Permian metabolic bone disease revealed by microCT: Paget’s disease-like pathology in vertebrae of an early amniote Yara Haridy, Florian Witzmann, Patrick Asbach, Robert R. Reisz Summarized by Time Scavenger collaborator Jen Bauer
Brief Summary: This study examined bone remodeling (how the bone fixes itself after disease or other events) in an amniote (animals such as birds, reptiles, and mammals) from the early Permian (289 million years ago). Through detailed measurements and 3D internal and external modeling of the bone the authors determined that this animal suffered from a metabolic bone disease similar to Paget’s disease in humans. This is the oldest evidence of viral infection in the fossil record!
What data were used? The authors were exploring two fused (pathological or abnormal) and one normal vertebra. Vertebrae are the interlocking bones that make up your spinal column. They were able to identify both specimens as being caudal vertebraes (vertebrae of the tail area) of a varanopid animal. For comparison, the authors also examined several other non-pathological caudal vertebrae of a similar animal for comparison to this abnormal specimen.
Varanopids are an extinct group of amniotes (animals that have a membrane around their embryos) that looked similar to extant (still alive) monitor lizards. The veranopids were alive from the late Carboniferous to the late Middle Permian (~300-260 million years ago).
Methods: Measurements of the specimens were done using ImageJ, a freely available imaging editing program that can be used for a variety of projects. The idea was to measure different thickness of the bones. There is bone repair due to the disease and the author’s were quantifying the difference in the diseased bone compared to the thicknesses of normal (non-diseased) bones. Specimens were also CT scanned at the Museum für Naturkunde Berlin and the models were visualized and analyzed in Volume Graphics Studio MAX 2.2. Computed Tomography (CT) allows for scientists to look inside the bones without cutting them into pieces, making it a non-destructive visualization technique. This is particularly helpful for looking at any internal bone structure and any possible abnormalities in the external or internal structure.
Results:The pathological (diseased) specimen is two vertebral centra completely fused together, with no trace of a previous suture between the bones. The internal bone structure is slightly different. The notochordal canal (where the notochord resides) is uniform where there is some tapering the non-pathological specimens. The micro-CT scans reveal the outer cortex of the vertebrae has been dramatically altered through bone remodeling and growth causing features to be thickened and misshapen.
Why is this study important? The oldest recorded case of Paget disease of bone (PBD)-like alteration was in a Late Jurassic (~150 million years ago) vertebrate of a dinosaur, so this new find pushes the interpretation back to the Permian (~290 million years ago) – a shift of 140 million years back! The other major finding is about how this disease affects animals. Certain organisms are susceptible to certain diseases more than others. This bone disease has been found in primates (including humans), extant (living) dogs, lizards and snakes, and a dinosaur. The new finding in a varanopid furthers the spread across the tree of life, meaning that the disease must have evolved in early amniotes before the split between the split of synapsids (mammals) and diapsids (reptiles and birds).
Citation: Haridy Y, Witzmann F, Asbach P, Reisz RR (2019) Permian metabolic bone disease revealed by microCT: Paget’s disease-like pathology in vertebrae of an early amniote. PLoS ONE 14(8): e0219662. https://doi.org/10.1371/journal.pone.0219662
Members of the Time Scavengers team are writing a ‘Applying to Grad School‘ series. These blog posts are written primarily for undergraduate students who are applying to graduate programs (but will be useful for any transitioning graduate or professional students), and will cover such topics as funding and stipends in grad school, how to write and build a CV, how to network with potential graduate advisors, and how to effectively write statements for your applications. This is the second post in the series on how to prepare and structure your CV for graduate applications.
Adriane and Jen here –
A good starting point for gearing up to find a STEM* (science, technology, engineering, math) graduate program is to get your Curriculum Vitae (CV) looking good. There are a variety of ways to do this in a handful of programs that may or may not give you templates. When emailing people about working with them in the future it is customary to include your interests and your CV so they can look at your experience. A CV should document all of your academic credentials, accomplishments, outreach and service, publications (of all types), and more! Read this online resource to learn more about how CV’s and resumes differ. *because we are all geoscience majors, the advice that follows is mostly applicable to STEM majors, check out CVs of people in your field by looking on their websites & research gate!
The additions to your CV all depend on what you are applying for and wish to do. If you are interested in a museum position, it’s a good idea to add when you have worked with collections, in what capacity, and for how long. Similarly, if you are applying for tech positions in a lab make sure you list out the equipment you have experience with and what you did with the machines. When applying for graduate schools specifically, what you really want to show is that you have a good, solid education, and that you are hard-working and can achieve tasks and goals.
We’ll go over some sections that should be included on your CV, but here are some general tips that apply to the entire document:
List the most important information first (Education, Professional and Work Experience), then go from there
Make sure the date for each item is very obvious and clear; provide a range of dates (e.g., 2013–2015), a year (e.g., 2016) or a specific semester (e.g., Fall 2015) for each item
Use italics and bolding, but do so in a manner that is appealing and does not distract from the overall appearance of the document
Make sure the text and any bullet points are aligned correctly throughout the entire CV
Use language that can be understood by the general public and doesn’t contain too much jargon; you don’t know who will be reviewing your application
Pick one font and stick with it
Using different sized fonts throughout is ok, but like italics and bolding, be sure this doesn’t distract from the overall look of the document
List your achievements (and other chronological things like community outreach, mentoring, etc.) in order from most recent to oldest last
As a disclaimer before diving into this post, we have been at the academic game for a long time. Do not feel discouraged if you don’t have as many lines on your CV. There are a million opportunities for you to expand your horizons and engage in research, award nominations, grants, and much more as you continue along your academic journey!
The heading on your CV should include your name, address, and contact information. Generally, your name can be in a bigger font so the reader is drawn to that first. You can list your home address, or the address to your university. I, Adriane, always include my phone number, email address (make sure it’s a professional email address), and my website URL. It is important to make sure you are using the designated header space on your document, as this ensures you have more space on each page of your CV. There are settings that allow you to have a different header on all subsequent pages so the first can be large and then you can switch to just your name so the person reviewing it doesn’t lose track of whose CV it is. Here’s an example of a formal header:
I (Adriane) also jazzed up my CV by adding in images of fossils that represent the two major time periods I work in. Stylistic features like this may be considered as unprofessional by others. So, ask those in your lab group or your supervisor/advisor for their input before doing something like this.
