Graduate and Professional Students Research Spotlight
The Research Committee of the GPSC presents the Research Spotlight, where we highlight the research carried out by one of our fellow graduate and professional students.
Want to be featured in a spotlight article? Fill out your information here! If you are interested and need more information you can contact our Research Committee Chair, Sarah Hartman, at email@example.com.
Volume 4, Issue 2
Posted: Thursday, March 2, 2017
Bassel Daher is a Research Associate at Texas A&M University’s Water-Energy-Food Nexus Research Group (since 2014), and pursuing his PhD in Water Management and Hydrologic Sciences at Texas A&M (2018). Daher’s work focuses on policy-oriented research in natural resource management, environmental sustainability, and resource security. He is particularly interested in developing Water-Energy-Food Nexus solutions that respond to biophysical, socioeconomic, governance, and financing constraints, at multiple scales, in the context of the Sustainable Development Goals. Daher also has expertise in water-energy-food nexus analytics and development of resources allocation assessment tools.
As part of his PhD, Bassel specifically focuses on three areas: 1) spatial and temporal modeling of trade-offs between competing, resource demanding, sectors, and quantifying the risks associated with “business-as-usual” growth trends; 2) modeling stakeholder behavior, interaction, interests, power dynamics, goals and values, and he uses game theory as a tool for assessing the potential and feasibility of different case-specific resource allocation problems; and 3) He is also interested in examining different governance structures and financing mechanisms that would be suitable for mobilizing “resource nexus solutions” at different scales.
He was most recently selected as one of 8 young water professionals globally to serve on the Young Scientific Committee for the 2016 Stockholm World Water Week. Daher has contributed to multiple chapters of the UN Global Sustainable Development Report, co-authored a report on “Renewable Energy and the Water, Energy, and Food Nexus” for the International Renewable Energy Agency (IRENA), and has multiple other journal articles, book chapters, and policy briefs relating to the interconnected water-energy-food securities and nexus assessment tools, including with Chatham House and Water International. Bassel is currently serving as the President of the Biological and Agricultural Engineering Graduate Student Association. He is also a member of the Legislative Committee of the Graduate and Professional Student Association.
Daher holds a B.Sc. in Civil and Environmental Engineering from the American University of Beirut (2010), and an MSE (2012) from Purdue University, Biological and Agricultural Engineering-Multi-Scale Hydrology Group. He was a Research Associate (2012-2014) with the Qatar Environment and Energy Research Institute, Doha.
Volume 4, Issue 1
Posted: Thursday, February 16, 2017
I am Mahdi Imani, a third year PhD student in department of Electrical and Computer Engineering, working under supervision of Dr. Ulisses Braga-Neto.
My research is focused on estimation and control of stochastic Boolean dynamical systems, with applications in genomic signal processing. Transcriptional regulatory circuits, also known as gene regulatory networks, govern the functioning of key cellular processes, such as the cell cycle, stress response, and DNA repair. In rational drug design, the objective is to determine optimal strategies for intervention into gene regulatory networks, which can shift the long-term behavior of cellular processes from malignant outcomes to benign ones, at the minimum possible risk to the patient.
Developing effective therapies require understanding the nature of cellular function and behavior of gene activities and interactions. It is often the case that the transcriptional state of each gene is represented by 0 (OFF) or 1 (ON), and the relationship among genes is described by logical gates updated at discrete time intervals. Accordingly, gene regulatory networks are modeled using partially-observed Boolean dynamical systems (POBDS), a class of models developed by our research group, which allow for uncertainty in state transition due to unmodeled system components as well as measurement noise. This mathematical modeling goes beyond most of the existing work by allowing gene states to be observed through noisy measurements, such as next-generation sequencing technologies for transcriptomics, also known as RNA-Seq.
My research can be divided into two main categories. The first category is estimation and filtering. I developed the optimal estimator of the transcriptional state of genes through noisy measurements, called the Boolean Kalman Smoother. Furthermore, I developed adaptive filters for estimating genes’ expression state simultaneously with the inference of the network topology and noise and expression parameters. My current research in this area is to design more efficient and practical filters to enable filtering and inference of large gene regulatory networks based on particle filters.
The second category is the optimal control of gene regulatory networks. In my latest publications, I discussed preliminary attempts to design appropriate intervention strategies to alter network dynamics beneficially, using time series data produced by next-generation sequencing technologies for transcriptomics. The goal of control is to shift the steady-state mass from undesirable cell transcriptional states, such as cell proliferation states that may be associated with cancer, to desirable states. My current research focuses on designing robust and efficient controllers to control the behavior of large gene regulatory networks, to have beneficial impact on translational medicine, drug design, and cancer treatment.
For more information about my research, visit http://people.tamu.edu/~m.imani88/.
Volume 3, Issue 6
John P John
Posted: Thursday, December 1, 2016
John P John is a doctoral student in Department of Aerospace Engineering under the mentorship of Dr. Diego Donzis. Dr. Donzis and his team at The Turbulence and Advanced Computations Laboratory (TACL), works on understanding fundamental issues in turbulence and turbulent mixing using massively parallel simulations of turbulent flows. In this issue of Research Spotlight, John writes about researchers’ fascination towards turbulence and his team’s contribution towards furthering the body of knowledge in this field.
Ever imagined the blood flow inside your heart, combustion process inside your car, air flow over an Air bus A380, the waves in an ocean, and formation of stars in an interstellar medium? All these have one feature in common; they are all turbulent in nature. Turbulence is ubiquitous and is part of our daily life. Yet, surprisingly, our knowledge is still very limited. We know about the fascination for turbulence as a phenomenon worth to be studied from early 1500, when Leonardo da Vinci described turbulent flow patterns in one of his illustrations. Nevertheless, the field of turbulence failed to keep up pace with the other fields of science. This lack of progress in the field of turbulence has left the scientific community visibly frustrated.
