Intensity perturbations due to the v3, v4 Coriolis interaction in methane

Formulas are obtained for the intensity asymmetry (Herman-Wallis) factors in the ν3 and ν4 fundamentals of methane due to the ζ34 Coriolis interaction. The results are also applicable to the ν3 and ν4 bands of SF6.

The infrared spectrum of silicon difluoride

The infrared spectrum of the stretching fundamentals of SiF2 has been obtained at a resolution of ≈ 0.1 cm−1 using a FTIR spectrometer. The spectrum has been analysed using computer simulation based on a coupled hamiltonian for v1 and v3, giving v1 = 855.01 cm−1 and v3 = 870.40 cm−1. The relative magnitude and sign of the vibrational transition moments has been determined from the ξC13 Coriolis coupling.

The infrared spectrum, equilibrium structure and harmonic and anharmonic force field of thioborine, HBS

Infrared spectra of the two stretching fundamentals of both HBS and DBS have been observed, using a continuous flow system through a multiple reflection long path cell at a pressure around 1 Torr and a Nicolet Fourier Transform spectrometer with a resolution of about 0•1 cm-1. The v3 BS stretching fundamental of DBS, near 1140 cm-1, is observed in strong Fermi resonance with the overtone of the bend 2v2. The bending fundamental v2 has not been observed and must be a very weak band. The analysis of the results in conjunction with earlier work gives the equilibrium structure (re(BH) = 1•1698(12) , re(BS) = 1•5978(3) ) and the harmonic and anharmonic force field.

The infrared spectrum of the ν2 and ν3 bands of H16OF, H18OF, and D16OF

Fourier transform IR spectra in the ν2 and ν3 regions between 800 and 1500 cm−1 have been measured of H16OF with a resolution of 0.007 cm−1 and of H18OF and DOF with a resolution of 0.040 cm−1. Ground state constants have been improved for H16OF and have been obtained for the first time for H18OF. Parameters of the v2 = 1 and v3 = 1 excited states have been determined from rovibrational analyses of ca. 1000 ν2/ν3 lines which were fitted with σ 0.36, 4.5, and 7.6 × 10−3 cm−1 for H16OF, H18OF, and D16OF, respectively. Band centers of ν2/ν3 are 1353.40466(5)/889.07974(6), 1350.3976(5)/862.2967(7), and 1002.0083(9)/891.0014(15) cm−1, respectively, for the three isotopic species. While ν2 and ν3 are sufficiently separated in HOF to be treated independently, a Coriolis resonance is evident in DOF, the interaction constant ξ23c = 0.19073(16) cm−1 being in agreement with the prediction from the harmonic force field.

Mapping the immune response to the outer domain of a human immunodeficiency virus-1 clade C gp120

The outer domain (OD) of human immunodeficiency virus (HIV)-1 gp120 represents an attractive, if difficult, target for a beneficial immune response to HIV infection. Unlike the entire gp120, the OD is structurally stable and contains the surfaces that interact with both the primary and secondary cellular receptors. The primary strain-specific neutralizing target, the V3 loop, lies within the OD, as do epitopes for two cross-reactive neutralizing monoclonal antibodies (mAbs), b12 and 2G12, and the contact sites for a number of inhibitory lectins. The OD is poorly immunogenic, at least in the context of complete gp120, but purposeful OD immunization can lead to a substantial antibody response. Here, we map the antibody generated following immunization with a clade C OD. In contrast to published data for the clade B OD, the majority of the polyclonal response to the complete clade C OD is to the V3 loop; deletion of the loop substantially reduces immunogenicity. When the loop sequence was substituted for the epitope for 2F5, a well-characterized human cross-neutralizing mAb, a polyclonal response to the epitope was generated. A panel of mAbs against the clade C OD identified two mAbs that reacted with the loop and were neutralizing for clade C but not B isolates. Other mAbs recognized both linear and conformational epitopes in the OD. We conclude that, as for complete gp120, V3 immunodominance is a property of OD immunogens, that the responses can be neutralizing and that it could be exploited for the presentation of other epitopes.

