Dynamic responses of the benthic bacterial community at the Western English Channel observatory site L4 are driven by deposition of fresh phytodetritus

The impact of the seasonal deposition of phytoplankton and phytodetritus on surface sediment bacterial abundance and community composition was investigated at the Western English Channel site L4. Sediment and water samples were collected from January to September in 2012, increasing in frequency during periods of high water column phytoplankton abundance. Compared to the past two decades, the spring bloom in 2012 was both unusually long in duration and contained higher than average biomass. Within spring months, the phytoplankton bloom was well mixed through the water column and showed accumulations near the sea bed, as evidenced by flow cytometry measurements of nanoeukaryotes, water column chlorophyll a and the appearance of pelagic phytoplankton at the sediment. Measurements of chlorophyll and chlorophyll degradation products indicated phytoplankton material was heavily degraded after it reached the sediment surface: the nature of the chlorophyll degradation products (predominantly pheophorbide, pyropheophorbide and hydroxychlorophyllone) was indicative of grazing activity. The abundance of bacterial 16S rRNA genes g−1 sediment (used as a proxy for bacterial biomass) increased markedly with the onset of the phytoplankton bloom, and correlated with measurements of chlorophyll at the surface sediment. Together, this suggests that bacteria may have responded to nutrients released via grazing activity. In depth sequencing of the 16S rRNA genes indicated that the composition of the bacterial community shifted rapidly through-out the prolonged spring bloom period. This was primarily due to an increase in the relative sequence abundance of Flavobacteria.

ROLE OF MULTIPLE TOLL-LIKE RECEPTOR ACTIVATION IN REGULATING CYTOTOXIC T CELL PRIMING TO LYMPOCYTIC CHORIOMENINGITIS VIRUS INFECTIONS

Foreign pathogens are recognized by toll-like receptors (TLR), present on various immune cells such as professional antigen-presenting cells (pAPCs). On recognition of its ligand, these receptors activate pAPCs, which may in turn influence naïve CD8+ T cell activation and affect their abilities to clear viral infection. However, how TLR ligands (TLR-L) can regulate CD8+ T cell responses have not been fully elucidated. This thesis will focus on examining how the presence of components from foreign pathogens, e.g. viral or bacterial infection, can contribute to shaping host immunity during concurrent viral infections. Since nitric oxide (NO), an innate effector immune molecule, was recently suggested to regulate proteasome activity; we sought to examine if NO can influence MHC-I antigen presentation during viral infections. The data in this section of the thesis provides evidence that combined TLR engagement can alter the presentation of certain CD8+ epitopes due to NO-induced inhibition in proteasome activity. Taken together, the data demonstrate that TLR ligation can influence the adaptive immune response due to induction of specific innate effector molecules such as NO. Next, the influence of combined TLR engagement on CD8+ T cell immunodominance hierarchies during viral infections was examined. In this section, we established that dual TLR2 and TLR3 stimulation alters immunodominance hierarchies of LCMV epitopes as a result of reduced uptake of cell-associated antigens and reduced cross-presentation of NP396 consequently suppressing NP396-specific CD8+ T cell responses. These findings are significant as they highlight a new role for TLR ligands in regulating anti-viral CD8+ T cell responses through impairing cross-presentation of cell-associated antigens depending on the type of TLR present in the environment during infections. Finally, we addressed TLR ligand induced type I interferon production and the signalling pathways that regulate them in two different mouse macrophage populations – those derived from the spleen or bone marrow. In this study, we observed that concomitant TLR2 stimulation blocked the induction of type I IFN induced by TLR4 in bone marrow-derived macrophages, but not spleen-derived macrophages in SOCS3-dependent manner. Taken together, the data presented in this thesis have defined new facets of how anti-viral responses are regulated by TLR activation, especially if multiple receptors are engaged simultaneously.

