Development of Gene Expression Markers of Acute Heat-Light Stress in Reef-Building Corals of the Genus Porites

Coral reefs are declining worldwide due to increased incidence of climate-induced coral bleaching, which will have widespread biodiversity and economic impacts. A simple method to measure the sub-bleaching level of heat-light stress experienced by corals would greatly inform reef management practices by making it possible to assess the distribution of bleaching risks among individual reef sites. Gene expression analysis based on quantitative PCR (qPCR) can be used as a diagnostic tool to determine coral condition in situ. We evaluated the expression of 13 candidate genes during heat-light stress in a common Caribbean coral Porites astreoides, and observed strong and consistent changes in gene expression in two independent experiments. Furthermore, we found that the apparent return to baseline expression levels during a recovery phase was rapid, despite visible signs of colony bleaching. We show that the response to acute heat-light stress in P. astreoides can be monitored by measuring the difference in expression of only two genes: Hsp16 and actin. We demonstrate that this assay discriminates between corals sampled from two field sites experiencing different temperatures. We also show that the assay is applicable to an Indo-Pacific congener, P. lobata, and therefore could potentially be used to diagnose acute heat-light stress on coral reefs worldwide.

Efficient numerical methods for the random-field Ising model: Finite-size scaling, reweighting extrapolation, and computation of response functions

It was recently shown [Phys. Rev. Lett. 110, 227201 (2013)] that the critical behavior of the random-field Ising model in three dimensions is ruled by a single universality class. This conclusion was reached only after a proper taming of the large scaling corrections of the model by applying a combined approach of various techniques, coming from the zero-and positive-temperature toolboxes of statistical physics. In the present contribution we provide a detailed description of this combined scheme, explaining in detail the zero-temperature numerical scheme and developing the generalized fluctuation-dissipation formula that allowed us to compute connected and disconnected correlation functions of the model. We discuss the error evolution of our method and we illustrate the infinite limit-size extrapolation of several observables within phenomenological renormalization. We present an extension of the quotients method that allows us to obtain estimates of the critical exponent a of the specific heat of the model via the scaling of the bond energy and we discuss the self-averaging properties of the system and the algorithmic aspects of the maximum-flow algorithm used.

Theory and Practice in Sustainability Science: Influence of Urban Form on the Urban Heat Island and Implications for Urban Systems

As the world population continues to grow past seven billion people and global challenges continue to persist including resource availability, biodiversity loss, climate change and human well-being, a new science is required that can address the integrated nature of these challenges and the multiple scales on which they are manifest. Sustainability science has emerged to fill this role. In the fifteen years since it was first called for in the pages of Science, it has rapidly matured, however its place in the history of science and the way it is practiced today must be continually evaluated. In Part I, two chapters address this theoretical and practical grounding. Part II transitions to the applied practice of sustainability science in addressing the urban heat island (UHI) challenge wherein the climate of urban areas are warmer than their surrounding rural environs. The UHI has become increasingly important within the study of earth sciences given the increased focus on climate change and as the balance of humans now live in urban areas.

In Chapter 2 a novel contribution to the historical context of sustainability is argued. Sustainability as a concept characterizing the relationship between humans and nature emerged in the mid to late 20th century as a response to findings used to also characterize the Anthropocene. Emerging from the human-nature relationships that came before it, evidence is provided that suggests Sustainability was enabled by technology and a reorientation of world-view and is unique in its global boundary, systematic approach and ambition for both well being and the continued availability of resources and Earth system function. Sustainability is further an ambition that has wide appeal, making it one of the first normative concepts of the Anthropocene.

Despite its widespread emergence and adoption, sustainability science continues to suffer from definitional ambiguity within the academe. In Chapter 3, a review of efforts to provide direction and structure to the science reveals a continuum of approaches anchored at either end by differing visions of how the science interfaces with practice (solutions). At one end, basic science of societally defined problems informs decisions about possible solutions and their application. At the other end, applied research directly affects the options available to decision makers. While clear from the literature, survey data further suggests that the dichotomy does not appear to be as apparent in the minds of practitioners.

