Characterization and comparative 3D modeling of CmPI-II, a novel 'non-classical' Kazal-type inhibitor from the marine snail Cenchritis muricatus (Mollusca)

The complete amino acid sequence obtained by electrospray ionization tandem mass spectrometry of the proteinase inhibitor CmPI-II isolated from Cenchritis muricatus is described. CmPI-II is a 5480-Da protein with three disulfide bridges that inhibits human neutrophil elastase (HNE) (K(i) 2.6+/-0.2 nM), trypsin (K(i) 1.1+/-0.9 nM), and other serine proteinases such as subtilisin A (K(i) 30.8+/-1.2 nM) and pancreatic elastase (K(i) 145.0+/-4.4 nM); chymotrypsin, pancreatic and plasma kallikreins, thrombin and papain are not inhibited. CmPI-II shares homology with the Kazal-type domain and may define a new group of 'non-classical' Kazal inhibitors according to its Cys(I)-Cys(V) disulfide bridge position. The 3D model of CmPI-II exhibits similar secondary structure characteristics to Kazal-type inhibitors and concurs with circular dichroism experiments. A 3D model of the CmPI-II/HNE complex provides a structural framework for the interpretation of its experimentally determined K(i) value. The model shows both similar and different contacts at the primary binding sites in comparison with the structure of turkey ovomucoid third domain (OMTKY3)/HNE used as template. Additional contacts calculated at the protease-inhibitor interface could also contribute to the association energy of the complex. This inhibitor represents an exception in terms of specificity owing to its ability to strongly inhibit elastases and trypsin.     

Infrequent and unidirectional colonization of hyperdiverse Papuadytes diving beetles in New Caledonia and New Guinea

We present a molecular phylogenetic analysis of 2808 aligned bp of rrnL, cox1, cob, H3 and 18S rRNA of all major morphological groups of Papuadytes diving beetles (Coleoptera: Dytiscidae) which are diverse in running water habitats throughout the Australian region. We focus on the origin of the fauna of the megadiverse islands of New Guinea and New Caledonia. Parsimony as well as Bayesian analyses suggest a basal position of Australian species in a paraphyletic series, with more recent nested radiations in New Caledonia and New Guinea. According to molecular clock analyses, both landmasses were colonized during the Miocene, which matches geological data and corroborates similar findings in other taxonomic groups. Our analyses suggest that dispersal played an important role in the formation of these large insular faunas, although successful colonization appears to be a rare event, and, in this case, is unidirectional. Whether or not a lineage is present on an island is due to chance: Papuadytes are absent from Fiji, where related Copelatus have radiated extensively in the same habitats occupied by Papuadytes in New Caledonia and New Guinea, while Copelatus are absent from New Caledonia. Lineages of Papuadytes apparently colonized New Caledonia twice, around 14 and 9 MYA according to the molecular calibration, and both lineages are derived from an Australian ancestor. The older clade is represented only by two apparently relictual mountain species (one morphologically strongly adapted to highly ephemeral habitats), while the younger clade contains at least 18 species exhibiting a great morphological diversity. The 150+ species in New Guinea are monophyletic, apparently derived from an Australian ancestor, and constitute a morphologically rather homogenous group. The tree backbone remains insufficiently supported under parsimony and Bayesian analyses, where shorter branches suggest a rapid sequence of major branching events.     

Quantification of darunavir (TMC114) in human plasma by high-performance liquid chromatography with ultra-violet detection

A precise and accurate high-performance liquid chromatography (HPLC) method with UV detection has been developed and validated for darunavir, a peptidic protease inhibitor. An internal standard, methylclonazepam, was added to 100 microL of plasma before a solid-phase extraction on C18 Bond Elut column. The eluted solutions were evaporated to dryness and reconstituted with 100 microL of mobile phase before being injected in the chromatographic system. The separation was performed on a C8 column using an acetonitrile and ultrapure water mixture (40:60, v/v) as mobile phase. All compounds were detected at a wavelength of 266 nm. The method was linear and validated over a concentration range of 0.25-20mg/L. The within-day precision, ranged from 3.0 to 7.9%, while the within-day accuracy ranged from -11.4 to 0.5%. The between day precision and accuracy were respectively less than 13.7 and -11.4%. The mean recovery was 75.7% for darunavir and 66.7% for methylclonazepam. This method provides a useful tool for therapeutic drug monitoring in HIV patients.     

Molecular and morphological patterns of introgression between two large white-headed gull species in a zone of recent secondary contact

Incomplete reproductive isolation promotes gene flow between diverging taxa. However, any gene encoding for traits involved in the reproductive barriers will be less prone to introgression than neutral markers. Comparing introgression rates among loci is thus informative of the number and functions of loci involved in the reproductive barriers. This study aimed at identifying possible mechanisms of restriction to gene flow across a zone of recent secondary contact between Larus argentatus and Larus cachinnans by comparing introgression patterns for nine microsatellite loci, a fragment of mitochondrial DNA and a set of phenotypic traits. The low linkage disequilibrium between neutral nuclear markers indicated introgression without any barrier to gene flow. However, asymmetric introgression of mitochondrial DNA suggested that interspecific crosses may be more successful in one direction. The introgression rate for phenotypic traits was variable and low compared to neutral molecular markers. This was particularly evident in colouration of bare parts: individuals with intermediate colouration were scarcer in sympatry than expected if the genomes recombined freely. We hypothesized that one of these variables, the orbital ring colour, may play a role in mate choice, acting as an incomplete premating barrier through assortative mating. This study emphasizes that multilocus approaches are useful to discriminate among possible mechanisms responsible for the maintenance of hybrid zones.     

