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ItemKarenia brevis allelopathy compromises the lipidome, membrane integrity, and photosynthesis of competitors (dataset)(Georgia Institute of Technology, 2015-12-17) Poulin, R. X. ; Kubanek, JuliaThe attached data files underlie the forthcoming publication, "Karenia brevis allelopathy compromises the lipidome, membrane integrity, and photosynthesis of competitors".
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ItemSustainable tilapia feed derived from urban food waste(Georgia Institute of Technology, 2015-12-08) Chaddick, Justin GarrettFinding an alternative to fishmeal and fish oil in animal feeds has been a topic of increasing interest due to the pressures being put on the ocean’s fisheries and the increasing world demand for animal protein. An often-overlooked source of nutrients is in the form of food waste. One third of all food produced globally ends up in landfills, wasting a huge amount of nutrients and embodied energy that could otherwise be redirected towards productive use. This study investigated the feasibility of feeding Hermetia illucens, the black soldier fly larvae (BSFL), grown on urban food waste, and Lemna minor, a species of duckweed, to tilapia in a recirculating aquaponic system as a compound feed. The study compared the growth of two groups of 58 tilapia over 44 days; one group was fed commercial pellets and the other a compound feed composed of BSFL and duckweed. The group fed the commercial pellets achieved heavier weight gain than the group fed the experimental feed but both groups resulted in steady weight gain and had similar mortality rates. Feeding the experimental feed composed of BSFL and duckweed to tilapia in an aquaponics system is an effective method of diverting food waste from the landfill and further research should be done to optimize this process.
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ItemFrom rivers to natural gas: The influence of allochthonous inputs on marine nitrogen fixation and the carbon cycle(Georgia Institute of Technology, 2015-12-04) Weber, Sarah C.The Western Tropical North Atlantic (WTNA) was once thought to be a net source of carbon dioxide (CO₂) to the atmosphere, but recent studies have shown that this Amazon River influenced region may actually act as a net sink for CO₂. During a 2010 research cruise to the WTNA, we characterized the impact of the Amazon River on offshore diazotrophy (N₂-fixation) and the resulting stimulation of biological carbon export from surface waters. Through the delivery of phosphate- and silicate-replete waters to the nitrogen (N) limited surface waters of the WTNA, the aging Amazon River plume promotes the growth of diatom-diazotoph associations (DDAs). Regions supporting large DDA blooms were associated with increased pCO₂ and DIC drawdown in the surface waters, reflecting the net export of carbon from the mixed layer. The existence of this biologically mediated linkage between the C and N cycles in productive surface waters is well known, but we have only recently discovered a stimulatory relationship in deep waters between oil/gas release and N₂-fixation. This association was first observed after the Deepwater Horizon oil spill in 2010 and we again saw evidence for it in the days following the Hercules 265 natural gas blowout. This blowout event was characterized by the release of an unknown quantity of natural gas into the shelf waters of the Northern Gulf of Mexico, but we detected a response from the marine microbial community within days. We observed a significant drawdown of dissolved oxygen and found biogeochemical evidence for the incorporation of methane-carbon into the food web, along with a modest stimulation of N₂-fixation. The episodic nature of anthropogenic blowouts makes them difficult to study, so we use cold seeps in the Gulf of Mexico as natural analogues. Interestingly, we have measured both methane oxidation and N₂-fixation at depth above some of the more active seeps. Using NanoSIMS analyses, we have taken the first steps towards physically characterizing the organisms utilizing these metabolisms. It appears that different organisms are carrying out these processes, with CH₄-assimilation occurring primarily in individual particles or small aggregates, whereas N₂-fixtion was associated with larger, sulfur-containing aggregates. Continued NanoSIMS work in combination with the use of microbial ID techniques will help to further characterize these unique deepwater diazotrophs.