The first section of your CV should be all about your education. Here, you’ll specify where you attended high school (or leave it off, it’s up to you) and the college and/or university you attended for your undergraduate degree. Within this section you can also include your overall GPA. If you are attending graduate school to further your e.g., geology undergraduate degree, you can also put your major GPA. I, Adriane, did this when applying for graduate programs because my total GPA was low, but my geology GPA was pretty high. Within this section, also be sure to include the dates for which you attended each institution. If you did an undergraduate thesis or research project, you can even include that information in this section. Here’s an example:
After this section, you can tailor your CV sections to best fit you, the position you are applying for, and your experience. As an undergraduate, it’s important you showcase your experiences and capabilities.
Professional and Work Experience
The next section on your CV could be ‘Professional and Work Experience’. Here, you can add in any formal or informal positions you have held. For example, if you volunteered as an undergraduate teaching assistant, you could add that to this section. If you held any jobs, add those as well! Jobs that showcase team building, management, and other useful life skills are important to add even if they aren’t relevant to your target job or career. Some academics will tell you to leave off jobs that don’t have anything to do with the degree you are seeking in graduate school. I, Adriane, still include the two assistant manager retail positions I held while going to community college. I worked hard at those jobs, and including them on my CV (hopefully) signals to others that I have leadership experience and have extensively worked in teams to accomplish tasks. Both of these qualities are important in academia, although they are hardly talked about. Adding in these other professional experiences also helps fill out your CV if you are really early in your career path or haven’t found a position that will pay you for your scientific expertise (as many lab positions are volunteer based).
Peer Reviewed Publications and Conference Abstracts
One of the next important sections you should include on your CV is any abstracts you authored or were included on for academic meetings. If you contributed to a peer-reviewed publication go ahead and include it here. It’s important to be consistent with the style you cite publications and abstracts in this section because it can look messy or be confusing otherwise. This section highlights that you’ve been involved with research, and have practice presenting your research to the scientific community. If you don’t have research experience, don’t fret! Many undergraduates who apply to graduate programs don’t have that experience just yet, and that’s ok!
If you have any other types of reviewed literature you can also include it in this section. Maybe you helped edit something for a companies big annual report or contributed to a local journal or newsletter. Writing is a really difficult skill to acquire and if you can showcase you have been practicing that is great!
Funding and Awards
Next, list any funding you have received for any research projects, events, or clubs/associations you were involved with. You can title this section something like ‘Funding Awarded’. This section shows your future graduate school advisor that you can win money (a very important skill in STEM fields). In the heading, be sure to include the total amount of money that you’ve won to date. Each item in this section should also include the amount for each award. It may not seem like it, but if your college/university has helped you pay for attending a meeting, that’s money you should include in this section as well!
If your CV is not super filled up it’s totally fine to combine sections. I, Jen, often suggest students to include funding and awards together – the heading could be funding and awards, achievements, whatever you think best describes what you are putting in the section. When you end up with more funding and/or award success it makes sense to split them into two sections so you can keep track of things. I called my Awards and Honors and also included any instance where I guest lectured for faculty members. I didn’t have another good place to put it in my subheaders so this seemed reasonable to me.
The next section you could include on a CV is any relevant coursework. For example, when I, Adriane, applied to paleontology programs, I included all the courses I took that were related to paleontology in any way (biology, invertebrate paleobiology, stratigraphy and sedimentology). Here, you can include the semester you took the course, and even a short two-sentence description of the class. If you gained specific skills in the class, it is best to include that in the short blurb. If you took a mineralogy course and also had the opportunity to prep and analyze samples for XRF or XRD, include that information!
Other Relevant Experience
The next section of your graduate school CV could include a section titled ‘Field Experience’ (or ‘Field and Lab Experience’, or ‘Lab Experience’). This section highlights the work you’ve done in the field/lab, when you did that work, and a short description of what it was you did. This section shows your future graduate school and advisor that you know your way around the lab or have experience doing science outdoors. Again, if you don’t have this experience, it’s not a huge deal!
I, Jen, have titled a similar section more broadly as ‘Research Experience’. Here I include when I worked with (1) specific fossil collections; (2) specialized equipment or instruments; (3) any other things that may not have fit within the job descriptions listed above but may be useful for potential advisors or PI’s to know about.
Academic and Community Service
After you’ve highlighted your education, work experience, the research you’ve done, and your coursework, there are a few other sections you can include on your CV if you have the experience. If you’ve won an award as an undergraduate student, include that in a section titled ‘Awards and Honors’. If you are part of an organization, for example, president of the Geology Club, that can be included in a section titled ‘Academic Service’. Academic Service is any activity you do within the science community as a volunteer. This differs from Volunteer Experience as these are things done outside of academia. While we’re talking about it, do include a section on your CV where you highlight any volunteer or outreach experiences you have. This could be as simple as talking to a K-12 class about science, or helping at a rock and fossil sale.
Professional Memberships Organizations
The last section on your CV should be titled ‘Professional Memberships and Organizations’. This is where you will list all the clubs, organizations, and associations you are a part of. This shows that you are an involved and active member of your scientific and local community, a networking skill that will become even more important in graduate school!
Other Potential Headers
The National Science Foundation has a series of headers in their short format CV requirements and I, Jen, have worked to adopt some of the language that this large organization uses. So, I have a big header called ‘Synergistic Activities’ this includes, programmatic events I organized, ways I engage my community, professional development opportunities that I’ve participated in, professional service, mentoring experience, and invited talks and lectures. Now, that’s a whole lot of stuff but the header is something that people may specifically look for when they are analyzing your CV.
I also have a section called ‘Courses taught as instructor of record’. This is handy when applying for teaching positions because right off the bat they can see that I have taught a full course and have experience in front of a class. I have another section for ‘Collections Curated’ this is for specimens that I took care of or managed in some way. As I was applying for museum and faculty positions, it was to by benefit to include this section and showcase what I had done.
Our last bit of advice is to seek out help with your CV! Reach out to your classmates, a trusted professor, or a graduate student for feedback. Your CV will likely go through several iterations until you end up with something you are happy with. Also, attend any resume or CV-building workshop on your campus or in your community if you can. You’ll likely receive additional advice than what we provided here, and also get really great feedback from others on your CV. And remember, your CV is a living document, meaning you should continually update it anytime you achieve something!