Immunogenicity of the outer domain of a HIV-1 clade C gp120

Background: The possibility that a sub domain of a C clade HIV-1 gp120 could act as an effective immunogen was investigated. To do this, the outer domain ( OD) of gp120(CN54) was expressed and characterized in a construct marked by a re-introduced conformational epitope for MAb 2G12. The expressed sequence showed efficient epitope retention on the isolated ODCN54 suggesting authentic folding. To facilitate purification and subsequent immunogenicity ODCN54 was fused to the Fc domain of human IgGl. Mice were immunised with the resulting fusion proteins and also with gp120(CN54)-Fc and gp120 alone. Results: Fusion to Fc was found to stimulate antibody titre and Fc tagged ODCN54 was substantially more immunogenic than non-tagged gp120. Immunogenicity appeared the result of Fc facilitated antigen processing as immunisation with an Fc domain mutant that reduced binding to the FcR lead to a reduction in antibody titre when compared to the parental sequence. The breadth of the antibody response was assessed by serum reaction with five overlapping fragments of gp120(CN54) expressed as GST fusion proteins in bacteria. A predominant anti-inner domain and anti-V3C3 response was observed following immunisation with gp120(CN54)-Fc and an anti-V3C3 response to the ODCN54-Fc fusion. Conclusion: The outer domain of gp120(CN54) is correctly folded following expression as a C terminal fusion protein. Immunogenicity is substantial when targeted to antigen presenting cells but shows V3 dominance in the polyvalent response. The gp120 outer domain has potential as a candidate vaccine component.

Glycosaminoglycans and protein disulfide isomerase-mediated reduction of HIV Env

Conformational changes within the human immunodeficiency virus-1 (HIV-1) surface glycoprotein gp120 result from binding to the lymphocyte surface receptors and trigger gp41-mediated virus/cell membrane fusion. The triggering of fusion requires cleavage of two of the nine disulfide bonds of gp120 by a cell-surface protein disulfide-isomerase (PDI). Soluble glycosaminoglycans such as heparin and heparan sulfate bind gp120 via V3 and, possibly, a CD4-induced domain. They exert anti-HIV activity by interfering with the HIV envelope glycoprotein ( Env)/cell-surface interaction. Env also binds cell-surface glycosaminoglycans. Here, using surface plasmon resonance, we observed an inverse relationship between heparin binding by gp120 and its thiol content. In vitro, and in conditions in which gp120 could bind CD4, heparin and heparan sulfate reduced PDI-mediated gp120 reduction by approximately 80%. Interaction of Env with the surface of lymphocytes treated using sodium chlorate, an inhibitor of glycosaminoglycan synthesis, led to gp120 reduction. We conclude that besides their capacity to block Env/cell interaction, soluble glycosaminoglycans can effect anti-HIV activity via interference with PDI- mediated gp120 reduction. In contrast, their presence at the cell surface is dispensable for Env reduction during the course of interaction with the lymphocyte surface. This work suggests that the reduction of exofacial proteins in various diseases can be inhibited by compounds targeting the substrates ( not by targeting PDI, as is usually done), and that glycosaminoglycans that primarily protect proteins by preserving them from proteolysis also have a role in preventing reduction.

Simulating the formation of secondary organic aerosol from the photooxidation of aromatic hydrocarbons

The formation and composition of secondary organic aerosol (SOA) from the photooxidation of benzene, p-xylene, and 1,3,5-trimethylbenzene has been simulated using the Master Chemical Mechanism version 3.1 (MCM v3.1) coupled to a representation of the transfer of organic material from the gas to particle phase. The combined mechanism was tested against data obtained from a series of experiments conducted at the European Photoreactor (EUPHORE) outdoor smog chamber in Valencia, Spain. Simulated aerosol mass concentrations compared reasonably well with the measured SOA data only after absorptive partitioning coefficients were increased by a factor of between 5 and 30. The requirement of such scaling was interpreted in terms of the occurrence of unaccounted-for association reactions in the condensed organic phase leading to the production of relatively more nonvolatile species. Comparisons were made between the relative aerosol forming efficiencies of benzene, toluene, p-xylene, and 1,3,5-trimethylbenzene, and differences in the OH-initiated degradation mechanisms of these aromatic hydrocarbons. A strong, nonlinear relationship was observed between measured (reference) yields of SOA and (proportional) yields of unsaturated dicarbonyl aldehyde species resulting from ring-fragmenting pathways. This observation, and the results of the simulations, is strongly suggestive of the involvement of reactive aldehyde species in association reactions occurring in the aerosol phase, thus promoting SOA formation and growth. The effect of NO, concentrations on SOA formation efficiencies (and formation mechanisms) is discussed.