Analyzing turbulence is not straightforward because it is governed by a set of 4-coupled partial differential equations known as Navier-Stokes (N-S) equations. Although N-S are deterministic in nature, its extreme sensitivity to initial conditions and boundary conditions make the phenomena of turbulence unpredictable in any deterministic way. These equations appear impenetrable to existing analytical techniques in mathematics. However the past few decades have witnessed tremendous increase in computing power. At TACL, we utilize this great advancement to mitigate the above limitations by solving N-S numerically using Direct Numerical Simulation (DNS) for idealistic flow conditions without any simplifications. These cutting edge tools help gain insights into phenomenon of turbulence.
DNS of turbulence by itself is challenging since turbulence is a multi-scale phenomenon and thus subjected to stringent resolution requirements. Turbulent flow exhibit a wide range of scales of motion which increases when Reynolds number (Re) increases or when turbulence in the flow increases. As a result the domain of the numerical model has to be greater than the largest scale involved and the grid size small enough to capture the smallest scales of motion. Thus most engineering codes used in industry for designing airplanes, gas turbines etc. do not simulate turbulence directly, but incorporate it’s effects based on empirical models and fundamental knowledge of turbulence. The DNS codes and simulations developed at TACL for idealized turbulence are used to gain insights and improve these engineering models.
The first objective of our research is to improve our physical understanding of turbulence. We use state of the art numerical techniques to solve N-S on the most powerful and fastest supercomputer platforms available today and analyze the results using advanced stochastic and visualization tools. The results are then combined with theory to answer some of the fundamental questions like universality, intermittency of turbulent flows and validate phenomenological theories (not derived directly from N-S), which are experimentally difficult to validate. Turbulence being ubiquitous interacts with other phenomena such as compressibilty, shocks,gravity, rotation of earth, electromagnetic fields etc.compressibility, shocks, gravity, rotation of earth, electro-magnetic fields etc. We study how turbulence modifies them and vice-versa. Some of our work includes the study of incompressible and compressible mixing which is important in combustion science and dispersion of particles in atmosphere. Another area of research is shock-turbulence interactions which are important in high speed flows generally observed in supersonic jets and scram jet combustion. We also have done research on interaction of turbulence with thermodynamic non-equilibrium, which has applications in hypersonic flights and reentry problems. Someof our work includes the study of incompressible and compressible mixing which is important in combustion science and dispersion of particles in atmosphere. Another area of research is shock-turbulence interactions which are important in high speed flows generally observed in supersonic jets and scram jet combustion. We also have done research on interaction of turbulence with thermodynamic non equilibrium which has applications in hypersonic flights and reentry problems.
A second objective of our research in TACL is to develop numerical algorithms for faster and accurate turbulence simulations. Over the years Dr Donzis and his group have developed highly portable and scalable hybrid code for simulating turbulence using MPI and OpenMP which can scale of the O(10^5) processors. One of the major bottlenecks in current algorithms that limits scalability is the time taken to share data between processors. Our group is developing a novel scheme based on asynchronous algorithms which avoids or delays the communication time between processors and decreasing the errors due to this delay. The project is still in this incipient stage where it is tested on simpler equations like the wave and diffusion equations. However the final aim is to develop such schemes for solving N-S. The outcomes or findings can be applied not only to turbulence simulation but for scientific computing as a whole.
Thus our research aims to satisfy an intellectual curiosity by understanding one of the most extraordinarily difficult topics in science. Moreover we believe this understanding can be used to improve current technologies or develop new ones like faster hypersonic flights in the future.
Volume 3, Issue 5
Posted: Thursday, November 10, 2016
Cheng Qian is a third year PhD student at Department of Electrical and Computer Engineering. Working in Dr. Mladen Kezunovic’s team at Smart Grid Center, he is delving into one of the most fundamental research efforts in modern Smart Grid: sensing and observation.
Electricity is what people tend to take for granted. And yet, the power grid is undergoing constant disturbances: whether they are local or wide-area, swift or prolonged, temporary or permanent, natural causes or malicious attacks. How to prevent outages has always been of utmost importance for power grid researchers. Over the course of over a hundred years, the power grid is steadily evolving to become more robust, resilient, and reliable. Most recently, the electric power grid is embracing a revolution from traditional power grid to “smart grid”.
The intelligence of smart grid is empowered by integrating intercommunication among generation, transmission, distribution, and consumption systems. This intercommunication is predominantly based on the data source from advanced sensing, observation, and measurement infrastructures, which is what Cheng is currently working on. With advanced sensing and timing technologies, snapshots of the power grid with higher accuracy and resolution can be acquired at a much higher rate and lower latency. It is apt to say, they are trying to take MRIs of the power grid at a pace faster enough to capture and track what the power grid is currently experiencing, so that appropriate control schemes can be applied to guarantee stability and prevent. The power system signals are sine waves infiltrated by a wide spectrum of harmonics, resulting from power system dynamics and fluctuations. How to extract useful information that represents power system states from noisy, distorted and contaminated raw samples, and more importantly, how to transform ideas and thoughts into concrete implementations that can actually be beneficial to people’s lives, are the essential topics of his research.
Like many other graduate students engaging in smart grid research, he is fascinated by the great potential of smart grid, and values working with researchers from diverse disciplinary backgrounds. Thanks to the cooperation with industry advisors and the excellent research resources in Dr. Kezunovic’s lab, Cheng enjoys doing research at Texas A&M University.
