NOVEL MECHANISMS OF ANTIGEN PROCESSING THAT ENHANCE BCG VACCINE EFFICACY

Mycobacterium tuberculosis, the causative agent of tuberculosis, is the most lethal single infectious agent afflicting man today causing 2 million deaths per year. The World Health Organization recommends a vaccine as the best option to prevent this disease. The current vaccine, BCG, has a variable efficacy and does not protect adults. It is known that BCG vaccine becomes sequestered in special phagosome compartments of macrophages that do not fuse with lysosomes. Since lysosome fusion is necessary for peptide production and T cell priming leading to protective TH1 immunity, we hypothesized that vaccine efficacy is reduced and occurs perhaps due to non-lysosome dependent mechanisms. We therefore proposed an in depth analysis of phagosome environment, and its proteome to unravel mechanisms of antigen processing and presentation. We initially discovered that three mechanisms of pH regulation including vacuolar proton ATPase, phagocyte oxidase and superoxide dismutase (SOD) secretion from BCG vaccine affect antigen processing within phagosomes. These studies led to the discovery that a mutant of BCG vaccine which lacked SOD was a better vaccine. Subsequently, the proteomic analysis of vaccine phagosomes led to the discovery of novel protease (γ-secretase) enriched on BCG vaccine phagosomes. We then demonstrated that these proteases generated a peptide from the BCG vaccine which was presented through the MHC-II pathway to T cells and induced a TH1 response. The specificity of antigen production from γ-secretase was confirmed through siRNA knockdown of the components of the protease namely, nicastrin, presenilin and APH, which led to a decrease in antigen presentation. We therefore conclude that, even though BCG phagosomes are sequestered and do not fuse with lysosomes to generate peptide antigens, there are complex and novel in situ mechanisms within phagosomes that are capable of generating an immune response. We conclude that TH1 immunity to BCG vaccine arises mostly due to non-lysosome dependent immune mechanisms of macrophages and dendritic cells.

Rhesus factors and ammonium: a function in efflux?

Completion of fungal, plant and human genomes paved the way to the identification of erythrocytic rhesus proteins and their kidney homologs as ammonium transporters. Ammonium is the preferred nitrogen source of bacteria and fungi, and plants acquire nitrogen from the soil in the form of ammonium [1]. In animals and humans, assimilated forms of nitrogen - amino acids - are much preferred for nutrition, and, in the case of ammonotelic animals, ammonium is used for the excretion of nitrogen instead. In the human kidney, ammonium is produced, reabsorbed and excreted as a means to maintain pH balance and to get rid of surplus inorganic nitrogen. Whether ammonium transport also has a role in the pH regulation of other organs is not known and the molecular mechanisms were not, up to now, understood.

Effects of CO2-driven ocean acidification on early life stages of marine medaka (Oryzias melastigma)

The potential effects of elevated CO2 level and reduced carbonate saturation state in marine environment on fishes and other non-calcified organisms are still poorly known. In present study, we investigated the effects of ocean acidification on embryogenesis and organogenesis of newly hatched larvae of marine medaka (Oryzias melastigma) after 21 d exposure of eggs to different artificially acidified seawater (pH 7.6 and 7.2, respectively), and compared with those in control group (pH 8.2). Results showed that CO2-driven seawater acidification (pH 7.6 and 7.2) had no detectable effect on hatching time, hatching rate, and heart rate of embryos. However, the deformity rate of larvae in pH 7.2 treatment was significantly higher than that in control treatment. The left and right sagitta areas did not differ significantly from each other in each treatment. However, the mean sagitta area of larvae in pH 7.6 treatment was significantly smaller than that in the control (p = 0.024). These results suggest that although marine medaka might be more tolerant of elevated CO2 than some other fishes, the effect of elevated CO2 level on the calcification of otolith is likely to be the most susceptibly physiological process of pH regulation in early life stage of marine medaka.