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ItemNeural Activation Patterns Arising From Gesture Recognition(Georgia Institute of Technology, 2015-12) Basunia, SumiaThe human brain is composed of a complex network of neurons that create a representation of the world through sensation and perception. This representation facilitates interacting with the environment and is thus vital to the human experience. One aspect that is crucial to normal functioning is the ability to identify and classify the different types of gestures we see every day. Broadly, gestures are classified into three categories: transitive, intransitive and neutral. Transitive gestures involve specific hand-object actions such as tool-use; while, intransitive gestures are communicative in nature. In this experiment, we propose that the main aspect of a gesture is the context in which the gesture is performed. For example, the gesture of waving goodbye to someone, an intransitive gesture, and the gesture of wiping a window, a transitive gesture, both involve the same biomechanics and motor control; however, they differ greatly based on the context in which they were performed. To understand and differentiate such kinematically similar gestures, the cerebral cortex or deep brain structures might exhibit unique patterns of activations specific to differentiating context. Therefore, the objective in this experiment is to map patterns of neural activation that specifically encode and differentiate context when viewing kinematically similar transitive and intransitive gestures. The participants recruited were 19 young adults between the ages 20 to 30. To map the pattern of neural activation, this experiment employed the use of a neuroimaging technique called functional magnetic resonance imaging or fMRI. fMRI indirectly measures the hemodynamic response that represents the flow of blood to specific regions of the brain that are active in response to the viewing a picture such as a particular type of gesture. Each participant was placed in an MRI machine and exposed to 75 images containing gestures in either a transitive, intransitive, or neutral context. For the purposes of this experiment, we defined the neutral context as a gesture devoid of any context. Once the data was collected, a Linux based software called FSL was used to analyze the data. Analysis thus far has displayed neural activation patterns for the three types of gestures primarily in the visual cortex, along the dorsal and ventral streams and along the primary motor cortex. When contrasting transitive and intransitive gestures, there is no difference in neural activation. Data from this experiment gives insight into the basic neuroscience of how the brain effortlessly recognizes daily gestures and has clinical implications towards ideomotor apraxia, a neurological disorder that is characterized by an inability to recognize and perform transitive gestures.
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ItemDeveloping Tools to Monitor Vibrio cholerae Type VI Secretion During Range Expansion on Solid Surfaces(Georgia Institute of Technology, 2015-12) Ng, Siu LungThe waterborne bacterium Vibrio cholerae causes the fatal cholera diarrhea, and thrives in aquatic environments attached to chitinous surfaces with other bacteria. V. cholerae has been used to study natural competence, which promotes DNA uptake through horizontal gene transfer (HGT). A newly described Type VI Secretion System (T6SS) that V. cholerae employ to kill neighboring cells could increase the chance for a competent V. cholerae to take up and utilize the released DNA. The T6SS apparatus, which is similar to a bacteriophage spike, injects toxic effector proteins into prey cells causing lysis that can aid V. cholerae in acquiring DNA from its neighbors. Although previous studies have investigated the regulation and mechanism of T6SS in V. cholerae at a single cell level, the role of T6SS in the dynamics of mixed bacterial populations, such as those found in the environment, remains poorly understood. Fluorescence microscopy was used in this study to determine the effect of T6SS by growing V. cholerae predators and isogenic prey populations on agar surfaces as a model for competitors undergoing spatial expansion. These conditions may mimic conditions encountered on chitinous surfaces in marine settings. In this study, plasmids expressing green and red fluorescent proteins were constructed to visualize the predator and prey populations. Preliminary spatial expansion experiments were ultimately performed using different fluorescent protein alleles that were encoded on the chromosome of competing bacteria. Preliminary results suggest that the presence of a functional T6SS plays an important role in competition. The tools developed for this study are now being used to study interaction between diverse V. cholerae isolates, and as a platform for experimental evolution.
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ItemModerately lower temperatures greatly extend the lifespan of Brachionus manjavacas (Rotifera): thermodynamics or gene regulation?(Georgia Institute of Technology, 2015-11-20) Johnston, Rachel KelseyEnvironmental temperature greatly affects lifespan in a wide variety of animals, but the exact mechanisms underlying this effect are still largely unknown. A moderate temperature decrease from 22°C to 16°C extends the lifespan of the monogonont rotifer Brachionus manjavacas by up to 163%. Thermodynamic effects on metabolism contribute to this increase in longevity, but are not the only cause. When rotifers are exposed to 16°C for four days and then transferred to 22°C, they survive until day 13 at nearly identical rates as rotifers maintained at 16°C continuously. This persistence of the higher survival for nine days after transfer to 22°C suggests that low temperature exposure alters the expression of genes that affect the rate of aging. The relative persistence of the gene regulation effect suggests that it may play an even larger role in slowing aging than the thermodynamic effects. The life extending effects of these short-term low temperature treatments are largest when the exposure happens early in the life cycle, demonstrating the importance of early development. There is no advantage to lowering the temperature below 16°C to 11° or 5°C. Rotifers exposed to 16°C also displayed increased resistance to heat, starvation, oxidative and osmotic stress. Reproductive rates at 16°C were lower than those at 22°C, but because they reproduce longer, there is no significant change in the lifetime fecundity of females. To investigate which genes contribute to these effects, the expression of specific temperature sensing genes was knocked down using RNAi. Of 12 genes tested, RNAi knockdown of four eliminated the survival enhancing effects of the four-day cold treatment: TRP7, forkhead box C, Y-box factor, and ribosomal protein S6. This demonstrates that active gene regulation is an important factor in temperature mediated life extension, and that these particular genes play an integral role in these pathways. As a thermoresponsive sensor, TRP7 may be responsible for triggering the signaling cascade contributing to temperature mediated life extension. The TRP genes may also provide especially promising candidates for targeted gene manipulations or pharmacological interventions capable of mimicking the effects of low temperature exposure. These results support recent theories of aging that claim rate of aging is determined by an actively regulated genetic program rather than an accumulation of molecular damage.
