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Regulation of the type VI secretion system in environmental isolates of vibrio cholerae

2017-12-14 , Hoffmann, Tobias

Vibrio cholerae is a human pathogen that causes the severe diarrheal disease cholera, but can also inhabit aquatic environments. The type-VI secretion system (T6SS) is a macromolecular contractile machine that injects neighboring cells with cytotoxic effector proteins. Clinical strains of V. cholerae express the T6SS only when exposed to high cell density and starvation conditions in the presence of chitin, a process regulated by the master regulator QstR. The atypical clinical strain V52 expresses its T6SS constitutively, a trait shared by many V. cholerae strains isolated from the environment. Recently it was discovered that the TfoY regulator controls T6SS expression independent of QstR in V52. In examining strains from environmental sources, I found that one constitutive environmental strain is also under TfoY control. However, I also uncovered that T6SS-mediated constitutive killing in four additional environmental strains was unaffected by a tfoY deletion. Furthermore, I demonstrated that other known regulators (TfoX, QstR, OscR) also played no role in T6SS expression in these strains. For example, the environmental strain BGT69 remains capable of T6SS-mediated killing when these four known T6SS regulators were deleted. These results suggest the presence of a novel regulatory pathway(s) for type-VI secretion in this and other environmental strains of V. cholerae.

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Unrecognized diversity of microbes linking methanotrophy to nitrogen loss in marine oxygen minimum zones

2017-11-13 , Padilla, Cory Cruz

Methane (CH4) is a potent greenhouse gas with 25 times the warming potential of carbon dioxide (CO2) on a per mol basis. Marine oxygen minimum zones (OMZs) are enriched in CH4 compared to oxygenated water columns and are predicted to expand under global warming. OMZs are also key sites for microbially-mediated nitrogen (N) loss, which has been shown in other systems to be linked to CH4 consumption. Diverse groups of microorganisms mediate the global cycling of both CH4 and N. Microbial genes encoding the enzyme used in CH4 oxidation, particulate methane monooxygenase (pmo), have previously been detected in OMZs. However, the genomic diversity and ecological importance of the OMZ CH4-cycling community are unclear, as is the mechanism by which CH4 consumption is carried out by these microbes. This thesis uses a combination of metagenomics, metatranscriptomics, and biogeochemical measurements to explore the activity and diversity of methanotrophic microbes in OMZs. OMZs were found to harbor at least two metabolic strategies for CH4 consumption. First, we found evidence that bacteria belonging to the recently discovered NC10 phylum are present and transcriptionally active at the functionally anoxic core of the OMZ. NC10 bacteria link anaerobic CH4 oxidation to nitrite (NO2-)-driven denitrification through a unique O2-producing intra-aerobic methanotrophy pathway. rRNA and mRNA transcripts assignable to NC10 peaked within the OMZ and included genes mediating this unique methanotrophic pathway. Second, metagenomic binning uncovered a separate and distinct methanotrophic strategy that is present and active within and just below the oxycline. In this strategy, gammaproteobacteria, designated phylogenetically as belonging to the OPU3 clade, were found to carry and express genes for methanotrophy and partial denitrification, thereby supporting respiration under low O2 concentrations and allowing for available O2 to be used directly for CH4 oxidation. These findings confirm OMZs as a niche for diverse and previously overlooked forms of denitrification-linked methanotrophy. Further characterization of these niches and the environmental constraints on OMZ CH4 consumption is critical for predicting the effects of OMZ expansion on global C cycling, greenhouse gas consumption, and N loss.

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Population genetics and genomics of eusocial animals

2017-11-09 , Chau, Linh M.

Major evolutionary transitions have been associated with increases in organismal complexity. One of the latest evolutionary transitions is from solitary life to eusociality. This transition led to a reproductive division of labor in which individuals are divided into castes. Reproductive castes are responsible for reproduction, while nonreproductive castes take part in colony maintenance and brood care. This division of labor represents a challenge to selection and has long been of curiosity to researchers. My dissertation research examined the population genetics and genomics of eusociality in a spectrum of eusocial species. First, I examined the population structure and genetic diversity of Vespula pensylvanica, a wasp native to North America that has invaded the Hawaiian archipelago. I found a lack of population structure in V. pensylvanica’s native range and determined how the population structure of invasive social insects can be shaped by geography. I also examined the population genetics of captive naked mole rats, one of the only known eusocial mammals. I sought to understand how captivity can shape the population structure of a eusocial animal. Interestingly, there was evidence that naked mole rat populations are not as inbred as previously theorized and that sex ratios are equal within captive colonies. Finally, I examined how the phenomenon of gene duplication can affect the evolution of castes in eusocial species. I uncovered a relationship between duplication rate and level of sociality across the bees. Also, I saw that duplicates were differently expressed across phenotypes compared to single copy genes. These studies provide insight on an array of population genetic and genomic questions concerning the evolution of eusociality. Therefore, this research furthers our understanding of the rare distribution of this social system across the tree of life.

