Characterisation of the plasma membrane subproteome of bloodstream form Trypanosoma brucei

Proteome analysis by conventional approaches is biased against hydrophobic membrane proteins, many of which are also of low abundance. We have isolated plasma membrane sheets from bloodstream forms of Trypanosoma brucei by subcellular fractionation, and then applied a battery of complementary protein separation and identification techniques to identify a large number of proteins in this fraction. The results of these analyses have been combined to generate a subproteome for the pellicular plasma membrane of bloodstream forms of T. brucei as well as a separate subproteome for the pellicular cytoskeleton. In parallel, we have used in silico approaches to predict the relative abundance of proteins potentially expressed by bloodstream form trypanosomes, and to identify likely polytopic membrane proteins, providing quality control for the experimentally defined plasma membrane subproteome. We show that the application of multiple high-resolution proteomic techniques to an enriched organelle fraction is a valuable approach for the characterisation of relatively intractable membrane proteomes. We present here the most complete analysis of a protozoan plasma membrane proteome to date and show the presence of a large number of integral membrane proteins, including 11 nucleoside/nucleobase transporters, 15 ion pumps and channels and a large number of adenylate cyclases hitherto listed as putative proteins.

Chemical studies of plasma etchants used in integrated circuit manufacture

Plasma or "dry" etching is an essential process for the production of modern microelectronic circuits. However, despite intensive research, many aspects of the etch process are not fully understood. The results of studies of the plasma etching of Si and Si02 in fluorine-containing discharges, and the complementary technique of plasma polymerisation are presented in this thesis. Optical emission spectroscopy with argon actinometry was used as the principle plasma diagnostic. Statistical experimental design was used to model and compare Si and Si02 etch rates in CF4 and SF6 discharges as a function of flow, pressure and power. Etch mechanisms m both systems, including the potential reduction of Si etch rates in CF4 due to fluorocarbon polymer formation, are discussed. Si etch rates in CF4 /SF6 mixtures were successfully accounted for by the models produced. Si etch rates in CF4/C2F6 and CHF3 as a function of the addition of oxygen-containing additives (02, N20 and CO2) are shown to be consistent with a simple competition between F, 0 and CFx species for Si surface sites. For the range of conditions studied, Si02 etch rates were not dependent on F-atom concentration, but the presence of fluorine was essential in order to achieve significant etch rates. The influence of a wide range of electrode materials on the etch rate of Si and Si02 in CF4 and CF4 /02 plasmas was studied. It was found that the Si etch rate in a CF4 plasma was considerably enhanced, relative to an anodised aluminium electrode, in the presence of soda glass or sodium or potassium "doped" quartz. The effect was even more pronounced in a CF4 /02 discharge. In the latter system lead and copper electrodes also enhanced the Si etch rate. These results could not be accounted for by a corresponding rise in atomic fluorine concentration. Three possible etch enhancement mechanisms are discussed. Fluorocarbon polymer deposition was studied, both because of its relevance to etch mechanisms and its intrinsic interest, as a function of fluorocarbon source gas (CF4, C2F6, C3F8 and CHF3), process time, RF power and percentage hydrogen addition. Gas phase concentrations of F, H and CF2 were measured by optical emission spectroscopy, and the resultant polymer structure determined by X-ray photoelectron spectroscopy and infrared spectroscopy. Thermal and electrical properties were measured also. Hydrogen additions are shown to have a dominant role in determining deposition rate and polymer composition. A qualitative description of the polymer growth mechanism is presented which accounts for both changes in growth rate and structure, and leads to an empirical deposition rate model.

