Oxymyohemerythrin: discriminating between O2 release and autoxidation

Myohemerythrin (Mhr) is a non-heme iron O2 carrier (with two irons in the active site) that is typically found in the retractor muscle of marine 'peanut' worms. OxyMhr may either release O2, or undergo an autoxidation reaction in which hydrogen peroxide is released and diferric metMhr is produced. The autoxidation reaction can also be promoted by the addition of certain anions to Mhr solutions. This work, using recombinant Themiste zostericola Mhrs, contrasts the results of environmental effects on these reactions. For the O2 release reaction, deltaVdouble dagger(21.5 degrees C) = +28+/-3 cm3 mol(-1), deltaHdouble dagger(1 atm) = +22+/-1 kcal mol(-1), and deltaSdouble dagger(1 atm) = +28+/-4 eu. The autoxidation reaction (pH 8.0, 21.5 degrees C, 1 atm) displays different kinetic parameters: deltaVdouble dagger = -8+/-2 cm3 mol(-1), deltaHdouble dagger = +24.1+/-0.7 kcal mol(-1), and deltaSdouble dagger = +1+/-1 eu. Autoxidation in the presence of sodium azide is orders of magnitude faster than solvolytic autoxidation. The deltaVdouble dagger parameters for azide anation and azide-assisted autoxidation reaction are +15+/-2 and +59+/-2 cm3 mol(-1), respectively, indicating that the rate-limiting steps for the Mhr autoxidation and anation reactions (including O2 uptake) are not associated with ligand binding to the Fe2 center. The L103V and L103N oxyMhr mutants autoxidize approximately 10(3)-10(5) times faster than the wild-type protein, emphasizing the importance of leucine-103, which may function as a protein 'gate' in stabilizing bound dioxygen.     

What a tangled web we weave: discriminating between malingering and anosmia

Two groups of normosmic subjects were instructed to feign a total olfactory loss when tested with the Olfactory Confusion Matrix (OCM). One of the groups was given specific instructions as to the number of odorants and trials in the test, as well as the number of items that might be expected to be correctly identified by chance. The responses of both groups of malingerers were compared with responses gathered from a group of anosmic patients. The groups did not differ in terms of performance level (percent correct). In spite of the similarity in terms of accuracy level, an analysis of the pattern of OCM responses to an irritant allowed the anosmic patients to be distinguished from subjects attempting to feign a loss. Subjects were given explicit details about the test performed at the same level as those simply told to feign a loss. These results suggest that the OCM is an effective tool in separating malingering from anosmia.     

Methodology capture: discriminating between the best and the rest of community practice

Background  

The methodologies we use both enable and help define our research. However, as experimental complexity has increased the choice of appropriate methodologies has become an increasingly difficult task. This makes it difficult to keep track of available bioinformatics software, let alone the most suitable protocols in a specific research area. To remedy this we present an approach for capturing methodology from literature in order to identify and, thus, define best practice within a field.     

A simple method for discriminating between full and partial inhibitors

A method is described which provides a more straightforward and reliable discrimination between full and partial inhibitors than do other available procedures. Its advantages are demonstrated by analysis of actual inhibition data. The proposed method proves in certain cases convenient also for the determination of inhibition constants.     

Lysosomal membrane proteins: life between acid and neutral conditions

Whereas we have a profound understanding about the function and biogenesis of the protein constituents in the lumen of the lysosomal compartment, much less is known about the functions of proteins of the lysosomal membrane. Proteomic analyses of the lysosomal membrane suggest that, apart from the well-known lysosomal membrane proteins, additional and less abundant membrane proteins are present. The identification of disease-causing genes and the in-depth analysis of knockout mice leading to mutated or absent membrane proteins of the lysosomal membrane have demonstrated the essential role of these proteins in lysosomal acidification, transport of metabolites resulting from hydrolytic degradation and interaction and fusion with other cellular membrane systems. In addition, trafficking pathways of lysosomal membrane proteins are closely linked to the biogenesis of this compartment. This is exemplified by the recent finding that LIMP-2 (lysosomal integral membrane protein type-2) is responsible for the mannose 6-phosphate receptor-independent delivery of newly synthesized β-glucocerebrosidase to the lysosome. Similar to LIMP-2, which could also be linked to vesicular transport processes in certain polarized cell types, the major constituents of the lysosomal membrane, the glycoproteins LAMP (lysosome-associated membrane protein)-1 and LAMP-2 are essential for regulation of lysosomal motility and participating in control of membrane fusion events between autophagosomes or phagosomes with late endosomes/lysosomes. Our recent investigations into the role of these proteins have not only increased our understanding of the endolysosomal system, but also supported their major role in cell physiology and the development of different diseases.     

Proteomic Helicobacter pylori biomarkers discriminating between duodenal ulcer and gastric cancer

Protein patterns of 129 Helicobacter pylori strains isolated from Korean and Colombian patients suffering from duodenal ulcer or gastric cancer were analyzed by the high-throughput methodology SELDI-TOF-MS. Eighteen statistically significant candidate biomarkers discriminating between the two clinical outcomes were selected by using the Mann–Whitney test. Three biomarker proteins were purified and identified as a neutrophil-activating protein NapA (HU HPAG1_0821), a RNA-binding protein (HPAG1_0813), and a DNA-binding histone-like protein HU, respectively (jhp0228). These novel biomarkers can be used for development of diagnostic assays predicting the evolution to gastric cancer in H. pylori-infected patients.     