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Dissecting the role of linker histone H1 variants in embryonic stem cells

2017-08-28 , Ho, Po-Yi

To further dissect the role of linker histone H1 in embryonic stem cells (ESCs), here, we have utilized a functional reconstitution approach to identify the regions of H1 proteins that are important to mediate neurite outgrowth during neural differentiation of ESCs. We first generated H1 reconstituted ESC lines by overexpressing exogenous H1d proteins in H1 depleted ESCs. We find that overexpression of H1d in H1 depleted ESCs significantly restored the neurite outgrowth capacity of embryoid bodies (EBs) formed from ESCs. Next, to dissect the role of individual domains of H1d in ESC differentiation, we constructed a series of vectors to express H1 deletion mutants in H1 depleted ESCs. Our results show that reconstitution with H1d-GD and H1d-NTD-GD increases neurite outgrowth of EBs, suggesting that the globular domain of H1d is critical in mediating the neurite outgrowth during neural differentiation of ESCs. Lastly, we investigated the potential role of H1 modifications in ESC differentiation. We constructed an expression vector encoding the H1d mutant (H1dK46R) containing a lysine-to-arginine mutation at site K46, and expressed H1dK46R in H1c/H1d/H1e triple knockout (H1 TKO) ESCs by stable transfection and analyzed chromatin binding and biochemical properties through HPLC analysis. Our results suggest that K46R mutation of H1d disrupts the function of H1d in mediating the neurite outgrowth of EBs, suggesting a critical role of post-translational modification(s) on H1d K46 in ESC differentiation. To further dissect the potential mechanisms underlying the defects of H1dK46R mutant, we set out to characterize and compare the mobility of H1dK46R and H1d in ESCs in vivo using fluorescent recovery after photobleaching (FRAP) assay. Results from FRAP assay suggest that K46R mutation decreases dynamic mobility of H1d in ESCs, which may partially contribute to the defects of H1dK46R in mediating proper ESC differentiation. In summary, through a series of studies aimed at dissection of different regions and sites of H1d, we pinpoint GD as a key domain of H1 in mediating neurite outgrowth during neural differentiation of ESCs. Furthermore, our results suggest that the modification(s) on K46 of H1d are critical for proper ESC differentiation and are likely to increase the dynamic plasticity of H1d.

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Rotifer Growth Under Astaxanthin Enrichment

2017-12 , Siegfried, Emma

Rotifers and astaxanthin both play an important part in the aquaculture industry. Rotifers are used as a substitute for copepods, the main source of food for larval fish in natural systems, due to the ease with which they can be cultured. Astaxanthin is a carotenoid and antioxidant which brightens the coloring of fish and improves fish health. Rotifers are believed to be a method through which astaxanthin can be bioencapsulated and vectored to larval fish. As a result, it is important to understand the effect of astaxanthin on rotifers themselves. This experiment uses a multitude of different protocols to determine how different astaxanthin compounds effects rotifers on both the individual and population levels. Reproductive tables and fluorescent imaging were used to assess the health of individual rotifers; population density measurements in mass cultures were used to assess rotifer population health. The reproductive ability of rotifers was significantly different from control under multiple astaxanthin treatments. Astaxanthin enrichment also created a higher stable population density in the mass cultures. The fluorescent imaging showed that the rotifers reached peak astaxanthin concentration within the rotifer gut after 3 hours, and but concentration returned to control levels within 24 hours of removal from astaxanthin. These results all point to the fact that astaxanthin helps to increase rotifer health and fitness, and that these rotifers could be used as a vector for astaxanthin to larval fish.