Wear and corrosion of mechanical seals

Mechanical seals are used extensively to seal machinery such as pumps, mixers and agitators in the oil, petrochemical and chemical industries. The performance of such machinery is critically dependent on these devices. Seal failures may result in the escape of dangerous chemicals, possibly causing injury or loss of life. Seal performance is limited by the choice of face materials available. These range from cast iron and stellited stainless steel to cemented and silicon carbides. The main factors that affect seal performance are the wear and corrosion of seal faces. This research investigated the feasibility of applying surface coating/treatments to seal materials, in order to provide improved seal performance. Various surface coating/treatment methods were considered; these included electroless nickel plating, ion plating, plasma nitriding, thermal spraying and high temperature diffusion processes. The best wear resistance, as evaluated by the Pin-on-Disc wear test method, was conferred by the sprayed tungsten carbide/nickel/tungsten-chromium carbide deposit, produced by the high energy plasma spraying (Jet-Kote) process. In general, no correlation was found between hardness and wear resistance or surface finish and friction. This is due primarily to the complexity of the wear and frictional oxidation, plastic deformation, ploughing, fracture and delamination. Corrosion resistance was evaluated by Tafel extrapolation, linear polarisation and anodic potentiodynamic polarisation techniques. The best corrosion performance was exhibited by an electroless nickel/titanium nitride duplex coating due to the passivity of the titanium nitride layer in the acidified salt solution. The surface coating/treatments were ranked using a systematic method, which also considered other properties such as adhesion, internal stress and resistance to thermal cracking. The sealing behaviour of surface coated/treated seals was investigated on an industrial seal testing rig. The best sealing performances were exhibited by the Jet-Kote and electroless nickel silicon carbide composite coated seals. The failure of the electroless nickel and electroless nickel/titanium nitride duplex coated seals was due to inadequate adhesion of the deposits to the substrate. Abrasion of the seal faces was the principal wear mechanism. For operation in an environment similar to the experimental system employed (acidified salt solution) the Jet-Kote deposit appears to be the best compromise.

Cracking in hydrogen ion-implanted Si/Si0.8Ge0.2/Si heterostructures

We demonstrate that a controllable cracking can be realized in Si with a buried strain layer when hydrogen is introduced using traditional H-ion implantation techniques. However, H stimulated cracking is dependent on H projected ranges; cracking occurs along a Si0.8Ge0.2 strain layer only if the H projected range is shallower than the depth of the strained layer. The absence of cracking for H ranges deeper than the strain layer is attributed to ion-irradiation induced strain relaxation, which is confirmed by Rutherford-backscattering-spectrometry channeling angular scans. The study reveals the importance of strain in initializing continuous cracking with extremely low H concentrations.

Measurement of HNE-protein adducts in human plasma and serum by ELISA-Comparison of two primary antibodies

There is increasing evidence that non-enzymatic post-translational protein modifications might play key roles in various diseases. These protein modifications can be caused by free radicals generated during oxidative stress or by their products generated during lipid peroxidation. 4-Hydroxynonenal (HNE), a major biomarker of oxidative stress and lipid peroxidation, has been recognized as important molecule in pathology as well as in physiology of living organisms. Therefore, its detection and quantification can be considered as valuable tool for evaluating various pathophysiological conditions.The HNE-protein adduct ELISA is a method to detect HNE bound to proteins, which is considered as the most likely form of HNE occurrence in living systems. Since the earlier described ELISA has been validated for cell lysates and the antibody used for detection of HNE-protein adducts is non-commercial, the aim of this work was to adapt the ELISA to a commercial antibody and to apply it in the analysis of human plasma samples.After modification and validation of the protocol for both antibodies, samples of two groups were analyzed: apparently healthy obese (n=62) and non-obese controls (n=15). Although the detected absolute values of HNE-protein adducts were different, depending on the antibody used, both ELISA methods showed significantly higher values of HNE-protein adducts in the obese group. © 2013 The Authors.