Seawater carbonate chemistry and biological processes of Mytilus edulis during experiments, 2010

Marine organisms are exposed to increasingly acidic oceans, as a result of equilibration of surface ocean water with rising atmospheric CO2 concentrations. In this study, we examined the physiological response of Mytilus edulis from the Baltic Sea, grown for 2 months at 4 seawater pCO2 levels (39, 113, 243 and 405 Pa/385, 1,120, 2,400 and 4,000 µatm). Shell and somatic growth, calcification, oxygen consumption and excretion rates were measured in order to test the hypothesis whether exposure to elevated seawater pCO2 is causally related to metabolic depression. During the experimental period, mussel shell mass and shell-free dry mass (SFDM) increased at least by a factor of two and three, respectively. However, shell length and shell mass growth decreased linearly with increasing pCO2 by 6-20 and 10-34%, while SFDM growth was not significantly affected by hypercapnia. We observed a parabolic change in routine metabolic rates with increasing pCO2 and the highest rates (+60%) at 243 Pa. excretion rose linearly with increasing pCO2. Decreased O:N ratios at the highest seawater pCO2 indicate enhanced protein metabolism which may contribute to intracellular pH regulation. We suggest that reduced shell growth under severe acidification is not caused by (global) metabolic depression but is potentially due to synergistic effects of increased cellular energy demand and nitrogen loss.

Seawater carbonate chemistry and biological processes of foraminifera, Globigerinoides ruber and Globigerinella siphonifera during experiments, 2011

Specimens of two species of planktic foraminifera, Globigerinoides ruber and Globigerinella siphonifera, were grown under controlled laboratory conditions at a range of temperatures (18-31 °C), salinities (32-44 psu) and pH levels (7.9-8.4). The shells were examined for their calcium isotope compositions (d44/40Ca) and strontium to calcium ratios (Sr/Ca) using Thermal Ionization Mass Spectrometry and Inductively Coupled Plasma Mass Spectrometry. Although the total variation in d44/40Ca (~0.3 per mill) in the studied species is on the same order as the external reproducibility, the data set reveals some apparent trends that are controlled by more than one environmental parameter. There is a well-defined inverse linear relationship between d44/40Ca and Sr/Ca in all experiments, suggesting similar controls on these proxies in foraminiferal calcite independent of species. Analogous to recent results from inorganically precipitated calcite, we suggest that Ca isotope fractionation and Sr partitioning in planktic foraminifera are mainly controlled by precipitation kinetics. This postulation provides us with a unique tool to calculate precipitation rates and draws support from the observation that Sr/Ca ratios are positively correlated with average growth rates. At 25 °C water temperature, precipitation rates in G. siphonifera and G. ruber are calculated to be on the order of 2000 and 3000 µmol/m**2/h, respectively. The lower d44/40Ca observed at 29 °C in both species is consistent with increased precipitation rates at high water temperatures. Salinity response of d44/40Ca (and Sr/Ca) in G. siphonifera implies that this species has the highest precipitation rates at the salinity of its natural habitat, whereas increasing salinities appear to trigger higher precipitation rates in G. ruber. Isotope effects that cannot be explained by precipitation rate in planktic foraminifera can be explained by a biological control, related to a vacuolar pathway for supply of ions during biomineralization and a pH regulation mechanism in these vacuoles. In case of an additional pathway via cross-membrane transport, supplying light Ca for calcification, the d44/40Ca of the reservoir is constrained as -0.2 per mill relative to seawater. Using a Rayleigh distillation model, we calculate that calcification occurs in a semi-open system, where less than half of the Ca supplied by vacuolization is utilized for calcite precipitation. Our findings are relevant for interpreting paleo-proxy data on d44/40Ca and Sr/Ca in foraminifera as well as understanding their biomineralization processes.

Gene expression changes in the coccolithophore Emiliania huxleyi after 500 generations of selection to ocean acidification

Coccolithophores are unicellular marine algae that produce biogenic calcite scales and substantially contribute to marine primary production and carbon export to the deep ocean. Ongoing ocean acidification particularly impairs calcifying organisms, mostly resulting in decreased growth and calcification. Recent studies revealed that the immediate physiological response in the coccolithophore Emiliania huxleyi to ocean acidification may be partially compensated by evolutionary adaptation, yet the underlying molecular mechanisms are currently unknown. Here, we report on the expression levels of 10 candidate genes putatively relevant to pH regulation, carbon transport, calcification and photosynthesis in E. huxleyi populations short-term exposed to ocean acidification conditions after acclimation (physiological response) and after 500 generations of high CO2 adaptation (adaptive response). The physiological response revealed downregulation of candidate genes, well reflecting the concomitant decrease of growth and calcification. In the adaptive response, putative pH regulation and carbon transport genes were up-regulated, matching partial restoration of growth and calcification in high CO2-adapted populations. Adaptation to ocean acidification in E. huxleyi likely involved improved cellular pH regulation, presumably indirectly affecting calcification. Adaptive evolution may thus have the potential to partially restore cellular pH regulatory capacity and thereby mitigate adverse effects of ocean acidification.