Volume 3, Issue 4
Posted: Monday, October 31, 2016
Kristen Hicks is a fourth year doctoral student in Nutrition, working with Dr. Peter Murano, in the Department of Nutrition and Food Science. Her research interest focuses on educating physicians about nutrition basics along with providing a practical approach and tools to incorporate nutrition counseling with patients. In a country where over two-thirds are overweight or obese along with a majority of the leading causes of death are attributed to nutrition, there is a clear need for nutrition intervention.
When Kristen came to Texas A&M University, she began working for Dr. Nancy Turner in the department, focusing on the dietary impact on gut microbiota and colon health. As a Registered Dietitian in Texas, she craved a research focus geared towards translational medicine and specifically a focus with direct impact on patient healthcare and delivery. After two years in her initial lab, she made the tough decision to transition into a new advisor, Dr. Peter Murano, to focus on research that had an education approach for teaching healthcare professionals. A former student in Dr. Murano’s lab, Laurie Shroads, had developed nutrition education courses for medical students attending Texas A&M University Medical School. Kristen had interest in expanding this research idea to be focused on physicians, the healthcare professional actively assisting patients. A unique concept of these courses is also to embrace the healthcare team approach, by encouraging physicians to refer patients to a Registered Dietitian for long term nutrition support. As a practicing Registered Dietitian, this research topic “hit home”. This research was both a personal and professional interest to increase nutrition education for physicians, a key component to the healthcare team. Kristen is paving an innovative path, create online continuing medical education (CME) courses. Physicians are required to complete CME’s annually, her accredited programs meet the standards to be counted for credit.
Kristen currently has two continuing education courses on both the Texas Medical Association’s education library and the Texas A&M University College of Medicine faculty education library. She plans to continue to expand these courses at the state level, to encourage physicians to increase education specific to nutrition and counseling with patients. Long term, she plans to create additional courses for physicians along with other healthcare staff to encompass the entire healthcare team approach when educating patients. Physicians are strapped for time and have a large patient load, requesting them to counsel patients on nutrition has been an obstacle in the way for decades. Yet with our American people at the highest level of chronic disease- the need for intervention has never been greater. Her objective is to find ways to improve the education offerings for all healthcare professionals, so the wellbeing of the population can return to a healthy state.
Volume 3, Issue 3
Posted: Thursday, October 20, 2016
Xun He is a fifth year Ph.D. candidate in the Department of Chemistry. Being impressed by how polymers improve the lives of human beings and how material science changes the world, he joined Prof. Karen L. Wooley’s lab and performed research on smart polymeric materials.
Xun is working on new approaches to print conductive materials that can be recycled and reprocessed. The sales of printable electronics has exceeded $23 billion in 2014, with a prediction of ca. 20% growth rates annually. Nevertheless, few efforts have been made towards the development of rewritable, repairable, or recyclable conductive materials, which may shape the future of green and smart electronics.
The challenges that need to be overcome include the development of new reversible surface patterning techniques, and processes to allow these techniques to be combined with conductive materials. Traditionally, a common practice to produce patterns with high spatiotemporal sensitivity and resolution is photo-patterning, which, however, has been challenging to print reprocessable and rewritable conductive materials, as the printing process typically relies on irreversible, and thus Ôdead’ reactions. “In order to address the above two challenges while taking advantage of photo-patterning, we need to have a smart design of materials on a molecular scale,” said Xun. “As members of Prof. Karen Wooley’s lab, we have been trained to synthesize polymers in a creative way to afford unique macromolecular structures and functionalities, from which we can deliver special properties and applications.
The interesting and exciting part of this research is the synergistic effect of two simple components to achieve a complicated process. “We made the polymers and conductive carbon nanotubes help each other to achieve photo-patterning,” said Xun. In this design, it was expected that a cascading series of events would occur, by which photo-thermal carbon nanotubes would absorb light and generate heat, to be absorbed by thermo-responsive hydrogelators, resulting in a triggered supramolecular assembly process and affording conductive, patterned, and flexible materials. Another advantage of this system is the facile and rapid curing into desired patterns with the potential to take advantage of the modern photo stereolithographic technologies, without the requirement of a pre-treated substrate or a specific irradiation wavelength. In addition, because the patterning is based on supramolecular assembly, which does not involve conversion of chemical bonds, the conductive patterns can be recycled due to the unique polymer property.
Based upon this new strategy, a broad scope of applications can be anticipated, including patternable and flexible conductive materials with various dimensions, injectable and near IR curable hydrogels for bioelectronics or tissue engineering, and 3D printing materials for permanent or temporary layers. A patent application has been filed and a paper has been published as Chemical Communications 2016, 52, 8455-8458. Xun said, “we would love to see the translation of this new design and platform into industrial production, or the development of a better system motivated by our idea, to deliver useful materials that serve society.”
Volume 3, Issue 2
Posted: Thursday, September 29, 2016
In this issue, the graduate student from the Geography Department, Trey Murphy wrote a narrative about his project:
I struggle to consider a more dangerous journey than traveling through an active oil and gas boom. During my first trip to the Eagle Ford Shale—one of the most productive oil and gas plays in the United States—in summer 2014, I was constantly jerking the steering wheel to evade the incessant stream of 18-wheelers lurching into oncoming traffic to pass me and whose drivers were ready to make nearly any sacrifice to get their laded trailers to the destinations on schedule. Their immense bravery was only matched by my immeasurable fear. Emotionally wrecked after several hours of driving, I pulled into a rest stop and decided to learn more about the Eagle Ford. It was in that Texas Monthly article that I read about a giddy “elderly rancher who walked into the bank, very pleased to be depositing a $100,000 [mineral lease] signing-bonus check, only to be pulled aside by the teller” and told that he was actually depositing a million dollar check. At that moment, I realized what the Eagle Ford Shale meant to the people of South Texas: an imagined opportunity to break from the risky, agriculturally based lifestyles of the past. But when I looked out the window at the speeding big-rigs, I wondered to myself where that money was actually going? Yes, some economic benefits were chasing those heedless truck drivers. And, at least according to some of the locals, there really were Jed Clampett-style stories of impoverished ranchers overwhelmed by their first mineral royalty checks. But there had to be more to this story. It was evident that the economic benefits were not evenly distributed across the rugged South Texas landscape.
