Halmos Researchers Demonstrate How Staghorn Coral Restoration Projects Show Promise in the Florida Keys

A new analysis of reef restoration projects in the Florida Keys National Marine Sanctuary suggests they could play a key role in helping staghorn coral recover after decades of decline. Steven Miller, Ph.D., a research scientist at NSU’s Halmos College; and his former master’s student, Matt Ware, Ph.D. (‘12); worked with their colleagues to present these findings in the open-access journal PLOS ONE on May 6, 2020.

Once widespread in Caribbean reefs, staghorn coral populations have declined by over 90 percent since the 1970s. After the species was listed as Threatened under the U.S. Endangered Species Act in 2006, the National Oceanic and Atmospheric Administration (NOAA) initiated a recovery plan. A central part of this plan is outplanting, in which corals are cultivated in an offshore nursery before being transplanted to restoration sites.

While outplanting efforts have been in place for many years, only recently has enough time passed to analyze their long-term potential. Now, Ware and colleagues have applied photographic monitoring and scuba diving  to assess 2,419 staghorn coral colonies outplanted to 20 different sites in the Florida Keys between 2007 and 2013 by the Coral Restoration Foundation.

The analysis revealed that survivorship – the percentage of colonies containing living tissue – was high for the first two years after outplanting, but declined in subsequent years. Survivorship among projects based on colony counts was highly variable, between 4% and 89% for seven projects with corals that survived at least five years. The researchers also used statistical modeling to predict future survivorship, finding that 0 to 10 percent of the colonies would survive seven years post-outplanting. This means that large numbers of colonies need to be outplanted to start, so ecologically relevant numbers survive longer-term. Coral growth rates were similar to the wild population.

The authors acknowledge some limitations of their analysis, including low or variable sample sizes among projects and the retrospective nature of their analyses that made it difficult to identify how different habitat types and reef locations affected survivorship

Still, the findings suggest that outplanting could help restore staghorn coral populations by protecting against local extinction and maintaining genetic diversity in the wild. Meanwhile, the same major stressors that have plagued these corals over the last few decades – disease and bleaching, both related to global warming – remain. The new findings support NOAA conclusions that mitigating these stressors is needed to achieve full, long-term recovery.

Citation: Ware M, Garfield EN, Nedimyer K, Levy J, Kaufman L, Precht W, Winters, RS, and Miller, SL. (2020) Survivorship and growth in staghorn coral (Acropora cervicornis) outplanting projects in the Florida Keys National Marine Sanctuary. PLoS ONE 15(5): e0231817. https://doi.org/10.1371/journal.pone.0231817

Halmos College Faculty and Students Present Protein Modeling at Virtual Conference

During April, a Halmos College faculty and student team was accepted to the National meeting of the American Society of Biochemistry and Molecular Biology. Originally the symposium was scheduled to be held in San Diego, but due to COVID-19, the event was moved to a virtual platform. The team prepared a video presentation and posted to YouTube to link to the nationwide event.

The team consisted of Halmos faculty members Arthur Sikora, Ph.D., Emily Schmitt Lavin, Ph.D. Halmos College undergraduate students: Feza Abbas, Matthew Hunt, Lyla Abbas, Helana Ghali, Alesa Chabbra, and Mina Ghali. The team modeled two well know inhibitors of HIV-1 protease called Darunavir and Ritonavir. They also used chemical elements of both inhibitors to design a hypothetical new inhibitor that they named “Sharkavir” in honor of the NSU Sharks. The group worked in conjunction with the Center for Biomolecular Modeling as part of their NSF funded project to develop protein modeling research through the CREST (Connecting Researchers, Educators, and STudents) Program.

Human immunodeficiency virus (HIV) affects approximately 37 million people worldwide and results in over 1 million deaths annually. A class of drugs first developed in 1995 inhibits the enzyme HIV-1 protease, thus preventing the maturation of an HIV precursor protein. There are now over 10 protease inhibitors available to treat HIV. Multiple mutations in the protein have made this treatment less effective. Darunavir is currently one of the strongest competitive inhibitors, as it binds effectively to the substrate envelope and has yielded a lower resistance for patients. The most effective treatment is a combination of two of these inhibitors: Darunavir and Ritonavir. In order to explain how these drugs work, the active site of the non-mutated wild-type HIV-1 protease was depicted as a binding box model. The protease inhibitors Darunavir, Ritonavir, and our hypothetical drug, “Sharkavir” were 3D printed to show how they fit into the protease active site. Details of the wild-type HIV-1 protease, as well as the drugs Darunavir, and Ritonavir, were found in the Protein Data Bank files. The new protease inhibitor molecule, “Sharkavir”, was designed as a combination of Darunavir and Ritonavir using Marvin Sketch: a software used to manipulate molecular structures.


