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Development of Biosensors to Measure the Spatial and Temporal Concentration Profiles of Inorganic Phosphate in Plants During Arbuscular Mycorrhizal Symbiosis
Biology; TAMU; https://hdl.handle.net/20.500.14641/599; DOE-Office Of Science
The concentration of inorganic phosphate (Pi) in the chloroplast stroma must be maintained within narrow limits to sustain photosynthesis and to direct the partitioning of fixed carbon. However, it is unknown if these limits or the underlying contributions of different chloroplastic Pi transporters vary throughout the photoperiod or between chloroplasts in different leaf tissues. To address these questions, we applied live Pi imaging to Arabidopsis (Arabidopsis thaliana) wild-type plants and 2 loss-of-function transporter mutants: triose phosphate/phosphate translocator (tpt), phosphate transporter 2;1 (pht2;1), and tpt pht2;1. Our analyses revealed that stromal Pi varies spatially and temporally, and that TPT and PHT2;1 contribute to Pi import with overlapping tissue specificities. Further, the series of progressively diminished steady-state stromal Pi levels in these mutants provided the means to examine the effects of Pi on photosynthetic efficiency without imposing nutritional deprivation. ?PSII and nonphotochemical quenching (NPQ) correlated with stromal Pi levels. However, the proton efflux activity of the ATP synthase (gH+) and the thylakoid proton motive force (pmf) were unaltered under growth conditions, but were suppressed transiently after a dark to light transition with return to wild-type levels within 2?min. These results argue against a simple substrate-level limitation of ATP synthase by depletion of stromal Pi, favoring more integrated regulatory models, which include rapid acclimation of thylakoid ATP synthase activity to reduced Pi levels.
Elucidation of a Eukaryotic Chemorepulsion Mechanism
Biology; TAMU; https://hdl.handle.net/20.500.14641/505; DHHS-NIH-National Institute of General Medical Science
There is good evidence that some cells secrete chemorepellents that cause specific cell types to move away from them. However, much remains to be understood about the identity of the chemorepellents, their receptors, and the mechanisms they use to direct cell motility. We found that proliferating Dictyostelium cells secrete a protein called AprA, and that AprA is an extracellular signal that functions as a chemorepellent. Although AprA has little sequence similarity to mammalian proteins, AprA has predicted structural similarity to the human secreted dipeptidyl protease DPPIV, and shares functional properties with DPPIV. We found that human DPPIV is a chemorepellent for human and mouse neutrophils, and when applied locally, DPPIV can induce neutrophils to leave a tissue in two mouse models of a lung disease called acute respiratory distress syndrome (ARDS), and a mouse model of rheumatoid arthritis. To gain insights into a fundamental mechanism used in morphogenesis, ways to induce neutrophils to leave a tissue, and how one could augment or diminish the effect of a chemorepellent, we propose three specific aims to elucidate the molecular mechanisms used by AprA and DPPIV to cause chemorepulsion. Aim 1 is to identify the AprA receptor, since this plays a key role in the Dictyostelium chemorepulsion mechanism. Our preliminary work has identified a predicted G protein- coupled receptor called GrlH as a possible AprA receptor. We will carefully test this, and if GrlH is not the receptor, we will use several approaches to identify the receptor. Aim 2 is to elucidate the AprA chemorepulsion signal transduction pathway. Our preliminary data indicate that some components of the chemorepulsion mechanism are different from components used by the chemoattraction mechanism that allows Dictyostelium cells to aggregate toward cAMP. We will determine the extent to which the chemorepulsion mechanism uses known components of the chemoattraction mechanism, as well as use the power of unbiased genetic screens in Dictyostelium to identify additional components of the chemorepulsion mechanism. Aim 3 is to test the hypothesis that DPPIV uses a G protein-coupled receptor called PAR2 to induce neutrophil chemorepulsion, and use what we learn about the Dictyostelium chemorepulsion mechanism to determine the similarities and differences between the Dictyostelium and the human neutrophil chemorepulsion mechanisms. Together, this work combining molecular biology, genetics, cell biology, and biochemistry will help to elucidate eukaryotic chemorepulsion mechanisms, and identify potential drug targets that could enhance or inhibit chemorepulsion.