Plasma vascular endothelial growth factor, angiopoietin-2, and soluble angiopoietin receptor tie-2 in diabetic retinopathy:effects of laser photocoagulation and angiotensin receptor blockade

Background: Proliferative diabetic retinopathy (PDR) may be a response to abnormal angiogenic growth factors such as vascular endothelial growth factor (VEGF), angiopoietin-2 (Ang-2), and the soluble angiopoietin receptor tie-2. The authors hypothesised the following: (a) there are differences in plasma levels of these growth factors in different grades of diabetic retinopathy; and (b) that the effects of intervention with panretinal laser photocoagulation (PRP) for PDR, and angiotensin receptor blockade (using eprosartan) for patients with other grades of diabetic retinopathy will be to reduce levels of the growth factors. Methods: Cross sectional and interventional study (using PRP and eprosartan) in diabetic patients. VEGF, Ang-2, and tie-2 were measured by ELISA. Results: VEGF (p<0.001) and Ang-2 levels (p<0.001) were significantly higher in 93 diabetic patients compared to 20 healthy controls, with the highest levels in grade 2 and grade 3 diabetic retinopathy (p<0.05). Tie-2 was lower in diabetics compared to controls (p = 0.008), with no significant differences between the diabetic subgroups. Overall, VEGF significantly correlated with Ang-2 (p<0.001) and tie-2 (p = 0.004) but the correlation between Ang-2 and tie-2 levels was not significant (p = 0.065). Among diabetic patients only, VEGF levels were significantly correlated with Ang-2 (p<0.001) and tie-2 (p<0.001); the correlation between Ang-2 and tie-2 levels was also significant (p<0.001). There were no statistically significant effects of laser photocoagulation on plasma VEGF, Ang-2, and tie-2 in the 19 patients with PDR, or any effects of eprosartan in the 28 patients with non-proliferative diabetic retinopathy. Conclusion: Increased plasma levels of VEGF and Ang-2, as well as lower soluble tie-2, were found in diabetic patients. The highest VEGF and Ang-2 levels were seen among patients with pre-proliferative and proliferative retinopathy, but there was no relation of tie-2 to the severity of retinopathy. As the majority of previous research into Ang-2 and tie-2 has been in relation to angiogenesis and malignancy, the present study would suggest that Ang-2 and tie-2 may be used as potential indices of angiogenesis in diabetes mellitus (in addition to VEGF) and may help elucidate the role of the angiopoietin/tie-2 system in this condition.

Transcriptome Analysis Reveals New Insights into the Modulation of Endometrial Stromal Cell Receptive Phenotype by Embryo-Derived Signals Interleukin-1 and Human Chorionic Gonadotropin: Possible Involvement in Early Embryo Implantation

The presence of the conceptus in uterine cavity necessitates an elaborate network of interactions between the implanting embryo and a receptive endometrial tissue. We believe that embryo-derived signals play an important role in the remodeling and the extension of endometrial receptivity period. Our previous studies provided original evidence that human Chorionic Gonadotropin (hCG) modulates and potentiates endometrial epithelial as well as stromal cell responsiveness to interleukin 1 (IL1), one of the earliest embryonic signals, which may represent a novel pathway by which the embryo favors its own implantation and growth within the maternal endometrial host. The present study was designed to gain a broader understanding of hCG impact on the modulation of endometrial cell receptivity, and in particular, cell responsiveness to IL1 and the acquisition of growth-promoting phenotype capable of receiving, sustaining, and promoting early and crucial steps of embryonic development. Our results showed significant changes in the expression of genes involved in cell proliferation, immune modulation, tissue remodeling, apoptotic and angiogenic processes. This points to a relevant impact of these embryonic signals on the receptivity of the maternal endometrium, its adaptation to the implanting embryo and the creation of an environment that is favorable for the implantation and the growth of this latter within a new and likely hostile host tissue. Interestingly our data further identified a complex interaction between IL1 and hCG, which, despite a synergistic action on several significant endometrial target genes, may encompass a tight control of endogenous IL1 and extends to other IL1 family members.