This blog post is the second in our series on how to reduce your carbon footprint! Find our first post by Sarah by clicking here.
Sometimes, you can’t reduce your footprint in all areas and that’s OK!
Many of our advances as a society have made life much better for people with a range of needs. A good example of this is plastic straws. Plastic straws, of course, contribute to our overall plastic waste, but there are many disabled people who rely on plastic straws as a safe and hygienic way to eat and drink. Alternatives like paper or metal straws aren’t always viable options for several reasons. Plastic straw bans can often hurt people who rely on straws for basic survival, so always make sure that while advocating for reducing waste, you’re not creating disadvantages for other groups of people. Advances in society have helped us live longer and better lives- some plastic waste is an inevitability. Do your best to reduce your footprint where you can, but don’t feel guilty if you can’t reduce it in every aspect of your life. And if you can cut out plastic straws, do so- but don’t take it away from people who need it!
This series is meant to be a series of ideas that you may or may not be able to employ in your daily lives but getting a better understanding and awareness is an excellent first step.
Jen & Jillian here –
Transportation can be a difficult area of your life to cut your carbon footprint. Not everyone, including us, can purchase an electric or hybrid vehicle, or choose to travel by train instead of plane, even knowing that transportation accounts for over a quarter of US carbon emissions (data from 2016). But there are other ways to reduce your carbon footprint while commuting or running errands. While not everyone lives somewhere where these are viable options, or is physically able to travel in certain ways, we encourage you to take an in-depth look at what’s in your area! In addition to reducing carbon emissions and working toward a more green future, many of these suggestions have the potential to improve your health by getting you moving, instead of a car.
Take public transportation more: Not only do gasoline vehicles emit greenhouse gases, they also are a major source of air pollution, which is linked to premature death and a myriad of systemic health problems. This is particularly important in areas that are prone to at-risk air conditions, like cities, or areas with climatic and geographic characteristics that lead to smog (like Los Angeles).
Riding public transit is easier than ever – many public transit systems utilize Transit App, which makes it very simple to find routes, plan trips, and in some cases, see real-time data on where vehicles are, or have their own in-house apps. Google Maps also offers transit instructions for a lot of cities too. Worried about getting stranded or needing your car in case of emergency? Many metropolitan planning commissions offer an emergency or guaranteed ride home program, like this one. Take a look at what’s in your area!
Riding public transit allows you to use your time for something else, be it napping, reading, or just relaxing, instead of paying attention to the road and dealing with the stress of traffic. More and more systems offer Wi-Fi and outlets or charging stations on their vehicles. Additionally, riding public transit will save you money over the long term. Data from 2016 indicates that money saved by commuting by public transit for a two-worker household is over $6000 annually – approximately the same amount spent on groceries (How public transit can (and must) help reduce carbon pollution). Additionally, many workplaces have pre-tax commuter benefits that can be used to pay for transit passes and many schools and universities have agreements that let students and/or staff ride for free with an appropriate ID.
Public transit also increases the efficiency of traffic, fewer vehicles promote fewer traffic jams and reduces fuel waste. In 2011, the American Public Transportation Association provided evidence that the use of public transportation ‘saved 865 million hours of travel time and 450 million gallons of fuel in 498 urban areas’ (Why is public transportation good for the environment?).
Jillian, before moving within walking distance of her job, commuted to work nearly every day by bus. She enjoyed letting the bus drivers deal with traffic and other drivers, zoning out instead of stressing out, and walking a little extra each day to get to and from the stops.
If you live in a bike/pedestrian-friendly area, start biking or walking more frequently! Not only are these activities good methods of exercise but they can reduce emissions from traffic congestion and fuel use (Reducing your Transportation Footprint). If you are concerned about safety, head to your local bicycle shop or bicycle advocacy organization to talk with people in the community. If there isn’t a local shop or organization by you, REI often offers bike classes. There are likely local resources to help you get started and give you ideas for safety precautions during your commute.
Check out TrailLink, a non-profit dedicated to developing trail networks across the United States. Another great resource is Google Maps. There is an option to include a layer with bike routes (head to the three horizontal bar dropdown in your browser to add it to your maps). This is an excellent planning tool and you can use street view to confirm your route before heading to the street or path. Many bus and train systems have bike racks in or on vehicles so you can become an expert multi-modal commuter!
This is Jen’s favorite method of commuting. She feels like she gets to work feeling fresh and a clear head to start the day. It takes time to really feel comfortable on the bike and the road but it is worth the effort. Make sure you have a helmet and proper lights/reflectors so that you stay visible. Also, it’s likely other people at your office are bike commuters, ask them for tips or see if they would ride with you the first few times. It’s always helpful to have someone guiding you.
There are bicycle collectives, cooperatives (co-ops), and communities all over the world. BikeCollectives has a comprehensive list of community bicycle organizations around the globe so you can look up your state or country to get more details on your local areas. In many cases, this will result in low-costs for transportation on your end and new friends and hobbies. Bike communities are very invested in sharing knowledge of bike maintenance and safety.
Carpool with coworkers or colleagues: Maybe you don’t live in a location that has good public transit or allows you to safely be a cyclist or walking pedestrian. Carpools or multiple occupancy-vehicles are an excellent way to reduce the number of cars/vehicles on the road and in turn minimize levels of pollution. This mode of transportation also saves money in terms of gas, vehicle maintenance, and parking fees. Many highways are adopting carpool lanes as an incentive for reducing the amount of vehicles on the road.
Larger workplaces often have carpool programs, and many metropolitan area planning commissions have programs to help commuters find a carpool buddy. Try searching for “find carpool [city name]” – here’s a program in Indianapolis.
Scooter and bicycle share programs: Many cities now have various programs that allow pedestrians to rent scooters or bicycles. These programs have an app that allows you to unlock and purchase a scooter or bike for a period of time for a fee. Some of these programs have docking stations scattered throughout the city for you to pick up or return the vehicle. Wikipedia has a description of bike-share systems and a detailed history, which you can read about by clicking here and a list of programs (click here). This can be an excellent mode of transportation for quick trips or recreation but make sure you return the vehicles to an appropriate spot, they can really clutter sidewalks and make things difficult for other pedestrians.