Epigenetic Regulation of Seasonal Behavior in Insects
Biology; TAMU; https://hdl.handle.net/20.500.14641/206; National Science Foundation
Many animals change their behavior in response to seasonal changes in the environment. The molecular nature of the changes that occur in the brain to alter behavior in a seasonal manner remains poorly understood. This project will examine epigenetic changes, i.e. changes in external modifications to DNA, that turn behavior-regulating genes on or off in a season-dependent manner. The work will be carried out using behavioral approaches and DNA sequencing of the genome of the long-distance migratory monarch butterfly, Danaus plexippus. The monarch exhibits extreme seasonal behavioral changes at the individual level in response to changing daylength and temperature. Migratory monarch butterflies accomplish an extraordinary journey of 2,000 miles from the United States to their overwintering sites in Mexico by flying southward in the fall. In the spring, migratory butterflies flip their flight orientation northward and return to the United States. This project will reveal seasonal epigenetic changes to the genome in the brains of these seasonal forms. These findings will provide insight into the molecular mechanisms underlying seasonal migration and the production of distinct seasonal flight orientations, and may be applicable to other migratory species. They could also have implications for conservation strategies to help preserve the iconic monarch migration, a spectacular yet threatened biological phenomenon. The project will provide valuable research training for students interested in animal behavior, neuroscience, and bioinformatics, including students from groups underrepresented in STEM fields. The researchers will also develop outreach activities devoted to increase public awareness for the need of monarch habitat conservation efforts. Seasonal behavioral adaptations are key to the ecological success of many animals. The behavioral plasticity observed in individuals in response to seasonal changes in the environment strongly suggests that epigenetics play a crucial role in shaping seasonal behavior. However, the epigenetic changes that link brain function to seasonal regulation of behavior remain largely unknown. This project will leverage the remarkable seasonal plasticity of monarch butterfly migratory behavior in response to seasonal changes in the environment (daylength, temperature) to delineate the genome-wide epigenetic architecture in the brain that underlies seasonal migratory behavior and flight orientation. The goal of the project is to identify active cis-regulatory elements (CREs) and putative transcription factors (TFs) that mediate differential gene expression in the brains of non-migrants, fall migrants and spring remigrants. The researchers will use fall migrants and fall migrants reprogrammed into spring remigrants in controlled conditions and a combination of next-generation sequencing technologies. Genes differentially expressed in the brains of these seasonal forms will be identified by RNA-seq, and open genomic regulatory regions and CREs that mediate this differential expression will be identified by ATAC-seq and ChIP-seq of histone marks. Candidate transcription factors (TFs) responsible for the seasonal behavioral reprogramming will ultimately be identified through DNA genomic footprinting within CREs. The project will have broad societal impacts through outreach activities devoted to increase public awareness for the need of monarch habitat conservation efforts, and research training of students interested in animal behavior, neuroscience, and bioinformatics. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
Epigenetic Regulation of Seasonal Behavior in Insects
Biology; TAMU; https://hdl.handle.net/20.500.14641/206; National Science Foundation
Many animals change their behavior in response to seasonal changes in the environment. The molecular nature of the changes that occur in the brain to alter behavior in a seasonal manner remains poorly understood. This project will examine epigenetic changes, i.e. changes in external modifications to DNA, that turn behavior-regulating genes on or off in a season-dependent manner. The work will be carried out using behavioral approaches and DNA sequencing of the genome of the long-distance migratory monarch butterfly, Danaus plexippus. The monarch exhibits extreme seasonal behavioral changes at the individual level in response to changing daylength and temperature. Migratory monarch butterflies accomplish an extraordinary journey of 2,000 miles from the United States to their overwintering sites in Mexico by flying southward in the fall. In the spring, migratory butterflies flip their flight orientation northward and return to the United States. This project will reveal seasonal epigenetic changes to the genome in the brains of these seasonal forms. These findings will provide insight into the molecular mechanisms underlying seasonal migration and the production of distinct seasonal flight orientations, and may be applicable to other migratory species. They could also have implications for conservation strategies to help preserve the iconic monarch migration, a spectacular yet threatened biological phenomenon. The project will provide valuable research training for students interested in animal behavior, neuroscience, and bioinformatics, including students from groups underrepresented in STEM fields. The researchers will also develop outreach activities devoted to increase public awareness for the need of monarch habitat conservation efforts. Seasonal behavioral adaptations are key to the ecological success of many animals. The behavioral plasticity observed in individuals in response to seasonal changes in the environment strongly suggests that epigenetics play a crucial role in shaping seasonal behavior. However, the epigenetic changes that link brain function to seasonal regulation of behavior remain largely unknown. This