Therefore, this part of my master’s research asked who are the main economic recipients of oil and gas royalties in the Eagle Ford Shale? This research question was difficult to answer, because there were no known published records on mineral wealth ownership dynamics, short of examining courthouse deed records or surveying mineral wealth owners— an approach unlikely to generate a useful response rate because of the confidential nature of mineral leases between the mineral owner and the company drilling the oil well. So, instead my co-collaborators and I decided to inspect publically available county tax appraisal records.
Our results were very surprising. Using data from a representative county in the Eagle Ford Shale (Live Oak County), we established that 96% of assessed mineral wealth concentrates mostly among energy firms and individuals in Texas metropolitan regions; 1.95% of mineral wealth remains “local” to the production county, challenging the common notion that the wealth produced from oil wells actually remain local to the site of production.
This research demonstrates how little we know about mineral ownership the United States. This was a study of a single county on the Eagle Ford Shale in South Texas. While the results are certainly important, we need to capitalize off of the methods and findings from this study to advance our knowledge of mineral wealth ownership across Texas and the United States. The U.S. is unique in that individuals, and not the government, owns the mineral wealth in many regions, but we know amazingly little about those mineral owners—especially since subsurface mineral estates can be so easily severed from the surface property and treated as distinct assets able to be bought and sold like any other property. Are mineral owners local landowners or do they live far away? Is the wealth held mostly by companies or by individuals? If a mineral owner or lessee does not live in the region, do they still have a positive economic impact in that locality? All of these questions and their associated answers will be important in determining how subsurface mineral properties function in the U.S.
Volume 3, Issue 1
Posted: Thursday, September 15, 2016
Grace Rivera is a second year graduate student working under the advisement of Dr. Rebecca Schlegel in the Psychology Department (in the area of Social and Personality Psychology) at Texas A&M University. Her research interests span a variety of literatures, including identity stereotypes, intergroup relations, self-knowledge, and psychological well-being. She is particularly interested in investigating how social and situational factors affect individuals who belong to stigmatised groups across various outcomes, including academic achievement and psychological well-being.
Recently, I worked on a project that examined factors predicting college student attrition within an access opportunity program, and received GPSC Travel Funding to present this research at the ACPA Conference in Montreal, Canada. This study was conducted in collaboration with Dr. Monica Schneider (SUNY Geneseo) and examined factors such as first generation status, socioeconomic status, and ethnicity/racial group as predictors of graduation and self-reported reasons for leaving college. We found evidence that suggests that minority and first generation students in AOP programs are more likely to leave college due to compounded effects of academic, family, and financial issues than their Caucasian or non-first generation peers. This suggests that resources and advisement geared towards managing challenges that occur simultaneously might be particularly beneficial for minority or first generation students, rather than treating each challenge as a separate issue.
Currently, I am working with Dr. Rebecca Schlegel (TAMU) and Dr. Phia Salter (TAMU) on a line of research that examines how our preferences for different messages about social inequalities shift as a function of situational factors, such as the race of a speaker espousing the message and the race of the audience receiving the message. With growing attention in the media around issues of race, social inequalities, and prejudice, people often turn to one of two explanations for why and how social inequalities exist. The first of these explanations blames the individual and calls for increased personal responsibility, while the second blames the system and calls for increased social responsibility (Feagin, 1972; Jones, 1991). I am particularly interested in examining endorsement of these explanations within the context of education, since education is historically entrenched in meritocratic philosophy (Meroe, 2014; Mijs, 2016) despite evidence that disparities in resource access and availability exist (Flores, 2007; Morgan, 2016).
In addition to wanting to understand how preferences for these different explanations change as a function of the race of the speaker and audience, I am interested in how these preferences relate to actual hiring decisions. Personal responsibility narratives in education suggest that if a student simply works hard and takes ownership of their education they will succeed, without acknowledging that not all students have access to the same opportunities and resources. Are we more likely to hire teachers who espouse personal responsibility narratives at the cost of teachers who cite the need for social responsibility? Additionally, since past research suggests that Black individuals who discuss discrimination incur social costs (Kaiser & Miller, 2001), we are also interested in testing whether people particularly dislike the social responsibility message if it is coming from Black teachers as opposed to White teachers.
As racial tensions in America continue to garner national attention, it becomes increasingly important to research the complex ways that race and identity play a role in the context of education. My goal in pursuing this type of research is to help find ways to make educational environments as supportive as possible, so that every person’s unique identity can be viewed as the value-adding factor it is, rather than a reason for division – so that everyone can have access to opportunity and success.
Volume 2, Issue 10
Sayyeda Marziya Hasan
Posted: Tuesday, May 3, 2016
Sayyeda Hasan is a doctoral student in the Department of Biomedical Engineering. She works in Dr. Duncan J. Maitland’s laboratory. She was one of the finalists for the 2015-2016 Texas A&M University 3 Minute Thesis Competition. Her 3MT title was “Self-Expanding Foams for Brain Aneurysm Treatment.” You can view her presentation on the OGAPS website.
Imagine you are going about your day and suddenly, you feel an intense pain running from your head to your spine. You immediately throw up. Your head is pounding with pain. 30 seconds later your face becomes numb and you lose hearing in your left ear. Before you can realize what is happening, you lose consciousness.