In Chapter 4, the UHI is first addressed at the synoptic, mesoscale. Urban climate is the most immediate manifestation of the warming global climate for the majority of people on earth. Nearly half of those people live in small to medium sized cities, an understudied scale in urban climate research. Widespread characterization would be useful to decision makers in planning and design. Using a multi-method approach, the mesoscale UHI in the study region is characterized and the secular trend over the last sixty years evaluated. Under isolated ideal conditions the findings indicate a UHI of 5.3 ± 0.97 °C to be present in the study area, the magnitude of which is growing over time.

Although urban heat islands (UHI) are well studied, there remain no panaceas for local scale mitigation and adaptation methods, therefore continued attention to characterization of the phenomenon in urban centers of different scales around the globe is required. In Chapter 5, a local scale analysis of the canopy layer and surface UHI in a medium sized city in North Carolina, USA is conducted using multiple methods including stationary urban sensors, mobile transects and remote sensing. Focusing on the ideal conditions for UHI development during an anticyclonic summer heat event, the study observes a range of UHI intensity depending on the method of observation: 8.7 °C from the stationary urban sensors; 6.9 °C from mobile transects; and, 2.2 °C from remote sensing. Additional attention is paid to the diurnal dynamics of the UHI and its correlation with vegetation indices, dewpoint and albedo. Evapotranspiration is shown to drive dynamics in the study region.

Finally, recognizing that a bridge must be established between the physical science community studying the Urban Heat Island (UHI) effect, and the planning community and decision makers implementing urban form and development policies, Chapter 6 evaluates multiple urban form characterization methods. Methods evaluated include local climate zones (LCZ), national land cover database (NCLD) classes and urban cluster analysis (UCA) to determine their utility in describing the distribution of the UHI based on three standard observation types 1) fixed urban temperature sensors, 2) mobile transects and, 3) remote sensing. Bivariate, regression and ANOVA tests are used to conduct the analyses. Findings indicate that the NLCD classes are best correlated to the UHI intensity and distribution in the study area. Further, while the UCA method is not useful directly, the variables included in the method are predictive based on regression analysis so the potential for better model design exists. Land cover variables including albedo, impervious surface fraction and pervious surface fraction are found to dominate the distribution of the UHI in the study area regardless of observation method.

Chapter 7 provides a summary of findings, and offers a brief analysis of their implications for both the scientific discourse generally, and the study area specifically. In general, the work undertaken does not achieve the full ambition of sustainability science, additional work is required to translate findings to practice and more fully evaluate adoption. The implications for planning and development in the local region are addressed in the context of a major light-rail infrastructure project including several systems level considerations like human health and development. Finally, several avenues for future work are outlined. Within the theoretical development of sustainability science, these pathways include more robust evaluations of the theoretical and actual practice. Within the UHI context, these include development of an integrated urban form characterization model, application of study methodology in other geographic areas and at different scales, and use of novel experimental methods including distributed sensor networks and citizen science.

Electric shock causes physiological stress responses in shore crabs, consistent with prediction of pain

Animal pain is defined by a series of expectations or criteria, one of which is that there should be a physiological stress response associated with noxious stimuli. While crustacean stress responses have been demonstrated they are typically preceded by escape behaviour and thus the physiological change might be attributed to the behaviour rather than a pain experience. We found higher levels of stress as measured by lactate in shore crabs exposed to brief electric shock than non-shocked controls. However, shocked crabs showed more vigorous behaviour than controls. We then matched crabs with the same level of behaviour and still found that shocked crabs had stronger stress response compared with controls. The finding of the stress response, coupled with previous findings of long-Term motivational change and avoidance learning, fulfils the criteria expected of a pain experience.