Simulating the detailed chemical composition of secondary organic aerosol formed on a regional scale during the TORCH 2003 campaign in the southern UK

Following on from the companion study (Johnson et al., 2006), a photochemical trajectory model (PTM) has been used to simulate the chemical composition of organic aerosol for selected events during the 2003 TORCH (Tropospheric Organic Chemistry Experiment) field campaign. The PTM incorporates the speciated emissions of 124 nonmethane anthropogenic volatile organic compounds (VOC) and three representative biogenic VOC, a highly-detailed representation of the atmospheric degradation of these VOC, the emission of primary organic aerosol (POA) material and the formation of secondary organic aerosol (SOA) material. SOA formation was represented by the transfer of semi and non-volatile oxidation products from the gas-phase to a condensed organic aerosol-phase, according to estimated thermodynamic equilibrium phase-partitioning characteristics for around 2000 reaction products. After significantly scaling all phase-partitioning coefficients, and assuming a persistent background organic aerosol (both required in order to match the observed organic aerosol loadings), the detailed chemical composition of the simulated SOA has been investigated in terms of intermediate oxygenated species in the Master Chemical Mechanism, version 3.1 ( MCM v3.1). For the various case studies considered, 90% of the simulated SOA mass comprises between ca. 70 and 100 multifunctional oxygenated species derived, in varying amounts, from the photooxidation of VOC of anthropogenic and biogenic origin. The anthropogenic contribution is dominated by aromatic hydrocarbons and the biogenic contribution by alpha-and beta-pinene (which also constitute surrogates for other emitted monoterpene species). Sensitivity in the simulated mass of SOA to changes in the emission rates of anthropogenic and biogenic VOC has also been investigated for 11 case study events, and the results have been compared to the detailed chemical composition data. The role of accretion chemistry in SOA formation, and its implications for the results of the present investigation, is discussed.

Simulating regional scale secondary organic aerosol formation during the TORCH 2003 campaign in the southern UK

A photochemical trajectory model has been used to simulate the chemical evolution of air masses arriving at the TORCH field campaign site in the southern UK during late July and August 2003, a period which included a widespread and prolonged photochemical pollution episode. The model incorporates speciated emissions of 124 nonmethane anthropogenic VOC and three representative biogenic VOC, coupled with a comprehensive description of the chemistry of their degradation. A representation of the gas/aerosol absorptive partitioning of ca. 2000 oxygenated organic species generated in the Master Chemical Mechanism (MCM v3.1) has been implemented, allowing simulation of the contribution to organic aerosol (OA) made by semi- and non-volatile products of VOC oxidation; emissions of primary organic aerosol (POA) and elemental carbon (EC) are also represented. Simulations of total OA mass concentrations in nine case study events (optimised by comparison with observed hourly-mean mass loadings derived from aerosol mass spectrometry measurements) imply that the OA can be ascribed to three general sources: (i) POA emissions; (ii) a '' ubiquitous '' background concentration of 0.7 mu g m(-3); and (iii) gas-to-aerosol transfer of lower volatility products of VOC oxidation generated by the regional scale processing of emitted VOC, but with all partitioning coefficients increased by a species-independent factor of 500. The requirement to scale the partitioning coefficients, and the implied background concentration, are both indicative of the occurrence of chemical processes within the aerosol which allow the oxidised organic species to react by association and/or accretion reactions which generate even lower volatility products, leading to a persistent, non-volatile secondary organic aerosol (SOA). The contribution of secondary organic material to the simulated OA results in significant elevations in the simulated ratio of organic carbon (OC) to EC, compared with the ratio of 1.1 assigned to the emitted components. For the selected case study events, [OC]/[EC] is calculated to lie in the range 2.7-9.8, values which are comparable with the high end of the range reported in the literature.

In vitro three-stage continuous fermentation of gluco-oligosaccharides produced by Gluconobacter oxydans NCIMB 4943 by the human colonic microflora

Gluco-oligosaccharides produced by Gluconobacter oxydans NCIMB 4943 from maltodextrin as the source, were evaluated for their fermentability by the human colonic microflora. The selectivity of growth of desirable bacteria in the human colon was studied in a three-stage continuous model of the human large intestine. Populations of bacteria, and their fluctuations as a response to the fermentation, were enumerated using fluorescent in situ hybridization (FISH). The gluco-oligosaccharides resulted in increases in numbers of bifidobacteria and the Lactobacillus/Enterococcus group in all 3 vessels of the system, representing the proximal, transverse and distal colonic areas. The prebiotic indices of the glucooligosaccharides were 2.29, 4.23 and 2.74 in V1, V2 and V3 respectively.

