Temperature and Salinity on the half shell: the synergistic effects of environmental change on oyster gene expression and physiology.

IMG_7414 (1)
Hollis Jones dissecting an eastern oyster, Crassostrea virginica, as part of her research on how environmental change impacts these ecologically and commercially important organisms.

Recently, we reached out to Hollis Jones, a recently graduated masters student from the Kelly Lab at LSU and current Knauss Fellow with NOAA SeaGrant to tell us more about her recently published article in Integrative and Comparative Biology. Her article is titled “Synergistic Effects of Temperature and Salinity on the Gene Expression and Physiology of Crassostrea virginica” and was published online on May 10, 2019.

What was the motivation to produce this work?

The Louisiana eastern oyster fishery provides 45% of the oysters consumed nationally (the largest contributor in the nation). Aside from their value as a fishery, the ecosystem services that they provide, such as shoreline stabilization, nursery habitat, and water filtration, have been valued at between $5,500 and $99,000/ha/year. River diversions and increased precipitation in the Southeastern United States has led to larger and longer pulses of freshwater in the northern Gulf of Mexico. This increased freshwater inflow combined with rising average temperatures in the Gulf of Mexico have had negative impacts on the eastern oyster across all life stages.

This study focused on the combined effects of heat and salinity stress on the eastern oyster, C. virginica, an ecologically, economically, and culturally important marine invertebrate inhabiting estuaries along the Gulf of Mexico. Our results suggest that timing and duration of freshwater events will have large impacts on eastern oyster recruitment and survival as temperatures gradually warm and push them closer to their tolerance thresholds.

What were some of the important or interesting discussions arose through and as a consequence of this work?

We can learn a lot about how an organism is dealing with stress by looking at what genes individuals express. Comparative transcriptomics allows us to compare gene expression profiles between treatments. In this study, we used a combination of comparative transcriptomics, physiological measurements, and field assessments to quantify the synergistic effects of combined temperature and salinity stress on adult C. virginica. Linking environment, physiology, and gene expression profiles provided a more complete picture of how climate change will impact these phenotypically plastic organisms. Temperature and salinity are only two of many shifting environmental variables and the cascading and sometimes unpredictable impacts of multiple stressors is why studies that measure responses to multiple variables will be key to predicting the effects of future environmental change.

What future directions do you hope to take in this area?

There is a need for the ability to assess oyster condition in the field after a stressful event like a hurricane or freshwater diversion. Our results suggests that the expression of select hypoosmotic stress genes could be used for this purpose.  The ability to quickly classify oyster condition using gene expression profiles would be useful for monitoring efforts and potentially identifying resilient stocks that could be used for effective oyster reef restoration projects.

What did you most enjoy about producing this work?

I was born and raised on the Louisiana coast; researching an organism that simultaneously plays a critical role in the health of our coastal ecosystems and my Christmas dinner was amazing. Most everyone has heard of oysters, and most recollect them on the half shell (although our younger audience usually response with a definitive “yuck!”), but being able to relate oysters to hurricane resiliency or juvenile red snapper habitat is really rewarding.

IMG_7052Are there any other advantages to working with oysters?

One of the perks of working with oysters is that they’re delicious. When we were sampling oysters in the wild, gill tissue was excised and stored within minutes of dredging in order to minimize changes in gene expression associated with handling. After we take the tissue sample, we’re done with the oyster and they make a great snack! #sampleyoursample!

You can read the original article by Hollis R. Jones et al. here: https://doi.org/10.1093/icb/icz035


Article in Focus: The Biota Project

The Biota Project aims to produce content and engage its audience in a way that is particularly cognizant of historically ignored demographics in science education and outreach media as a means of celebrating the underappreciated power these demographics hold.

The start of something new:

The Biota Project was initiated in the Fall of 2013 by filmmaker J. Abubo and scientist Sabah Ul-Hasan. Many ecosystems showcased in media center on exotic locales that indirectly remind viewers of their socioeconomic dispositions.
Abubo and Ul-Hasan related to this as individuals growing up in homes with limited resources and thus wanted to create a space in media that encourages its viewers to embrace their local landscapes as stewards of the land. Having both grown up in an “undesirable” part of Salt Lake City, across the highway and near industrial factories, the two joined heads to produce a fresh take on how we view ecosystems in our own backyards.