Fly less: Jet fuel is a high-carbon energy source so reducing the amount of flights you take per year can greatly reduce your impact. This also means that booking direct flights reduces your impact. The larger and heavier the aircraft, the more fuel is consumed. This means that even packing efficiently and light will have an impact (Reducing your Transportation Footprint). Some are deciding to completely abstain from flying (a task that is definitely easier in Europe, which has a strong passenger rail infrastructure).
Regulating the environmental impact of air travel is quite complicated. It’s difficult to have an excellent, green alternative for shuttling millions of people around the world every day. Click here to read a comprehensive article that explores some of the major issues. This article also highlights that the complexity should not deter us from working to learn more.
What is your favorite aspect of being a scientist, and how did you become interested in science?
My favorite part about being a scientist is undoubtedly getting to do research for a living. While there are many stressful aspects associated with being a scientist, at the end of the day I get to spend most of my time learning about things that are deeply interesting to me. Science has also allowed me to travel the world and meet some of the most inspirational people I would have otherwise never crossed paths with.
What do you do?
When people hear the word “biogeochemistry” for the first time, the general response I get is “biogeo-what? Are you a biologist, geologist or chemist? Couldn’t you just pick one?” While this is a fair question, it is unfortunately not how the Earth system works.
I work specifically in the field of paleoceanography, the branch of science concerned with the ancient oceans and their role in climate. My research aims to understand the evolution of polar North Atlantic Ocean circulation over geological warm periods that occurred hundreds of thousands of years ago. The ocean, however, is an interconnected mess of physical, chemical and biological phenomena. To thoroughly investigate oceanographic processes, it is therefore necessary for scientists to have a broad and multidisciplinary understanding of all aspects of marine science.
As a biogeochemist, I work mainly with organic matter preserved in microfossils called foraminifera. The composition of this organic matter reflects historic upper-ocean biochemistry recorded during the foraminifer’s lifetime, which allows me to make observations about the chemical conditions of the ancient surface waters. The surface-ocean chemistry of this particular region is subsequently controlled by waters mixing together, which makes foraminifera-bound organic matter a useful proxy to reconstruct physical mixing processes in the upper-ocean water column.
But who cares about what the surface of the polar North Atlantic used to look like? Because this is where southern-sourced Atlantic waters sink and return to tropical latitudes (the so-called “ocean conveyor belt”), this one region actually governs the strength of the entire Atlantic circulation in addition to a variety of global climatic phenomena that we are just beginning to understand. Studying how Atlantic waters used to move during past warm periods therefore allows us to get an approximate idea of how the Atlantic may continue to change in the near future, and its greater effects on Earth’s climate.
What are your data, and how do you obtain them?
My data are mostly measurements of stable nitrogen isotopes of organic matter contained within foraminifera shells, which dominate sediment core samples from the polar North Atlantic region. This isotopic signature, or the ratio of heavy to light nitrogen atoms, is a proxy for surface nutrient processes affected by upper-ocean nutrient mixing. Because foraminifera contain only miniscule amounts of organic nitrogen, extracting this organic material and turning it into a measurable form requires intensive laboratory and chemical work. I therefore spend most of my time in the laboratory rather than on a boat, which is unfortunately slightly less scenic.
How does your research contribute to the understanding of climate change?
There are now several lines of evidence which indicate that ocean circulation in the polar North Atlantic is slowing down, likely as a result of human-caused global warming. While today’s rate of warming is unique in the recent geological history of Earth, our planet has experienced intense warm events in the past. By investigating the behavior of the Atlantic circulation in the past, we are able to better understand the long-term climatic and oceanographic implications of our current warming. For example, we hope our research will shed light on the extent to which the modern ocean circulation will slow down, and what this slowing means for other aspects of Earth’s climate in the long term.
What advice do you have for aspiring scientists?
Stay curious and keep an open mind! I switched my major several times throughout my undergraduate career before I discovered my passion for science.
Don’t let previous failures detract from your goals. Often times, we see the finished product of science in the form of a published, peer-reviewed journal article. What we don’t see in that article is all of the failed experiments and misguided hypotheses leading to its production. Doing science means falling short many times, recognizing mistakes, learning from them and continuing to improve. The most important thing you can do is to not give up and to keep trying, because one day this stuff will work out.
What is your favorite part about being a scientist and how did you get interested in science in general?
My favorite part about being a scientist is going into the lab, doing an experiment, and discovering something that nobody else knows. My uncle was in grad school when I was a kid. He studied fracture mechanics in metals, or crackology, as I like to call it. I visited his lab and he showed me his million-dollar microscope. He was getting a Ph.D. so I decided I would, too. I wasn’t interested in engineering. I liked watching nature shows on PBS and biology in school. In high school, I learned about DNA replication. DNA has directionality and can only be replicated in one direction but there are two strands held together in the opposite direction. When you separate the DNA there isn’t enough space to copy the other strand. The cell solves this problem by making short sections of DNA of the strand that is facing the opposite direction and then gluing them together. These are called Okazaki fragments and I thought that was cool. Also, in that class, my teacher showed us statistics on how many people get undergraduate, masters, and Ph.D. degrees and all the different careers you could do with those degrees. So at 16, I decided to get a Ph.D. and do research in biochemistry. I searched for schools that had strong undergraduate research in a real biochemistry program. I didn’t want chemistry and biology class, but a dedicated program. Once I did start a biochemistry project, I decided that wasn’t for me. Biochemistry involves reducing reactions to their bare minimums, but life isn’t like that. So, I traded the cold room and purified proteins for genetics. I like asking the questions and having the cells tell me the answers.
In laymen’s terms, what do you do?
I investigate why genetically diverse individuals respond differently to the same stress, usually a chemical. Every chemical is a poison in the right dose but also can be a medicine. Water is essential for life is also toxic in high doses. Drowning is a leading cause of premature death. The stress response is a complex reaction. The first thing that happens is that cell growth is arrested. It’s like if your house is on fire. Once you see the fire, you don’t finish washing the dishes and then find the fire extinguisher. There are common responses to stress and then there are specific ones. To find out how the cell’s response to a specific stress, we exploit genetic variation within a species. I compare cells that can successfully deal with the stress to ones that can’t and determine what are the underlying differences that govern that. Depending on the stress we sequence genomes, measure the changes in gene expression or proteins. We work on yeast because in general people don’t appreciate being poisoned and don’t reproduce as fast as in the lab. Yeast have a generation every 90 minutes. Yeast are fungi and are more related to us than to bacteria. They have important applications in baking, brewing, and biotechnology. Yeast share many biochemical pathways with us and so by studying them, we can then extrapolate that to humans. In my lab we are working on glyphosate, the active ingredient in RoundUp, MCHM, a coal-cleaning chemical, and copper nanoparticles, a novel antimicrobial material.
