Regulation of pyridoxal $5\prime$-phosphate biosynthesis in {\it Escherichia coli\/} K-12

Vitamin B$\sb6$ (or pyridoxal 5$\sp\prime$-phosphate, PLP) is an essential, ubiquitous coenzyme that affects many aspects of amino acid and cellular metabolism in all organisms. The goal of this thesis is to examine the regulation of PLP biosynthesis in Escherichia coli K-12. First, PdxH oxidase is a PLP biosynthetic enzyme, which uses molecular oxygen as an electron acceptor under aerobic assay conditions. To test if facultative anaerobic E. coli uses another enzyme to replace the function of PdxH oxidase anaerobically, suppressors of a pdxH null mutant were isolated anaerobically after 2-aminopurine or spontaneous mutagenesis. Only one specific bypass mutation in another PLP biosynthetic gene pdxJ was found, suggesting that PdxH oxidase is able to function anaerobically and PdxT utilizes D-1-deoxyxyulose as a substrate. Second, regulation of the serC (pdxF)-aroA operon, which is involved the biosynthesis of L-serine, PLP and aromatic compounds was examined. A serC (pdxF) single gene transcript and a serC (pdXf)-aroA cotranscript initiated at P$\sb{serC\ (pdxF)}$ upstream of serC (pdxF) were detected. The expression of the operon is activated by leucine responsive regulatory protein (LRP) and repressed by cAMP receptor protein-cAMP complex (CRP$\cdot$cAMP) at the transcriptional level. LRP activates the operon by directly binding to the upstream consensus box. Binding of CRP$\cdot$cAMP to the upstream CRP box diminishes the activation effect of LRP. However, deletion of the CRP box did not affect the repression of CRP$\cdot$cAMP, suggesting that CRP$\cdot$cAMP may repress the operon indirectly by stimulating the activity or level of an unidentified repressor. The overall effect of this regulation is to maximize the expression of the operon when the cells are growing in minimal-glucose medium. In addition, the binding and the transcription of P$\sb{serC\ (pdxF)}$ by RNA polymerase require a supercoiled circular DNA, indicating that DNA supercoiling affects the transcription of the operon. Third, regulation of another PLP biosynthetic gene gapB was also examined. gapB is activated by CRP$\cdot$cAMP and repressed by catabolic repressor activator protein (CRA). However, the activation of CRP$\cdot$cAMP is epistatic to the repression of CRA. Due to the CRA repression, gapB was expressed at a low level in all the media tested, suggesting that it may be the rate-limiting step of PLP biosynthesis. In summary, unlike genes in many biosynthetic pathways, PLP biosynthetic genes are regulated by global regulators that are important for carbon and amino acid metabolism, instead of the end product(s) of the pathway. ^

Ice Core Paleovolcanic Records from the St. Elias Mountains, Yukon, Canada

We previously reported a record of regionally significant volcanic eruptions in the North Pacific using an ice core from Eclipse Icefield (St. Elias Mountains, Yukon, Canada). The acquisition of two new ice cores from Eclipse Icefield, along with the previously available Eclipse Icefield and Mount Logan Northwest Col ice cores, allows us to extend our record of North Pacific volcanism to 550 years before present using a suite of four ice cores spanning an elevation range of 3 - 5 km. Comparison of volcanic sulfate flux records demonstrates that the results are highly reproducible, especially for the largest eruptions such as Katmai ( A. D. 1912). Correlation of volcanic sulfate signals with historically documented eruptions indicates that at least one-third of the eruptions recorded in St. Elias ice cores are from Alaskan and Kamchatkan volcanoes. Although there are several moderately large ( volcanic explosivity index (VEI) >= 4) eruptions recorded in only one core from Eclipse Icefield, the use of multiple cores provides signals in at least one core from all known VEI >= 4 eruptions in Alaska and Kamchatka since A. D. 1829. Tephrochronological evidence from the Eclipse ice cores documents eruptions in Alaska (Westdahl, Redoubt, Trident, and Katmai), Kamchatka (Avachinsky, Kliuchevoskoi, and Ksudach), and Iceland (Hekla). Several unidentified tephra-bearing horizons, with available geochemical evidence suggesting Alaskan and Kamchatkan sources, were also found. We present a reconstruction of annual volcanic sulfate loading for the North Pacific troposphere based on our ice core data, and we provide a detailed assessment of the atmospheric and climatic effects of the Katmai eruption.

