New technology for the detection of pH

The measurement of pH is the most widely employed test for (bio-)chemical lab. Since the first use of glass electrode to detect pH, new techniques and methods have broaden the scope of pH detection. Metal/metal oxide, ion sensitive field-effect transistors (ISFET), fibre-optical techniques, nanotechniques, and conducting polymer techniques have been extensively developed. This review covers the various methods for pH detection. New development trends were discussed.     

New insights into the nature of the wool fibre surface

Wool fibres have been treated to remove the covalently bound lipid and characterised using lipid analysis, wettability and scanning probe microscopy. A model substrate consisting of alternating stripes of hydrophobic (predominantly CH₃ terminated molecules) and hydrophilic (COOH terminated molecules) surfaces, micro-printed onto a gold-coated mica surface was assessed using the SPM techniques of adhesion, friction and phase imaging and showed that SPM can easily distinguish these surfaces. When KOH/methanol treated wool fibres were examined, SPM showed an increase in coefficient of friction and a decrease in adhesion as the lipid is removed. The increased friction is consistent with studies on the model surface and confirms the hypothesis that the lipid layer decreases the surface friction of fibres. The decreased adhesion is consistent with results in the literature on hair, but is at odds with the results on the model surface. The strong contrast shown between the methyl and carboxylic acid surfaces in the friction image of the micro-patterned surface, and the complete absence of any such contrast developing with time of treatment of the wool fibres strongly suggests that the surface lipid is not present as a discrete outer layer on the fibre. A new model is proposed in which the lipid is intimately associated with the surface proteins and allows for changes in lipid concentration at the surface in response to changes in environmental conditions.     

New insights into the regulation of apoptosis,necroptosis, and pyroptosis by receptor interacting protein kinase 1 and caspase-8

Necroptosis and pyroptosis are inflammatory forms of regulated necrotic cell death as opposed to apoptosis that is generally considered immunologically silent. Recent studies revealed unexpected links in the pathways regulating and executing cell death in response to activation of signaling cascades inducing apoptosis, necroptosis, and pyroptosis. Emerging evidence suggests that receptor interacting protein kinase 1 and caspase-8 control the cross-talk between apoptosis, necroptosis, and pyroptosis and determine the type of cell death induced in response to activation of cell death signaling.     

Separate Gating Mechanisms Mediate the Regulation of K2P Potassium Channel TASK-2 by Intra- and Extracellular pH

TASK-2 (KCNK5 or K_2P5.1) is a background K⁺ channel that is opened by extracellular alkalinization and plays a role in renal bicarbonate reabsorption and central chemoreception. Here, we demonstrate that in addition to its regulation by extracellular protons (pH_o) TASK-2 is gated open by intracellular alkalinization. The following pieces of evidence suggest that the gating process controlled by intracellular pH (pH_i) is independent from that under the command of pH_o. It was not possible to overcome closure by extracellular acidification by means of intracellular alkalinization. The mutant TASK-2-R224A that lacks sensitivity to pH_o had normal pH_i-dependent gating. Increasing extracellular K⁺ concentration acid shifts pH_o activity curve of TASK-2 yet did not affect pH_i gating of TASK-2. pH_o modulation of TASK-2 is voltage-dependent, whereas pH_i gating was not altered by membrane potential. These results suggest that pH_o, which controls a selectivity filter external gate, and pH_i act at different gating processes to open and close TASK-2 channels. We speculate that pH_i regulates an inner gate. We demonstrate that neutralization of a lysine residue (Lys²⁴⁵) located at the C-terminal end of transmembrane domain 4 by mutation to alanine abolishes gating by pH_i. We postulate that this lysine acts as an intracellular pH sensor as its mutation to histidine acid-shifts the pH_i-dependence curve of TASK-2 as expected from its lower pK_a. We conclude that intracellular pH, together with pH_o, is a critical determinant of TASK-2 activity and therefore of its physiological function.     