The scenario I just described is a typical brain aneurysm rupture and there’s a 30% chance that you may not wake up again. An aneurysm is a ballooning of the blood vessel, which affects about 6 million people in the United States. Often times, people are not even aware that they have an aneurysm. Each year, 30,000 people will experience an aneurysm rupture. This means that there is an aneurysm bleed once every 18 minutes. The key is to catch and treat an aneurysm before it ruptures to prevent internal bleeding into the brain, which can cause permanent brain damage or even death. My research consists of collaborating with a team of doctors and engineers to develop a new device that will treat the aneurysm through a minimally invasive surgical procedure.
We have developed a self-expanding foam that can be delivered to the aneurysm through a small delivery tube where it will expand to fill the sac, form a clot, and reinstate normal use of the blood vessel. Our foams have a far superior short and long term healing response compared to other treatment products in the market today.
My research, specifically, is to design the foams to have controllable expansion times. Ideally, the foam can be molded into a small shape, the size of a pencil lead, but when exposed to heat, such as body heat in our case, the foam will rapidly expand to the size of a marble. If the expansion time is too low then the foams open too quickly and become stuck in the delivery tube. This is a significant hurdle for device development, which my thesis addressed.
My work focused on changing the base chemistry to tailor the expansion time of the foams. This chemical optimization allowed me to control the expansion time of the foams so that they could be delivered to various parts of the body. Through this approach, I was able to develop a self-expanding foam that the surgeon could now easily deliver to the aneurysm without the foam opening too quickly and getting stuck in the delivery tube.
This means that our loved ones, who may one day need to get an aneurysm treated, will have this smart technology available for a safe and effective treatment. Our devices may save thousands of lives by treating brain aneurysms and eliminate the horrifying reality of an unexpected rupture.
Volume 2, Issue 9
Posted: Thursday, April 28, 2016
Huinan Li is a fifth year Ph.D student in the Department of Biology in Dr. Mark Harlow’s lab.
Synaptic transmission enables neurons to communicate with each other in the brain, as well as the communication between neurons and muscles cells all over our body. When this process is disrupted or compromised, at any cellular level or molecular level, neurological diseases will happen – for the brain, there are Alzheimer’s Disease, Parkinson’s Disease, Autism Spectrum Disorder, the list goes on and on; for peripheral nervous system, there are neuromuscular dystrophy and myasthenia gravis. Although scientists have been working on these neurological diseases for decades, there is still no cure for all of them. One main reason is that it is actually not even fully understood how normal neurons communicate and maintain their functions, so there is no reference to see what goes wrong in neurological diseases. My research focus is to understand how normal synaptic transmission works at cellular and molecular level.
Working in the neurobiology field, trying to understand how synaptic transmission happens at the cellular and molecular level is fascinating. It is a relatively new field. With the recent advancement of modern techniques, we are able to address more questions than ever. Working in Dr. Mark Harlow’s Lab, we seek to understand an essential component during the synaptic transmission process, called synaptic vesicles. They are subcellular organelles trafficking inside the neurons containing neurotransmitters. The interesting and exciting part of my research is that over the last five years, we have made significant discoveries about synaptic vesicles, neither of which were ever thought or imagined before. These discoveries will impact how we think about synaptic transmission; therefore, more things are taken into consideration when treating any neurological diseases. It has been assumed that each synaptic vesicle has one and only one neurotransmitter transporter, and therefore all the drugs probably only doses against one or two transporters, but we have demonstrated and published that actually, there are more than one, and furthermore, there are at least four different kinds of neurotransmitter transporters on each individual synaptic vesicle. So now you can imagine why most of the drugs don’t work well, because either dosage is not high enough, or there should be more than one type of drug in the pills. Furthermore, it is widely accepted, even dogmatic that synaptic vesicles contain and release neurotransmitters, and seemingly only release neurotransmitters.
In our lab, yet again, we have successfully demonstrated that there are small RNA molecules inside as well. Now you see how many more things we simplified and how much more we have to keep on learning. This discovery was published in the prestigious Nature Publishing Group member – Scientific Reports recently. Because of our discovery, people now cannot ignore the fact that small RNAs may play an essential role during synaptic transmission. During neurological diseases, is it possible that those released RNAs are made, packed or released wrong? Why are they there in the first place? This very discovery of mine has been selected for a talk in the past 45th International Society for Neuroscience Annual Conference, and received many positive feedbacks.
I enjoy the feeling of discovering new mechanisms in neurons and thus eventually help us to understand our brains. Just imagining someone else feeling enlightened after reading my paper gives me goosebumps. A better understanding of normal synaptic transmission will help to explain what has gone wrong in the disease state. However, we do have a long way to go to gain full understanding of our intricate brain, as there are so many signaling pathways maintaining the normal functioning of our brain. And there are many limitations of the tools available, not to mention we cannot easily use human brains to do experiments. So we have to make the most of model organisms including mice, flies and worms. But I am hopeful that in the near future, we will understand so much that we can come up with better treatment of every single neurodegenerative diseases. To diagnose, then to treat them.
Volume 2, Issue 8
Ian W. Smith
Posted: Thursday, April 21, 2016
Ian Smith is a third year Neuroscience Ph.D. student at the Texas A&M Institute for Neuroscience (TAMIN). Ian works in the Neuromuscular Laboratory of Dr. Wesley J. Thompson. Dr. Thompson is appointed as a Distinguished Faculty in TAMIN as well as the Department of Biology. Research in Dr. Thompson’s lab covers a wide range of neuromuscular-related questions, from how synaptic connections are formed between motor neurons and muscle during mammalian development to how these synapses break down and degenerate in old age.