Camerawoman, Alondra Romero, snaps a shot of director Manny Collazo IV capturing screenwriter Nicholas Dove and host Sabah Ul-Hasan at Hetch Hetchy for Episode 2: The Sierra Nevada. From the Biota Project Newsletter.
What is The Biota Project?
Over the past five years, we as a science education and communication organization have used multiple approaches of achieving this aim. We consistently strive to practice what we preach by ensuring our team demography is 85% or more representative of overlooked communities in the sciences. We also reflect this in who we interview, how we use language, and the material we release through various forms of art (music, film, blogging, vlogging, 2-dimensional art, and so forth).

Art highlighting symbioses, with the young trevally fish swimming inside a jellyfish – likely a parasitic relationship (Above) and symbiotic slug (below) both made by Leesa
How does the Biota Project work?
As one of our previous team members has referred to us, we are a “radically democratic” bottom-up group. While we hold certain leadership titles for the function of organization formality, we strongly believe in the ideology of every voice being equally heard in order to ensure the integrity and strength of our products.
Going forward, we plan to expand our team’s practices as we continue to gain credibility and immediately share this space by bringing visibility and funding to incoming science communication initiatives. Through these approaches, we ultimately aim to “symbiotically” contribute to bridging the gap between scientists and general public.

The Biota Project has a recently accepted article featured in ICB highlighting their work:
The Biota Project thus sets a symbiotic tone for re-calibrating the balance between academics, researchers, and local communities. When science is made relevant through understanding, its quality and significance are enhanced, and public recognition of its value is increased.

Trainee Tuesday: Callie Crawford

Gugenheim - CopyCallie Crawford (@CallieHCrawford) is a newly minted PhD Candidate in the department of Biological Sciences at the New Jersey Institute of Technology (@NJIT).  Her work, “using hillstream loaches to study the evolution of terrestrial locomotion from a biomechanics viewpoint”, is being conducted in the laboratory of Brooke Flammang (@FlammangLab ).  Her plan is to use a variety of tools (including CT scanning, kinematics, phylogenetics, and electromyography) to study how these fishes are capable of terrestrial locomotion. ,

Callie did not start out a New Jersey resident. She’s making her way through the US, being originally from Kentucky; she completed her BS in Marine Biology with minors in Leadership Studies and Wildlife & Conservation Biology at the University of Rhode Island and then moved to Charleston, South Carolina to complete her master’s degree in Marine Biology, “studying the variation in skeletal morphology in cartilaginous fishes (sharks, skates, rays, and chimaeras).”

She’s been in Dr. Flammang’s lab for two years now.  “While looking at labs in which to do a PhD, a friend/mentor who was nearing the end of his PhD recommended I look into Brooke’s lab, both because of the type of research, and because he felt we would work well together. After reading up on her work and meeting her at the SICB conference in Portland about a month before interviews, I felt working with Brooke would be a great opportunity to build on my skills from my master’s degree in addition to gaining new tools for my toolkit. “

One of the most interesting parts of her research is the “opportunity to work towards answering questions that are still within the realm of the unknown, and to learn new tools that build upon skills I developed during my masters research.”

Grad school (as we know) has its high and low points, moments that make us stronger and love our science. I asked her what her favorite part of grad school has been thus far. “Being able to continue to learn new things every day while working and networking with like minded individuals. I have constant opportunities to learn from researchers, students, and instructors in addition to learning from my advisor’s collaborators and visiting speakers.” Graduate school definitely lends itself to opening up different avenuesIMG_6221 for collaborations and learning. However, sometimes that can also be a least favorite part of grad school. “The number of directions I am pulled every day and having to remain focused and not jump on every side project that comes my way. The opportunity for side projects and working on other projects is wonderful, but trying to rein myself in is the difficult part!” Not a bad least-favorite part of grad school!

Callie has done and will continue to do a lot of travelling for her research. She has traveled to Duke University to complete microCT scans of fish borrowed from the Smithsonian Museum of Natural History.  Additionally, she has some collaborations throughout the east coast: “I have traveled to Maryland and to Stockton University in NJ to complete CT scans of Mola mola (the ocean sunfish) and various varanid lizards, respectively.”

