Sub-cellular localization of membrane proteins

In eukaryotes, numerous complex sub-cellular structures exist. The majority of these are delineated by membranes. Many proteins are trafficked to these in order to be able to carry out their correct physiological function. Assigning the sub-cellular location of a protein is of paramount importance to biologists in the elucidation of its role and in the refinement of knowledge of cellular processes by tracing certain activities to specific organelles. Membrane proteins are a key set of proteins as these form part of the boundary of the organelles and represent many important functions such as transporters, receptors, and trafficking. They are, however, some of the most challenging proteins to work with due to poor solubility, a wide concentration range within the cell and inaccessibility to many of the tools employed in proteomics studies. This review focuses on membrane proteins with particular emphasis on sub-cellular localization in terms of methodologies that can be used to determine the accurate location of membrane proteins to organelles. We also discuss what is known about the membrane protein cohorts of major organelles.

Cloud computing : what upstream oil and gas can learn from other industries

The topic of “the cloud” has attracted significant attention throughout the past few years (Cherry 2009; Sterling and Stark 2009) and, as a result, academics and trade journals have created several competing definitions of “cloud computing” (e.g., Motahari-Nezhad et al. 2009). Underpinning this article is the definition put forward by the US National Institute of Standards and Technology, which describes cloud computing as “a model for enabling ubiquitous, convenient, on-demand network access to a shared pool of configurable computing resources that can be rapidly provisioned and released with minimal management effort or service provider interaction” (Garfinkel 2011, p. 3). Despite the lack of consensus about definitions, however, there is broad agreement on the growing demand for cloud computing. Some estimates suggest that spending on cloudrelated technologies and services in the next few years may climb as high as USD 42 billion/year (Buyya et al. 2009).

How does innovation happen in the upstream oil & gas industry? Insights from a global survey

Few would argue that the upstream oil & gas industry has become more technology-intensive over the years. But how does innovation happen in the industry? Specifically, what ideas and inputs flow from which parts of the sector’s value network, and where do these inputs go? And how do firms and organizations from different countries contribute differently to this process? This paper puts forward the results of a survey designed to shed light on these issues. A joint research initiative between the Society of Petroleum Engineers and the Queensland University of Technology, the survey was sent to 469 executives and senior managers who played a significant role with regards to R&D and/or technology deployment in their respective business units. A total of 199 responses were received from a broad range of organizations and countries around the world. Several interesting themes and trends emerge from the results, including: (1) service companies tend to file considerably more patents per innovation than other types of organization; (2) over 63% of the deployed innovations reported in the survey originated in service companies; (3) neither universities nor government-led research organizations are considered to be valuable sources of new information and knowledge in the industry’s R&D initiatives; and (4) despite the increasing degree of globalization in the marketplace, the USA still plays an extremely dominant role in the industry’s overall R&D and technology deployment activities. By providing a detailed snapshot of how innovation happens in the upstream oil & gas sector, this paper provides a valuable foundation for future investigations and discussions aimed at improving how R&D and technology deployment are managed within the industry.

Dying feet in ICU : why might extracorporeal membrane oxygenation machines cause necrotic feet?

Background Extracorporeal membrane oxygenation (ECMO) is used for severe lung and/or heart failure in intensive care units (ICU). The Prince Charles Hospital (TPCH) has one of the largest ECMO units in Australia. Its use rapidly increased during the H1N1 (“swine flu”) pandemic and an increase in pedal complications resulted. The relationship between ECMO and pedal complications has been described, particularly in children, though no strong data exists. This paper presents a case series of foot complications in patients having received ECMO treatment. Methods We present nine cases of severe foot complications resulting from patients receiving ECMO treatment at TPCH in 2009–2012. Results Case ages ranged from 16 - 58 years and three were male. Six cases had an unremarkable medical history prior to H1N1 or H1N2 infection, one had Cardiomyopathy, one had received a lung transplant, and one had multi-organ failure post-sepsis. Common medications prescribed included vasopressors, antibiotics, and sedatives. All cases showed signs of markedly impaired peripheral perfusion whilst on ECMO and seven developed increasing areas of foot necrosis. Outcomes include two bilateral below knee amputations, two multiple digital amputations, one Reflex Sympathetic Dystrophy Syndrome, three pressure injuries, and three deaths. Conclusion Necrosis of the feet appears to occur more readily in younger people requiring ECMO treatment than others in ICU. The authors are conducting further studies to investigate associations between particular infections, medical history, medications, or machine techniques and severe foot complications. Some of these early results will also be presented at this conference.