Ian studies how synapses between motor neurons and muscle fibers (Neuromuscular Junctions) are formed and refined during development. Specifically, his research project is aimed at understanding the process by which neuromuscular synapses form, focusing on a particular period of early development commonly referred to as synapses elimination. “It’s very interesting, at birth there are multiple motor neurons making synaptic connections with the same muscle fiber, but by the time the synapse is mature all but one of those neurons have been lost from the muscle. It boils down to a competitive process, where only the correct motor neuron will remain to synapse onto the muscle fiber, a survival of the “fittest” so to speak,” said Ian. In order to examine this process of elimination and competition, Ian utilizes a variety of techniques aimed at identifying the key factors in the process of neuromuscular synapse formation including; immunohistochemistry, wide field light microscopy, confocal microscopy, and especially serial transmission electron microscopy.
As the fundamental unit of neuromuscular transmission the NMJ is vital to proper functioning in daily life, as many neuromuscular diseases are the result of improper synapse assembly. Thus, elucidating the molecular and cellular interactions responsible for proper synapse development will provide a, “…Blue-print of sorts for understanding how normal development proceeds, allowing us to identify what factors specifically run awry in different disease models.”, says Smith. As such, Ian’s work complements that of others in his lab focused on aspects of aging and disease at the neuromuscular junction. A more complete understanding of the phenomenon known as synapse elimination would contribute greatly to the field of synapse development and in doing so will help us understand neuromuscular pathologies that are often associated with developmental abnormalities at the NMJ such as various muscular dystrophies, myasthenia gravis and spinal muscular atrophy.
When asked about why he chose to work in this field, Ian says, “I remember being fascinated with the nervous system after taking my first undergraduate course in neuroscience and immediately searching for a lab to work in on campus. My background in athletics and biology are probably what sparked my interest in neuromuscular systems initially.” Ian’s passion for life and science are evident when speaking with him and the high quality of his research is clear from viewing his publication record and CV. As a third year student Ian has been an author on three publications with a fourth in the works, and his work has not gone unnoticed as he has compiled an impressive list of awards including a 3rd place finish in an international scientific imaging-excellence competition last year.
Although Ian’s career as a scientist has started in impressive fashion, his greatest contributions may extend beyond the laboratory. In his time at Texas A&M Ian has gone above and beyond to serve and contribute to others on campus. His commitment is clear when considering the various positions he has held: Representative Society for Neuroscience- Texas A&M Chapter, Student Body President for TAMIN, and Neuroscience Delegate for Graduate and Professional Student Council. Despite holding all of these positions, Ian is most proud of his work in founding an original student organization on campus, Students for Advancing Neuroscience Discovery and Innovation (SANDI). When asked about SANDI, Smith says, “I wanted to create an organization that was focused on bringing the students within the realm of neuroscience together in order to promote interdisciplinary collaboration, peer support, professional development and community service.” SANDI membership is open to undergraduates, graduates and faculty/staff, for more information please visit https://stuactonline.tamu.edu/app/organization/profile/public/id/1702.
For more information on Ian’s research in the Thompson lab and neuroscience research here at Texas A&M, visit http://tamin.tamu.edu.
Volume 2, Issue 7
Posted: Thursday, April 14, 2016
Haley Harwell is a sixth year Economics Ph.D. student at Texas A&M University. She is an experimental economist using lab and field experiments to study cooperation and pro-social behavior. Her adviser is Dr. Catherine Eckel. Dr. Eckel is the Sarah and John Lindsey Professor in Liberal Arts as well as the director of the Behavioral Economics and Policy Program (BEPP) at Texas A&M University.
Haley’s research is shaped by human behavior and economic decision-making. Behavior is shaped both by individual preferences and social norms, and these two factors are present in her research. The specific topic areas she addresses include public goods, trust, and charitable giving in the lab; and risk sharing and variation in risk-sharing norms in the field. One research project observes the effects of successful fundraising campaigns on individuals’ philanthropic behavior. In her paper “Did the Ice Bucket Challenge Drain the Philanthropic Reservoir?” she uses a controlled lab experiment to investigate the source of funds that are raised in successful campaigns. Ultimately, she asks in particular whether new funds are raised, or if individuals instead merely redirect funds from contributions to other organizations. The results show that a successful campaign increases funds raised by the charity. However, the increase in giving to the target charity comes entirely at the expense of the other charities. “This paper highlights my interest in using lab experiments to test important policy-related questions,” said Haley.
Another avenue of Haley’s research uses lab experiments run in the field on average adults. This research examines the impact that formal financial institutions have on informal networks of risk sharing. Individuals in developing countries as well as poor urban areas in developed countries use alternatives to formal market options to insure and overcome possible poor outcomes. These individuals assist each other when a bad outcome happens to a member of their group. They share their own resources allowing the unlucky individual to obtain a better outcome; much like insurance offers individuals in formal financial institutions.
Recently Haley received her first publication in a journal. This paper is a replication of four classic public goods experiments, and is published recently in Research in Experimental Economics. This work replicates four highly-cited studies in the provision of public goods, using procedures as close as possible to the original studies. The results show patterns that are similar to the original studies, but with smaller treatment effects in all cases. We observe a pronounced “Texas effect” with higher contributions and less free riding than in the original studies. This research contributes to the discussion of the influence of unobserved heterogeneity in institutional lab environments.
Haley has recently accepted a job at the University of Richmond in the Jepson School of Leadership Studies. “I am looking forward to moving to Richmond, and teaching undergraduates about experimental and behavioral economics,” she said.
Volume 2, Issue 6
Posted: Thursday, April 7, 2016
“Birds have always interested me and I knew I would like to work with them when I grew up,” says Zaria Torres, a sixth year PhD student in the Department of Wildlife Fisheries Sciences at Texas A&M University. After completing her Bachelor’s in Biomedical Science at Texas A&M, she moved on to graduate school to pursue her long-cherished passion.