To learn more about Callie and her research, please follow her at @CallieHCrawford. 






Article in Focus: Neural Crest Transplantation Reveals Key Roles in the Evolution of Cavefish Development

Fish living in caves often show adaptations to this unusual environment, including loss of eyes. The neural crest (a temporary group of cells that, during development, gives rise to structures such as the craniofacial bone and cartilage) is important for the development of eyes and other features – but what is the role of the neural crest in the evolution and development of cavefish? In this study, the authors transplanted neural crests between fish and embryos of Astyanax cavefish. Their results suggest that cavefish neural crest cells are defective in forming optic derivatives, and that neural crest cells are also implicated in a loss of pigmentation. In sum, neural crest cells play key roles in the evolution of cavefish development.
Lead author Masato Yoshizawa (University of Hawai’i at Mānoa) tells us more about this project:
img7999_6283l.jpg“Eye degeneration in cave animals has made researchers wonder for a long time, even since the era of Charles Darwin. Our group and other researchers have revealed that eye regression is promoted by lens apoptosis; altered Shh/Fgf8 signaling and HSP90 pathways; standing genetic variation in surface-dwelling ancestors; and even epigenetics. Despite these findings, we still do not fully understand its evolutionary mechanism, perhaps due to its multi-genetic nature and how natural selection carefully promotes eye degeneration without perturbing the functions of other organs. Genetics and genomics cannot provide a full view of this phenomenon. We decided that careful tracking of each cell, and developmental, trascriptomic, metabolomic and epigenetic analyses, would highlight further processes that could be crucial for the evolution of eye degeneration.
“Our motivation in conducting this study was first to see if we could highlight the contribution of the neural crest cells in the eye development of cavefish. It is known that, in vertebrates, neural crest cells differentiate into cornea, iris and scleral bones. Since cavefish have reduced numbers of pigment cells, which are also derived from neural crest cells (McCauley et al., 2004), we hypothesized that altered neural crest cells may also contribute to eye regression in cavefish.
Astyanax mexicanus cavefish (picture: Wikimedia Commons)
Thus far in cave animal studies there has been no genetic or transcriptomic research that indicated the involvement of neural crest cells in eye-size regression. The classic microsurgery experiment we undertook revealed the significant contribution of neural crest cells. From this, we will further investigate the role of neural crest cells in cave adaptation. We were surprised that, if we just based our hypothesis on the latest genetic and transcriptomic evidence, we could have overlooked the adaptive contribution of the altered neural crest cells!
“I most enjoyed using a classic technique of developmental biology, and showing that it is still valid to test modern hypotheses. I was just thrilled what I have seen and learnt from this study!”
Neural crest cells (picture: Dr. Masato Yoshizawa)

Article in Focus: High temperature, oxygen, and performance: Insights from reptiles and amphibians

Post written by Dr. Eric Gangloff

Elgaria multicarinata, the Southern Alligator Lizard. Photo: E. Gangloff & R. Telemeco

While graduate students at Iowa State University, Rory and I participated in many discussion groups and conferred about new and exciting ideas in eco-physiology. From these conversations naturally flowed research collaborations. At one point we became intensely interested in the oxygen- and capacity-limited thermal tolerance (OCLTT) hypothesis, as put forth by Hans-Otto Pörtner and colleagues, about which there has been much lively debate. We realized that this hypothesis was relatively unexplored in reptiles, our taxa of preference, and set out to design experiments to test this hypothesis. We also became excited about some of the new possibilities to gain high-throughput physiological data. Rory had recently conducted an experiment with alligator lizards (Elgaria coerulea and E. multicarinata), designed to test for variation in response to thermal stress in these two closely-related species. With samples of skeletal muscle from this experiment, we utilized a metabolomics approach to identify differences in metabolites between heat-stressed and non-stressed animals and between species (Telemeco et al. J Anim Ecol 2017). Concurrently, we tested the hormonal and metabolic response to garter snakes (Thamnophis elegans) exposed to extreme but sub-lethal temperatures (Gangloff et al. J Exp Biol 2016). To our surprise, the results of both experiments provided rather robust results refuting the importance of the OCLTT mechanism in setting thermal tolerance limits in these species. So what then? We continued our discussions and collaborations, both on classroom whiteboards and over beers, and decided to challenge ourselves with a review/commentary paper.