Novel dipeptidyl peptidase IV resistant analogues of glucagon-like peptide-1(7-36)amide have preserved biological activities in vitro conferring improved glucose-lowering action in vivo

Although the incretin hormone glucagon-like peptide-1 (GLP-1) is a potent stimulator of insulin release, its rapid degradation in vivo by the enzyme dipeptidyl peptidase IV (DPP IV) greatly limits its potential for treatment of type 2 diabetes. Here, we report two novel Ala(8)-substituted analogues of GLP-1, (Abu(8))GLP-1 and (Val(8) GLP-1 which were completely resistant to inactivation by DPP IV or human plasma. (Abu(8))GLP-1 and (Val(8))GLP-1 exhibited moderate affinities (IC50: 4.76 and 81.1 nM, respectively) for the human GLP-1 receptor compared with native GLP-1 (IC50: 0.37 nM). (Abu(8))GLP-1 and (Val(8))GLP-1 dose-dependently stimulated cAMP in insulin-secreting BRIN BD11 cells with reduced potency compared with native GLP-1 (1.5- and 3.5-fold, respectively). Consistent with other mechanisms of action, the analogues showed similar, or in the case of (Val(8))GLP-1 slightly impaired insulin releasing activity in BRIN BD11 cells. Using adult obese (ob/ob) mice, (Abu(8))GLP-1 had similar glucose-lowering potency to native GLP-1 whereas the action of (Val(8))GLP-1 was enhanced by 37%. The in vivo insulin-releasing activities were similar. These data indicate that substitution of Ala(8) in GLP-1 with Abu or Val confers resistance to DPP IV inactivation and that (Val(8))GLP-1 is a particularly potent N-terminally modified GLP-1 analogue of possible use in type 2 diabetes.

Functional characterization of a Kar3/Vik1-like Kinesin-14 heterodimer from the filamentous multinucleate fungus Ashbya gossypii

Kinesins are motor proteins that convert chemical energy from ATP hydrolysis into mechanical energy used to generate force along microtubules, transporting organelles, vesicles, and proteins within the cell. Kar3 kinesins are microtubule minus-end-directed motors with pleiotropic functions in mating and mitosis of budding and fission yeast. In Saccharomyces cerevisiae, Kar3 is multifunctionalized by two non-catalytic companion proteins, Vik1 and Cik1. A Kar3-like kinesin and a single Vik1/Cik1 ortholog are also expressed by the filamentous fungus Ashbya gossypii, which exhibits different nuclear movement challenges and unique microtubule dynamics from its yeast relatives. We hypothesized that these differences in A. gossypii physiology could translate into interesting and novel differences in its versions of Kar3 and Vik1/Cik1. Presented here is a structural and functional analysis of recombinantly expressed and purified forms of these motor proteins. Compared to the previously published S. cerevisiae Kar3 motor domain structure (ScKar3MD), AgKar3MD displays differences in the conformation of the ATPase pocket. Perhaps it is not surprising then that we observed the maximal microtubule-stimulated ATPase rate (kcat) of AgKar3MD to be approximately 3-fold slower than ScKar3MD, and that the affinity of AgKar3MD for microtubules (Kd,MT) was lower than ScKar3MD. This may suggest that elements that compose the ATPase pocket and that participate in conformational changes required for efficient ATP hydrolysis or products release work differently for AgKar3 and ScKar3. There are also subtle structural differences in the disposition of the secondary structural elements in the small lobe (B1a, B1b, and B1c) at the edge of the motor domain of AgKar3 that may reflect the enhanced microtubule-depolymerization activity that we observed for this motor, or they could relate to its interactions with a different regulatory companion protein than its budding yeast counterpart. Although we were unable to gain experimentally determined high-resolution information of AgVik1, the results of Phyre2-based bioinformatics analyses may provide a structural explanation for the limited microtubule-binding activity we observed. These and other fundamental differences in AgKar3/Vik1 could explain divergent functionalities from the ScKar3/Vik1 and ScKar3/Cik1 motor assemblies.

Effect of chronic angiotensin converting enzyme inhibition on spatial memory and anxiety-like behavours in rats

Angiotensin converting enzyme inhibitors (ACEis) are widely used anti-hypertensive agents that are also reported to have positive effects on mood and cognition. The present study examined the influence of the ACEi, perindopril, on cognitive performance and anxiety measures in rats. Two groups of rats were treated orally for one week with the ACEi, perindopril, at doses of 0.1 and 1.0mg/kg/day. Learning was assessed by the reference memory task in the water maze, comparing treated to control rats. Over five training days both perindopril-treated groups learnt the location of the submerged platform in the water maze task significantly faster than control rats. A 60s probe trial on day 6 showed that the 1.0mg/kg/day group spent significantly longer time in the training quadrant than control rats. This improved performance in the swim maze task was not due to the effect of perindopril on motor activity or the anxiety levels of the rats as perindopril-treated and control animals behaved similarly in activity boxes and on the elevated+maze. These results confirm the anecdotal human studies that ACEis have a positive influence on cognition and provide possibilities for ACEis to be developed into therapies for memory loss.