Zaria is studying ecotoxicology, which can be defined as “studying the effects of toxic substances and especially pollutants on the environment”. She also studies stable isotope ecology (trace details of element cycling in the environment). She is currently working in Dr. Miguel Mora’s lab at Texas A&M University. She chose this particular lab as it would give her the opportunity to go out into the field for sample collection and getting the chance to handle birds. Moreover, “ecotoxicology and stable isotope ecology are both diverse fields that have not yet bored me,” she adds. During her PhD program, Zaria worked on two different projects. For her first project, she studied the likeliness of American white pelicans acquiring mercury from their wintering grounds in Lake Chapala, which is the largest freshwater lake in Mexico. For her second project, she studied ‘Attwater’s prairie chicken’, an endangered species of bird found in Texas.
While giving more details about her work, Zaria says, “The most interesting part of my project would be studying an endangered species of bird, Attwater’s prairie chicken, which once ranged all along the coast of Texas and Louisiana. For this project I analyzed the bird’s feathers and blood, and then compared those values to their diet which consists of plants and insects. My job is to see what type of plants or insects they prefer to eat once they are released onto the wild by using stable isotopes carbon and nitrogen. I also collected museum feather samples and compared them to recently collected samples. With this information I will be able to see if the past birds’ diet is different from those today.”
Zaria’s research aims at finding if the Attwater’s prairie chicken’s current diet is a contributing factor to its population decline. She explains, “A big problem this bird is facing in the wild is that their chicks are not surviving to adulthood. We think that the mothers are not getting the proper nutrition to have healthy young, and we are doing this diet study to determine whether this is true or not.”
Zaria faced many obstacles with data collection. When asked about the hurdles of sampling in the wild, she explains, “Being in wildlife you are at the mercy of the environment your field collection takes place. For instance, I tried collecting insects and plants during certain times of the year, but I would come up short a few times. Winter turns out to be not a good time for insect collection, so sometimes I only came back with plant samples. Also, on my last day of field work they decided to do prescribed burning on one of my collection sites, hence I could not go and collect since the whole field was on fire. You just learn how to deal with the unexpected as a wildlife scientist.”
If Zaria’s work finds the relationship between the bird’s diet and its declining population, the findings could potentially help aid in the population recovery of this endangered species. For further details please visit: http://agrilife.org/ecotoxicology/
Volume 2, Issue 5
Posted: Thursday, March 31, 2016
Joseph Modarelli is a second year Genetics PhD student who had has a passion for diagnostics. He spent his undergraduate years studying Lyme disease, a tick-borne disease. It is one of the most well-known tick-borne disease, though there are several other organisms carried by ticks which infect animals and people. Working with the TVMDL (Texas A&M Veterinary Medical Diagnostics Laboratory) through undergrad, he began to see the big picture: how prevalent these diseases are, yet unnoticed, and so wanted to play a role in uncovering them.
What has been most interesting for Joseph in this field is how genetically similar these tick-borne diseases are, yet how many different ways they can make people and animals feel sick! Genetically speaking, small variations in an organism’s DNA can produce large changes in how they behave in nature. In the case of a particular tick-borne disease, a few DNA alterations have resulted in bacteria that become “invisible” to your immune system.
Joseph is interested in Tick-Borne Relapsing Fever (TBRF) is a condition caused by a type of bacteria that in essence uses multiple disguises against our immune system. Initially, our immune system focuses on the most obvious disguise of the bacteria and eliminates it. Meanwhile, other forms are growing in the background without being targeted to die. Thus, a relapsing effect occurs when the bacteria continually takes on a different appearance to confuse the body.
Joseph told us that some of the obstacles in his field are that molecular diagnostics rely heavily on ongoing surveillance efforts as bacteria adapt to various environments. These adaptations come from small changes in their DNA, and require continued modification of current testing methods to maintain effectiveness. This makes surveillance studies vital to keeping the field of diagnostics current with the most accurate testing methods.
Joseph hopes to contribute to the field of diagnostics with more efficient approaches and cheaper tests. Currently, he is developing a test to detect TBRF and other bacteria in a clinical veterinary environment. As current diagnostic tests for TBRF are limited by its relapsing effect, Joseph says our only best option is to tackle this problem genetically by designing a test that detects the presence of the organism’s DNA in individual patients. Joseph’s main focus is utilizing genetic tools to detect multiple diseases carried by ticks at one time and within a single sample from a patient. This will hopefully lower costs associated with testing, reducing the costs and financial burden on the client. Additionally, Joseph’s research aims to give us a better understanding of these diseases within our state.
The more ticks Joseph and his team finds or receives, the better.
If you find a tick on your animal please reach out to the TAMU Lyme Lab http://vetmed.tamu.edu/labs/lyme-lab, or think they are suffering from a tick-borne disease, please refer to the TVMDL for testing options. http://tvmdl.tamu.edu./
Volume 2, Issue 4
Posted: Thursday, March 24, 2016
Payman Dehghanian is a 4th year PhD student at the Department of Electrical and Computer Engineering at Texas A&M University. He is supervised by Prof. Mladen Kezunovic in Power System Protection and Control Laboratory.
Payman’s research is focused on a paradigm shift regarding how the electricity flows in the electricity grid, so called “topology control” or “transmission line switching” which is a feature how a “smarter electricity grid” can be realized. According to what he explains, “As electricity flows through transmission lines (similar to goods carried by trucks), my research tries to offer a fast decision making solution for predicting severe events (such as adverse weather conditions) in advance and efficiently re-routing the electricity (similar to various routes for trucks to get to a destination) in recovering from such disasters”. By changing the way how electricity flows through the electricity grid, Payman believes that his proposed research can be employed either in emergency scenarios (to alleviate violations, overloading conditions, or outages), or during normal operating conditions for higher economic benefits.
