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Announcing the Student Cohort for Undergraduate Research in Marine Biosciences Abroad (SCUBA) - Thursday, September 27, 2018
Coral reef ecosystems are endangered world-wide. Understanding the current status, trends, and prognosis of coral reef health might eventually lead to repairing damaged coral reefs. The (UT) LSAMP- STEM Pathways project offers an exciting opportunity for undergraduate students to participate in one of a number of marine bioscience field research experiences at a location in the Caribbean Sea related to coral reef ecosystems. A small group of qualified students will be selected to a.) contribute to a research project led by Midland College and the University of Texas at Arlington, or b.) design & execute their own research project (with prior approval from the SCUBA director). Preference will be given, but not limited to, qualified community college applicants. If you are ready for adventure and meet the minimum requirements (below) you should apply!

A list of the ongoing Midland College / UT-Arlington coral reef ecosystem research projects available for students to participate in are:

General assessment of the status of the coral reef’s health
Coral tissue inflammation / susceptibility to disease
Phytoplankton enumeration / characterization in ocean water.
Marine bacteria isolation / characterization (both in ocean water and in coral mucus)
Marine bacteria genetics
Coral genetic variation
Marine ion-nutrient measurements (both in ocean water and in coral mucus)
Water quality measurements (i.e. ocean water temperature, pH, dissolved oxygen, oxidation-reduction potential, conductivity, turbidity, etc.)
Marine engineering (the development of low cost, autonomous, sensors; the development of new coral health assessment tools)

More in-depth descriptions of these research projects can be found below:
Coral reefs are a diverse and complex ecosystem that impact the world’s macro environment. It is estimated that 50% of the planet’s oxygen is generated via photosynthesis within phytoplankton in the ocean. A large part of phytoplankton is within the coastal reef areas. In addition, coral reefs provide safe environments for juvenile fish to grow and other fish to reproduce. Without these environments, a large portion of the food-chain for human consumption would be disrupted. Coral themselves are the integral part of building and maintaining the reef ecosystem.
In recent decades, coral reef ecosystems have become stressed or endangered via myriad of inter-related threats: natural processes such as El Nino events and hurricanes; and man-made stresses such as industrial induced climate change, overfishing of coastal waters, and land based discharge of fertilizers & waste.

Research mentors at Midland College and UT-Arlington offer students from a wide scope of STEM majors the opportunity to expand their knowledge in their respective field of study as it is applied to the coral reef ecosystem. STEM areas of study include; Chemistry, Engineering/Physics, Computer Science, Environmental Science, Biology, Genetics, and Microbiology, A short synopsis of mentor led projects is listed below. Students will have access to multiple data sets to examine possible cross-correlations, so interdisciplinary interactions will occur.

Coral Immunity
Laura Mydlarz (Ph.D.) – University of Texas at Arlington / coral disease
(for extensive information, see the web-site: http://www.themydlarzlab.com/ )

Corals and other invertebrates must be able to defend themselves against infection, predation, competition and abiotic stressors to maintain homeostasis. Much advancement has been made on the elucidation of pathways and phenotypes involved in both resistance to, and active response to infection in corals and other reef inhabitants. We are interested in immunorecognition, signaling pathways, effector responses as well as putting immunity in the context of organismal studies, such as life-history tradeoffs and effects of the environment on immunity. See our page (link above) dedicated to Cnidarian Immunity for more information.

Specific projects - - - -

Effects of temperature on coral immunity *********************************************************************************************
The Caribbean has suffered from two unprecedented bleaching events, one in 2005 and one in 2010. We have worked on these naturally bleached corals to assess the effects of bleaching and oxidative stress on coral immunity and disease outbreaks. We have also experimentally stressed corals with temperature and pathogens recognition molecules and found supression of immunity.

Coral immunity and life history - why do corals differ in disease susceptibility? ***********************************************************
We are looking at how immunocompetence varies between species with different morphology, growth rates, reproduction and susceptibility to disease and bleaching.

Symbiodinium recognition and coral immunity*********************************************************************************************
Corals rely on a symbiotic relationship with an immotile dinoflagellate known as Symbiodinium. Using Symbiodinium cultures we are comparing the response of several types of Symbiodinium to temperature and pathogen stress. We are measuring growth rates, production and release of reactive oxygen and antioxidants as well as proteomics to look at responses.