Kit-like immunopositive cells in sheep mesenteric lymphatic vessels.

Recent electrophysiological studies have suggested that there is a subpopulation of cells in lymphatic vessels which act as pacemakers controlling the characteristic spontaneous contractile activity in this tissue. In this study, electron microscopy and immunohistochemical techniques were used on sheep mesenteric lymphatic vessels to investigate the morphology of the cells comprising the lymphatic wall. The smooth muscle cells were not orientated in circular and longitudinal layers as is seen in the gastrointestinal tract, but were arranged in bundles which interlock and cross over in a basket-weave fashion. Antibodies to Kit and vimentin, which are widely used to label specialised pacemaking cells in the gastrointestinal tract (known as interstitial cells of Cajal), demonstrated the existence of an axially orientated subpopulation of cells lying between the endothelium and the bulk of the smooth muscle. Examination of this area using electron microscopy showed cells which were electron dense compared to the underlying smooth muscle and contained caveolae, Golgi complexes, mitochondria, 10-nm filaments, a well-developed endoplasmic reticulum and a basal lamina. The smooth muscle cells typically contained caveolae, dense bodies, mitochondria, abundant filaments, sER and basal laminae. Cells dispersed for patch-clamp studies were also stained for vimentin and myosin. Myosin-staining cells had the typical spindle appearance of smooth muscle cells whereas the vimentin-positive cells could either be branched or more closely resemble the smooth muscle cells. The present study provides the first morphological evidence that specialised cells exist within the vascular system which have the ultrastructural characteristics of pacemaker cells in other tissues and are vimentin and Kit positive.

Emission lines of Na-like ions in spectra obtained with the Solar EUV Research Telescope and Spectrograph (SERTS)

Theoretical emission-line ratios involving transitions in the 236-412 Angstrom wavelength range are presented for the Na-like ions Ar viii, Cr xiv, Mn xv, Fe xvi, Co xvii, Ni xviii and Zn xx. A comparison of these with an extensive data set of the solar active region, quiet-Sun, subflare and off-limb observations, obtained during rocket flights by the Solar EUV Research Telescope and Spectrograph (SERTS), reveals generally very good agreement between theory and experiment. This indicates that most of the Na-like ion lines are reliably detected in the SERTS observations, and hence may be employed with confidence in solar spectral analyses. However, the features in the SERTS spectra at 236.34 and 300.25 Angstrom, originally identified as the Ni xviii 3p (2) P-3/2 -3d (2) D- 3/2 and Cr xiv 3p (2) P-3/2 -3d (2) D-5/2 transitions, respectively, are found to be due to emission lines of Ar xiii (236.34 Angstrom) and possibly S v or Ni vi (300.25 Angstrom). The Co xvii 3s (2) S-3p (2) P-3/2 line at 312.55 Angstrom is always badly blended with an Fe xv feature at the same wavelength, but Mn xv 3s (2) S-3p (2) P-1/2 at 384.75 Angstrom may not always be as affected by second-order emission from Fe xii 192.37 Angstrom as previously thought. On the other hand, we find that the Zn xx 3s (2) S-3p (2) P-3/2 transition can sometimes make a significant contribution to the Zn xx/Fe xiii 256.43- Angstrom blend, and hence care must be taken when using this feature as an Fe xiii electron density diagnostic. A line in the SERTS-89 active region spectrum at 265.00 Angstrom has been re-assessed, and we confirm its identification as the Fe xvi 3p (2) P-3/2 -3d (2) D-3/2 transition.

Radiation damping effects on L-shell photoionization cross- sections of O-like Fe xix and N-like recombination rate coefficients for Fe xx

Photoionization cross-sections out of the fine-structure levels (2S(2)2p(4) P-3(2,0,1)) of the O-like Fe ion Fe XIX have been reinvestigated. Data for photoionization out of each of these finestructure levels have been obtained, where the calculations have been performed with and without the inclusion of radiation damping on the resonance structure in order to assess the importance of this process. Recombination rate coefficients are determined using the Milne relation, for the case of an electron recombining with N-like Fe ions (Fe XX) in the ground state to form O-like Fe (Fe XIX) existing in each of the fine- structure ground-state levels. Recombination rates are presented over a temperature range similar to 4.0 less than or equal to log T-e less than or equal to 7.0, of importance to the modelling of X-ray emission plasmas.