Development of a high- versus low-pathogenicity model of the free-living amoeba Naegleria fowleri

Species in the genus Naegleria are free-living amoebae of the soil and warm fresh water. Although around 30 species have been recognized, Naegleria fowleri is the only one that causes primary amoebic meningoencephalitis (PAM) in humans. PAM is an acute and fast progressing disease affecting the central nervous system. Most of the patients die within 1-2 weeks of exposure to the infectious water source. The fact that N. fowleri causes such fast progressing and highly lethal infections has opened many questions regarding the relevant pathogenicity factors of the amoeba. In order to investigate the pathogenesis of N. fowleri under defined experimental conditions, we developed a novel high- versus low-pathogenicity model for this pathogen. We showed that the composition of the axenic growth media influenced growth behaviour and morphology, as well as in vitro cytotoxicity and in vivo pathogenicity of N. fowleri. Trophozoites maintained in Nelson's medium were highly pathogenic for mice, demonstrated rapid in vitro proliferation, characteristic expression of surface membrane vesicles and a small cell diameter, and killed target mouse fibroblasts by both contact-dependent and -independent destruction. In contrast, N. fowleri cultured in PYNFH medium exhibited a low pathogenicity, slower growth, increased cell size and contact-dependent target cell destruction. However, cultivation of the amoeba in PYNFH medium supplemented with liver hydrolysate (LH) resulted in trophozoites that were highly pathogenic in mice, and demonstrated an intermediate proliferation rate in vitro, diminished cell diameter and contact-dependent target cell destruction. Thus, in this model, the presence of LH resulted in increased proliferation of trophozoites in vitro and enhanced pathogenicity of N. fowleri in mice. However, neither in vitro cytotoxicity mechanisms nor the presence of membrane vesicles on the surface correlated with the pathologic potential of the amoeba. This indicated that the pathogenicity of N. fowleri remains a complex interaction between as-yet-unidentified cellular mechanisms.

The Forensic Reference Phantom-a new tool for quality assurance of attenuation measurements in forensic radiology

Introduction The purpose of this paper is to present the technical specifications of the Forensic Reference Phantom (FRP), to test its behavior relative to organic test materials, and discuss potential applications of the phantom in forensic radiology. Materials and method The FRP prototype is made of synthetic materials designed to simulate the computed tomography (CT) attenuation of water. It has six bore holes that accommodate multiuse containers. These containers were filled with test materials and scanned at 80 kVp, 120 kVp, and 140 kVp. X-ray attenuation was measured by two readers. Intra- and inter-reader reliability was assessed using the intra-class correlation coefficient (ICC). Significance levels between mean CT numbers at 80 kVp, 120 kVp, and 140 kVp were assessed with the Friedman-test. The T-test was used to assess significance levels between the FRP and water. Results Overall mean CT numbers ranged from −3.0–3.7HU for the FRP; −1000.3–−993.5HU for air; −157.7– −108.1HU for oil; 35.5–42.0HU for musle tissue; and 1301.5–2354.8HU for cortical bone. Inter-reader and intra-reader reliability were excellent (ICC>0.994; and ICC=0.999 respectively). CT numbers were significantly different at different energy levels. There was no significant difference between the attenuation of the FRP and water. Conclusions The FRP is a new tool for quality assurance and research in forensic radiology. The mean CT attenuation of the FRP is equivalent to water. The phantom can be scanned during routine post-mortem CT to assess the composition of unidentified objects. In addition, the FRP may be used to investigate new imaging algorithms and scan protocols in forensic radiology.

Culture of ovine bone marrow-derived macrophages and evidence for serum factors distinct from M-CSF contributing to their propagation in vitro.