New insights into the regulation of plant immunity by amino acid metabolic pathways

Besides defence pathways regulated by classical stress hormones, distinct amino acid metabolic pathways constitute integral parts of the plant immune system. Mutations in several genes involved in Asp‐derived amino acid biosynthetic pathways can have profound impact on plant resistance to specific pathogen types. For instance, amino acid imbalances associated with homoserine or threonine accumulation elevate plant immunity to oomycete pathogens but not to pathogenic fungi or bacteria. The catabolism of Lys produces the immune signal pipecolic acid (Pip), a cyclic, non‐protein amino acid. Pip amplifies plant defence responses and acts as a critical regulator of plant systemic acquired resistance, defence priming and local resistance to bacterial pathogens. Asp‐derived pyridine nucleotides influence both pre‐ and post‐invasion immunity, and the catabolism of branched chain amino acids appears to affect plant resistance to distinct pathogen classes by modulating crosstalk of salicylic acid‐ and jasmonic acid‐regulated defence pathways. It also emerges that, besides polyamine oxidation and NADPH oxidase, Pro metabolism is involved in the oxidative burst and the hypersensitive response associated with avirulent pathogen recognition. Moreover, the acylation of amino acids can control plant resistance to pathogens and pests by the formation of protective plant metabolites or by the modulation of plant hormone activity.     

New insights into the mechanism of odorant detection by the malaria-transmitting mosquito Anopheles gambiae

Anopheles gambiae mosquitoes that transmit Plasmodium falciparum malaria use a series of olfactory cues present in human sweat to locate their hosts for a blood meal. Recognition of these odor cues occurs through the interplay of odorant receptors and odorant-binding proteins (OBPs) that bind to odorant molecules and transport and present them to the receptors. Recent studies have implicated potential heterodimeric interactions between two OBPs, OBP1 and OBP4, as important for perception of indole by the mosquito (Biessmann, H., Andronopoulou, E., Biessmann, M. R., Douris, V., Dimitratos, S. D., Eliopoulos, E., Guerin, P. M., Iatrou, K., Justice, R. W., Kröber, T., Marinotti, O., Tsitoura, P., Woods, D. F., and Walter, M. F. (2010) PLoS ONE 5, e9471; Qiao, H., He, X., Schymura, D., Ban, L., Field, L., Dani, F. R., Michelucci, E., Caputo, B., della Torre, A., Iatrou, K., Zhou, J. J., Krieger, J., and Pelosi, P. (2011) Cell. Mol. Life Sci. 68, 1799–1813). Here we present the 2.0 Å crystal structure of the OBP4-indole complex, which adopts a classical odorant-binding protein fold, with indole bound at one end of a central hydrophobic cavity. Solution-based NMR studies reveal that OBP4 exists in a molten globule state and binding of indole induces a dramatic conformational shift to a well ordered structure, and this leads to the formation of the binding site for OBP1. Analysis of the OBP4-OBP1 interaction reveals a network of contacts between residues in the OBP1 binding site and the core of the protein and suggests how the interaction of the two proteins can alter the binding affinity for ligands. These studies provide evidence that conformational ordering plays a key role in regulating heteromeric interactions between OBPs.     

New insights into the archaeal diversity of a hypersaline microbial mat obtained by a metagenomic approach

A metagenomic approach was carried out in order to study the genetic pool of a hypersaline microbial mat, paying more attention to the archaeal community and, specifically, to the putatively methanogenic members. The main aim of the work was to expand the knowledge of a likely ecologically important archaeal lineage, candidate division MSBL1, which is probably involved in methanogenesis at very high salinities.     

Diphenhydramine inhibits voltage-gated proton channels (Hv1) and induces acidification in leukemic Jurkat T cells- New insights into the pro-apoptotic effects of antihistaminic drugs

An established characteristic of neoplastic cells is their metabolic reprogramming, known as the Warburg effect, with greater reliance on energetically less efficient pathways (such as glycolysis and pentose phosphate shunt) compared with oxidative phosphorylation. This results in an overproduction of acidic species that must be extruded to maintain intracellular homeostasis. We recently described that blocking the proton currents in leukemic cells mediated by Hv1 ion channels triggers a marked intracellular acidification and apoptosis induction. Moreover, histamine H1-receptor antagonists were found to induce apoptosis in tumoral cells but the mechanism is still unclear. By using Jurkat T cells, we now show how diphenhydramine inhibits Hv1 mediated currents, inducing a drop in intracellular pH and cellular viability. This provides evidence of a new target structure responsible of the known pro-apoptotic action of antihistaminic drugs.     

