientific curiosity? Neither did the scientists initially studying these and yet now this research is considered foundational in immunology and human psychology.
Those are just some examples of the type of research honored at the yearly Golden Goose awards. Check out this years and previous awardees here: https://www.goldengooseaward.org/
The stories told in the short videos highlight the importance of continuing funding for basic research. Not only does it broaden our knowledge of the world, you also never know what will lead to a groundbreaking innovation. As Stanley Cohen describes it in the Golden Goose Award video: “Scientific discovery is like growing a tree. New things keep popping up along the way and create new branches, and then you have to explore the branches. Every once in a while you will find a branch with a lot of nice fruits, but you don’t know in advance which branch that will be.”
Keep following your basic curiosity in science!