An in vitro system allowing the culture of ovine bone marrow-derived macrophages (BMMs) is described. Bone marrow (BM) cells from the sternum of 4- to 9-month-old sheep were cultured in liquid suspension in hydrophobic bags with medium containing 20% autologous serum and 20% fetal calf serum (FCS). Cells with macrophage characteristics were positively selected and increased four- to five-fold between day (d) 0 and d18. Granulocytes and cells of lymphoid appearance including progenitor cells were negatively selected and were diminished 50-fold during this 18-d culture. The addition of macrophage colony-stimulating factor (M-CSF)-containing supernatants to liquid cultures did not significantly improve the yield of BMM in 18-d cultures. In contrast, cell survival at d6 and macrophage cell yield at d18 depended on the concentration and source of serum in the culture medium. FCS and 1:1 mixtures of FCS and autologous serum were superior to autologous serum alone. Analysis of growth requirements of ovine BMMs suggested that they are under more complex growth control than their murine counterparts. In an [3H]thymidine incorporation assay with BM cells collected at different times of culture, d3 or d4 BM cells responded to human recombinant M-CSF, human recombinant granulocyte-macrophage colony-stimulating factor (GM-CSF), bovine GM-CSF, murine M-CSF or murine M-CSF-containing supernatants, and bovine interleukin 1 beta (IL-1 beta) in decreasing order of magnitude. Likewise, pure murine BMM populations harvested at d6 responded to homologous GM-CSF, IL-3, and human or murine M-CSF. FCS did not stimulate the proliferation of murine BMMs (d6) and of ovine BM cells (d3 or d4). In contrast, ovine BM cells harvested at d12 responded to FCS by proliferation in a dose-dependent manner but failed to proliferate in the presence of human or murine M-CSF or M-CSF-containing supernatants of mouse and sheep fibroblasts containing mouse macrophage growth-promoting activity. Likewise, various cytokine-containing supernatants and recombinant cytokines (murine IL-3, murine and human GM-CSF, murine and bovine IL-1 beta) did not promote proliferation of ovine d12 BM cells to an extent greater than that achieved with 15% FCS alone. Thus, ovine BMM proliferation is under the control of at least two factors acting in sequence, M-CSF and an unidentified factor contained in FCS. The ovine BMM culture system may provide a model for the analysis of myelomonocytopoiesis in vitro.

Multiyear predictability of tropical marine productivity

With the emergence of decadal predictability simulations, research toward forecasting variations of the climate system now covers a large range of timescales. However, assessment of the capacity to predict natural variations of relevant biogeochemical variables like carbon fluxes, pH, or marine primary productivity remains unexplored. Among these, the net primary productivity (NPP) is of particular relevance in a forecasting perspective. Indeed, in regions like the tropical Pacific (30°N–30°S), NPP exhibits natural fluctuations at interannual to decadal timescales that have large impacts on marine ecosystems and fisheries. Here, we investigate predictions of NPP variations over the last decades (i.e., from 1997 to 2011) with an Earth system model within the tropical Pacific. Results suggest a predictive skill for NPP of 3 y, which is higher than that of sea surface temperature (1 y). We attribute the higher predictability of NPP to the poleward advection of nutrient anomalies (nitrate and iron), which sustain fluctuations in phytoplankton productivity over several years. These results open previously unidentified perspectives to the development of science-based management approaches to marine resources relying on integrated physical-biogeochemical forecasting systems.

​Indole is an essential herbivore-induced volatile priming signal in maize

Herbivore-induced volatile organic compounds prime non-attacked plant tissues to respond more strongly to subsequent attacks. However, the key volatiles that trigger this primed state remain largely unidentified. In maize, the release of the aromatic compound ​indole is herbivore-specific and occurs earlier than other induced responses. We therefore hypothesized that ​indole may be involved in airborne priming. Using ​indole-deficient mutants and synthetic indole dispensers, we show that herbivore-induced ​indole enhances the induction of defensive volatiles in neighbouring maize plants in a species-specific manner. Furthermore, the release of ​indole is essential for priming of mono- and homoterpenes in systemic leaves of attacked plants. ​Indole exposure markedly increases the herbivore-induced production of the stress hormones ​jasmonate-isoleucine conjugate and ​abscisic acid, which represents a likely mechanism for ​indole-dependent priming. These results demonstrate that ​indole functions as a rapid and potent aerial priming agent that prepares systemic tissues and neighbouring plants for incoming attacks.

Commensal bacteria protect against food allergen sensitization.

Environmentally induced alterations in the commensal microbiota have been implicated in the increasing prevalence of food allergy. We show here that sensitization to a food allergen is increased in mice that have been treated with antibiotics or are devoid of a commensal microbiota. By selectively colonizing gnotobiotic mice, we demonstrate that the allergy-protective capacity is conferred by a Clostridia-containing microbiota. Microarray analysis of intestinal epithelial cells from gnotobiotic mice revealed a previously unidentified mechanism by which Clostridia regulate innate lymphoid cell function and intestinal epithelial permeability to protect against allergen sensitization. Our findings will inform the development of novel approaches to prevent or treat food allergy based on modulating the composition of the intestinal microbiota.