Seawater carbonate chemistry and processes during experiments with coral Acropora eurystoma, 2006

The rise in atmospheric CO2 has caused significant decrease in sea surface pH and carbonate ion (CO3-2) concentration. This decrease has a negative effect on calcification in hermatypic corals and other calcifying organisms. We report the results of three laboratory experiments designed specifically to separate the effects of the different carbonate chemistry parameters (pH, CO3-2, CO2 [aq], total alkalinity [AT], and total inorganic carbon [CT]) on the calcification, photosynthesis, and respiration of the hermatypic coral Acropora eurystoma. The carbonate system was varied to change pH (7.9-8.5), without changing CT; CT was changed keeping the pH constant, and CT was changed keeping the pCO2 constant. In all of these experiments, calcification (both light and dark) was positively correlated with CO3-2 concentration, suggesting that the corals are not sensitive to pH or CT but to the CO3-2 concentration. A decrease of ~30% in the CO3-2 concentration (which is equivalent to a decrease of about 0.2 pH units in seawater) caused a calcification decrease of about 50%. These results suggest that calcification in today's ocean (pCO2 = 370 ppm) is lower by ~20% compared with preindustrial time (pCO2 = 280 ppm). An additional decrease of ~35% is expected if atmospheric CO2 concentration doubles (pCO2 = 560 ppm). In all of these experiments, photosynthesis and respiration did not show any significant response to changes in the carbonate chemistry of seawater. Based on this observation, we propose a mechanism by which the photosynthesis of symbionts is enhanced by coral calcification at high pH when CO2(aq) is low. Overall it seems that photosynthesis and calcification support each other mainly through internal pH regulation, which provides CO3-2 ions for calcification and CO2(aq) for photosynthesis.

Adaptation of a globally important coccolithophore to ocean warming and acidification

Regulating intracellular pH (pHi) is critical for optimising the metabolic activity of corals, yet mechanisms involved in pH regulation and the buffering capacity within coral cells are not well understood. Our study investigated how the presence of symbiotic dinoflagellates affects the response of pHi to pCO2-driven seawater acidification in cells isolated from Pocillopora damicornis. Using the fluorescent dye BCECF-AM, in conjunction with confocal microscopy, we simultaneously characterised the response of pHi in host coral cells and their dinoflagellate symbionts, in symbiotic and non-symbiotic states under saturating light, with and without the photosynthetic inhibitor DCMU. Each treatment was run under control (pH 7.8) and CO2 acidified seawater conditions (decreasing pH from 7.8 - 6.8). After two hours of CO2 addition, by which time the external pH (pHe) had declined to 6.8, the dinoflagellate symbionts had increased their pHi by 0.5 pH units above control levels. In contrast, in both symbiotic and non-symbiotic host coral cells, 15 min of CO2 addition (0.2 pH unit drop in pHe) led to cytoplasmic acidosis equivalent to 0.4 pH units. Despite further seawater acidification over the duration of the experiment, the pHi of non-symbiotic coral cells did not change, though in host cells containing a symbiont cell the pHi recovered to control levels. This recovery was negated when cells were incubated with DCMU. Our results reveal that photosynthetic activity of the endosymbiont is tightly coupled with the ability of the host cell to recover from cellular acidosis after exposure to high CO2 / low pH.

Seawater carbonate chemistry and biological processed during experiments with corals Porites sp. & Stylophora pistillata, 2010