Climate change and IMO technical and operational measures for reduction of emissions of greenhouse gas from ships

According to a study conducted by the International Maritime organisation (IMO) shipping sector is responsible for 3.3% of the global Greenhouse Gas (GHG) emissions. The 1997 Kyoto Protocol calls upon states to pursue limitation or reduction of emissions of GHG from marine bunker fuels working through the IMO. In 2011, 14 years after the adoption of the Kyoto Protocol, the Marine Environment Protection Committee (MEPC) of the IMO has adopted mandatory energy efficiency measures for international shipping which can be treated as the first ever mandatory global GHG reduction instrument for an international industry. The MEPC approved an amendment of Annex VI of the 1973 International Convention for the Prevention of Pollution from Ships (MARPOL 73/78) to introduce a mandatory Energy Efficiency Design Index (EEDI) for new ships and the Ship Energy Efficiency Management Plan (SEEMP) for all ships. Considering the growth projections of human population and world trade the technical and operational measures may not be able to reduce the amount of GHG emissions from international shipping in a satisfactory level. Therefore, the IMO is considering to introduce market-based mechanisms that may serve two purposes including providing a fiscal incentive for the maritime industry to invest in more energy efficient manner and off-setting of growing ship emissions. Some leading developing countries already voiced their serious reservations on the newly adopted IMO regulations stating that by imposing the same obligation on all countries, irrespective of their economic status, this amendment has rejected the Principle of Common but Differentiated Responsibility (the CBDR Principle), which has always been the cornerstone of international climate change law discourses. They also claimed that negotiation for a market based mechanism should not be continued without a clear commitment from the developed counters for promotion of technical co-operation and transfer of technology relating to the improvement of energy efficiency of ships. Against this backdrop, this article explores the challenges for the developing counters in the implementation of already adopted technical and operational measures.

Intranasal immunization with C. muridarum major outer membrane protein (MOMP) and cholera toxin elicits local production of neutralising IgA in the prostate

Successful control of sexually transmitted diseases (STDs) through vaccination will require the development of vaccine strategies that target protective immunity to both the female and male reproductive tracts (MRT). In the male, the immune privileged nature of the male reproductive tract provides a barrier to entry of serum immunoglobulins into the male reproductive ducts, thereby preventing the induction of protective immunity using conventional injectable vaccination techniques. In this study we investigated the potential of intranasal (IN) immunization to elicit anti-chlamydial immunity in BALB/c male mice. Intranasal immunization with Chlamydia muridarum major outer membrane protein (MOMP) admixed with cholera toxin (CT) resulted in high levels of MOMP-specific IgA in prostatic fluids (PF) and MOMP-specific IgA-secreting cells in the prostate. Prostatic fluid IgA inhibited in vitro infection of McCoy cells with C. muridarum. Using RT-PCR we also show that mRNA for the polymeric immunoglobulin receptor (PIgR), which transports IgA across mucosal epithelia, is expressed only in the prostate but not in other regions of the male reproductive ducts upstream of the prostate. These data suggest that using intranasal immunization to target IgA to the prostate may protect males against STDs while at the same time maintaining the state of immune privilege within the MRT.

A randomised controlled trial of amniotic membrane in the treatment of a standardised burn injury in the merino lamb

Burn injury is associated with disabling scar formation which impacts on many aspects of the patient's life. Previously we have shown that the fetus heals a deep dermal burn in a scarless fashion. Amniotic membrane (AM) is the outermost fetal tisue and has beeen used as a dressing in thermal injuries, though there is little data to support this use. To assess the efficacy of AM in scar minimisation after deep dermal burn wound, we conducted a randomised controlled study in the 1-month lamb. Lambs were delivered by caesarian section and the amniotic membranes stored after which lambs were returned to their mothers post-operatively. At 1 month, a standardised deep dermal burn was created under general anaesthesia on both flanks of the lamb. One flank was covered with unmatched AM, the other with paraffin gauze. Animals were sequentially euthanased from Day 3-60 after injury and tissue analysed for histopathology and immunohistochemically for alpha-smooth muscle actin (alphaSMA) content. AM resulted in reduced scar tissue as assessed histopathologically and reduced alphaSMA content. This study provides the first laboratory evidence that AM may reduce scar formation after burn injury.