Pre-therapy inflammation and coagulation activation and long-term CD4 count responses to the initiation of antiretroviral therapy

OBJECTIVES Pre-antiretroviral therapy (ART) inflammation and coagulation activation predict clinical outcomes in HIV-positive individuals. We assessed whether pre-ART inflammatory marker levels predicted the CD4 count response to ART. METHODS Analyses were based on data from the Strategic Management of Antiretroviral Therapy (SMART) trial, an international trial evaluating continuous vs. interrupted ART, and the Flexible Initial Retrovirus Suppressive Therapies (FIRST) trial, evaluating three first-line ART regimens with at least two drug classes. For this analysis, participants had to be ART-naïve or off ART at randomization and (re)starting ART and have C-reactive protein (CRP), interleukin-6 (IL-6) and D-dimer measured pre-ART. Using random effects linear models, we assessed the association between each of the biomarker levels, categorized as quartiles, and change in CD4 count from ART initiation to 24 months post-ART. Analyses adjusted for CD4 count at ART initiation (baseline), study arm, follow-up time and other known confounders. RESULTS Overall, 1084 individuals [659 from SMART (26% ART naïve) and 425 from FIRST] met the eligibility criteria, providing 8264 CD4 count measurements. Seventy-five per cent of individuals were male with the mean age of 42 years. The median (interquartile range) baseline CD4 counts were 416 (350-530) and 100 (22-300) cells/μL in SMART and FIRST, respectively. All of the biomarkers were inversely associated with baseline CD4 count in FIRST but not in SMART. In adjusted models, there was no clear relationship between changing biomarker levels and mean change in CD4 count post-ART (P for trend: CRP, P = 0.97; IL-6, P = 0.25; and D-dimer, P = 0.29). CONCLUSIONS Pre-ART inflammation and coagulation activation do not predict CD4 count response to ART and appear to influence the risk of clinical outcomes through other mechanisms than blunting long-term CD4 count gain.

Nck-interacting Ste20 kinase couples Eph receptors to c-Jun N-terminal kinase and integrin activation.

The mammalian Ste20 kinase Nck-interacting kinase (NIK) specifically activates the c-Jun amino-terminal kinase (JNK) mitogen-activated protein kinase module. NIK also binds the SH3 domains of the SH2/SH3 adapter protein Nck. To determine whether Nck functions as an adapter to couple NIK to a receptor tyrosine kinase signaling pathway, we determined whether NIK is activated by Eph receptors (EphR). EphRs constitute the largest family of receptor tyrosine kinases (RTK), and members of this family play important roles in patterning of the nervous and vascular systems. In this report, we show that NIK kinase activity is specifically increased in cells stimulated by two EphRs, EphB1 and EphB2. EphB1 kinase activity and phosphorylation of a juxtamembrane tyrosine (Y594), conserved in all Eph receptors, are both critical for NIK activation by EphB1. Although pY594 in the EphB1R has previously been shown to bind the SH2 domain of Nck, we found that stimulation of EphB1 and EphB2 led predominantly to a complex between NIK/Nck, p62(dok), RasGAP, and an unidentified 145-kDa tyrosine-phosphorylated protein. Tyrosine-phosphorylated p62(dok) most probably binds directly to the SH2 domain of Nck and RasGAP and indirectly to NIK bound to the SH3 domain of Nck. We found that NIK activation is also critical for coupling EphB1R to biological responses that include the activation of integrins and JNK by EphB1. Taken together, these findings support a model in which the recruitment of the Ste20 kinase NIK to phosphotyrosine-containing proteins by Nck is an important proximal step in the signaling cascade downstream of EphRs.

Less is More: Treatment with BTH and Laminarin Reduces Herbivore-Induced Volatile Emissions in Maize but Increases Parasitoid Attraction

Chemical plant strengtheners find increasing use in agriculture to enhance resistance against pathogens. In an earlier study, it was found that treatment with one such resistance elicitor, BTH (benzo-(1, 2, 3)-thiadiazole-7-carbothioic acid S-methyl ester), increases the attractiveness of maize plants to a parasitic wasp. This surprising additional benefit of treating plants with BTH prompted us to conduct a series of olfactometer tests to find out if BTH and another commercially available plant strengthener, Laminarin, increase the attractiveness of maize to three important parasitic wasps, Cotesia marginventris, Campoletis sonorensis, and Microplitis rufiventris. In each case, plants that were sprayed with the plant strengtheners and subsequently induced to release volatiles by real or mimicked attack by Spodoptera littoralis caterpillars became more attractive to the parasitoids than water treated plants. The elicitors alone or in combination with plants that were not induced by herbivory were not attractive to the wasps. Interestingly, plants treated with the plant strengtheners did not show any consistent increase in volatile emissions. On the contrary, treated plants released less herbivore-induced volatiles, most notably indole, which has been reported to interfere with parasitoid attraction. The emission of the sesquiterpenes (E)-β-caryophyllene, β-bergamotene, and (E)-β-farnesene was similarly reduced by the treatment. Expression profiles of marker genes showed that BTH and Laminarin induced several pathogenesis related (PR) genes. The results support the notion that, as yet undetectable and unidentified compounds, are of major importance for parasitoid attraction, and that these attractants may be masked by some of the major compounds in the volatile blends. This study confirms that elicitors of pathogen resistance are compatible with the biological control of insect pests and may even help to improve it.