Uptake of anthropogenic CO2 by the oceans is altering seawater chemistry with potentially serious consequences for coral reef ecosystems due to the reduction of seawater pH and aragonite saturation state (omega arag). The objectives of this long-term study were to investigate the viability of two ecologically important reef-building coral species, massive Porites sp. and Stylophora pistilata, exposed to high pCO2(or low pH) conditions and to observe possible changes in physiologically related parameters as well as skeletal isotopic composition. Fragments of Porites sp. and S. pistilata were kept for 6-14 months under controlled aquarium conditions characterized by normal and elevated pCO2 conditions, corresponding to pHTvalues of 8.09, 7.49, and 7.19, respectively. In contrast with shorter, and therefore more transient experiments, the long experimental timescale achieved in this study ensures complete equilibration and steady state with the experimental environment and guarantees that the data provide insights into viable and stably growing corals. During the experiments, all coral fragments survived and added new skeleton, even at seawater omega arag <1, implying that the coral skeleton is formed by mechanisms under strong biological control. Measurements of boron (B), carbon (C) and oxygen (O) isotopic composition of skeleton, C isotopic composition of coral tissue and symbiont zooxanthellae, along with physiological data (such as skeletal growth, tissue biomass, zooxanthellae cell density and chlorophyll concentration) allow for a direct comparison with corals living under normal conditions and sampled simultaneously. Skeletal growth and zooxanthellae density were found to decrease, whereas coral tissue biomass (measured as protein concentration) and zooxanthellae chlorophyll concentrations increased under high pCO2 (low pH) conditions. Both species showed similar trends of delta11B depletion and delta18O enrichment under reduced pH, whereas the delta13C results imply species-specific metabolic response to high pCO2 conditions. The skeletal delta11B values plot above seawater delta11B vs. pH borate fractionation curves calculated using either the theoretically derived deltaB value of 1.0194 (Kakihana et al., Bull. Chem. Soc. Jpn. 50(1977), 158) or the empirical deltaB value of 1.0272 (Klochko et al., EPSL 248 (2006), 261). However, the effective deltaB must be greater than 1.0200 in order to yield calculated coral skeletal delta11B values for pH conditions where omega arag >1. The delta11B vs. pH offset from the literature seawater delta11B vs. pH fractionation curves suggests a change in the ratio of skeletal material laid down during dark and light calcification and/or an internal pH regulation, presumably controlled by ion-transport enzymes. Finally, seawater pH significantly influences skeletal delta13C and delta18O. This must be taken into consideration when reconstructing paleo-environmental conditions from coral skeleton

Seawater carbonate chemistry and clownfish Amphiprion percula size and otholith development during experiments, 2011

Calcification in many invertebrate species is predicted to decline due to ocean acidification. The potential effects of elevated CO2 and reduced carbonate saturation state on other species, such as fish, are less well understood. Fish otoliths (earbones) are composed of aragonite, and thus, might be susceptible to either the reduced availability of carbonate ions in seawater at low pH, or to changes in extracellular concentrations of bicarbonate and carbonate ions caused by acid-base regulation in fish exposed to high pCO2. We reared larvae of the clownfish Amphiprion percula from hatching to settlement at three pHNBS and pCO2 levels (control: ~pH 8.15 and 404 µatm CO2; intermediate: pH 7.8 and 1050 µatm CO2; extreme: pH 7.6 and 1721 µatm CO2) to test the possible effects of ocean acidification on otolith development. There was no effect of the intermediate treatment (pH 7.8 and 1050 µatm CO2) on otolith size, shape, symmetry between left and right otoliths, or otolith elemental chemistry, compared with controls. However, in the more extreme treatment (pH 7.6 and 1721 µatm CO2) otolith area and maximum length were larger than controls, although no other traits were significantly affected. Our results support the hypothesis that pH regulation in the otolith endolymph can lead to increased precipitation of CaCO3 in otoliths of larval fish exposed to elevated CO2, as proposed by an earlier study, however, our results also show that sensitivity varies considerably among species. Importantly, our results suggest that otolith development in clownfishes is robust to even the more pessimistic changes in ocean chemistry predicted to occur by 2100.

Analysis of Alpha CA Genes in Early Vertebrates and ; High-Invertebrates

Carbonic anhydrases are enzymes that are ubiquitously found in all organisms that are engaged in catalyzing the hydration of carbon dioxide to form bicarbonate and proton and vice versa. They are crucial in the process of respiration, bone resorption, pH regulation, ion transport, and photosynthesis in plants. Out of the five classes of carbonic anhydrase α, β, γ, δ, ζ this study focused in the α carbonic anhydrases. This class of CAs constitute of 16 subfamilies in mammals that include 3 non-active enzymes known as Carbonic Anhydrase Related Proteins. The inactiveness of these enzymes is due to the loss of one or more Histidine residues in the active site. This thesis was conducted based on the aim of studying evolutionary analysis of carbonic anhydrase sequences from organisms spanning from the Cambrian age. It was carried out in two phases. The first phase was the sequence collection, which involved many biological sequence databases as a source. The scope of this segment included sequence alignments and analysis of the sequence manually and in an automated form incorporating few analysis tools. The second Phase was phylogenetic analysis and exploring the subcellular location of the proteins, which was key for the evolutionary analysis. Through the medium of the methods conducted with respect to the phases mentioned above, it was possible to accomplish the desired result. Certain thought-provoking sequences were come across and analyzed thoroughly. Whereas, Phylogenetics showed interesting results to bolster previous findings and new findings as well which lay bedrock for future intensified studies.