Data compilation on the biological response to ocean acidification: environmental and experimental context of data sets and related literature

The exponential growth of studies on the biological response to ocean acidification over the last few decades has generated a large amount of data. To facilitate data comparison, a data compilation hosted at the data publisher PANGAEA was initiated in 2008 and is updated on a regular basis (doi:10.1594/PANGAEA.149999). By January 2015, a total of 581 data sets (over 4 000 000 data points) from 539 papers had been archived. Here we present the developments of this data compilation five years since its first description by Nisumaa et al. (2010). Most of study sites from which data archived are still in the Northern Hemisphere and the number of archived data from studies from the Southern Hemisphere and polar oceans are still relatively low. Data from 60 studies that investigated the response of a mix of organisms or natural communities were all added after 2010, indicating a welcomed shift from the study of individual organisms to communities and ecosystems. The initial imbalance of considerably more data archived on calcification and primary production than on other processes has improved. There is also a clear tendency towards more data archived from multifactorial studies after 2010. For easier and more effective access to ocean acidification data, the ocean acidification community is strongly encouraged to contribute to the data archiving effort, and help develop standard vocabularies describing the variables and define best practices for archiving ocean acidification data.

Mineralogy and petrology of Black Sea Basin sediments

The origin and modes of transportation and deposition of inorganic sedimentary material of the Black Sea were studied in approximately 60 piston, gravity, and Kasten cores. The investigation showed that the sediment derived from the north and northwest (especially from the Danube) has a low calcite-dolomite ratio and a high quartz-feldspar ratio. Rock fragments are generally not abundant; garnet is the principal heavy mineral and illite is the predominant clay mineral. This sedimentary material differs markedly from that carried by Anatolian rivers, which is characterized by a high calcite-dolomite ratio and a low quartz-feldspar ratio. Rock fragments are abundant; pyroxene is the principal heavy mineral and montmorillonite is the predominant clay mineral. In generel, the clay fraction is large in all sediments (27.6-86.9 percent), and the lateral distributian indicates an increase in clay consent from the coasts toward two centers in the western and eastern Black Sea basin. Illite is the most common clay mineral in the Black Sea sediments. The lateral changes in composition of the clay mineral can easily be traced to the petrologic character of northern (rich in illite) and southern (rich in montmorillonite) source areas. In almost all cores, a rhythmic change of the montmorillonite-illite ratio with depth was observed. These changes may be related to the changing influence of the two provinces during the Holocene and late Pleistocene. Higher montmorillonite content seems to indicate climctic changes, probably stages of glaciation end permafrost in the northern area, at which time the illite supply was diminished to a large extent. The composition of the sand fraction is relatad to the different petrologic and morphologic characteristics of two major source provimces: (1) a northern province (rich in quartz, feldspars, and garnet) characterized by a low elevation, comprising the Danube basin area and the rivers draining the Russian platform; and (2) a southern province (rich in pyroxene and volcanic and metamorphic rocks) in the mountainous region of Anatolia and the Caucasus, characterized by small but extremely erosive rivers. The textural properties (graded bedding) of the deep-sea send layers clearly suggest deposition from turbidity currents. The carbonate content of the contemporary sediments ranges from 5 to 65 percent. It increases from the coast to a maximum in two centers in the western and eastern basin. This pattern reflects the distribution of the <2-µm fraction. The contemporary mud sedimentation is governed by two important factors: (1) the deposition of terrigenous allochthonous material of low carbonate content originating from the surrounding hinterland (northern and southern source areas), and (2) the autochthonous production of large quantities of biogenic calcite by coccolithophores during the last period of about 3,000-4,000 years.

Hydrological and sedimentological investigation of Radok Lake, Amery Oasis, East Antarctica

Radok Lake in Amery Oasis, East Antarctica, has a water depth of ca. 360 m, making it the deepest non-subglacial lake in Antarctica. Limnological analyses revealed that the lake had, despite a 3 m thick ice cover, a completely mixed water column during austral summer 2001/2002. High oxygen contents, low ion concentrations, and lack of planktonic diatoms throughout the water column indicate that Radok Lake is ultra-oligotrophic today.The late glacial and postglacial lake history is documented in a succession of glacial, glaciolimnic, and limnic sediments at different locations in the lake basin. The sediments record regional differences and past changes in allochthonous sediment supply and lake productivity. However, the lack of age control on these changes, due to extensive sediment redeposition and the lack of applicable dating methods, excluded Radok Lake sediments for advanced paleoenvironmental reconstructions.