Improved determination of sterile neutrino dark matter spectrum

The putative recent indication of an unidentified 3.55 keV X-ray line in certain astrophysical sources is taken as a motivation for an improved theoretical computation of the cosmological abundance of 7.1 keV sterile neutrinos. If the line is interpreted as resulting from the decay of Warm Dark Matter, the mass and mixing angle of the sterile neutrino are known. Our computation then permits for a determination of the lepton asymmetry that is needed for producing the correct abundance via the Shi-Fuller mechanism, as well as for an estimate of the non-equilibrium spectrum of the sterile neutrinos. The latter plays a role in structure formation simulations. Results are presented for different flavour structures of the neutrino Yukawa couplings and for different types of pre-existing lepton asymmetries, accounting properly for the charge neutrality of the plasma and incorporating approximately hadronic contributions.

Effect of the Tiger Stripes on the water vapor distribution in Enceladus' exosphere

The jet activity emanating from Enceladus' exosphere south pole region observed by Cassini is a subject of intensive study. The in situ and remote sensing observations performed since 2005 triggered an active modeling campaign. Such modeling is essential for better understanding of the measurements performed by individual instruments as well as to link them for a more complete picture of the volatile and ice grain distribution in Enceladus' exosphere. This paper is focused on the investigation of the effect that diffuse gas sources along the Tiger Stripes have on distribution of the water vapor in Enceladus' exosphere using the updated version of our multiplume model. We have found that accounting for the gas production by Tiger Stripes is critical for interpretation of the Cassini data. According to our calculations, sources along the Tiger Stripes (apart from those originally identified by Spitale and Porco (2007)) must contribute about 23–32% to the total plume source rate, which varies in the range of (6.4–29) ×1027 s−1. The effect of the previously unidentified source suggested in the paper is found to be critical for explaining the Ultraviolet Imaging Spectrograph 2007 and 2010 observations in the whole range of the elapsed times.

Nitrogen-Doping in ZnO via Combustion Synthesis?

We report the synthesis and characterization of colored ZnO-based powders via solution combustion reaction of urea and zinc nitrate hexahydrate in varying molar ratios between 1:1 and 10:1. Among other techniques, we employ X-ray diffraction, nuclear magnetic resonance, and Raman spectroscopy to characterize the products. Within a narrow range of reactant ratios, we reproducibly find an unidentified, crystalline precursor phase related to isocyanuric acid next to ZnO. Finally, we complement our investigations by performing Prompt Gamma Activation Analysis (PGAA) on selected products in order to directly determine elemental bulk compositions and compare these with X-ray photoelectron spectroscopy (XPS) measurements. Our data show traces of nitrogen mainly on the surface of the particles, and thus we question the solution combustion method as a reliable synthesis toward N-doped ZnO. Furthermore, we exclude nitrogen as being responsible for the appearance of the four controversially discussed Raman bands superimposed onto the spectrum of pure ZnO (at 275, 510, 582, and 643 cm–1) and show that the combination of PGAA and XPS is an excellent and complementary method to obtain information about the distribution of the elements in question.

Migration of encephalitogenic CD8 T cells into the central nervous system is dependent on the α4β1-integrin

Although CD8 T cells are key players in neuroinflammation, little is known about their trafficking cues into the central nervous system (CNS). We used a murine model of CNS autoimmunity to define the molecules involved in cytotoxic CD8 T-cell migration into the CNS. Using a panel of mAbs, we here show that the α4β1-integrin is essential for CD8 T-cell interaction with CNS endothelium. We also investigated which α4β1-integrin ligands expressed by endothelial cells are implicated. The blockade of VCAM-1 did not protect against autoimmune encephalomyelitis, and only partly decreased the CD8(+) T-cell infiltration into the CNS. In addition, inhibition of junctional adhesion molecule-B expressed by CNS endothelial cells also decreases CD8 T-cell infiltration. CD8 T cells may use additional and possibly unidentified adhesion molecules to gain access to the CNS.