Marine Chemistry
Thomas Ready (Ph.D.) – Midland College / Marine Chemistry

Coral & phytoplankton (algae) both depend on dissolved nutrients (i.e. Nitrate NO3-, Nitrite NO2-, Phosphate PO4-3, Bicarbonate HCO3-, Carbonate CO3-2, and others) to maintain growth and sustainability. There are complex interplays between coral and phytoplankton. On the one hand, symbiodinium algae imbed themselves in the coral tissue and assist coral acquisition and metabolism of nutrients via photosynthesis. On the other hand, phytoplankton in the ocean compete with coral for dissolved nutrients. Likewise, mature plant-like algae also compete with coral for space. In broad terms, high concentrations of nutrients tend to favor the growth of phytoplankton / algae while low concentrations tend to favor healthy coral. The concentration of these nutrients vary with depth. Students will measure the concentrations of the dissolved nutrients at different depths & within coral mucus and attempt to develop correlations between nutrient concentrations and coral health /phytoplankton biomass / coral mucus microbiota / water quality. Students will practice assay protocols during the academic year prior to the Caribbean trip on samples acquired from fresh water lakes in Texas and New Mexico as well as the Texas Coast.

Water Quality
Greg Larson (M.S.) – Midland College / Marine Environmental Science

Water quality parameters include: temperature, pH, dissolved oxygen concentration, Reduction/oxidation potential, conductivity (salinity), turbidity, current flow rate, nitrate concentration, phytoplankton biomass. Changes from the norm in any of these parameters can adversely affect both coral health and phytoplankton populations. Climate change is presumed to be actively affecting these parameters. Students will measure these water quality parameters by deploying a submersible autonomous sonde as well as custom-built sensor packages. Students will compare these measurements to the historical values in an attempt to determine trends as well as correlations between each parameter and changes in coral health / changes in phytoplankton populations / changes in dissolved or coral mucus nutrients / coral mucus microbiota.

Marine Bacteria / Genetics
Ethel Matthews (M.S.) – Midland College / Marine Microbiology
Marlana Mertens (M.S.) – Midland College / Marine Microbiology

In many higher life forms, including humans, there is a microbiota community that populates the host. The native microbiota often plays a role in the host’s ability to maintain health (ie. Human gut microbiota). Disturbances in the native microbiota or invasion of non-native bacteria can cause infection or disease. This is also the case for coral. There is a microbiota community that dwell within the mucous that is normally secreted by coral. This microbiota community is different for each species of coral and in many cases not well characterized.

Coral disease has been credited as a cause of the decline of coral reef health. Stressed coral releases mucus as a protective measure against many threats to coral health. They also secrete mucus under normal conditions to capture bacteria and other small zooplankton as food. White Plague Disease (WPD), Black Band Disease (BBD), and others have been linked to the decimation of corals in many coastal reef systems. Though the causative agent of these diseases has not been elucidated due to the variety of microbes identified in association with these diseases, Cyanobacteria has been strongly linked to BBD. It is not known if the Cyanobacteria are part of the normal flora and opportunistic, or if they are causative in the disease process. Cyanobacteria mats are found to be increased in areas where coral is on the decline. Many benthic Cyanobacteria mats (BCM) contain only Cyanobacteria where other BCM contain diverse consortia of microbes.

This particular part of the SCUBA program will use molecular techniques to show the presence of Cyanobacteria in the water surrounding the coral reef and in the mucus on diseased and healthy coral. The water, at depths of 20m, 40m, and 60m above the coral reef, were tested with Cyanobacteria specific primers for the presence of planktonic Cyanobacteria. Mucus samples collected from diseased and healthy coral, as well as visually diseased and visually healthy areas of a single coral species, will be evaluated for Cyanobacteria species.

PCR reactions using five primer sets for the 16S rDNA of Cyanobacteria have been selected from currently available literature, will possibly confirm the presence of Cyanobacteria mats in coral communities. PCR reactions using two primer sets targeting the microcystin synthase gene have selected to evaluate the possibility of microcystin toxin in the area of the coral reef.