project will leverage the remarkable seasonal plasticity of monarch butterfly migratory behavior in response to seasonal changes in the environment (daylength, temperature) to delineate the genome-wide epigenetic architecture in the brain that underlies seasonal migratory behavior and flight orientation. The goal of the project is to identify active cis-regulatory elements (CREs) and putative transcription factors (TFs) that mediate differential gene expression in the brains of non-migrants, fall migrants and spring remigrants. The researchers will use fall migrants and fall migrants reprogrammed into spring remigrants in controlled conditions and a combination of next-generation sequencing technologies. Genes differentially expressed in the brains of these seasonal forms will be identified by RNA-seq, and open genomic regulatory regions and CREs that mediate this differential expression will be identified by ATAC-seq and ChIP-seq of histone marks. Candidate transcription factors (TFs) responsible for the seasonal behavioral reprogramming will ultimately be identified through DNA genomic footprinting within CREs. The project will have broad societal impacts through outreach activities devoted to increase public awareness for the need of monarch habitat conservation efforts, and research training of students interested in animal behavior, neuroscience, and bioinformatics. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
I-Corps: Hand-held Assistive Mobility Device for the Visually Impaired Using Sensors to Feel Obstacles From a Distance and Track Their Movements
Biology; TAMU; https://hdl.handle.net/20.500.14641/548; National Science Foundation
The broader impact/commercial potential of this I-Corps project is the development of a hand-held assistive mobility device for the visually impaired. The Center for Disease Control (CDC) estimates that approximately 12 million people over the age of 40 suffer from visual impairment in the United States. Vision impairment and loss of sight are among the top 10 disabilities for individuals over the age of 18 and can have a substantial social and economic toll including, but not limited to, significant loss of productivity and diminished quality of life. Further, the annual economic impact of major vision problems in those 40 and older is estimated to be $145 billion. The proposed device holds the potential to significantly improve mobility, accessibility, and quality of life for the millions of people with no or low-vision that currently use an assistive mobility device such as the widely used ?white cane.? The technology also offers potential benefits to people working in low-visibility or disaster conditions, such as emergency first-responders or military personnel. This I-Corps project is based on the development of a hand-held device that uses remote sensing technology to control a dynamic tactile display on the hand, allowing the visually impaired to detect and classify obstacles in their environment sooner and more broadly than is possible using current assistive technology devices. Unlike existing technologies that involve touching or poking items with a white cane or rely on the individual to follow auditory cues, this device may enable individuals to feel the presence of obstacles and targets from a distance, including the relative location of multiple obstacles and being able to track the relative movements of nearby obstacles and targets. The proposed technology is an extension of research into optimized graphical displays of information derived from Sound Navigation and Ranging (SONAR) and Light Detection and Ranging (LIDAR)-based sensor systems. People in low-vision situations may be better equipped to rapidly process and exploit multi-channel spatial information when it is delivered via the hand instead of the ear. The proposed technology exploits the natural active-sensing behaviors used by humans when they reach out to explore their environment. This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
LTREB: Social, Environmental, and Evolutionary Dynamics of Replicated Hybrid Zones in Swordtails (Teleostei: Xiphophorus) of Mexicos Sierra Madre Oriental
Biology; TAMU; https://hdl.handle.net/20.500.14641/337; National Science Foundation
The study of natural hybridization - the exchange of genetic information between species - is fundamental to further understanding how genes function within organisms and within the environment. Hybrids - crosses between different species - can also be used to identify specific genes associated with traits of interest and how these genes interact with environmental variation, ultimately shedding light on the genetic basis of disease and adaptation to environmental change. This project studies changes in behavioral decisions, communication signals, heat and cold tolerance, and population structure over 10 years in natural and experimental populations of swordtail fish, a longstanding model in genetics, physiology, and behavior. The two parent species are found at high and low elevations, hybrids at intermediate elevations. Experimental populations will seed first-generation hybrids along an elevation gradient. The predicted response at the high elevation site is that genes associated with cold tolerance will spread along with the communication signals and behavioral biases of the high-elevation species, and vice-versa at the low elevation site. The study will identify novel genes involved with decision-making, communication, and temperature tolerance, which may lead to applications in medicine and agriculture. Further, the data will address the extent to which specific, identifiable parts of the genome are responsible for adaptation to various environments. Collection and analysis of data will be accomplished with a structured summer mentorship program between undergraduate students and local K-12 students. Because of the long-term nature of the study, K-12 trainees will have the opportunity to become mentors themselves later in the project.