Bacterial biofilms in the human gastrointestinal tract

Microbial biofilms were first described in 1936 and subsequent research has unveiled their ubiquity and physiological distinction from free-living (planktonic) microorganisms. In light of their emerging significance this review examines the bacterial biofilms within the human gastrointestinal tract. Attention is paid to the nature of these mucosally- associated populations, focusing on the protected environment afforded by the continual secretion of mucus by host epithelial cells. It also examines the attributes possessed by various bacterial species that facilitate habitation of this microenvironment. Additionally, contrasts are drawn between planktonic bacteria of the lumen and sessile (biofilm) bacteria growing in close association with host cells and food particles. In particular the different fermentation profiles exhibited by these two fractions are discussed. The potential role of these communities in host health and disease, as well as the stabilisation of the lumenal population, is also considered. Reference is made to the state of mutualism that exists between these little understood populations and the host epithelia, thus highlighting their ecological significance in terms of gastrointestinal health.

Mapping of domains on HIV envelope protein mediating association with calnexin and protein-disulfide isomerase.

The cell catalysts calnexin (CNX) and protein-disulfide isomerase (PDI) cooperate in establishing the disulfide bonding of the HIV envelope (Env) glycoprotein. Following HIV binding to lymphocytes, cell-surface PDI also reduces Env to induce the fusogenic conformation. We sought to define the contact points between Env and these catalysts to illustrate their potential as therapeutic targets. In lysates of Env-expressing cells, 15% of the gp160 precursor, but not gp120, coprecipitated with CNX, whereas only 0.25% of gp160 and gp120 coprecipitated with PDI. Under in vitro conditions, which mimic the Env/PDI interaction during virus/cell contact, PDI readily associated with Env. The domains of Env interacting in cellulo with CNX or in vitro with PDI were then determined using anti-Env antibodies whose binding site was occluded by CNX or PDI. Antibodies against domains V1/V2, C2, and the C terminus of V3 did not bind CNX-associated Env, whereas those against C1, V1/V2, and the CD4-binding domain did not react with PDI-associated Env. In addition, a mixture of the latter antibodies interfered with PDI-mediated Env reduction. Thus, Env interacts with intracellular CNX and extracellular PDI via discrete, largely nonoverlapping, regions. The sites of interaction explain the mode of action of compounds that target these two catalysts and may enable the design of further new competitive agents.

The efficacy of Salenvac, a Salmonella enterica subsp. Enterica serotype Enteritidis iron-restricted bacterin vaccine, in laying chickens

The protective effect of two vaccination regimes using Salenvac, a commercially available iron-restricted Salmonella enterica subsp. Enterica serotype Enteritidis PT4 bacterin vaccine, was verified in laying birds. Immunization was intramuscular at 1 day old and again at 4 weeks of age (V2), or at 1 day and 4 weeks with a third dose at 18 weeks of age (V3). Challenge S. Enteritidis (5 to 7.5) x 10(7) colony forming units) was given intravenously at 8, 17, 23, 30 and 59 weeks of age. For all age groups, both vaccination regimes reduced significantly the number of tissues and faecal samples that were culture positive for the challenge strain. For laying birds, fewer eggs (P < 0.001) were culture positive for S. Enteritidis after challenge from vaccinated laying birds ( 56/439 batches of eggs) than unvaccinated birds (99/252 batches). The data give compelling evidence that the vaccine is efficacious and may contribute to the reduction of layer infection and egg contamination.

Building resilience in the face of recurring environmental crisis in African Sahel

The present food shortages in the Horn of Africa and the West African Sahel are affecting 31 million people. Such continuing and future crises require that people in the region adapt to an increasing and potentially irreversible global sustainability challenge. Given this situation and that short-term weather and seasonal climate forecasting have limited skill for West Africa, the Rainwatch project illustrates the value of near real-time monitoring and improved communication for the unfavourable 2011 West African monsoon, the resulting severe drought-induced humanitarian impacts continuing into 2012, and their exacerbation by flooding in 2012. Rainwatch is now coupled with a boundary organization (Africa Climate Exchange, AfClix) with the aim of integrating the expertise and actions of relevant institutions, agencies and stakeholders to broker ground-based dialogue to promote resilience in the face of recurring crisis.