Ideas flowing. Photo: E. Gangloff & R. Telemeco

After graduating, Rory took a post-doc position at the University of Washington where he conducted further work in this area. This included one study with lizard (Sceloporus tristichus) eggs, providing support for oxygen capacity playing an important role setting tolerance limits in lizard embryos (Smith et al. Biol Lett 2015). With this result and some other studies published around the same time, our ideas began to germinate. By combining current theoretical work on thermal tolerance limits in fishes with decades of great physiological studies in reptiles and amphibians, we could propose an integrative framework to predict when and how different mechanisms would set thermal tolerance limits. The broad ideas were there, we had lots of papers to read, so then…we just needed to figure out how to make time to put it all together. Last winter, we were able to arrange for Rory to give a departmental seminar at Iowa State University – where I was working as a post-doc – which allowed us to spend a week working on this manuscript. We hunkered down for the most part in a basement room with a couple computers and a whiteboard, hashing out ideas. It proved to be enormously productive (and fun!). We set a timetable to complete a full draft of the manuscript within a couple months. We were able to do this just as I began a new post-doc position at the Station d’Ecologie Théorique et Expérimentale du CNRS in Moulis, France. Here, I am studying how oxygen limitation interacts with temperature regime to limit high-altitude colonization in the lizard Podarcis muralis (read more about this work in the project’s blog). Perfect!

After several rounds of re-naming, we are now very pleased to present the Hierarchical Mechanisms of Thermal Limits (HMTL) hypothesis with our paper: “High temperature, oxygen, and performance: Insights from reptiles and amphibians.” With this commentary, we seek to integrate ideas about how either subcellular components or organ systems first suffer under exposure to high temperatures and thus set thermal limits in ectotherms. Furthermore, we hope to merge the well-established thermal performance curve paradigm with these ideas of the proximal mechanisms setting thermal limits. As we outline in the paper, this framework combines a variety of observations in reptiles and amphibians and points to exciting new directions and untested questions. For example, what is the factor that signals animals to reduce their preferred temperature in hypoxia? Is the lethal thermal limit always lower when it is determined by oxygen capacity rather than subcellular components? Does maximum aerobic capacity underlie whole-organism thermal optima? Will species that invade high-elevation habitats suffer reduced performance as oxygen availability decreases? While reptiles and amphibians provide a great diversity of ecological and ontogenetic contexts in which to test these ideas, we think they are broadly applicable to many ectothermic taxa. As Rory begins his new position as assistant professor at California State University, Fresno, and I continue my post-doc work here, we are excited to begin empirical studies that further test and develop these ideas.

We are most thankful to our families for support and patience while we spent long hours debating these ideas in the basement of Bessey Hall at Iowa State University. We are also grateful to M. Angilletta, B. Bodensteiner, and J. VandenBrooks for comments on earlier drafts of the manuscript, and for the support of A. Bronikowski, T. Schwartz, and A. Toth.

R.S.T. received support from Auburn University and California State University, Fresno. E.J.G. was supported by the U.S. National Science Foundation (IOS-1558071 to A. Bronikowski), the “Laboratoire d’Excellence (LABEX)” TULIP (ANR-10-LABX-41), and the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 752299.