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Transposable element polymorphisms and human genome regulation

2017-11-13 , Wang, Lu

Transposable elements (TEs) are DNA sequences that are capable of moving from one genomic location to another. A large proportion of the human genome is derived from TEs, and TE-derived sequences have been shown to contribute to genome regulation in a variety of ways. There are several active families of human TEs, primarily the Alu, LINE-1 (L1), and SVA retrotransposons, which generate structural variations that segregate as polymorphisms within and between human populations. Given the known regulatory properties of human TEs, considered together with the fact that TE insertion activity is a source of population genetic variation, I hypothesized that TE polymorphisms can lead to gene regulatory differences among human individuals with health related phenotypic consequences. I evaluated this hypothesis via a series of genome-wide association screens aimed at assessing: (1) how the human genome regulates TE activity, and (2) how TE activity impacts human genome regulation and health related phenotypes. Expression quantitative trait loci (eQTL) analysis was used to discover a number of novel genetic modifiers of L1 element expression, including genes encoding for transcription factors and chromatin associated proteins. Human TE polymorphisms were shown to participate in population-specific gene regulation, with the potential to coordinately modify transcriptional networks. The regulatory effects of human TE polymorphisms were linked to immune system function, and related diseases, via insertions into cell type-specific enhancers. Results from my novel genome-wide approach to the study of human TE activity underscore the ability of TEs to effect health related phenotypes by virtue of changes to the regulatory landscape of the genome.

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Neurobehavioral quantification of the transition to explicit awareness in skilled motor learning: Implications for rehabilitation

2017-11-08 , Lawson, Regan

We often take for granted the ability to learn and execute sequential movements in a smooth, automatic manner on a continual daily basis. Unfortunately, many patient populations exhibit deficits in motor learning, impairing the ability to develop such sequential motor skills. Understanding the individual neural progression associated with sequential learning in healthy individuals may provide valuable insights of motor learning as well as identify factors that can impede learning. Recent studies have indicated potential therapeutic benefits to the incidental development of explicit awareness during a motor learning task, but have not addressed the potential confound of variability in individual learning rates. We identified an individualized indicator of incidentally developed explicit awareness to more precisely examine the neurobehavioral changes associated with sequential motor learning to a level of explicit awareness. EEG results revealed the presence of a facilitative frontoparietal network for subjects demonstrating awareness, that was not present for those failing to develop awareness. Additional neurobehavioral correlations provided evidence for the impact of working memory on the ability to acquire initial explicit awareness, and the impact of learning strategy on the ability to successfully transfer the newly learned skill to a novel, more complex motor task. Finally, a multimodal approach examined eye-tracking, kinematics and neural activity changes for prosthesis users and intact control subjects when learning a sequential motor task. Prosthesis users demonstrated neurobehavioral patterns reflective of enhanced visual reliance for motor control, impacting motor learning progression. It was additionally noted that prosthesis users developing awareness appeared to engage in behaviors which introduced additional sensorimotor information relevant to motor learning. The individualized approach in the presented work provide insight into rehabilitative interventions with which to assist individuals experiencing motor learning deficits.

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Predation, competition, and facilitation on tropical reefs: implications for corals as reefs degrade 

2017-11-13 , Clements, Cody Shane

Tropical coral reefs are among the most diverse and productive ecosystems on Earth, but reefs worldwide have experienced dramatic declines in coral and often transitioned from coral- to macroalgal dominance. As local and global threats to corals increase in severity and frequency, there is an urgent need to understand how reef degradation, as well as efforts to manage and restore corals, are reshaping ecological interactions that are critical to the function of coral reef ecosystems. Here, I utilize a range of experimental approaches to investigate how interactions between corals, competing macroalgae, and coral predators (i.e. corallivores) are being altered within mosaics of coral reef habitat characterized by different levels of degradation and local protection in the tropical Pacific. I first demonstrate, via a series of field observations and experiments, the direct negative effects of competition for corals competing with macroalgae that commonly dominate degraded reefs, including the spatial and temporal constraints of these competitive interactions, as well as the indirect positive effects that can arise due to the presence of a common coral predator, the crown-of-thorns sea star (Acanthaster cf. planci). I also provide observational and experimental evidence that protected reefs can help alleviate predation by corallivorous snails (Coralliophila violacea) for some stress-tolerant corals (Porites cylindrica), but that stark habitat contrasts between coral-dominated protected reefs and macroalgal-dominated fished reefs can simultaneously attract and concentrate feeding by other corallivores (Acanthaster cf. planci) – potentially contributing to coral demise and compromising the conservation value of small Marine Protected Areas. Lastly, I use a field-based manipulative experiment to explore the implications of coral species loss for ecosystem function on degraded reefs; demonstrating that greater coral species richness can enhance coral growth and survivorship, and reduced colonization by competing macroalgae. Together, these studies highlight the need to better understand the novel and context-dependent role of ecological interactions – both for fundamental ecology and effective management – in rapidly changing ecosystems subject to increasing disturbances.