A simple method for discriminating between cell membrane and cytosolic proteins

* Transgenic plants expressing either green fluorescent protein (GFP)-genomic DNA or GFP-cDNA fusions have been used as powerful tools to define the subcellular localization of many proteins. Because most plant cells are highly vacuolated, the cytosol is confined to a thin layer at the periphery of the cells, making it very difficult to distinguish among cell wall, cell membrane and cytosolic GFP-fusion proteins. * Plasmolysis tests inform about cell-wall localization of GFP-tagged proteins, but they do not discriminate between its cell membrane and/or cytoplasmic localization. By observing the GFP signal in transgenic protoplasts placed at a hypotonic solution, it was possible to distinguish between cell membrane and cytosolic GFP-tagged proteins. * The osmotic disruption of the protoplast vacuole in the hypotonic solution allows the diffusion of the GFP signal from the cell periphery to the central part of the cell volume when the GFP is fused to a soluble protein. By contrast, such diffusion does not occur when the protein under study is attached to the cell membrane. * The present method is easier, faster and cheaper than subcellular fractionating studies and/or immunoelectron microscopy, which have been traditionally used to discern between cell membrane and cytosolic proteins.     

Physicochemical factors for discriminating between soluble and membrane proteins: hydrophobicity of helical segments and protein length

The average hydrophobicity of a polypeptide segment is considered to be the most important factor in the formation of transmembrane helices, and the partitioning of the most hydrophobic (MH) segment into the alternative nonpolar environment, a membrane or hydrophobic core of a globular protein may determine the type of protein produced. In order to elucidate the importance of the MH segment in determining which of the two types of protein results from a given amino acid sequence, we statistically studied the characteristics of MH helices, longer than 19 residues in length, in 97 membrane proteins whose three-dimensional structure or topology is known, as well as 397 soluble proteins selected from the Protein Data Bank. The average hydrophobicity of MH helices in membrane proteins had a characteristic relationship with the length of the protein. All MH helices in membrane proteins that were longer than 500 residues had a hydrophobicity greater than 1.75 (Kyte and Doolittle scale), while the MH helices in membrane proteins smaller than 100 residues could be as hydrophilic as 0.1. The possibility of developing a method to discriminate membrane proteins from soluble ones, based on the effect of size on the type of protein produced, is discussed.     

The mechanical properties of simple epithelial keratins 8 and 18: discriminating between interfacial and bulk elasticities

The abundance and cytoplasmic organization of keratin filaments enables them to contribute to the maintenance of structural integrity in epithelial tissues. Co-polymers of the type II keratin 8 and type I keratin 18 form the major intermediate filament network in simple epithelia. We investigated the mechanical properties of K8-K18 filament suspensions using rheological assays in conjunction with light and electron microscopy. Suspensions of K8-K18 filaments behave like a viscoelastic solid under standard assembly conditions. Bulk elasticity is weakly dependent on deformation frequency but is very sensitive to the concentration (G' approximately C1.5) and size of individual keratin polymers, in agreement with recent models of semiflexible-polymer physics. K8-K18 filaments can self-organize to form a bundled network that exhibits gel-like mechanical properties. In all cases the mechanical properties of the suspensions correlate with the structural features of individual polymers, as seen under light and electron microscopy. Importantly, these bulk viscoelastic properties of K8-K18 filaments are revealed only when interfacial elastic effects are minimized by the application of phospholipids at the air-liquid interface. Suspensions of K5-K14 and vimentin filaments also exhibit interfacial elasticity, which distorts the interpretation of the viscoelastic moduli as determined by standard rheometry. The potential for modulation of mechanical properties through self-organization may be a general property of keratin polymers and contribute to their organization and function in vivo.     

A simple and reliable method for discriminating between Helicoverpa armigera and Helicoverpa assulta (Lepidoptera: Noctuidae)

Abstract The cotton bollworm Helicoverpa armigera and the oriental tobacco budworm H. assulta are sibling species, both being important agricultural pests. Morphologically, the two insects are almost indistinguishable at the egg, larval and pupal stages. One of the big challenges in the study of these insects, in particular in integrated pest management, is a timely and dependable identification of these insects at their early stages of development. Here, we report a H. armigera‐specific nuclear DNA marker, and demonstrate that it can be employed to reliably discriminate between H. armigera and H. assulta by simple polymerase chain reaction amplification experiment.     

A quantitative measure for discriminating between self and non-self antigens in immune response

We present a new theory of how lymphocyte–antigen interaction is governed. We present ‘chronicity’, a quantitative record of previous lymphocyte–antigen interactions, which is used to regulate lymphocyte behavior. When the chronicity of a lymphocyte increases with the interaction and gets beyond the lower threshold, the lymphocyte can proliferate. Non-self antigens cause lymphocyte proliferation which destroys the antigen. However, self antigens are not destroyed. When the chronicity gets beyond the upper threshold, the lymphocytes get in the tolerance state ensuring non-destruction of self antigens. The discrimination between self and non-self results from the difference in the termination process between self and non-self antigens, caused by the difference in the frequency between interaction of lymphocyte with both antigens.     

Cryptic species identification: a simple diagnostic tool for discriminating between two problematic bumblebee species

Distinguishing between cryptic species is a perennial problem for biologists. Bombus ruderatus and Bombus hortorum are two species of bumblebee, which can be indistinguishable from their morphology. The former species is in decline, whereas the latter is ubiquitous. In the UK, isolated records of B. ruderatus occur amongst many for B. hortorum. For ecological studies of B. ruderatus to be feasible, the two species need to be reliably distinguishable. We present a diagnostic tool for quick and reliable identification of problematic individuals based on a restriction enzyme digest of the cytochrome b region of mitochondrial DNA.