What are your data and how do you obtain them?
I am an experimental geneticist. We have tens of thousands of different yeast strains in the lab. Most of these yeast come from other labs. The yeast community is generous, and these are all freely shared. To understand how RoundUp resistance occurs in nature, we also collect yeast from different environments. We have several sites with different RoundUp exposures. We started with a reclaimed strip coal mine, a state park, and the university organic farm. We have taken the public and students from local public schools to collect samples from these areas. We bring the samples to the lab and teach them how to coax the yeast out and then purify their DNA so we can sequence them. We thought that the mine would have the highest frequency of RoundUp resistant yeast because they spray that area every year with RoundUp. The park has been a state park since the 1930s and RoundUp was invented in the 1970s. RoundUp is a synthetic herbicide and not included in the list of herbicides and pesticides permitted on organic foods. We were completely shocked when we found that the organic farm had the highest number of RoundUp yeast and the mine had the fewest. There could be several explanations. One is that the yeast weren’t specifically resistant to RoundUp but whatever genetic changes that had been selected togave it a selective advantage in that environment also conferred resistance. When we further investigated the histories of these sites we came up with another idea. The organic farm wasn’t always an organic farm. Two decades ago it was a conventional farm and from that previous exposure, the yeast became resistant and never lost it. The state park routinely uses RoundUp to combat invasive plants. There is also a power line that spans the canyon and they use helicopters to spray RoundUp so that trees don’t grow into the power line. The mine is used as a study site to find genes that are important for trees to grow on poor soil so that biofuels can be made. They started that study the year before I started collecting yeast so only a year of exposure was not enough to select for resistance. So now we have an even better study. We can go back every year to the mine and collect yeast. We can track RoundUp resistance as it happens.
How does your research contribute to the betterment of society in general?
We are exposed to and consume chemicals every day. Differences in how we respond to those chemicals in part depend on small differences in our genome. We use these genetic differences to find out how cells are metabolizing chemicals successfully and survive or unsuccessfully and die. When the human genome was sequenced, we thought that all its secrets would be unlocked. While tremendous advances in biomedical research could only have been done with this information, there is so much that we don’t know how to read. It’s like finally getting the keys to the entire library but all the books are written in a language that you taught yourself and they’re words that you don’t know how to translate. Based on a sequenced genome, we are not yet able to predict a person’s medical conditions or how a person will respond to drugs. The chemicals that we study are important agricultural and industrial chemicals. With the overuse of herbicides, we are now facing RoundUp resistant weeds. We don’t know how to combat this because we only partially understand how weeds become resistant. The active ingredient in RoundUp inhibits a biochemical pathway that plants, bacteria, and yeast have but humans do not. Therefore, it has been challenging to study possible effects of RoundUp exposure in humans. All known acute poisonings have been from the inactive ingredients and not the glyphosate. However, chronic exposure is time-consuming and complicated to study. We are using yeast to determine if there are other biochemical targets of RoundUp in yeast that humans may have. These studies can’t be done in plants because RoundUp exposure is lethal and prevents the synthesis of nutrients but yeast can be supplemented with the nutrients that RoundUp suppresses. Other chemicals like MCHM have limited toxicological information. Several years ago, a massive chemical spill contaminated the water supply in West Virginia. It caused headaches, nausea, and rashes and nobody knew why. MCHM changes how proteins fold and doesn’t have a specific target like RoundUp. By using this chemical we are studying how changes in protein folding regulate metal and amino acid levels in the cells. Fungal infections are difficult to treat because they are immune to antibiotics. Antibiotics work because they exploit fundamental differences in the metabolism of bacteria from humans. Yeast are more closely related to humans so there are fewer druggable targets. Copper is an effective antifungal material, but it is expensive, and metal has several drawbacks. By incorporating copper into cellulose-based nanoparticles, cheap, moldable, and biodegradable materials can reduce food spoilage and infections from medical devices.
What advice would you give to aspiring scientists?
Be prepared to fail. Failure is an opportunity to learn. In the example of the RoundUp resistance, the results were the opposite of what we thought. We can’t change the results, but we did further investigation and found an even more interesting story. I think of this as lost keys. My keys are always in the last place that I look. Why? Because I stop looking when I find them. If you think you know the answer, you stop searching. There is so much to discover and so many connections of which we are not aware. By challenging how you think about something you can overcome your assumptions and chip away at the unknown.
Head to Jen’s faculty page to learn more about her and her research by clicking here.
A new stemmed echinoderm from the Furongian of China and the origin of Glyptocystitida (Blastozoa, Echinodermata) S. Zamora, C.D. Sumrall, X-J. Zhu, and B. Lefebvre Summarized by Time Scavengers contributor, Sarah Sheffield
What data were used? A single, beautifully preserved echinoderm (relatives of sea stars and sea urchins) fossil from South China, named Sanducystis sinensis. Rhombiferans are extinct types of echinoderms with diamond shaped plates.
Methods: The new rhombiferan fossil was examined for all preserved features on its body; these features were ‘coded’ as characters for an evolutionary analysis. An example of a character: Does this have a stem? Yes=0; No=1. These characters were also used to code multiple other species of rhombiferan echinoderms. The reason for this was to figure out to what Sanducystis sinensis was most closely related. Computer programs, like PAUP*, take all of the characters coded and determine evolutionary relationships, based on the shared similarities between the species used in the analysis.
Results:Sanducystis sinensis falls within a large group of rhombiferan echinoderms called “Glyptocystitida” (similar to how humans are a large group of mammals). It’s an important find, as its place within the evolutionary tree of life is representative of a type of transitional fossil between a group of early rhombiferans that lack specialized breathing apparati and a group of more advanced, or derived, rhombiferans.
Why is this study important? This study paints a more complete story of how rhombiferans evolved through the Cambrian. It was not clear how the transition from rhombiferans without specialized breathing apparati gave rise to the more derived forms that we saw after the late Cambrian. This new find, Sanducystis sinensis, helps us to understand how that transition happened.