Aside from Cyanobacteria, there is a plethora of other species of bacteria in coral mucus. It is estimated that less than 1% of the coral mucus microbiota has been able to be cultured in a laboratory setting. In this ambitious part of the science, Mathews / Mertens will lead an effort to elucidate aspects of coral microbiota populations. Students will participate in the acquisition of coral mucous from select coral species. In the Roatan Institute of Marine Science (RIMS) laboratory, the coral mucous will be 1.) inoculated onto growth media, attempting to isolate specific colonies of bacteria, 2.) isolated bacteria strains will be subjected to standard protocols to determine are gram-positive or gram-negative, 3.) Attempts will be made to extract DNA from isolated bacteria strains so that it can be sent to the U.S. for sequencing and gene bar-coding.

Terrestrial Plant Genetics
Paul Mangum (Ph.D.) – Midland College / Plant Genetics near marine environments

The coast-lines along coral reefs have a huge diversity of plant life. These plants play a role in absorbing & re-cycling nutrients that run-off of land into the waters above coral reefs. Not all of these plants have been fully characterized.
Students who participate in this project will 1.) isolate DNA from plant leaf material, 2.) use PCR on the DNA to amplify part of the ribulose-bisphosphate carboxylate gene (rbcL), Send the PCR product to GeneWiz for sequencing.

Algae Science / Genetics
Philip Lee (Ph.D.) – Midland College / Marine Genetics/Biology (specializing in algae & phytoplankton)

Phytoplankton populations are integrally connected to the overall health of the coral reef environment. Because phytoplankton use photosynthesis to process nutrients for growth, these populations decrease with depth. Students will participate in the characterization of phytoplankton in terms of overall total biomass as well as individual species populations (when possible). Species identification may involve extraction/amplification of algal DNA for transport to U.S. laboratories for sequencing and gene bar-coding and/or flow cytometry and other microscopic evaluations. Students will attempt to draw correlations with both water quality parameters / nutrient concentrations and coral health.

Additionally, since phytoplankton are primary producers at the bottom of the food chain many organisms prey on them. These organisms include viruses, bacteria, and fungi that infect or parasitize phytoplankton. Others are consumers of phytoplankton such as single celled protozoa and multicellular zooplankton. These interactions are vital in the reef environment to maintain balance in the ecosystem, but are also industrially important to understand for commercial growers of algae. Thus, populations of phytoplankton predators will also be identified microscopically and by DNA sequencing.

Marine Engineering/Physics/Mathematics/Computer Science
Brian Flowers (Ph.D.) – Midland College / Marine Engineering / Physics / Computer Science
Michael Gibbons (Ph.D.) – Midland College / Marine Engineering / Physics / Computer Science

Midland College is active in developing low cost, autonomous, in situ sensor arrays to measure a variety of water quality parameters; temperature, pH, dissolved oxygen concentration, Reduction/oxidation potential, conductivity (salinity), turbidity, current flow rate, nitrate concentration, phytoplankton biomass. Other measurements are also in the design phase. These sensors must produce both high quality data and withstand a high external hydrodynamic pressure, and a corrosive aqueous environment. Students will participate in the design/fabrication/testing of their own sensor package. This may include (Arduino / Raspberry Pi) computer programming. Testing of sensor package prototypes will take place during the academic year at fresh-water lakes in Texas and New Mexico.

The most commonly utilized method for assessing coral health is to photograph sections of the coral reef (called a transect line) and assess the health by reviewing the photographs manually. This can be laborious. There are computer programs which can assess the photographs digitally and make assessments based on mathematical algorithms. Most of these programs have deficiencies. Midland College would like to develop its own program/algorithm for assessing coral health from digital photographs. Students involved with this project would acquire the transect line data and construct computer code to interpret the photographic data.

A separate engineering project related to the transect line analysis involves the design/fabrication/testing of novel photo-grid quadrants to be utilized for the assessment of overall coral health. Current technologies (transect lines and or small photo-grids) have limitations either in dimensions of the grid or the inherent biases in grid placement. The ultimate goal for this project is to build a light-weight, collapsible, 8-meter x 8-meter grid framework that will be used in making a photographic record of reef sites. This is a daunting engineering challenge as the collapsible grid must fit on the dive boat, be transportable underwater by divers to the study site, be expandable to 64 m2 by divers underwater, float 3 feet above the reef so as not to damage the coral underneath, be retracted and delivered back to the dive boat in 40 minutes of total dive time. Testing of grid prototypes will take place during the academic year at fresh-water lakes in Texas and New Mexico.

What will your summer entail?