When asked about the motivations for his research, Payman explained, “Electricity fuels our existence. Living without it is hard to imagine. While it is essential to keep the lights on at all times, severe climate and adverse weather conditions are frequently experienced leading to loss of electricity in some cases. From 1980 to 2014, a total of 178 weather disasters occurred in the US alone (8 of which occurred in 2014) with the overall damages exceeding US$ 1 trillion. As a disastrous consequence of such electricity outages, various industries were halted for hours resulting in significant economic loss and hundreds of people in need of specific health care lost their lives as the electricity was not restored fast enough”.
Thanks to the excellent advisorship and research resources in Dr. Kezunovic’s Lab and the ECEN department, he enjoys a stimulating collaborative environment for both learning and teaching that he is offered so far at Texas A&M University.
Volume 2, Issue 3
Posted: Thursday, March 3, 2016
In this week’s Research Spotlight, we are highlighting the work of our GPSC Quality of Life Committee Chair, Lindsay Porter in support of her dissertation defense next week. Lindsay is in her final year of her Ph.D program in the College of Veterinary Medicine in Dr. Mulenga’s lab.
Ticks are blood-sucking parasites that feed on animals primarily, but often times feed on humans too. In veterinary health, ticks are a significant source of distress, disease, and even death to many different types of animals. In public health, ticks can pass along dozens of different disease-causing organisms to humans, and they are responsible for at least 14 different diseases in the United States alone. While controlling ticks currently relies primarily on applying chemicals to humans, animals, and the environment, ticks have started to grow resistant to these chemicals. This in combination with the potential for chemical contamination to the environment or to food and water sources is a major drive to develop alternative tick control methods. One such possible alternative is to design an anti-tick vaccine. By designing a vaccine against ticks instead of the disease-causing organisms they transmit, we have the potential to block ticks from transmitting any organism it might be carrying. We also have the potential to target many tick species with just one vaccine, since we have found there are some genetic components that are similar across tick species.
Many vaccines are made using proteins from the organism the vaccine protects against. But research in our lab has shown that ticks make thousands of different proteins, so we need to decide which ones can be used in an anti-tick vaccine. We can start by using a national database of protein sequences, GenBank, to see which tick proteins are similar across species. If we use these proteins, we might be able to target multiple tick species with one vaccine. From this list we need to identify tick proteins that can cause antibody production in humans and animals. We accomplish this in the lab by extracting antibodies from animals that have already been exposed to ticks, and have therefore made anti-tick antibodies. We can then screen tick proteins with these antibodies, to see which tick proteins the antibodies recognize. The next step is to produce these proteins in large quantities in the lab, using bacteria cells as small protein factories. Once we have made the protein we are ready to test it out as a vaccine.
While tick control remains a priority for our lab, we have also found that some tick proteins may be useful in the medical field. This is because in order to feed ticks need to fight back against the human and animal immune system. They fight the immune system by injecting proteins into humans and animals that prevent inflammation, blood coagulation, and pain sensation. If we can isolate and mass-produce those injected tick proteins, we may be able to provide new pharmaceuticals to the medical field that can fight coagulation disorders, control diseases related to inflammation, and assist with pain management.
Volume 2, Issue 2
Travis D. Goode
Posted: Thursday, February 25, 2016
Travis Goode is a fourth year Neuroscience Ph.D. student at the Texas A&M Institute for Neuroscience (TAMIN). Travis works in the Emotion and Memory Systems Laboratory of Dr. Stephen Maren. Dr. Maren is a member of TAMIN and currently serves as the Claude H. Everett, Jr. ’47 Chair of Liberal Arts for the Department of Psychology. Research in Dr. Maren’s lab seeks to identify and characterize brain circuits and systems involved in states of fear and anxiety.
Travis’ research is centered on the ‘extended amygdala’ of the brain, which is present in both humans and other animals. “Students may have heard of the ‘amygdala,’ but a lesser known brain region is the ‘extended amygdala,’ which plays many different, but important roles in regulating fear and anxiety-like behaviors.” Travis studies how particular regions of the extended amygdala may contribute to the stress-induced return of fear. “Not only can stress facilitate the formation of fear memories, but stress can also interfere with fear suppression that normally follows therapeutic interventions,” said Travis. To accomplish their research goals, Dr. Maren’s laboratory utilizes various advanced neuroscience research techniques including; reversible brain lesions, chemo- and optogenetics, intracranial pharmacology, electrophysiology, and immunohistochemistry.
By studying unknown functions of the extended amygdala in various learning and memory tasks, Travis hopes to improve upon future brain treatments for anxiety. “Our brains all share common structures for processing emotions, giving us potential points of intervention,” described Travis. “As technologies advance to allow us to selectively treat particular brain regions, we may be able improve treatment efficacy and reduce side effects by tending to the neural structures that are at the heart of the illness.”
When asked about what motivates his research, Travis explained, “It’s an unfortunate reality that mental illness is common in our society. Basic science is critically important for advancing our theories and treatments for disorders.” Travis’ commitment to science is a very personal journey for him. “Growing up, I saw firsthand the kind of impact that mental illnesses—such as addiction—can have on a family. It has now become very important to me to make an impact on our understanding of neural basis of mental illness, so that we may continue to build better therapies.”
Recently, Travis was awarded a prestigious predoctoral National Research Service Award from the National Institute of Mental Health. These are highly competitive grants that provide full stipend support for graduate training in the biomedical sciences. Dr. Maren will serve as his Sponsor for the award, and Dr. Jun Wang (Assistant Professor in the Department of Neuroscience and Experimental Therapeutics [NExT], and also a member of TAMIN) will serve as his Co-Sponsor. “This is a tremendous opportunity and honor,” said Travis. “This award will allow me to further expand on our knowledge of the brain circuits that contribute to persistence of fear and anxiety states.”