Isoprene: New insights into the control of emission and mediation of stress tolerance by gene expression

Isoprene is a volatile compound produced in large amounts by some, but not all, plants by the enzyme isoprene synthase. Plants emit vast quantities of isoprene, with a net global output of 600 Tg per year, and typical emission rates from individual plants around 2% of net carbon assimilation. There is significant debate about whether global climate change resulting from increasing CO₂ in the atmosphere will increase or decrease global isoprene emission in the future. We show evidence supporting predictions of increased isoprene emission in the future, but the effects could vary depending on the environment under consideration. For many years, isoprene was believed to have immediate, physical effects on plants such as changing membrane properties or quenching reactive oxygen species. Although observations sometimes supported these hypotheses, the effects were not always observed, and the reasons for the variability were not apparent. Although there may be some physical effects, recent studies show that isoprene has significant effects on gene expression, the proteome, and the metabolome of both emitting and nonemitting species. Consistent results are seen across species and specific treatment protocols. This review summarizes recent findings on the role and control of isoprene emission from plants.     

New insights into the structure and hydration of a stratum corneum lipid model membrane by neutron diffraction

The structure and hydration of a stratum corneum (SC) lipid model membrane composed of N-(-hydroxyoctadecanoyl)-phytosphingosine (CER6)/cholesterol (Ch)/palmitic acid (PA)/cholesterol sulfate (ChS) were characterized by neutron diffraction. The neutron scattering length density across the SC lipid model membrane was calculated from measured diffraction peak intensities. The internal membrane structure and water distribution function across the bilayer were determined. The low hydration of the intermembrane space is a major feature of the SC lipid model membrane. The thickness of the water layer in the SC lipid model membrane is about 1 Å at full hydration. For the composition 55% CER6/25% Ch/15% PA/5% ChS, in a partly dehydrated state (60% humidity) and at 32°C, the lamellar repeat distance and the membrane thickness have the same value of 45.6 Å . The hydrophobic region of the membrane has a thickness of 31.2 Å . A decrease of the Ch content increases the membrane thickness. The water diffusion through the SC lipid model multilamellar membrane is a considerably slow process relative to that through phospholipid membranes. In excess water, the membrane hydration follows an exponential law with two characteristic times of 93 and 44 min. At 81°C and 97% humidity, the membrane separates into two phases with repeat distances of 45.8 and 40.5 Å . Possible conformations of CER6 molecules in the dry and hydrated multilayers are discussed.     

New insights into the mechanisms involved in renal proximal tubular damage induced in vitro by ochratoxin A

The mycotoxin ochratoxin A is a contaminant of human and animal food products. It is a potent nephrotoxin known to damage the proximal tubule. The aim of this work was to investigate the effects of ochratoxin A on a porcine renal proximal tubular epithelial cell line (LLC-PK1), and to identify sensitive endpoints revealing damage at the epithelial barrier level and at the molecular level. Cells exposed for 24 h to 5-10 microM ochratoxin indicated a clear damage to the intactness of the epithelial barrier, as shown by measurements of trans-epithelial resistance and zonula occludens-1 protein expression. At the mitochondrial level we observed alterations of the normal functions, such as an increase of the membrane potential, the formation of straight extensions, and the formation of giant mitochondria. At higher ochratoxin concentrations (50 microM), at which cytotoxicity assays revealed a significant toxicity, alterations of the cytoskeleton organization and induction of apoptosis were evident. In addition, we analyzed the expression of genes by using a cDNA macroarray. Our data indicate that ochratoxin-induced nephrotoxicity can be detected at the barrier and at the mitochondrial level at rather low concentrations, at which conventional cytotoxicity assays are unable to reveal toxic effects.     

New insights into the type A glycan modification of Clostridioides difficile flagellar protein flagellin C by phosphoproteomics analysis

The type A glycan modification found in human pathogen Clostridioides difficile consists of a monosaccharide (GlcNAc) that is linked to an N-methylated threonine through a phosphodiester bond. This structure has previously been described on the flagellar protein flagellin C of several C. difficile strains and is important for bacterial motility. The study of post-translational modifications often relies on some type of enrichment strategy; however, a procedure for enrichment of this modification has not yet been demonstrated. In this study, we show that an approach that is commonly used in phosphoproteomics, Fe³⁺-immobilized metal affinity chromatography, also enriches for peptides with this unique post-translational modification. Using LC–MS/MS analyses of immobilized metal affinity chromatography–captured tryptic peptides, we observed not only type A-modified C. difficile flagellin peptides but also a variety of truncated/modified type A structures on these peptides. Using an elaborate set of mass spectrometry analyses, we demonstrate that one of these modifications consists of a type A structure containing a phosphonate (2-aminoethylphosphonate), a modification that is rarely observed and has hitherto not been described in C. difficile. In conclusion, we show that a common enrichment strategy results in reliable identification of peptides carrying a type A glycan modification, and that the results obtained can be used to advance models about its biosynthesis.     