SCUBA Students and research mentors will spend two weeks in the summer months at a Caribbean location for field research. During these two weeks, students will: a) acquire data / samples as part of a marine science project and b) analyze the data / samples collected.

Acquiring data and samples will require scuba diving. It is anticipated that 90% of the sample/data analysis will occur at the field site.

Transportation, meals, and lodging for the field study will be provided by the SCUBA program. In addition, each student in the SCUBA cohort will receive a stipend of $2000.

Each student in the SCUBA cohort will present results from their marine science project in at least one (1) scientific conference following their summer experience. It is anticipated that this work will eventually be included in a peer-reviewed publication.

Prior to departure, SCUBA cohort students will be required to:

1) Have regular contact with the SCUBA director and their respective research mentor(s). These communications will include: internet contact via e-mail/skype; tutorials on the background science, any laboratory assays to be performed, data/sample collection, and international travel.
2) Travel to a practice dive site (at least once in Spring 2019). This event will entail two things; a check-out of the student’s competence in basic diving/safety skills* and practice on underwater maneuvers for data/sample collection with the entire SCUBA group. The cost(s) of the practice dive trip (estimated = $500) will be borne by the student’s home institution.
3) Secure a passport, secure health insurance card, secure a diver certification card, secure a secondary identification card (i.e. a driver’s license).

Minimum Qualifications for successful SCUBA candidates (at the time of departure for field research):

1) Full-time status majoring in a STEM (i.e. Science, Technology, Engineering, or Mathematics) field
2) have at least 28 college credit hours
3) have at least 16 college credit hours in science.
4) have a 3.2 GPA
5) Be certified for “open water” scuba diving (down to a 60 ft depth).
6) Be 18 years of age or older
7) Be a U.S. citizen or a permanent resident of the U.S.
8) Agree to all pre-departure requirements, especially those regarding diving certification*

*Even though the student may be certified for open water diving, it is imperative that their diving/safety skills be compatible with other divers in the SCUBA group. If diving/safety skills are deemed inadequate by the SCUBA director and Midland College staff, remedial practice may be in order. Ultimately, the SCUBA director will decide whether the student is allowed to dive with the SCUBA group.


The deadline for applications to be submitted for the Summer 2019 expedition is December 15th, 2018.
The deadline for both letters of recommendation in support of a student’s application is Jan. 1st, 2019.


Announcing the 2019 UT-System Summer Research Academy Abroad (SRA Abroad) - Thursday, September 13, 2018

If you’re interested in combining your passion for science with exploration of a new culture, you should consider applying to the 2019 SRA Abroad. Even if you don’t speak another language, your prior research knowledge and the fact that most research groups conduct their work in English means that you could have an incredible experience for your professional development and growth as a scientist or engineer.

What is the SRA Abroad?
Eight students from LSAMP partner schools will be selected for the eight-week long program that takes place abroad each summer. The students prepare to go abroad as a group through participation in a spring 2019 seminar via videoconference from their respective campuses. This seminar prepares participants for both the scientific and cultural components of the program. For the summer, students are placed in individual, independent research experiences in labs or research groups at institutions abroad. Ideally, participants are paired by location/city in order to share accommodations, although they will not necessarily be placed in the same lab or even at the same institution. The primary focus in summer will be participating in research, but students will also be required to blog about their time abroad, writing about what they’re learning both in and out of the lab. Upon their return to the U.S., SRA Abroad students will be invited to participate, all expenses paid, in the annual UT System Student Research Conference that takes place each September.

Students selected for the SRA Abroad will receive:

• A summer stipend ($4,000)
• Roundtrip international airfare
• Housing and food allowance

All applicants must meet the following requirements:

• Full-time status majoring in a STEM (i.e. Science, Technology, Engineering, or Mathematics) field
• Sophomore or junior status. Students who will graduate prior to the summer experience abroad are not eligible to apply.
• Prior UT System LSAMP research experience (must include participation for at least one summer or one full academic year).
• U.S. citizens or permanent residents of the U.S.

To apply, visit the UT System LSAMP web page at: http://lsamp.utep.edu. Applications for the SRA Abroad must be submitted on-line via the link at the above website. The application deadline is Friday, October 19, 2018.  On-line recommendation from your research supervisor is due Friday, October 26, 2018.

For more information contact Lynda Gonzales, SRA Abroad Program Coordinator, at lyndag@austin.utexas.edu or 512-232-8345.

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