Coupling short-term (B2G model) and long-term (g-function) models for ground source heat exchanger simulation in TRNSYS. Application in a real installation

Ground-source heat pump (GSHP) systems represent one of the most promising techniques for heating and cooling in buildings. These systems use the ground as a heat source/sink, allowing a better efficiency thanks to the low variations of the ground temperature along the seasons. The ground-source heat exchanger (GSHE) then becomes a key component for optimizing the overall performance of the system. Moreover, the short-term response related to the dynamic behaviour of the GSHE is a crucial aspect, especially from a regulation criteria perspective in on/off controlled GSHP systems. In this context, a novel numerical GSHE model has been developed at the Instituto de Ingeniería Energética, Universitat Politècnica de València. Based on the decoupling of the short-term and the long-term response of the GSHE, the novel model allows the use of faster and more precise models on both sides. In particular, the short-term model considered is the B2G model, developed and validated in previous research works conducted at the Instituto de Ingeniería Energética. For the long-term, the g-function model was selected, since it is a previously validated and widely used model, and presents some interesting features that are useful for its combination with the B2G model. The aim of the present paper is to describe the procedure of combining these two models in order to obtain a unique complete GSHE model for both short- and long-term simulation. The resulting model is then validated against experimental data from a real GSHP installation.

Shock Train/Boundary-Layer Interaction in Rectangular Scramjet Isolators

Numerous studies of the dual-mode scramjet isolator, a critical component in preventing inlet unstart and/or vehicle loss by containing a collection of flow disturbances called a shock train, have been performed since the dual-mode propulsion cycle was introduced in the 1960s. Low momentum corner flow and other three-dimensional effects inherent to rectangular isolators have, however, been largely ignored in experimental studies of the boundary layer separation driven isolator shock train dynamics. Furthermore, the use of two dimensional diagnostic techniques in past works, be it single-perspective line-of-sight schlieren/shadowgraphy or single axis wall pressure measurements, have been unable to resolve the three-dimensional flow features inside the rectangular isolator. These flow characteristics need to be thoroughly understood if robust dual-mode scramjet designs are to be fielded. The work presented in this thesis is focused on experimentally analyzing shock train/boundary layer interactions from multiple perspectives in aspect ratio 1.0, 3.0, and 6.0 rectangular isolators with inflow Mach numbers ranging from 2.4 to 2.7. Secondary steady-state Computational Fluid Dynamics studies are performed to compare to the experimental results and to provide additional perspectives of the flow field. Specific issues that remain unresolved after decades of isolator shock train studies that are addressed in this work include the three-dimensional formation of the isolator shock train front, the spatial and temporal low momentum corner flow separation scales, the transient behavior of shock train/boundary layer interaction at specific coordinates along the isolator's lateral axis, and effects of the rectangular geometry on semi-empirical relations for shock train length prediction. A novel multiplane shadowgraph technique is developed to resolve the structure of the shock train along both the minor and major duct axis simultaneously. It is shown that the shock train front is of a hybrid oblique/normal nature. Initial low momentum corner flow separation spawns the formation of oblique shock planes which interact and proceed toward the center flow region, becoming more normal in the process. The hybrid structure becomes more two-dimensional as aspect ratio is increased but corner flow separation precedes center flow separation on the order of 1 duct height for all aspect ratios considered. Additional instantaneous oil flow surface visualization shows the symmetry of the three-dimensional shock train front around the lower wall centerline. Quantitative synthetic schlieren visualization shows the density gradient magnitude approximately double between the corner oblique and center flow normal structures. Fast response pressure measurements acquired near the corner region of the duct show preliminary separation in the outer regions preceding centerline separation on the order of 2 seconds. Non-intrusive Focusing Schlieren Deflectometry Velocimeter measurements reveal that both shock train oscillation frequency and velocity component decrease as measurements are taken away from centerline and towards the side-wall region, along with confirming the more two dimensional shock train front approximation for higher aspect ratios. An updated modification to Waltrup \& Billig's original semi-empirical shock train length relation for circular ducts based on centerline pressure measurements is introduced to account for rectangular isolator aspect ratio, upstream corner separation length scale, and major- and minor-axis boundary layer momentum thickness asymmetry. The latter is derived both experimentally and computationally and it is shown that the major-axis (side-wall) boundary layer has lower momentum thickness compared to the minor-axis (nozzle bounded) boundary layer, making it more separable. Furthermore, it is shown that the updated correlation drastically improves shock train length prediction capabilities in higher aspect ratio isolators. This thesis suggests that performance analysis of rectangular confined supersonic flow fields can no longer be based on observations and measurements obtained along a single axis alone. Knowledge gained by the work performed in this study will allow for the development of more robust shock train leading edge detection techniques and isolator designs which can greatly mitigate the risk of inlet unstart and/or vehicle loss in flight.