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ItemINTERACTIVE EFFECTS OF DISTURBANCE AND DISPERSAL ON COMMUNITY ASSEMBLY(Georgia Institute of Technology, 2015-11-18) Bannister, Miriam Nozomi OjimaThe traditional debate on alternative community states has been over whether or not they exist. Recent studies have focused on the role of assembly history in dictating community divergence, but the context in which assembly history becomes important is a continued topic of interest. In this study, we created communities of bacterivorous ciliated protists in laboratory microcosms and manipulated assembly history, disturbance frequency, and the presence of dispersal among local communities to investigate the mechanisms behind community divergence. Specifically, we sought to understand how the role of assembly history changed in response to disturbance, dispersal, and the combination of the two. Assembly history determined the identity of the dominant species through priority effects, and dispersal and disturbance showed interactive effects on both alpha and beta diversity. Dispersal increased alpha diversity, but only in the absence of disturbance, and it reduced beta diversity, but not in the presence of low or mixed disturbance treatments. These results show that the role of assembly history and the strength of priority effects are dependent on community context. Each factor cannot be viewed in isolation, and understanding the interaction between them is important for understanding how communities assemble, which lends insight into how ecological restoration should be approached.
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ItemSpatiotemporal patterns of parietofrontal activity and eye movements underlying the visual perception of complex human tool use(Georgia Institute of Technology, 2015-11-16) Natraj, NikhileshWhen watching a child learning to use a spoon, a mother is immediately able to recognize the error when the child grabs the bowl rather than the stem, or when the child uses the spoon to try and scoop paper. Recognizing proper tool grasp-postures and use-contexts is an ability vital for daily life and can be lost due to brain injury. A better understanding of how the brain encodes contextual and grasp-specific tool-use not only furthers basic neuroscience, but also has strong relevance to deficits arising from neural pathologies. However, the majority of research till date has studied the neural response to viewing tools in isolation or viewing simple tool-grasps. These studies have shown that the recognition of tools to be a complex visuomotor process, as not only was the visual cortex engaged but also parietal and frontal regions that underlie actual tool-use. The recognition of tools therefore involves automatically recalling their motor information (graspability and manipulability) via activation of parietofrontal motor regions, a property called action affordances. Yet, it is still unclear how parietofrontal regions encode the combination of contextual and grasp-specific tool-use scenes. In addition, parietofrontal regions are multifaceted and also underlie visuospatial attention and eye movements. It is possible a relationship might exist between eye movements, attention and tool-use understanding over parietofrontal regions. Therefore the overall goal of this thesis was to understand the spatiotemporal patterns of parietofrontal activity and eye movements underlying the perceptual of contextual and grasp-specific static tool use images. Electroencephalography (EEG) was used to measure neural activity, combined with eye tracking to measure fixation and saccades. Overall, results from this thesis present evidence that the affordances of non-functional grasp-postures perturbed an observer from understanding the contextual uses of tools, with corresponding unique patterns of parietofrontal activity and eye movements. This effect was most robust when the tool was placed in contexts that afforded a certain degree of tool-use. Results also revealed a relationship between attention, eye movements and action perception over parietofrontal regions. Specifically, saccades perturbed activity over frontal regions during the perception of non-functional grasp postures and in addition, there was greater engagement of the left precuneus in the superior parietal lobe if the observer had to quickly parse the scene information using peripheral vision and rely on short term memory. In contrast, there was greater engagement of the left middle temporal gyrus if the observer had the ability to parse scene information continuously using foveal attention. Results in this thesis shed light on the neural and visual mechanisms in understanding the affordances of non-functional grasp postures, and the relation between the two mechanisms. The automatic sensitivity in understanding the intent of non-functional grasp-postures may correspond to a lifetime of learning the affordances of grasp-specific action outcomes with tools. Such cognitive motor knowledge may be vital in navigating a human environment almost entirely constructed on advanced tool-use knowledge and findings from this thesis have many potential applications in the field of neuro-rehabilitation.