Trainee Tuesday: Beth Reinke

BethBeth Reinke (@BA_Reinke) is a new postdoctoral fellow at Penn State University in Dave Miller’s lab. Miller focuses on population and community ecology in managed systems. Beth considers herself “an evolutionary ecologist with an interest especially in the evolution of animal coloration.” “My current postdoc work is on growth and senescence modeling using long-term data. Though these sound like disparate topics, I find that part of the fun in research is finding ways to connect my existing knowledge with new skills. Developing these quantitative modeling skills is necessary given that I plan to continue my painted turtle mark-recapture project and I am able to incorporate physiology and evolutionary biology into the interpretations of the models. The Miller Lab is extremely diverse, with everyone working on population ecology from different perspectives and with different species, so this is a great place to learn and teach.”F
Her work originally started when she was an undergrad at Indiana University as an assistant for a graduate student in a zooarchaeology lab.  “She inspired me to pursue my own project early in my undergraduate career and her support and enthusiasm was absolutely a huge part of why I’ve stuck with research.”  Interestingly, they ended up working together again, as she was Beth’s first postdoc supervisor. As an undergrad, Beth assisted with two very different graduate projects and developed an honors thesis from three years of field data. That project was the beginning of a mark-recapture study of painted turtles that she is still continuing – this summer will be its ninth year. Her PhD
work was at Dartmouth in the lab of Ryan Calsbeek.
Beth, like many of us, had a penchant for science and research that started as a child.  “I IMG_6309 copyremember poring over library books as a kid, trying to absorb as many reptile facts as possible and not understanding that there is a whole world of primary literature I was missing out on.” She knew she always wanted to work with animals, but not as a veterinarian.
Her experience as both a postdoc and graduate researcher makes her poised to provide valuable advice.  “I don’t feel that I’m the most qualified to give advice, not being far along this path myself. But the most helpful advice I’ve been given is to be flexible. You never know where your research is headed and forcing it in a particular direction is not likely to be the most fruitful approach. You have to always be curious and follow as many lines of inquiry as possible.”
At times, it is difficult to know where your research is heading. I asked Beth, “Where do you see your research heading?” “I’m not sure that that’s something I can easily predict. From where I stand now, I plan to connect my work on animal coloration with the skills I’m currently developing by incorporating color data into long-term studies and demographic models. Because the functions of animal coloration are so diverse, the IMG_6310 (1)utility of that approach will vary with the species but I’d like to continue to use macroevolutionary and experimental approaches to address questions about the evolution of coloration and color diversity in a broad range of species.”
Beth is an early career scientist hoping to land a tenure-track faculty position. She enjoys both teaching and research, and hopes in 5 years to be at a university where she could do both.”In the meantime, I will continue to conduct research and follow where my curiosity leads!” 
To learn more about Beth and her research follow her at @BA_Reinke and check out her www.bethreinke.com

Brooke Flammang: When the research ‘sucks’

2015-042I met Dr. Brooke Flammang while I was a doctoral student at New Jersey Institute of Technology, where I walked into the aquarium room and noticed a large tank with remora (fish whose dorsal fin has a suction disc that can take a firm hold against the skin of larger marine animals). Normally, we housed different species of weakly electric fish, and the remora’s presence signaled that our new faculty had started to set up her lab.

Dr. Flammang was one of the first female research faculty in the biology department and from my first encounter I knew she was a powerhouse. Her energy, her interest in research, and zest for teaching was evident through her interactions with me. I defended my thesis in March of 2015, and soon after we had a great afternoon discussing post-doc life, science, and everything in between. She took me under her wing, having only met me less than a year before (and not even working in the same field – neuroscience). Little did she know that she had made a great impact on both my scientific career and my life. I knew that she would be one of the mentors I turn to during the path throughout my academic career.

Brooke Flammang is an assistant professor in the biology department at the New Jersey mezzanine_751Institute of Technology in Newark, New Jersey. Her lab (https://web.njit.edu/~flammang/), the Fluid Locomotion Laboratory, focuses on functional morphology and biomechanics. Specifically, her current research is comparative biomechanics and the evolution of functional novelties. More specifically, she is interested in the morphological features of fishes that afford them performance advantages. Currently work in her lab focuses on remora adhesion, terrestrial walking in fishes, and mola and frogfish bioinspired robotics. Not being an expert in the field myself, I asked how she was drawn into this line of research and if any particular classes that helped peek her interest in research, “I pursued my Masters degree thinking I was going to be an ecologist studying deep sea catsharks, but then I took a fish biomechanics course from Lara Ferry (now at Arizona State) and it blew my mind. All of a sudden, here was the science that kept me awake at night, the science that made me wake up at 3 am with interesting questions. Using math and physics to approach biology made sense to me and helped me to understand and explain evolutionary patterns in a way that had not been possible before. Lara pointed me towards the Friday Harbor Labs fish course, taught by Adam Summers, which was a transformative experience. The FHL fish class was a biomechanics boot camp for me and gave me a strong foundation in experimental research. Its also where I made one of my first scientific discoveries that paved the way for my future career.”