Combustion Instability and Active Control: Alternative Fuels, Augmentors, and Modeling Heat Release

Experimental and analytical studies were conducted to explore thermo-acoustic coupling during the onset of combustion instability in various air-breathing combustor configurations. These include a laboratory-scale 200-kW dump combustor and a 100-kW augmentor featuring a v-gutter flame holder. They were used to simulate main combustion chambers and afterburners in aero engines, respectively. The three primary themes of this work includes: 1) modeling heat release fluctuations for stability analysis, 2) conducting active combustion control with alternative fuels, and 3) demonstrating practical active control for augmentor instability suppression. The phenomenon of combustion instabilities remains an unsolved problem in propulsion engines, mainly because of the difficulty in predicting the fluctuating component of heat release without extensive testing. A hybrid model was developed to describe both the temporal and spatial variations in dynamic heat release, using a separation of variables approach that requires only a limited amount of experimental data. The use of sinusoidal basis functions further reduced the amount of data required. When the mean heat release behavior is known, the only experimental data needed for detailed stability analysis is one instantaneous picture of heat release at the peak pressure phase. This model was successfully tested in the dump combustor experiments, reproducing the correct sign of the overall Rayleigh index as well as the remarkably accurate spatial distribution pattern of fluctuating heat release. Active combustion control was explored for fuel-flexible combustor operation using twelve different jet fuels including bio-synthetic and Fischer-Tropsch types. Analysis done using an actuated spray combustion model revealed that the combustion response times of these fuels were similar. Combined with experimental spray characterizations, this suggested that controller performance should remain effective with various alternative fuels. Active control experiments validated this analysis while demonstrating 50-70\% reduction in the peak spectral amplitude. A new model augmentor was built and tested for combustion dynamics using schlieren and chemiluminescence techniques. Novel active control techniques including pulsed air injection were implemented and the results were compared with the pulsed fuel injection approach. The pulsed injection of secondary air worked just as effectively for suppressing the augmentor instability, setting up the possibility of more efficient actuation strategy.

Post-shock thermochemistry in hypervelocity CO2 and air flow

This work represents ongoing efforts to study high-enthalpy carbon dioxide flows in anticipation of the upcoming Mars Science Laboratory (MSL) and future missions to the red planet. The work is motivated by observed anomalies between experimental and numerical studies in hypervelocity impulse facilities for high enthalpy carbon dioxide flows. In this work, experiments are conducted in the Hypervelocity Expansion Tube (HET) which, by virtue of its flow acceleration process, exhibits minimal freestream dissociation in comparison to reflected shock tunnels. This simplifies the comparison with computational result as freestream dissociation and considerable thermochemical excitation can be neglected. Shock shapes of the MSL aeroshell and spherical geometries are compared with numerical simulations incorporating detailed CO2 thermochemical modeling. The shock stand-off distance has been identified in the past as sensitive to the thermochemical state and as such, is used here as an experimental measurable for comparison with CFD and two different theoretical models. It is seen that models based upon binary scaling assumptions are not applicable for the low-density, small-scale conditions of the current work. Mars Science Laboratory shock shapes at zero angle of attack are also in good agreement with available data from the LENS X expansion tunnel facility, confi rming results are facility-independent for the same type of flow acceleration, and indicating that the flow velocity is a suitable first-order matching parameter for comparative testing. In an e ffort to address surface chemistry issues arising from high-enthalpy carbon dioxide ground-test based experiments, spherical stagnation point and aeroshell heat transfer distributions are also compared with simulation. Very good agreement between experiment and CFD is seen for all shock shapes and heat transfer distributions fall within the non-catalytic and super-catalytic solutions. We also examine spatial temperature profiles in the non-equilibrium relaxation region behind a stationary shock wave in a hypervelocity air Mach 7.42 freestream. The normal shock wave is established through a Mach reflection from an opposing wedge arrangement. Schlieren images confirm that the shock con guration is steady and the location is repeatable. Emission spectroscopy is used to identify dissociated species and to make vibrational temperature measurements using both the nitric oxide and the hydroxyl radical A-X band sequences. Temperature measurements are presented at selected locations behind the normal shock. LIFBASE is used as the simulation spectrum software for OH temperature-fitting, however the need to access higher vibrational and rotational levels for NO leads to the use of an in-house developed algorithm. For NO, results demonstrate the contribution of higher vibrational and rotational levels to the spectra at the conditions of this study. Very good agreement is achieved between the experimentally measured NO vibrational temperatures and calculations performed using an existing state-resolved, three-dimensional forced harmonic oscillator thermochemical model. The measured NO A-X vibrational temperatures are significantly higher than the OH A-X temperatures.