Big picture: Rocks from the late Cambrian (~500-480 million years ago) are very rare worldwide; this, of course, means that there are also very few fossils from this time as well. The late Cambrian is a very important time in Earth’s history, however, so finding fossils preserved from this time is critical towards understanding the evolution of life. Fossil finds, such as Sanducystis sinensis, have the potential to completely change what we currently know about how and when different groups of organisms on Earth evolved.
Members of the Time Scavengers team are writing a ‘Applying to Grad School‘ series. These blog posts are written primarily for undergraduate students who are applying to graduate programs (but will be useful for any transitioning graduate or professional student), and will cover such topics as funding and stipends in grad school, how to write and build a CV, how to network with potential graduate advisors, and how to effectively write statements for your applications. This is the first post in the series on various ways you can get paid to attend graduate school in STEM (science, technology, engineering, math) fields.
Jen, Adriane, and Sarah here –
Attending graduate school is an exciting prospect, but you can quickly become overwhelmed with deadlines, things to do, but mostly by the expense of it all. It’s no secret that today’s college undergraduate students are facing increasing tuition costs along with inflated interest rates on loans. Within public 4-year universities and colleges alone, tuition and fees rose on average 3.1% per year from the period of 2008 to 2019. Even within 2-year public colleges (such as community colleges), tuition and fees rose on average 3.0% per year within the same period of time! For student loans, interest rates range from 4.5% to as high as 7%, and that interest is usually compounding (meaning you will pay interest on the interest that your loan accrues over time). It can seem like there’s no way to escape college and obtain an education without paying dearly for it, especially if you want to attend graduate school right or soon after your undergraduate degree.
But fear not, there are several ways in which you can avoid taking out loans while pursuing a graduate degree, both MS and PhD. Since we are all geoscience majors, the advice and information we provide herein is more applicable to graduate degrees in STEM (science, technology, engineering, math) fields. Below, we discuss a few options to reduce the cost of attending graduate school. We also are very transparent about the debt we accrued during our undergraduate degrees and how that compounded over time. But mainly, we want to explain how you can get paid (yes, you read that correctly!) to go to graduate school.
First, we’ll discuss the different types of assistance you can be granted to go to graduate school. We’d like to stress that we do not advocate for paying for graduate school out of your own money if you’re majoring in a STEM field*, as you should be able to get an assistantship to pay for your tuition and provide a stipend (living expenses)**. *we’re uncertain about non-STEM fields-please look for good resources to help you understand how tuition waivers and stipends work in other fields!
**some STEM industries will pay for their employees to go back to graduate school. This is an awesome option, but not available to everyone.
Assistance within the University
Teaching assistants (TA for short) are graduate (MS and PhD) students who are paid to help teach classes and labs at their university. For example, Adriane taught Historical Geology lab sections at UMass Amherst, and had a blast doing it (so many cool field trips!). As a teaching assistant, you will also be involved with setting up experiments for labs, grading students’ assignments, helping on field trips, or even leading your own field trips! Being a teaching assistant can be a ton of work, but it is a great way to make money and sharpen your skills as an educator (important for folks who want to continue teaching in any capacity after their degree). There may also be opportunities to continue working as a TA over the summer, as these jobs usually do not include summer stipends.
Teaching assistantships often include tuition remission, meaning you are not expected to pay for your education. This is important when you are looking for graduate positions in the university. You want to ensure that you are receiving a stipend and tuition remission. Even though you are getting your education paid for there often are still associated fees you have to pay each semester. These fees can range from 100’s to 1000’s of dollars every semester and cover transportation, athletic, heath, and building fees on campus.
A research assistant (RA) are graduate students who are funded to do research or work on some aspect of a project. Usually, the money to fund an RA comes from the student’s primary academic advisor, or it could come from some other professor in the department. In most cases, an RA is only funded during the academic year, but it’s not uncommon that money for an RA is budgeted to fund the student over the summer. For example, Adriane and Jen were each funded for an entire year from their MS advisor’s NSF (National Science Foundation) grant, where they were able to build a website while working on their own research. The benefit of RA positions is that they are usually more flexible as to when you can get your work done. When Adriane was doing her MS degree as a research assistant, she would spend an entire two days of the week doing RA stuff, that way she had huge chunks of time to focus on her research. The downside to being an RA is that you don’t receive teaching experience or get to interact with students in a formal setting. This isn’t a huge deal, as there are usually opportunities to help professors out teaching their courses while they are away at conferences, doing field work, etc.
Internal University or Departmental Fellowships
Internal fellowships (and grants) are small to large pots of money that you can win from within your university or college. You have to do some research and keep up with deadlines on these because often they have specific requirements. While Jen was at UTK there were several extra fellowships you could apply for as a graduate student. Some were specifically for MS students others for PhD students – some were mixed! One was only for students in their first year and one was only for students in their last year. Jen was fortunate enough to apply for an receive a fellowship through the university to fund the last year of her dissertation. This allowed her to reduce her teaching load and focus more on writing. You can read about it by clicking here.
External Funding Options
There are fellowships, like NSF’s Graduate Research Fellowship Program (GRFP for short)-you write a proposal for the research you want to work on and submit it. It’s reviewed by experts in the field you want to specialize in. These are incredibly competitive across a national or even international scope, but they are great ways to fund your research! Often, you have to apply to these either before you begin your graduate program or early into your program, so look into it as soon as possible!
There are other options to acquire competitive fellowships, often to finish off your dissertation without being restricted by teaching or other responsibilities that take time away from completing your projects. NASA has a program that graduate students can apply for, but there are restrictions – you already have to be enrolled and your project has to fit whatever the theme of their solicitation is that cycle. Adriane won a similarly competitive fellowship for foraminiferal research, which you can read about by click here.
In some jobs and careers, your employer will reimburse your tuition costs. These are often to benefit your employer, as investing in your education and training will make you a more well-rounded and specialized employee in your field. The amount that your employer will reimburse you also varies; some may provide 50% remission or 100%. This amount can also vary depending on the number of courses you take during your graduate career. If you think your employer offers tuition remission, it is best to have an open and honest conversation with them about how much they will reimburse you for, and how many classes or credits they will cover.
The Cost of Graduate School: Examples
Below is an outline of how each of us paid for our undergraduate, masters (MS), and doctor of philosophy (PhD) degrees.