Electrocatalytically switchable CO2 capture : first principle computational exploration of carbon nanotubes with pyridinic nitrogen

Carbon nanotubes with specific nitrogen doping are proposed for controllable, highly selective, and reversible CO2 capture. Using density functional theory incorporating long-range dispersion corrections, we investigated the adsorption behavior of CO2 on (7,7) single-walled carbon nanotubes (CNTs) with several nitrogen doping configurations and varying charge states. Pyridinic-nitrogen incorporation in CNTs is found to induce an increasing CO2 adsorption strength with electron injecting, leading to a highly selective CO2 adsorption in comparison with N2. This functionality could induce intrinsically reversible CO2 adsorption as capture/release can be controlled by switching the charge carrying state of the system on/off. This phenomenon is verified for a number of different models and theoretical methods, with clear ramifications for the possibility of implementation with a broader class of graphene-based materials. A scheme for the implementation of this remarkable reversible electrocatalytic CO2-capture phenomenon is considered.

Vaccination of koalas with a recombinant Chlamydia pecorum major outer membrane protein induces antibodies of different specificity compared to those following a natural live infection

Chlamydial infection in koalas is common across the east coast of Australia and causes significant morbidity, infertility and mortality. An effective vaccine to prevent the adverse consequences of chlamydial infections in koalas (particularly blindness and infertility in females) would provide an important management tool to prevent further population decline of this species. An important step towards developing a vaccine in koalas is to understand the host immune response to chlamydial infection. In this study, we used the Pepscan methodology to identify B cell epitopes across the Major Outer Membrane Protein (MOMP) of four C. pecorum strains/genotypes that are recognized, either following (a) natural live infection or (b) administration of a recombinant MOMP vaccine. Plasma antibodies from the koalas naturally infected with a C. pecorum G genotype strain recognised the epitopes located in the variable domain (VD) four of MOMP G and also VD4 of MOMP H. By comparison, plasma antibodies from an animal infected with a C. pecorum F genotype strain recognised epitopes in VD1, 2 and 4 of MOMP F, but not from other genotype MOMPs. When Chlamydia-free koalas were immunised with recombinant MOMP protein they produced antibodies not only against epitopes in the VDs but also in conserved domains of MOMP. Naturally infected koalas immunised with recombinant MOMP protein also produced antibodies against epitopes in the conserved domains. This work paves the way for further refinement of a MOMP-based Chlamydia vaccine that will offer wide cross-protection against the variety of chlamydial infections circulating in wild koala populations.

Experimental evaluation of an autonomous surface vehicle for water quality and greenhouse gas emission monitoring

This paper describes the experimental evaluation of a novel Autonomous Surface Vehicle capable of navigating complex inland water reservoirs and measuring a range of water quality properties and greenhouse gas emissions. The 16 ft long solar powered catamaran is capable of collecting water column profiles whilst in motion. It is also directly integrated with a reservoir scale floating sensor network to allow remote mission uploads, data download and adaptive sampling strategies. This paper describes the onboard vehicle navigation and control algorithms as well as obstacle avoidance strategies. Experimental results are shown demonstrating its ability to maintain track and avoid obstacles on a variety of large-scale missions and under differing weather conditions, as well as its ability to continuously collect various water quality parameters complimenting traditional manual monitoring campaigns.

Ultraviolet action spectroscopy of iodine labeled peptides and proteins in the gas phase

Structural investigations of large biomolecules in the gas phase are challenging. Herein, it is reported that action spectroscopy taking advantage of facile carbon-iodine bond dissociation can be used to examine the structures of large molecules, including whole proteins. Iodotyrosine serves as the active chromophore, which yields distinctive spectra depending on the solvation of the side chain by the remainder of the molecule. Isolation of the chromophore yields a double featured peak at ∼290 nm, which becomes a single peak with increasing solvation. Deprotonation of the side chain also leads to reduced apparent intensity and broadening of the action spectrum. The method can be successfully applied to both negatively and positively charged ions in various charge states, although electron detachment becomes a competitive channel for multiply charged anions. In all other cases, loss of iodine is by far the dominant channel which leads to high sensitivity and simple data analysis. The action spectra for iodotyrosine, the iodinated peptides KGYDAKA, DAYLDAG, and the small protein ubiquitin are reported in various charge states. © 2012 American Chemical Society.

Characterisation of the ionic products arising from electron photodetachment of simple dicarboxylate dianions