EXPOSURE TO EXTREME HEAT EVENTS AND CHRONIC RESPIRATORY DISEASES AMONG A NATIONALLY REPRESENTATIVE SAMPLE OF THE UNITED STATES POPULATION

Previous studies have shown that extreme weather events are on the rise in response to our changing climate. Such events are projected to become more frequent, more intense, and longer lasting. A consistent exposure metric for measuring these extreme events as well as information regarding how these events lead to ill health are needed to inform meaningful adaptation strategies that are specific to the needs of local communities. Using federal meteorological data corresponding to 17 years (1997-2013) of the National Health Interview Survey, this research: 1) developed a location-specific exposure metric that captures individuals’ “exposure” at a spatial scale that is consistent with publicly available county-level health outcome data; 2) characterized the United States’ population in counties that have experienced higher numbers of extreme heat events and thus identified population groups likely to experience future events; and 3) developed an empirical model describing the association between exposure to extreme heat events and hay fever. This research confirmed that the natural modes of forcing (e.g., El Niño-Southern Oscillation), seasonality, urban-rural classification, and division of country have an impact on the number extreme heat events recorded. Also, many of the areas affected by extreme heat events are shown to have a variety of vulnerable populations including women of childbearing age, people who are poor, and older adults. Lastly, this research showed that adults in the highest quartile of exposure to extreme heat events had a 7% increased odds of hay fever compared to those in the lowest quartile, suggesting that exposure to extreme heat events increases risk of hay fever among US adults.

Heat dissipation from carbon nano-electronics

The incorporation of graphitic compounds such as carbon nanotubes (CNTs) and graphene into nano-electronic device packaging holds much promise for waste heat management given their high thermal conductivities. However, as these graphitic materials must be used in together with other semiconductor/insulator materials, it is not known how thermal transport is affected by the interaction. Using different simulation techniques, in this thesis, we evaluate the thermal transport properties - thermal boundary conductance (TBC) and thermal conductivity - of CNTs and single-layer graphene in contact with an amorphous SiO2 (a-SiO2) substrate. First, the theoretical methodologies and concepts used in our simulations are presented. In particular, two concepts are described in detail as they are necessary for the understanding of the subsequent chapters. The first is the linear response Green-Kubo (GK) theory of thermal boundary conductance (TBC), which we develop in this thesis, and the second is the spectral energy density method, which we use to directly compute the phonon lifetimes and thermal transport coefficients. After we set the conceptual foundations, the TBC of the CNT-SiO2 interface is computed using non- equilibrium molecular dynamics (MD) simulations and the new Green-Kubo method that we have developed. Its dependence on temperature, the strength of the interaction with the substrate, and tube diameter are evaluated. To gain further insight into the phonon dynamics in supported CNTs, the scattering rates are computed using the spectral energy density (SED) method. With this method, we are able to distinguish the different scattering mechanisms (boundary and CNT-substrate phonon-phonon) and rates. The phonon lifetimes in supported CNTs are found to be reduced by contact with the substrate and we use that lifetime reduction to determine the change in CNT thermal conductivity. Next, we examine thermal transport in graphene supported on SiO2. The phonon contribution to the TBC of the graphene-SiO2 interface is computed from MD simulations and found to agree well with experimentally measured values. We derive the theory of remote phonon scattering of graphene electrons and compute the heat transfer coefficient dependence on doping level and temperature. The thermal boundary conductance from remote phonon scattering is found to be an order of magnitude smaller than that of the phonon contribution. The in-plane thermal conductivity of supported graphene is calculated from MD simulations. The experimentally measured order of magnitude reduction in thermal conductivity is reproduced in our simulations. We show that this reduction is due to the damping of the flexural (ZA) modes. By varying the interaction between graphene and the substrate, the ZA modes hybridize with the substrate Rayleigh modes and the dispersion of the hybridized modes is found to linearize in the strong coupling limit, leading to an increased thermal conductance in the composite structure.