Body measurements and blood plasma lipid, PCB and OH-PCB content of polar bear (U. maritimus) mothers and cubs, Svalbard

The aim of this study was to examine the plasma concentrations and prevalence of polychlorinated biphenyls (PCBs) and hydroxylated PCB-metabolites (OH-PCBs) in polar bear (Ursus maritimus) mothers (n = 26) and their 4 months old cubs-of-the-year (n = 38) from Svalbard to gain insight into the mother-cub transfer, biotransformation and to evaluate the health risk associated with the exposure to these contaminants. As samplings were performed in 1997/1998 and 2008, we further investigated the differences in levels and pattern of PCBs between the two sampling years. The plasma concentrations of Sum(21)PCBs (1997/1998: 5710 ± 3090 ng/g lipid weight [lw], 2008: 2560±1500 ng/g lw) and Sum(6)OH-PCBs (1997/1998: 228 ± 60 ng/g wet weight [ww], 2008: 80 ± 38 ng/g ww) in mothers were significantly lower in 2008 compared to in 1997/1998. In cubs, the plasma concentrations of Sum(21)PCBs (1997/1998: 14680 ± 5350 ng/g lw, 2008: 6070 ± 2590 ng/g lw) and Sum(6)OH-PCBs (1997/1998: 98 ± 23 ng/g ww, 2008: 49 ± 21 ng/g ww) were also significantly lower in 2008 than in 1997/1998. Sum(21)PCBs in cubs was 2.7 ± 0.7 times higher than in their mothers. This is due to a significant maternal transfer of these contaminants. In contrast, Sum(6)OH-PCBs in cubs were approximately 0.53 ± 0.16 times the concentration in their mothers. This indicates a lower maternal transfer of OH-PCBs compared to PCBs. The majority of the metabolite/precursor-ratios were lower in cubs compared to mothers. This may indicate that cubs have a lower endogenous capacity to biotransform PCBs to OH-PCBs than polar bear mothers. Exposure to PCBs and OH-PCBs is a potential health risk for polar bears, and the levels of PCBs and OH-PCBs in cubs from 2008 were still above levels associated with health effects in humans and wildlife.

Effect of the Electrolyte Formulation on the Performances of Edlc and Li-Ion Batteries

One of the most important components in electrochemical storage devices (batteries and supercapacitors) is undoubtedly the electrolyte. The basic function of any electrolyte in these systems is the transport of ions between the positive and negative electrodes. In addition, electrochemical reactions occurring at each electrode/electrolyte interface are the origin of the current generated by storage devices. In other words, performances (capacity, power, efficiency and energy) of electrochemical storage devices are strongly related to the electrolyte properties, as well as, to the affinity for the electrolyte to selected electrode materials. Indeed, the formulation of electrolyte presenting good properties, such as high ionic conductivity and low viscosity, is then required to enhance the charge transfer reaction at electrode/electrolyte interface (e.g. charge accumulation in the case of Electrochemical Double Layer Capacitor, EDLC). For practical and safety considerations, the formulation of novel electrolytes presenting a low vapor pressure, a large liquid range temperature, a good thermal and chemical stabilities is also required.