Science in the Sierra Madre: Developing Infrastructure for Multidisciplinary Research at the CICHAZ Field Station -
Biology; TAMU; https://hdl.handle.net/20.500.14641/337; National Science Foundation
This FSML improvement grant proposal addresses the infrastructure and shared instrumentation needs of the Centro de Investigaciones Cientificas de las Huastecas "Aguazarca" (CICHAZ) field station located in the Sierra Madre Oriental (http://www.cichaz.org/). CICHAZ is located in the unique Sierra y Huasteca region of central Mexico, an area high in biological and cultural diversity but devoid of academic and research institutions. This field station is associated with Texas A&M University and hosts an increasing number of scientists annually who need a broad array of scientific resources. Since its founding in 2005, CICHAZ has hosted over 150 researchers in the natural and social sciences from over 30 institutions internationally, fostered 9 Ph.D. and two Master's theses, and attracted 11 NSF-funded projects. CICHAZ has provided research and cultural experiences for undergraduates, local residents, and members of the U.S. public. In addition to long-term lodging for up to 11 researchers, the station has built up facilities including an indoor fishroom, an array of 24 aquatic mesocosms, and a small laboratory for molecular biology. This award will provide the infrastructure and equipment for collecting and analyzing genomic data; controlled husbandry of plants and animals; and ecological and evolutionary studies in the region. With this grant, an existing laboratory will be converted into a standard molecular wet lab, featuring a MinIon genome sequencer. This will enable researchers to collect and analyze nucleic acid data in situ within the course of a field stay. Two new greenhouse facilities will be erected to house animals and plants for controlled studies, as well as sustainable improvements to address the anticipated increase in energy needs. Finally, the station will acquire a mobile laboratory flexibly equipped with instruments for stream sampling, water quality analysis, and sedimentary core extraction. These proposed improvements have fundamental impacts on outreach efforts, and will ensure success of broader impacts initiatives including research experiences for US and Mexican undergraduates, and for local K-12 students, focused on integrating field and environmental approaches with state-of-the-art techniques for measurement and analysis. The mobile laboratory will revolutionize engagement with schools and with remote indigenous communities, by enabling visiting researchers to work with staff in designing outreach programs in local communities.
Systems Biology of the Circadian Clock Output Network
Biology; TAMU; https://hdl.handle.net/20.500.14641/678; DHHS-NIH-National Institute of General Medical Science
DESCRIPTION (provided by applicant): The circadian clock is an evolutionarily conserved time-keeping mechanism that, through the regulation of rhythmic gene expression, coordinates the physiology of an organism with daily environmental cycles. Because virtually all aspects of human physiology and behavior are linked to the clock, abnormalities in the circadian system are associated with a wide range of diseases, including metabolic syndrome that affects up to 40% of adults over the age of 50. Thus, knowing what genes are regulated by the clock, and the mechanisms of this regulation, are necessary to understand clock-associated diseases. Furthermore, clock-controlled transcripts peak at all possible phases of the circadian cycle; however, we lack a basic understanding of what controls phase. To begin to understand the circadian output gene network, we identified the direct targets of the core clock component and transcription factor (TF) WCC in Neurospora crassa, and found an overrepresentation of TFs in the roughly 200 direct targets. Among these first tier TFs, ADV-1 was shown to be robustly rhythmic, defective in clock-controlled development, and closely linked to the downstream metabolic network. We also discovered that in addition to WCC, several first tier TFs bind to the adv-1 promoter, and that ADV-1 feeds back to bind to the promoters of these same TFs. These same TFs also bind and potentially co- regulate each other, and the direct targets of ADV-1. In addition, our analysis of the direct targets of ADV-1 revealed enrichment for genes involved in development, metabolism, and transcription control. Together, these data suggest a complex regulatory network linking WCC to ADV-1 and to downstream developmental and metabolic genes. Our data also suggest that one function of this network is to generate distinct temporal dynamics of gene expression critical to robust rhythms in biological functions. By combining computational and experimental biology, we will directly test this idea in our specific aims. We will determine how the upstream network sculpts the rhythms in ADV-1 (Aim1), and how the ADV-1 downstream network generates distinct temporal patterns of gene expression (Aim 2). We will combine the upstream and downstream network models to predict and validate which genetic changes will selectively alter the phase of expression of specific metabolic pathways that are rhythmically controlled by ADV-1 (Aim 3). As such, one major outcome of this work is the exciting potential to develop interventions to diminish the serious effects of disruption of the clock on human disease, such as metabolic syndrome associated with shift work.

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