Undergraduate: Once I left home I was given access to funds from my parents that I could use to pay for school. I lived in the dorms my first two years which used up a lot of this money. I then moved into an apartment and took up three part-time jobs (lifeguard, gym manager, research assistant) to maintain my living and school expenses. This allowed me to save the remainder of the money in my college fund and use it to move to Ohio for my MS program. MS: My first year at Ohio University I was a TA. My first semester I taught lab for Introduction to Paleontology and my second semester I taught Intro to Geology and Historical Geology. My second year I was on an NSF grant as an RA and worked on the Ordovician Atlas project for Alycia. Both summers I was awarded summer pay through this NSF project. My pay at OU was ~$14,000/year. My student fees at OU were ~$600/semester (summer was less like ~$200). Instead of taking out loans I took advantage of a loophole and paid late. There was a payment system but it cost extra. There was no fee (at the time) for simply paying a month late. It took some serious budgeting but was possible to slowly save for these extra fees. PhD: I was a TA all four years at UTK and taught a variety of classes: Intro to Paleontology, Earth’s Environments, Earth, Life, and Time, Dinosaur Evolution. During my time here my department stipend was $15,000 and I earned another $5,000 annual award from the university. I was able to split my pay over 12 months rather than 9 months. I was also able to work extra jobs over the summer at the university to augment my pay. Year 1 I was TA for a 4-week summer course for an extra $1000. Year 2 I taught a 4-week summer course as instructor for $3000. Year 3 I taught governor’s school (4-week program for high school students) for $2000. Year 4 I taught a paleontology summer camp at the local natural history museum for $500 (but also had the fellowship, where I got $10k but was reduced teaching so only received $7.5k from department).
Undergraduate: Full need based scholarship (shout out to UNC Chapel Hill for making my education possible!). My scholarship covered everything but summer school for the most part and I was hired as a federal work study student to pay for books and other necessities. I worked other jobs at the same time-I worked as a geology tutor and a lab instructor, namely, to cover other needs (medical care that wasn’t covered by insurance, transportation, etc.). I took out $7,000 in federally subsidized (i.e., interest doesn’t accrue until you begin paying) to cover summer classes and a required field camp. MS: I was paid as a half RA/half TA for one semester. I worked the remaining 3 semesters as a full TA teaching 3–4 lab courses per semester (I was paid extra to teach in the summer). My base pay was $14,000/year in Alabama. I worked as a tutor for the athletics department one summer to help pay for groceries. I did not take out loans for my degree, though I was not able to save much money. PhD: I was an RA on my advisor’s NSF grant for 2 years and a TA for two years. I also worked as a TA or a full course instructor for 3 of the 4 years. My base pay was $15,000/year in Tennessee. I took out $15,000 total in federally unsubsidized loans (i.e., loan interest began accruing immediately) to cover unexpected medical, family, and car emergencies. I also did small jobs, like tutoring individual students, helping professors, and babysitting to make a little extra money-my PhD department had a rule that we weren’t allowed to work outside tax-paying jobs on top of our assistantships.
AS (Associate of Social Science): I spent four years in community college, and lived at home while doing so. I worked 20–30 hours a week at a retail store to pay for courses and books. My grandmother did help me significantly during this time, so I was able to save up a bit for my BS degree when I transferred. Undergraduate (Bachelor of Science): I took out loans for 3 years worth of classes and research at a public 4-year university, in total about $40,000. I received a research fellowship ($3500) to stay and do research one summer. I still worked at my retail job the first summer and on holidays to make some extra money. MS: The first year I was a teaching assistant and my stipend was about $14,000 for the year. Over the summer, I won a grant from the university ($3000) that covered rent and living expenses. The second year I was a research assistant and made about the same as I did the first year. I think I took out about $5,000 worth of loans to help cover university fees and supplies. PhD: Throughout my first 3.5 years, I was funded as a teaching assistant making $25,000 the first two years, then was bumped up to $28,000 the third year (the teaching assistants at my university are in a union, so we won a huge pay increase). For the last year of my PhD, I won a fellowship (click here to read about it) from a research foundation ($35,000) that pays for my stipend, research expenses, and travel to research conferences. Early in the degree, I took out about $5,000 worth of loans to help cover fees and supplies.
Last December I got a chance to do two things I have never done before: Visit Washington D.C. and attend the American Geophysical Union (AGU) fall meeting. The AGU fall meeting is one of the biggest geology conferences and is held every year in December. This year they broke records with 26,000+ attendees and 28,000+ abstracts submitted!
My advisor was working on a project which required surveying attendees of the meeting and he was able to pay for me to come as well to help out with that. While I had to spend much of my time there at the Earth Science Information Partners (ESIP) Data Help Desk in the exhibit hall, I was able to get away and attend some talks and poster sessions. The project I was helping with was asking scientists who came for help at the Help Desk about their experiences, so we can figure out how to make the Help Desk more relevant and helpful for scientists at future meetings.
I flew in a whole day early so I could explore around D.C., because I knew once the conference started there would be so much going on it would be hard to get away. It was quite cold out so I bundled up in my jacket, hat, and scarf and headed out to see what I could find. I headed toward the National Mall, excited to finally visit the Smithsonian and all the memorials. I walked all the way to the far end of the mall first so I could see the various memorials. I visited the World War II, Korean War, Vietnam War, Lincoln, and Martin Luther King Jr. memorials. As a geologist, my favorite was the WWII memorial because of the variety of rocks used in cool ways. I also learned that besides the regular Vietnam War memorial wall, there is a memorial to the women who served the country and made great contributions during that time.
Next I visited the National Museum of Natural History. I had seen it in movies, but I was excited to see all the exhibits in person. This being AGU week, the most packed section was the rock and mineral exhibit. There was a line to even get in, and once in the excitement in the room was quite noticeable. It was so fun to see everyone excitedly discussing the different minerals, where they came from, and why they looked the way they did. These are the things we do for fun when you get a bunch of geologists together!
At the conference, while I did spend most of my time working in the exhibit hall, I had picked a few sessions of science talks to attend. The cool thing about conferences like these is that there are many simultaneous sessions in multiple fields of geology, so I could go see talks on anything I want. I often hop around to talks in fields other than what I work on, but since I had limited time to see talks this time I picked a few planetary science sessions to go see, and a few in areas that are important to me, like promoting equity and inclusion and dealing with sexual harassment in the geosciences. One of my favorite sessions was a lunchtime special session on the last day. AGU held a session celebrating the start of their 100th year, where they had speakers from many of their 25 sections give talks on how our scientific understanding has changed in the last 100 years in their field.