Halmos Faculty Participates in NSF STEM for All Video Showcase

From May 5 to May 12, Halmos Faculty Member Arthur Sikora, Ph.D. collaborated with faculty around the country to present their video entitled, “Rich Collaborations Yield More than Expected: BASIL lab. This curriculum from the BASIL (Biochemistry Authentic Scientific Inquiry Laboratory) collaboration aims to get students to transition from thinking like students to thinking and acting like scientists. Students will analyze proteins with known structure but unknown function using both computational and wet-lab techniques. BASIL is designed for undergraduate biochemistry lab courses but can be adapted to first year (or even high school) settings, as well as upper-level undergraduate or graduate coursework. It is targeted to students in biology, biochemistry, chemistry, or related majors.

Sikora stated, “We have been fortunate to have robust anticipated learning outcomes that were developed by our collaborators at Purdue. The full set is published in “Anticipated Learning Outcomes for a Biochemistry Course-Based Undergraduate Research Experience Aimed at Predicting Protein Function from Structure: Implications for Assessment Design” Irby et al BAMBED 2018. Several members of the group have started working with these ALOs to design targeted assessments.”

The 2020 National Science Foundation (NSF) STEM for All Video Showcase is an annual online event. Each year, it hosts between 100-200 three-minute video presentations from federally funded projects that aim to improve STEM (Science, Technology, Engineering, and Mathematics) and computer science education. During the seven days of this online event, Principal Investigators, practitioners, administrators, researchers, policy makers, industry and the public at large are encouraged to participate. All participants will be able to view the video presentations, post to the facilitated discussions related to each video, and vote for the videos that are most effective in conveying the creative work being done. All videos and discussions will be archived for perpetual future access. In addition, all videos from this Showcase will be added to the collection in the STEM for All Multiplex after the online May event.

Physical Distancing May Be New for Humans, 
Not So Much For Whale Sharks

When it comes to physical (social) distancing, humans could learn a thing or two from whale sharks. Seeing one in the ocean is a rare occurrence, indeed, and a big deal – so much so that a recent sighting off the west coast of Florida made several news reports.

For a group of research scientists, “Rio Lady” is one whale shark that shows just how physical distancing works. She was originally ‘tagged’ in 2007 and hadn’t been seen since her tag popped off a few months later. That was until 2011. And she’s since been “re-tagged,” this time with a satellite tag that is showing some remarkable results.

You can read the full press release ONLINE. In addition, enclosed are high resolution photos you can use and here’s a link to b-roll video from the Guy Harvey Ocean Foundation.



Halmos Undergraduate Co-Authors an Article in a Bioanalytical Chemistry Journal

This spring, Halmos College Biology major Elaine Ognjanovski (minors in Psychology and Experiential Leadership) co-authored a publication with Richard H. Perry, Ph.D. entitled, “Identification of lipid biomarkers of metastatic potential and gene expression (HER2/p53) in human breast cancer cell cultures using ambient mass spectrometry”, which was published in the journal Analytical and Bioanalytical Chemistry. Dr. Perry, a faculty member in the Department of Chemistry and Physics, worked with Elaine on developing a desorption electrospray ionization mass spectrometry method that enables the identification of lipid biomarkers of HER2/p53 expression, metastatic potential, and disease state in monolayer, suspension, and spheroid human breast cancer cell cultures.