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Quadrupedal locomotion with a unilateral bone-anchored transtibial prosthesis in the cat

2017-11-10 , Jarrell, Joshua Ryan

Bone-anchored limb prostheses offer numerous advantages over conventional socket-supported prostheses. As opposed to socket prostheses, loads on a bone-anchored prosthetic limb during natural activities are directly transmitted to the residual bone, which prevents damage of skin and other soft tissues. Despite this and other documented advantages, however, bone-anchored prostheses have been limited in their availability in the United States due to an increased risk of skin and deep tissue infection through the skin-implant interface. A novel porous titanium pylon, the skin- and bone-integrating pylon (SBIP), has been developed to promote deeper tissue integration with the percutaneous implant and thereby reduce the risk of infection (Farrell et al., 2014c; Pitkin et al., 2009; Pitkin, 2012). Further research is needed to examine if the SBIP can be utilized for anchoring a limb prosthesis in natural load bearing applications. In veterinary medicine, gait changes in animals after limb loss and subsequent prosthesis intervention have not been extensively investigated. In addition, it is not completely understood how the motor system adapts to a loss of sensory feedback from the distal leg and to a reduced ability to absorb and generate mechanical energy for locomotion. Currently, detailed biomechanical analyses of such adaptations are missing. Therefore, the overall goal of my research was to investigate the effects of walking with a unilateral, transtibial, bone-anchored via SBIP prosthesis on mechanics and stability of quadrupedal locomotion and on tissue integration with the SBIP implant. The general hypothesis tested was that the SBIP would provide secure, infection free anchoring of a transtibial prosthesis and that would permit the cats to adopt the prosthesis for stable quadrupedal locomotion. In Specific Aim 1, I examined the ability of the SBIP to serve as attachment for a unilateral, transtibial bone-anchored prosthesis during walking in the cat. In Specific Aim 2, I investigated dynamic stability by analyzing margins of dynamic stability and changes in angular impulse during quadrupedal walking with a unilateral bone-anchored passive transtibial prosthesis. In Specific Aim 3, I determined the amount of skin and bone ingrowth into the SBIP after the residual tibia had been loaded during natural motor activities including level and slope walking. The results of these investigations showed purposeful adoption of the bone-anchored prosthesis into the animals’ chosen gait strategies. More specifically, normal ground reaction forces produced by the prosthetic limb were of substantial magnitudes (at least 50% of the pre implantation level), and tangential ground reaction forces, while significantly reduced, were statistically greater than zero and in the appropriate direction and timing across the gait cycle. Frontal-plane stability metrics deviated from the intact values to a lesser extent than in similar studies in human prosthetic gait. The histological results revealed deep bone and skin integration highly correlated with the duration of implantation and exceeded ingrowth of in a non-locomotive subject of similar implantation times. This study has provided important new information about the ability of the novel SBIP implants to be utilized for anchoring limb prostheses and about how the motor system of a quadrupedal animal adapts to a partial loss of the limb’s ability to absorb and generate mechanical energy for locomotion.

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Neuromechanical activity of the wrist muscles during stabilization tasks

2017-08-28 , Brown, Ellenor J.

Wrist joint stability is vital to hand function and thus overall upper limb function. The overarching goal of the study is to understand the neuromuscular control and mechanical properties of the wrist muscles for wrist stabilization. Aim 1 focuses on development of an analysis method for ultrasound elastography images toward estimating individual muscle force changes in a wrist muscle. The application of multiple forces and torques at the hand and the activity of several forearm muscles to maintain stability necessitated the development of a new method of capturing and analyzing individual muscle activity. Aim 2 focuses on neural oscillations and amplitudes of muscle activity during co-contraction (i.e. simultaneous contraction for joint stability) of a wrist flexor and extensor for wrist flexion-extension stabilization and when extra afferent input is applied to the muscles. Aim 3 addresses modulation of the amplitudes of motor output via recurrent inhibition during co-activation (i.e. simultaneous activation for movement, joint stability, etc.) of a wrist flexor and extensor muscle working as synergists or antagonists for wrist stabilization. The contributions of this dissertation include new insights into the spinal and cortical control of wrist stabilization and an analysis method for capturing the activity and mechanical properties of the wrist muscles during complex wrist stabilization.

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