Near-infrared Instrumentation For Rapid-response Astronomy

Ɣ-ray bursts (GRBs) are the Universe's most luminous transient events. Since the discovery of GRBs was announced in 1973, efforts have been ongoing to obtain data over a broader range of the electromagnetic spectrum at the earliest possible times following the initial detection. The discovery of the theorized ``afterglow'' emission in radio through X-ray bands in the late 1990s confirmed the cosmological nature of these events. At present, GRB afterglows are among the best probes of the early Universe (z ≳ 9). In addition to informing theories about GRBs themselves, observations of afterglows probe the circum-burst medium (CBM), properties of the host galaxies and the progress of cosmic reionization. To explore the early-time variability of afterglows, I have developed a generalized analysis framework which models near-infrared (NIR), optical, ultra-violet (UV) and X-ray light curves without assuming an underlying model. These fits are then used to construct the spectral energy distribution (SED) of afterglows at arbitrary times within the observed window. Physical models are then used to explore the evolution of the SED parameter space with time. I demonstrate that this framework produces evidence of the photodestruction of dust in the CBM of GRB 120119A, similar to the findings from a previous study of this afterglow. The framework is additionally applied to the afterglows of GRB 140419A and GRB 080607. In these cases the evolution of the SEDs appears consistent with the standard fireball model. Having introduced the scientific motivations for early-time observations, I introduce the Rapid Infrared Imager-Spectrometer (RIMAS). Once commissioned on the 4.3 meter Discovery Channel Telescope (DCT), RIMAS will be used to study the afterglows of GRBs through photometric and spectroscopic observations beginning within minutes of the initial burst. The instrument will operate in the NIR, from 0.97 μm to 2.37 μm, permitting the detection of very high redshift (z ≳ 7) afterglows which are attenuated at shorter wavelengths by Lyman-ɑ absorption in the intergalactic medium (IGM). A majority of my graduate work has been spent designing and aligning RIMAS's cryogenic (~80 K) optical systems. Design efforts have included an original camera used to image the field surrounding spectroscopic slits, tolerancing and optimizing all of the instrument's optics, thermal modeling of optomechanical systems, and modeling the diffraction efficiencies for some of the dispersive elements. To align the cryogenic optics, I developed a procedure that was successfully used for a majority of the instrument's sub-assemblies. My work on this cryogenic instrument has necessitated experimental and computational projects to design and validate designs of several subsystems. Two of these projects describe simple and effective measurements of optomechanical components in vacuum and at cryogenic temperatures using an 8-bit CCD camera. Models of heat transfer via electrical harnesses used to provide current to motors located within the cryostat are also presented.