One of the coolest things I got to do was on the last day, right before we left D.C. My advisor knows someone who works at the Library of Congress (LOC) with the map collection, so we got to go and get a behind the scenes tour at the LOC. I loved seeing all the old and unusual maps they have there. The room where they store the maps is as long as 3 football fields! As a geologist it was especially exciting to see their collection of notes and maps from Marie Tharp, who used data from instruments on research ships to produce the first scientific map of the seafloor. This map was important because it showed us where the seafloor was spreading and gave us more evidence for plate tectonics.
I am so glad I was able to go to AGU in D.C. for the start of their Centennial celebrations, and I look forward to going again!
What is your favorite part about being a scientist and how did you get interested in science in general?
I enjoy exploring in the field to help find clues that support our theory and understanding of how our world works and using that experience to formulate better hypotheses and tests that will push the science forward. Our world is a fascinating place with endless opportunities to learn. Learning is humbling (“The more I learn, the more I realize how much I don’t know” -Einstein).
In laymen’s terms, what do you do?
I study streamflow generation in mountain environments of the western U.S. Or how snow(melt) becomes (stream)flow. Learn more about streamflow and the water cycle by clicking here. Mountains of the world have been termed ‘water towers for humanity’ due to the variety of downstream users reliant on water that originates as high-elevation snowpack. Population growth and migration combined with a warming climate is putting additional stresses on water resources originating from mountain snowpack, thus it is critical we have a thorough knowledge of how and where our streamflow originates.
There are a variety of approaches and scales used to study hydrology. I generally work at the watershed scale to perform stream gaging and measure natural tracers of the water cycle (electrical conductivity and water isotopes). Combining stream discharge and tracer data allows you to separate streamflow into different origins. Learn more about the field of hydrology by clicking here.
How does your research contribute to the understanding of climate change?
When temperatures warm, mountain snowpack begins melting earlier in the year. Earlier snowmelt and subsequent streamflow response has a variety of consequences ranging from biological impairment associated with changes to the natural flow regime to shifts in the timing and magnitude of water available for downstream reservoirs and irrigation. Importantly, earlier snowmelt often results in lower summer streamflow which can have detrimental effects in arid regions with an increasing demand for water. Part of my research aims to identify areas where this earlier shift in snowmelt is having the most adverse effects on summer streamflow by conducting an empirical, retrospective analysis from hundreds of stream gages in the western U.S.
What are your data and how do you obtain your data?
I use a combination of data I collect myself from field work in the Snowy Range of Wyoming, streamflow data from the United States Geological Survey (USGS), and snowpack data from the Natural Resources Conservation Service (NRCS). The USGS and NRCS data can be easily obtained from packages in R (‘dataRetrieval’ and ‘RNRCS’) but is less satisfying than digging 10 feet to install your own data loggers.
What advice would you give to young aspiring scientists?
I would advise young aspiring scientists to become proficient in a programming language (preferably several) as soon as possible. As computing power and data continue to grow, it is important that we make efficient use of our time. Also make sure you do not lose sight of the passions that drove you to pursue your career in the first place.
Creating a poster for class, a workshop, or a professional conference can be a daunting task. No matter what I’m creating the poster for, I try to stick with a simple and clean background and then once the organizational structure is in place, start to fill it in. This usually results in huge changes as I progress through the content but that’s okay!
Before getting started on your poster there are a few major things you should think about:
What program do I want to make my poster in? Google Slides integrates well with Google Sheets (free), Microsoft Powerpoint is pretty easy to manipulate (not free), and Adobe Illustrator is excellent for really detailed work (not free). There are many other programs, such as Canva (free), that offer lots of integration for images, line drawings, and more.
Who is in your audience? This will help you tailor language, depth of content, and figure detail on your poster.
Are there poster requirements? Size can be dramatically different and it’s always easiest to start with the biggest poster allowed and cut it down if you don’t need the space.
Generally, I like to work with boxes. Boxes help keep the organization of the poster nice and tidy. A major title box at the top that includes your poster title, authors, affiliations, and abstract number (if relevant). I usually aim to have the title in 72 point font and then everything else is a bit less. Having your regular text between 18-24 point font is a pretty good range and headers somewhere in the 40s-50s.
The rest of the poster is subdivided into larger boxes for each part of your project. These generally include but are not limited to: Introduction, Methods, Results, Conclusions, and Acknowledgments. Obviously, science and other projects don’t fit neatly into these categories but it’s a good starting place and titles can always be changed! It often helps just to get something on the page and then you can modify things later.
It’s always good to make sure your poster can stand alone when you aren’t there to walk viewers through the content. This means I usually include introductory or background text to help set the stage for the reader and reduce the text throughout the rest of the poster. This means shorter text, phrases, or bullets through the methods and results to concisely walk the reader through your content. Full sentences can be useful for discussion, conclusions, and/or broad implications of your work but sometimes bullets are plenty! Once you get to creating, it should be clear how much or how little you need to say.
Don’t forget to include references and people who have helped you out in your acknowledgments section. If people are interested in how you phrased something they may want to look up a reference that dives more deeply into the content. You can use regular in-text citations on your poster or superscripts to keep it neat and tidy. It’s good to include funding, departmental (internal or external) equipment that helped with analyses, and anyone who helped you run the machines or gain access to specimens!
The other major thing about posters is color schemes. Sometimes your supervisor or department may urge you to use school colors, this is fine but make sure you are following brand/logo policies (because they are confusing and there are a lot of rules). I like to throw in a lot of color wherever I can. It may be because I work on fossils and they are gray and often dreary-looking but I do believe that if your poster is visually appealing at first glance it will draw people over to you!
Quick Tips and Tricks
Make sure to include your affiliation (organization or institution)
Include logos of institutions or funding that helped support your project
Use colors that you like but that also help draw people to your poster
Send it to your friends and co-authors to edit before finalizing it
Always save it as a pdf when you send it off to be printed
Sometimes printing can take long, make sure you have enough time
Have fun, posters are an excellent networking opportunity
If you click here you can go to a template Sarah and I made when we were teaching a summer course. You can save a copy of this template to your Google Drive to play around with the different elements.