The article’s abstract states: “In breast cancer, overexpression of human epidermal growth factor receptor 2 (HER2) correlates with overactivation of lipogenesis, mutation of tumor suppressor p53, and increased metastatic potential. The mechanisms through which lipids mediate p53, HER2, and metastatic potential are largely unknown. We have developed a desorption electrospray ionization mass spectrometry (DESI-MS) method to identify lipid biomarkers of HER2/p53 expression, metastatic potential, and disease state (viz. cancer vs. non-cancerous) in monolayer and suspension breast cancer cell cultures (metastatic potential: MCF-7, T-47D, MDA-MB-231; HER2/p53: HCC2218 (HER2+++/p53+), HCC1599 (HER2−/p53−), HCC202 (HER2++/p53−), HCC1419 (HER2+++/p53−) HCC70 (HER2−/p53+++); non-cancerous: MCF-10A). Unsupervised principal component analysis (PCA) of DESI-MS spectra enabled identification of twelve lipid biomarkers of metastatic potential and disease state, as well as ten lipids that distinguish cell lines based on HER2/p53 expression levels (> 200 lipids were identified per cell line). In addition, we developed a DESI-MS imaging (DESI-MSI) method for mapping the spatial distribution of lipids in metastatic spheroids (MDA-MB-231). Of the twelve lipids that correlate with changes in the metastatic potential of monolayer cell cultures, three were localized to the necrotic core of spheroids, indicating a potential role in promoting cancer cell survival in nutrient-deficient environments. One lipid species, which was not detected in monolayer MDA-MB-231 cultures, was spatially localized to the periphery of the spheroid, suggesting a potential role in invasion and/or proliferation. These results demonstrate that combining DESI-MS/PCA of monolayer and suspension cell cultures with DESI-MSI of spheroids is a promising approach for identifying lipid biomarkers of specific genotypes and phenotypes, as well as elucidating the potential function of these biomarkers in breast cancer.”


Citation: Heather M. Robison, Corryn E. Chini, Troy J. Comi, Seung Woo Ryu, Elaine Ognjanovski and Richard H. Perry *, Analytical and Bioanalytical Chemistry, 2020, 412, 2949–2961. DOI: https://doi.org/10.1007/s00216-020-02537-4

Halmos Mathematics Student Accepted into Ph.D. Program

Halmos College Mathematics and Chemistry double major, Nikhil Nagabandi will head this fall to the University of North Carolina at Chapel Hill where he has been accepted with funding to pursue his Ph.D. in mathematics at one of the top graduate programs in the nation.

Nikhil has worked under the mentorship of Mathematics faculty member Ricardo Carrera, Ph.D. (first as Razor’s mentor and now as the Honors in Major mentor). He is graduating this May. He was accepted to Ph.D. programs at Louisiana State University and the University of Pittsburgh. Halmos College is always proud of our graduates and we feel we have prepared them well for a successful future.

Ocean Glider Found After Being Lost at Sea

The ocean circulation on the Southeast Florida shelf is complex due to the Gulf Stream. Oceanographic measurements have always been a challenge in this area. The currents can be so strong that even the National Data Buoy Center does not take a risk deploying their buoys in the Gulf Stream. As a result, the South Florida shelf is still a “desert” for oceanographic observations.  At the same time, this is the area of significant commercial and recreational activities. To address this situation, NSU’s Halmos College of Natural Sciences and Oceanography has been developing observational capabilities in the Straits of Florida employing state-of-the-art technologies including robotic instrumentation.

This spring, Halmos College became a center of robotic oceanography. In cooperation with Teledyne Webb Research (TWR), the Halmos College Physical Oceanography Laboratory pioneered the application of the new family of ocean gliders that, for the first time, could operate in strong currents like the Gulf Stream. These robotic instruments provide an unprecedented spatial resolution and report data through a satellite.

The Halmos College is now operating two gliders on the Ft. Lauderdale-Miami coastal area. Physical Oceanography Lab Senior Ocean Engineer Geoffrey Morrison said, “Gliders operate in the area of intense ship traffic and small recreational and fishing boat activities. Gliders show up on the surface for a few minutes to transmit the data through satellite and then dive for the next mission. We have had a case where a glider surfaced near a fishing boat and good Samaritans tried to keep it on the surface thinking that the instrument was in distress. After reading the contact information on the glider, they called us. We asked them to release it and this robotic instrument then went underwater for the next mission.”

While out on a cruise last week, the glider had what appeared to be fishing line tangled around its propeller. “The fishing line was probably tangled around one of the subsurface buoys,” said Halmos College Ph.D. student John A. Kluge who facilitates this project. “After dropping the emergency ballast, the glider surfaced around 4 am on Monday, April 20 and started sending telemetry. The folks from Teledyne kept the glider on the surface and guided the researchers until they found it. This glider is OK and will continue operation. We are reading telemetry and we will soon have a better idea of what really happened.”

Halmos faculty member and primary investigator Alexander Soloviev, Ph.D. said, “An important function of the Physical Oceanography Lab is to prepare the new generation of oceanographers who are proficient with new ocean technologies. Student involvement in field projects is a way to achieve this goal.”