Like many of us, Brooke had ups and downs during her career and periods of feeling like she did not belong. Rather than let those hinder, she used those moments as strengths and learning experiences. I was interested in understanding how she dealt with these problems and when she faced them. Walking into Harvard, was one of the first moments she was lost in her career. She was a first generation college student from a small town, who had chosen “their academic career thus far based on financial aid and part-time (really full-time) job opportunities.”

When you first get to know Brooke, and discuss her research you think that she was always a strong and confident scientist, however, it wasn’t always the case. “It took years for me to feel comfortable speaking freely about my thoughts and feeling like they might be taken seriously.”  She dealt with imposter syndrome that consumed her during times at scientific conferences. We have all been there questioning our career path. “It still happens from time to time: we set ourselves up to be judged every time we submit a paper or a grant; it’s just the nature of the beast.” This leads us to the advice that she gives her grad students and postdocs, “You are the world’s expert on the thing you are researching. Own that and have confidence in yourself and seek to be the foremost authority on that thing. This is a commitment you are making so make sure that you love the thing you are doing. And make sure you check in on your mental health and create some time for yourself.”

She was fortunate to have many mentors who influenced her career and supported her, “George Lauder provided me with every opportunity for research success while promoting work-life balance, including being flexible with working from home and welcoming my infant into the lab so my productivity wasn’t impacted.” Others include Karel Liem and Farish Jenkins, who “were always available to discuss my ideas in earnest. Beth Brainerd, Lara Ferry, Alice Gibb, Miriam Ashley-Ross, and Patricia Hernandez continue to be strong examples of women in science whom have provided me with a lot of support over the years. Adam Summers is a tremendous advocate for junior colleagues in the field. Peter Girguis has always provided sage advice on how to navigate academia.”

Brooke is a leading authority in her field, shown by her numerous publications, grants, interviews, and awards. One award she received, the Carl Gans Award, conferred by the Society for the Integrative and Comparative Biology, was “one of the proudest momentsroboshark_lab_logo of my career to date.” “When I’m working in research, I feel like I am making an exciting new discovery but I always wonder if it will be meaningful to others. To have my research acknowledged as ‘distinguished contributions to the field of comparative biomechanics’ gave me an overwhelming sense of validation that maybe I can get the hang of this, after all.” But awards aren’t the most rewarding part of her research. In addition to answering the “why” questions that many of us pose, she loves that the “discoveries in fish biomechanics holds the possibility of unlocking novel technological applications that can benefit humankind.”

She has been at NJIT for almost four years, and during that time has taught many classes, had students in her lab (graduate and undergraduate), supported postdocs, and published. I asked if there was a single moment during her time as a professor that has been her favorite, or if any stand out the most to her. Some of the moments she shared have come from her Comparative Biomechanics and Bioinspired Robotics courses in which her students develop their own research projects. During their experimental work, students have an ” ’a-ha!’ moment; to see their excitement as they suddenly get it right is the reason I like to teach these courses. How does one know when they are making an impact or if their students are taking away valuable lessons?” Brooke described one of those moments, and I imagine that it would be a moment of pride for any of us. “I had one group who was working on a flying cockroach robot (cockroaches fly like the chickens of the insect world) and in order to make sure they had the wing beat programming right they went out on their own and collected and analyzed a bunch of kinematic data over spring break.” Undergrads usually take their spring break to catch up on sleep, marathon that show on Netflix, or socialize, however, “they were so enthralled about what they were learning in the course that this seemed like the most exciting way for them to spend the vacation.”

Brooke continues to push the boundaries of her research and being a strong force in the comparative biomechanics field. A big part of pushing those boundaries is just knowing downloadthe “why?” What direction does she see the field moving in? “A lot of work in comparative biomechanics has been the foundation for developing novel technologies in medicine, defense, robotics, etc. I see no reason this trend should decrease as the applicability of research and its ability to solve a specific problem is highly motivational (and fundable). However, it is exceedingly important to note that the biological principles that these technologies are based on are almost unanimously the by-product of curiosity-driven basic research. It is imperative that the freedom to ask “why” just for the sake of knowing be supported.”