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ItemNeuromechanics of locomotion: Insights from the walk-to-run transition in amputees and pedaling in able-bodied individuals(Georgia Institute of Technology, 2015-10-16) Norman, Tracy L.Afferent feedback is important for modulating locomotion and maintaining stability. Studying locomotor extremes and applying perturbations to normal locomotion allows us to probe the effects of afferent feedback on the control of normal gait. Investigating the walk-to-run gait transition specifically provides a unique locomotor event to investigate the fundamental determinants of legged locomotion (walking or running) and identify the sensory inputs important to the ongoing neuromuscular control of walking and running. The first goal of this dissertation was to investigate the contributions of plantarflexor muscles during stance (Aim 1) and flexor muscles during swing (Aim 2) to the walk-to-run transition. To accomplish this I used unilateral, transtibial amputee subjects as a means to assess the affects of unilaterally eliminating plantarflexor propulsive force production and below-knee flexor activation on the walk-to-run transition speed. The main objective of Aim 1 was to determine the preferred gait transition speeds of unilateral, transtibial amputee subjects, and the influence of kinetics on the walk-to-run gait transition speed. Unilateral, transtibial amputee subjects transition between gaits at a lower speed than able-bodied controls and are still able to generate higher propulsive forces walking at speeds above their preferred gait transition speed. This finding indicates that their walk-to-run transition is not likely dictated by the force-length-velocity characteristics of the intact plantarflexor muscles. Thus, as an experimental model, unilateral, transtibial amputee subjects can provide unique insights for decoupling the previously identified performance limit of plantarflexor muscles from the preferred gait transition speed in order to probe other potential determinants. The main objective of Aim 2 was to quantify the muscle activation during walking and running gaits relative to the walk-to-run gait transition speed for unilateral, transtibial amputee subjects. The swing phase tibialis anterior muscle activation is a major determinant of the walk-to-run transitions in unilateral, transtibial amputee subjects. Swing phase dorsiflexion moments alone do not explain these results and additional work is necessary to probe potential mechanical and neural explanations. Furthermore, in unilateral, transtibial amputee subjects, swing-phase rectus femoris and biceps femoris long head activations and their respective joint moments are a function of changes in absolute speed and thus not indicative of their significantly lower gait transition speed. The second goal of this dissertation was to probe the potential contributions of afferent feedback to the underlying neuromuscular mechanism ultimately responsible for the transition (Aim 3). The main objective of Aim 3 was to evaluate the effects of contralateral sensory loss on the motor output of the ipsilateral leg. Unilateral below-knee, ischemic deafferentation has significant effects on both inter- and intra- limb motor output. The net effect of contralateral sensory loss below the knee is a significant decrease in ipsilateral flexor muscle activations during the transition from flexion to extension in pedaling (Q1). Due to the rapid time course of these responses, I speculate either i) contralateral below-knee afferents (most likely Ia and/or cutaneous) have a net excitatory effect on the ipsilateral flexor muscles or ii) contralateral above knee afferents (most likely Ib) have an inhibitory effect on the ipsilateral flexor muscles.
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ItemTranslational bioinformatics for personalized medicine and integrative biology: Data integration, extraction, knowledge discovery, and visualization(Georgia Institute of Technology, 2015-10-13) Uppal, KaranThis thesis focuses on developing a computational framework to support the Precision Medicine Initiative. The newly developed tools and algorithms use machine learning, text mining and visualization techniques for extracting salient information from heterogeneous sources such as scientific literature, clinical text, and –omics technologies to enhance clinical decision making and improve the quality of healthcare. Various advances in biomedical technologies have enhanced our ability to study disease processes at different molecular levels (genes, metabolites, histones, etc.). Similarly, technological advances in healthcare domain such as adoption of Electronic Health Record systems (EHRs) provide us a unique opportunity to develop a learning healthcare system where intelligent tools and algorithms can be utilized to extract information from clinical notes, patient medication records, laboratory results, etc. for early detection of medical risks and prevention of adverse drug events. The key novel contributions of this thesis are: a) development of novel full-text summarization algorithms that have been incorporated into a web application (CoReViz) for visualizing clinically relevant information and extracting relevant sentences from clinical text and scientific articles; b) development of novel association mining algorithms and graph summarization techniques incorporated into a web application (SEACOIN2.0) for interactive drill-down summarization and hypothesis generation to extend the functionality of PubMed; c) introduction of the concept of literature based Phenotype-wide Association Studies (Lit-PheWAS); d) development of an ensemble feature selection framework for biomarker discovery using agent-based modeling and stochastic optimization techniques.