Much of what we currently understand about the structure and energetics of multiply charged anions in the gas phase is derived from the measurement of photoelectron spectra of simple dicarboxylate dianions. Here we have employed a modified linear ion-trap mass spectrometer to undertake complementary investigations of the ionic products resulting from laser-initiated electron photodetachment of two model dianions. Electron photodetachment (ePD) of the \[M-2H](2-) dianions formed from glutaric and adipic acid were found to result in a significant loss of ion signal overall, which is consistent with photoelectron studies that report the emission of slow secondary electrons (Xing et al., 2010 \[201). The ePD mass spectra reveal no signals corresponding to the intact \[M-2H](center dot-) radical anions, but rather \[M-2H-CO2](center dot-) ions are identified as the only abundant ionic products indicating that spontaneous decarboxylation follows ejection of the first electron. Interestingly however, investigations of the structure and energetics of the \[M-2H-CO2](center dot-) photoproducts by ion-molecule reaction and electronic structure calculation indicate that (i) these ions are stable with respect to secondary electron detachment and (ii) most of the ion population retains a distonic radical anion structure where the radical remains localised at the position of the departed carboxylate moiety. These observations lead to the conclusion that the mechanism for loss of ion signal involves unimolecular rearrangement reactions of the nascent \[M-2H](center dot-) carbonyloxyl radical anions that compete favourably with direct decarboxylation. Several possible rearrangement pathways that facilitate electron detachment from the radical anion are identified and are computed to be energetically accessible. Such pathways provide an explanation for prior observations of slow secondary electron features in the photoelectron spectra of the same dicaboxylate dianions. (C) 2013 Elsevier B.V. All rights reserved.

Direct Observation of Photodissociation Products from Phenylperoxyl Radicals Isolated in the Gas Phase

Gas phase peroxyl radicals are central to our chemical understanding of combustion and atmospheric processes and are typically characterized by strong absorption in the UV (lambda(max) approximate to 240 nm). The analogous maximum absorption feature for arylperoxyl radicals is predicted to shift to the visible but has not previously been characterized nor have any photoproducts arising from this transition been identified. Here we describe the controlled synthesis and isolation in vacuo of an array of charge-substituted phenylperoxyl radicals at room temperature, including the 4-(N,N,N-trimethylammonium)methyl phenylperoxyl radical cation (4-Me3N[+]CH2-C6H4OO center dot), using linear ion-trap mass spectrometry. Photodissociation mass spectra obtained at wavelengths ranging from 310 to 500 nm reveal two major photoproduct channels corresponding to homolysis of aryl-OO and arylO-O bonds resulting in loss of O-2 and O, respectively. Combining the photodissociation yields across this spectral window produces a broad (FWHM approximate to 60 nm) but clearly resolved feature centered at lambda(max) = 403 nm (3.08 eV). The influence of the charge-tag identity and its proximity to the radical site are investigated and demonstrate no effect on the identity of the two dominant photoproduct channels. Electronic structure calculations have located the vertical (B) over tilde <- (X) over tilde transition of these substituted phenylperoxyl radicals within the experimental uncertainty and further predict the analogous transition for unsubstituted phenylperoxyl radical (C6H5OO center dot) to be 457 nm (2.71 eV), nearly 45 nm shorter than previous estimates and in good agreement with recent computational values.

Direct Detection of a Persistent Carbonyloxyl Radical in the Gas Phase

Long lived: Carbonyloxyl radicals (RCO2 .) are reactive intermediates that play key roles in initiating polymerization reactions. This reactivity also makes their direct observation difficult. For the first time a persistent organic RCO2 . radical is detected in the gas phase, its extraordinary longevity is attributed to the high barrier towards fragmentation owing to the endothermicity of the decarboxylation products. Grant Numbers ARC/DP0986738, ARC/DP120102922, ARC/DE120100467

Hydroxyl radical formation in the gas phase oxidation of distonic 2-methylphenyl radical cations

The reactions of distonic 4-(N, N, N-trimethylammonium)-2-methylphenyl and 5-(N, N, N-trimethylammonium)-2-methylphenyl radical cations (m/z 149) with O-2 are studied in the gas phase using ion-trap mass spectrometry. Photodissociation (PD) of halogenated precursors gives rise to the target distonic charge-tagged methylphenyl radical whereas collision-induced dissociation (CID) is found to produce unreactive radical ions. The PD generated distonic radicals, however, react rapidly with O-2 to form \[M + O2](center dot+) and \[M + O-2 - OH](center dot+) ions, detected at m/z 181 and m/z 164, respectively. Quantum chemical calculations using G3SX(MP3) and M06-2X theories are deployed to examine key decomposition pathways of the 5-(N, N, N-trimethylammonium)-2-methylphenylperoxyl radical and rationalise the observed product ions. The prevailing product mechanism involves a 1,5- H shift in the peroxyl radical forming a QOOH-type intermediate that subsequently eliminates (OH)-O-center dot to yield charge-tagged 2-quinone methide. Our study suggests that the analogous process should occur for the neutral methylphenyl + O-2 reaction, thus serving as a plausible source of (OH)-O-center dot radicals in combustion environments. Grants: ARC/DP0986738, ARC/DP130100862