This lecture will be focused on the effect of the electrolyte formulation on the performances of electrochemical storage devices (Li-ion batteries and supercapacitors). During which, a summary of the physical, thermal and electrochemical data obtained by our group, recently, on the formulation of novel electrolyte-based on the mixture of an ionic liquid (such as EmimNTf2 and Pyr14NTf2) and carbonate or dinitrile solvents will be presented and commented. The impact of the electrolyte formulation on the storage performances of EDLC and Li-ion batteries will be also discussed to further understand the relationship between electrolyte formulation and electrochemical performances. This talk will also be an opportunity to further discuss around the effects of additives (SEI builder: fluoroethylene carbonate and vinylene carbonate), ionic liquids, structure and nature of lithium salt (LiTFSI vs LiPF6) on the cyclability of negative electrode to then enhance the electrolyte formulation. For that, our recent results on TiSnSb and graphite negative electrodes will be presented and discussed, for example 1,2.

1-C. Marino, A. Darwiche1, N. Dupré, H.A. Wilhelm, B. Lestriez, H. Martinez, R. Dedryvère, W. Zhang, F. Ghamouss, D. Lemordant, L. Monconduit “ Study of the Electrode/Electrolyte Interface on Cycling of a Conversion Type Electrode Material in Li Batteries” J. Phys.chem. C, 2013, 117, 19302-19313

2- Mouad Dahbi, Fouad Ghamouss, Mérièm Anouti, Daniel Lemordant, François Tran-Van “Electrochemical lithiation and compatibility of graphite anode using glutaronitrile/dimethyl carbonate mixtures containing LiTFSI as electrolyte” 2013, 43, 4, 375-385.

Assessing the Legacy of Red Mud Pollution in a Shallow Freshwater Lake: Arsenic Accumulation and Speciation in Macrophytes

Little is known about long-term ecological responses in lakes following red mud pollution. Among red mud contaminants, arsenic (As) is of considerable concern. Determination of the species of As accumulated in aquatic organisms provides important information about the biogeochemical cycling of the element and transfer through the aquatic food-web to higher organisms. We used coupled ion chromatography and inductively coupled plasma mass spectrometry (ICP-MS) to assess As speciation in tissues of five macrophyte taxa in Kinghorn Loch, UK, 30 years following the diversion of red mud pollution from the lake. Toxic inorganic As was the dominant species in the studied macrophytes, with As species concentrations varying with macrophyte taxon and tissue type. The highest As content measured in roots of Persicaria amphibia (L.) Gray (87.2 mg kg-1) greatly exceeded the 3 - 10 mg kg-1 range suggested as a potential phytotoxic level. Accumulation of toxic As species by plants suggested toxicological risk to higher organisms known to utilise macrophytes as a food source.

Electric field strengths and ion trajectories in sharp-edge field ionization sources

On the presumption that a sharp edge may be represented by a hyperbola, a conformal transformation method is used to derive electric field equations for a sharp edge suspended above a flat plate. A further transformation is then introduced to give electric field components for a sharp edge suspended above a thin slit. Expressions are deduced for the field strength at the vertex of the edge in both arrangements. The calculated electric field components are used to compute ion trajectories in the simple edge/flat-plate case. The results are considered in relation to future study of ion focusing and unimolecular decomposition of ions in field ionization mass spectrometers.

Insulator-to-metal transition in vanadium supersaturated silicon: variable-range hopping and Kondo effect signatures

We report the observation of the insulator-to-metal transition in crystalline silicon samples supersaturated with vanadium. Ion implantation followed by pulsed laser melting and rapid resolidification produce high quality single-crystalline silicon samples with vanadium concentrations that exceed equilibrium values in more than 5 orders of magnitude. Temperature-dependent analysis of the conductivity and Hall mobility values for temperatures from 10K to 300K indicate that a transition from an insulating to a metallic phase is obtained at a vanadium concentration between 1.1 × 10^(20) and 1.3 × 10^(21) cm^(−3) . Samples in the insulating phase present a variable-range hopping transport mechanism with a Coulomb gap at the Fermi energy level. Electron wave function localization length increases from 61 to 82 nm as the vanadium concentration increases in the films, supporting the theory of impurity band merging from delocalization of levels states. On the metallic phase, electronic transport present a dispersion mechanism related with the Kondo effect, suggesting the presence of local magnetic moments in the vanadium supersaturated silicon material.