Volatility Spillover and Multivariate Volatility Impulse Response Analysis of GFC News Events

This paper applies two measures to assess spillovers across markets: the Diebold Yilmaz (2012) Spillover Index and the Hafner and Herwartz (2006) analysis of multivariate GARCH models using volatility impulse response analysis. We use two sets of data, daily realized volatility estimates taken from the Oxford Man RV library, running from the beginning of 2000 to October 2016, for the S&P500 and the FTSE, plus ten years of daily returns series for the New York Stock Exchange Index and the FTSE 100 index, from 3 January 2005 to 31 January 2015. Both data sets capture both the Global Financial Crisis (GFC) and the subsequent European Sovereign Debt Crisis (ESDC). The spillover index captures the transmission of volatility to and from markets, plus net spillovers. The key difference between the measures is that the spillover index captures an average of spillovers over a period, whilst volatility impulse responses (VIRF) have to be calibrated to conditional volatility estimated at a particular point in time. The VIRF provide information about the impact of independent shocks on volatility. In the latter analysis, we explore the impact of three different shocks, the onset of the GFC, which we date as 9 August 2007 (GFC1). It took a year for the financial crisis to come to a head, but it did so on 15 September 2008, (GFC2). The third shock is 9 May 2010. Our modelling includes leverage and asymmetric effects undertaken in the context of a multivariate GARCH model, which are then analysed using both BEKK and diagonal BEKK (DBEKK) models. A key result is that the impact of negative shocks is larger, in terms of the effects on variances and covariances, but shorter in duration, in this case a difference between three and six months.

Oral vaccination with heat inactivated Mycobacterium bovis activates the complement system to protect against tuberculosis

Tuberculosis (TB) remains a pandemic affecting billions of people worldwide, thus stressing the need for new vaccines. Defining the correlates of vaccine protection is essential to achieve this goal. In this study, we used the wild boar model for mycobacterial infection and TB to characterize the protective mechanisms elicited by a new heat inactivated Mycobacterium bovis vaccine (IV). Oral vaccination with the IV resulted in significantly lower culture and lesion scores, particularly in the thorax, suggesting that the IV might provide a novel vaccine for TB control with special impact on the prevention of pulmonary disease, which is one of the limitations of current vaccines. Oral vaccination with the IV induced an adaptive antibody response and activation of the innate immune response including the complement component C3 and inflammasome. Mycobacterial DNA/RNA was not involved in inflammasome activation but increased C3 production by a still unknown mechanism. The results also suggested a protective mechanism mediated by the activation of IFN-γ producing CD8+ T cells by MHC I antigen presenting dendritic cells (DCs) in response to vaccination with the IV, without a clear role for Th1 CD4+ T cells. These results support a role for DCs in triggering the immune response to the IV through a mechanism similar to the phagocyte response to PAMPs with a central role for C3 in protection against mycobacterial infection. Higher C3 levels may allow increased opsonophagocytosis and effective bacterial clearance, while interfering with CR3-mediated opsonic and nonopsonic phagocytosis of mycobacteria, a process that could be enhanced by specific antibodies against mycobacterial proteins induced by vaccination with the IV. These results suggest that the IV acts through novel mechanisms to protect against TB in wild boar.

Global transcriptome analysis of Lactococcus garvieae strains in response to temperature

Lactococcus garvieae is an important fish and an opportunistic human pathogen. The genomic sequences of several L. garvieae strains have been recently published, opening the possibility of global studies on the biology of this pathogen. In this study, a whole genome DNA microarray of two strains of L. garvieae was designed and validated. This DNA microarray was used to investigate the effects of growth temperature (18°C and 37°C) on the transcriptome of two clinical strains of L. garvieae that were isolated from fish (Lg8831) and from a human case of septicemia (Lg21881). The transcriptome profiles evidenced a strain-specific response to temperature, which was more evident at 18°C. Among the most significant findings, Lg8831 was found to up-regulate at 18°C several genes encoding different cold-shock and cold-induced proteins involved in an efficient adaptive response of this strain to low-temperature conditions. Another relevant result was the description, for the first time, of respiratory metabolism in L. garvieae, whose gene expression regulation was temperature-dependent in Lg21881. This study provides new insights about how environmental factors such as temperature can affect L. garvieae gene expression. These data could improve our understanding of the regulatory networks and adaptive biology of this important pathogen.