New insights into the ultrastructure, permeability, and integrity of conodont apatite determined by transmission electron microscopy

New crystalline structures have been observed in argon ion‐milled conodont elements from a diverse suite of Ordovician taxa (‘Cordylodus robustus’, Drepanoistodus suberectus, Panderodus gracilis, Plectodina? sp., Aphelognathus sp., Periodon aculeatus), using transmission electron microscopy (TEM). Electron diffraction patterns of albid tissue reveal that the component crystals are extraordinarily large, in the order of hundred(s) of microns. These large albid crystals show typical cancellate porosity, although a distinctly lamellar structure has also been observed within a large albid crystal positioned between hyaline lamellar and cancellate albid tissues. There is a distinct absence of ‘interlamellar space’ within all hyaline tissues examined, which are characterized by a polycrystalline matrix of micron‐scale elongate crystals that are both strongly aligned and tightly bound within a broader lamellar structure. Optical opacity, caused by light scattering within large (≥ 0.5 µm) pores, is also a feature of both albid and polycrystalline lamellar crown tissues. Accordingly, conodont hard tissues are differentiated by crystal size and shape, as well as inter‐ and intracrystalline porosity. These new observations highlight the structural complexities of conodont histologies and the need for more comprehensive investigations particularly of transitional crown tissues, which are not well defined by terms typically used in the literature. Their histological structures are interpreted to be a product of in vivo crystallization and thus provide new insights into the relative porosity, permeability, and inherent integrity of the tissues as well as their growth relationships. Accordingly, these data not only have implications for earlier histological and palaeobiological interpretations of conodont hard tissues but are also fundamental in determining their chemical integrity, which is crucial for characterizing palaeoseawater composition and palaeoenvironmental change. The potential for conodont apatite to retain primary chemical information depends on crystal size and permeability, so the large albid crystal domains are consistent with parallel geochemical studies that suggest that cancellate albid crown is more resistant to diagenetic modification.     

New insights into the migration and habitat use by bream and white bream in the floodplain of the River Rhine

Bream Abramis brama , white bream Blicca bjoerkna and roach Rutilus rutilus all undertook spawning migrations from the River Rhine into oxbows. Adult white bream and roach returned to the river after spawning. This indicates an annual change of habitat allowing the use of optimal conditions in oxbows for spawning and growth of juvenile fish, and the use of feeding grounds rich in benthos in the main river by the adults. In contrast, adult bream were still present in large numbers in the oxbows over the summer. Juvenile bream (0+ and 1+) migrated to the main river. Bream aged 2+ to 4+ were not found in the oxbows, whereas they occurred frequently in the river. Thus bream show ontogenetic changes in their use of the main river and oxbows. The young fish spend their long juvenile phase in the river after leaving the oxbows. Reproduction in oxbows is ensured by mature fish migrating in for a short period from the river as well as by other adults (≥5+) that live permanently in the oxbows. The strong tendency of adult bream to develop permanent stocks in the oxbows gives this species a reproductive advantage, since many oxbows are accessible to Rhine fish only occasionally in the present hydrological situation.     

New insights into early sequential PrPsc accumulation in scrapie infected mouse brain evidenced by the use of streptomycin sulfate

To investigate the amplifying potentialities of streptomycin sulfate in the immunohistochemical (IHC) detection of the abnormal prion protein (PrPsc), we used a sequential brain sampling from C506M3 scrapie strain inoculated C57Bl/6 mice. The weekly removed brains, from 7 to 63 days post intra-cranial inoculation were analysed using PrPsc IHC. The introduction of streptomycin sulfate, a technique developed for accurate cellular and regional mapping of PrPsc deposition in several animal TSEs, revealed a substantial amplifying effect and a clear specific PrPsc detection as early as 28 days post inoculation. The location of the first detected PrPsc deposits suggests a possible involvement of the cerebrospinal fluid in the early dissemination of the infectious agent. The meaning of these newly accessible PrPsc deposits is discussed in relation to a possible nascent form of PrPsc molecules detected in situ for the first time. Altogether, these findings argue that this method can be highly useful to study the early stages after infection with prion agents.