Effective collision strengths for electron impact excitation of Si VIII

Effective collision strengths for electron-impact excitation of the nitrogen-like ion Si VIII are presented over the wide range of electron temperatures log T(K) = 4.0-6.5. All 231 fine- structure transitions among the 22 fine-structure levels arising from the lowest 11 LS target states (2s(2)2p(3), 2s2p(4), 2p(5), and 2s(2)2p(2)3s) are considered in the tabulation. The collision strengths are evaluated in a multi- channel R-matrix approach, and the corresponding effective collision strengths are obtained by averaging these over a Maxwellian distribution of electron velocities. Comparisons are made with recent distorted-wave results at high incident electron energies. Differences of up to 20% are found, particularly for some allowed transitions. (C) 2003 Elsevier Inc. All rights reserved.

Energy dependence for pair production with electron capture in relativistic heavy-ion collisions

In 'Charge transfer from the negative-energy continuum: alternative mechanism for pair production in relativistic atomic collisions', Eichler (1995 Phys. Rev. Lett. 75 3653) proposes an alternative mechanism for capture by pair production, and from it derives an analytic expression for the total cross section with a surprisingly strong energy dependence. We show that, in fact, there is no alternative mechanism; rather the above mechanism may be more transparently viewed as an ionization-like transition in one centre with inclusion of continuum distortion by the second centre. We further show that to Centre the initial and final states on the target and projectile leads to confusion in the momentum transfer vectors, and hence, respectively that the alleged high-energy behaviour is erroneous.

Electron impact ionization of hydrogen-like molybdenum ions

The electron impact ionization cross sections of hydrogen-like molybdenum ions were measured with an electron beam ion trap at the electron energies of 49.4, 64.4 and 79.6 keV The results are 2.82(22) x 10(-23), 3.13(29) x 10(-23) and 3.23(51) x 10(-23) cm(2), respectively. These results are compared with the experimental results measured previously. The agreement with the results obtained with, scaling formulae is also discussed.

Electron-impact ionization of hydrogen-like iron ions

Electron-impact ionization cross sections have been determined for hydrogen like iron ions at selected electron energies between 1.45 and 4.3 times the threshold energy. The cross sections were obtained by measuring the equilibrium ionization balance in an electron beam ion trap. This ionization balance is obtained from x-ray measurements of radiative recombination into the K-shell of hydrogen-like and bare iron ions. The measured cross sections are compared with distorted-wave calculations and several semiempirical formulations.

The measurement of the dielectronic recombination in He-like Fe ions

We have studied the dielectronic recombination process in He-like Fe ions and have obtained the resonant strengths of the KLn (3 less than or equal to, n less than or equal to, 5) resonances. This measurement was performed with the use of an electron beam ion trap by measuring the x-ray energy emitted from highly charged ions simultaneously with the electron beam energy scanned during the measurement. The total resonant strengths obtained are 5.0 x 10(-19), 2.1 x 10(-19) and 1.1 X 10(-19) cm(2) eV, for KLM, KLN and KLO, respectively.

The role of target polarization in electron-ion recombination

We investigate the role of dynamic polarization of the target electrons in the process of recombination of electrons with multicharged ions (polarizational recombination). Numerical calculations carried out for a number of Ni- and Ne-like ions demonstrate that the inclusion of polarizational recombination leads to a noticeable increase (up to 30%) in the cross sections for incident electron energies outside the regions of dielectronic resonances. We also present a critical analysis of theoretical approaches used by other authors to describe the phenomenon of polarizational recombination.

Dielectronic recombination in highly charged He-like ions

We have determined resonant strengths of the KLn (2 less than or equal to n less than or equal to 5) resonances for helium-like Ti ions and (3 less than or equal to n less than or equal to 5) resonances for helium-like Fe ions. The results were obtained using the Tokyo electron beam ion trap. Characteristic X-rays from both dielectronic recombination and radiative recombination were detected as the electron beam energy was scanned through the resonances. (C) 2003 Elsevier Science B.V. All rights reserved.