Halmos Researcher Chimes In On Field Research and Social Distancing

Summer is the field research season. This year, CONVID 19 has stopped the season in its tracks. For more senior academic researchers, this cancellation is disappointing, summer is the main time they get to do it. For graduate students who may only get one or two field seasons to collect all the data they need for their thesis research, the loss of a summer field season can be a disaster, adding even more trouble to an incredibly stressful time.

This month, the American Scientist published an article discussing the subject. Entitled “Data Collection During Social Distancing”, Halmos College faculty member David Kerstetter, Ph.D. was interviewed. If graduate students aren’t able to collect or analyze data, one of the main goals of graduate school isn’t achieved.

“Especially in fisheries biology, there’s a strong component of professional training that goes beyond the required graduate-level coursework, including field techniques and data analysis,” said Kerstetter. “Not having data means fewer publications, the currency of academia, which also affects future placement into doctoral programs. Not having field data collection experience would be a caution flag for any potential employee or prospective doctoral student in a position that would involve extensive fieldwork, even if that lack was due to something beyond everyone’s control.”

The article continues with giving potential solutions.

 Halmos Undergraduate Co-Author of Chronic Fatigue Journal Article

This spring, Halmos undergraduate biology major Mina Bekheit was a co-author of the publication with Dr. Lubov Nathanson from the Institute for Neuro Immune Medicine (Dr. Kiran C. Patel College of Osteopathic Medicine). The article is entitled “Unravelling myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS): Gender‐specific changes in the microRNA expression profiling in ME/CFS” and was published in the Journal of Cellular and Molecular Medicine. In addition to Mina Bekheit, who significantly assisted in the data analysis, other Halmos undergraduates worked on the project. Leah Orton and Anna Movila participated in the literature search and analysis, Kenza Schreiber and Angelica Darmenko helped with the data input and analysis. Leah, Anna, Kenza and Angelica are acknowledged in the publication.

The articles abstract states: Myalgic encephalomyelitis/chronic fatigue syndrome (ME/CFS) is a multisystem illness characterized by medically unexplained debilitating fatigue with suggested altered immunological state. Our study aimed to explore peripheral blood mononuclear cells (PBMCs) for microRNAs (miRNAs) expression in ME/CFS subjects under an exercise challenge. The findings highlight the immune response and inflammation links to differential miRNA expression in ME/CFS. The present study is particularly important in being the first to uncover the differences that exist in miRNA expression patterns in males and females with ME/CFS in response to exercise. This provides new evidence for the understanding of differential miRNA expression patterns and post‐exertional malaise in ME/CFS. We also report miRNA expression pattern differences associating with the nutritional status in individuals with ME/CFS, highlighting the effect of subjects’ metabolic state on molecular changes to be considered in clinical research within the NINDS/CDC ME/CFS Common Data Elements. The identification of gender‐based miRNAs importantly provides new insights into gender‐specific ME/CFS susceptibility and demands exploration of sex‐suited ME/CFS therapeutics.

Halmos Student and Faculty Publish Sea Grass Article in Conjunction with USGS

This spring, Halmos Graduate student Erin M. Smith, with principle investigator (PI) Amy Hirons, Ph.D., co-PIs Dimitrios Giarikos, Ph.D. and Andre Daniels published an article entitled, “Heavy Metal Accumulation in Seagrasses in Southeastern Florida” in the Journal of Marine Biology and Oceanography.

Seagrass beds are among the most ecologically important systems in the marine environment. Seagrass environments also serve as critical habitat at some point in the life cycle of many species targeted for recreational and commercial fishing, as well as a major food source in the coastal ecosystem, with over 154 marine species known to feed on living seagrass. This provides a pathway for contaminants in the seagrasses to enter the marine food web. This study assessed the heavy metal concentrations in the three main seagrass species found in southeastern Florida seagrass beds.

The results show that the seagrasses in southeastern Florida waters do contain various concentrations of heavy metals. Higher concentrations of heavy metals were found during the wet season, while Zinc in seagrasses was at significantly higher concentrations during the dry season. The research detected that heavy metals were highest in leaves with attached epiphytes. Epiphytes in marine systems are species of algae, bacteria, fungi, sponges, and any other sessile organism that grows on the surface of a plant, typically seagrasses or algae. These epiphytes on southeastern Florida seagrasses contribute to heavy metals.

Seagrass beds provide important habitat for a wide range of marine species. Especially important in south Florida is the impact these beds have on sea turtles and manatees.

Hirons and Giarikos are faculty with Halmos College. Daniels is with the U.S. Geological Survey (USGS) which is located in the NSU Center for Collaborative Research on the Fort Lauderdale/Davie campus.

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