Molecular evolution of the H-NS protein: interaction with Hha-like proteins is restricted to enterobacteriaceae

We show here that chromosomal hha-like genes are restricted to the Enterobacteriaceae. The H-NS N-terminal domain of members of this family includes an unaltered seven-amino-acid sequence located between helixes 1 and 2, termed the Hha signature, that contains key residues for H-NS-Hha interaction.     

Critical role of electrostatic interactions of amino acids at the cytoplasmic region of helices 3 and 6 in rhodopsin conformational properties and activation

The cytoplasmic sides of transmembrane helices 3 and 6 of G-protein-coupled receptors are connected by a network of ionic interactions that play an important role in maintaining its inactive conformation. To investigate the role of such a network in rhodopsin structure and function, we have constructed single mutants at position 134 in helix 3 and at positions 247 and 251 in helix 6, as well as combinations of these to obtain double mutants involving the two helices. These mutants have been expressed in COS-1 cells, immunopurified using the rho-1D4 antibody, and studied by UV-visible spectrophotometry. Most of the single mutations did not affect chromophore formation, but double mutants, especially those involving the T251K mutant, resulted in low yield of protein and impaired 11-cis-retinal binding. Single mutants E134Q, E247Q, and E247A showed the ability to activate transducin in the dark, and E134Q and E247A enhanced activation upon illumination, with regard to wild-type rhodopsin. Mutations E247A and T251A (in E134Q/E247A and E134Q/T251A double mutants) resulted in enhanced activation compared with the single E134Q mutant in the dark. A role for Thr(251) in this network is proposed for the first time in rhodopsin. As a result of these mutations, alterations in the hydrogen bond interactions between the amino acid side chains at the cytoplasmic region of transmembrane helices 3 and 6 have been observed using molecular dynamics simulations. Our combined experimental and modeling results provide new insights into the details of the structural determinants of the conformational change ensuing photoactivation of rhodopsin.     

Application of acetamidomethyl and 9-fluorenylmethyl groups for efficient side protection of penicillamine in solid-phase peptide synthesis

Synthesis of S-acetamidomethyl and S-fluorenylmethyl derivatives of penicillamine is described. Both groups are completely stable to all the usual reagents in solid-phase peptide synthesis, including the HF cleavage step, and show an excellent degree of orthogonality to each other. Treatment of the protected peptides Ac-L-Pen(X)-L-Pro-D-Val-L-Cys(X)-NH2 with thallium (III) trifluoroacetate or iodine for X = Acm or piperidine/DMF (1:1) for X = Fm induced with good yield the formation of the intramolecular disulfide bridge. This cyclic peptide appears to assume a type II beta-turn conformation in d6-DMSO as evidenced by 1H-NMR spectra.     

Roundness variation in JPEG images affects the automated process of nuclear immunohistochemical quantification: correction with a linear regression model

The volume of digital image (DI) storage continues to be an important problem in computer-assisted pathology. DI compression enables the size of files to be reduced but with the disadvantage of loss of quality. Previous results indicated that the efficiency of computer-assisted quantification of immunohistochemically stained cell nuclei may be significantly reduced when compressed DIs are used. This study attempts to show, with respect to immunohistochemically stained nuclei, which morphometric parameters may be altered by the different levels of JPEG compression, and the implications of these alterations for automated nuclear counts, and further, develops a method for correcting this discrepancy in the nuclear count. For this purpose, 47 DIs from different tissues were captured in uncompressed TIFF format and converted to 1:3, 1:23 and 1:46 compression JPEG images. Sixty-five positive objects were selected from these images, and six morphological parameters were measured and compared for each object in TIFF images and those of the different compression levels using a set of previously developed and tested macros. Roundness proved to be the only morphological parameter that was significantly affected by image compression. Factors to correct the discrepancy in the roundness estimate were derived from linear regression models for each compression level, thereby eliminating the statistically significant differences between measurements in the equivalent images. These correction factors were incorporated in the automated macros, where they reduced the nuclear quantification differences arising from image compression. Our results demonstrate that it is possible to carry out unbiased automated immunohistochemical nuclear quantification in compressed DIs with a methodology that could be easily incorporated in different systems of digital image analysis.     

The role of low avidity T cells in the protection against type 1 diabetes: a modeling investigation

Cytotoxic T lymphocytes (CTLs) play a dominant role in the pathogenesis of autoimmune diabetes, commonly denoted Type 1 Diabetes (T1D). These CTLs (notably CD8⁺ T cells) recognize and kill insulin-secreting pancreatic β cells, reducing their number by ∼90%. The resulting reduction of insulin secretion causes the defective regulation of glucose metabolism, leading to the characteristic symptoms of diabetes. Recognition of β cells as targets by CTLs depends on the interactions between MHC-peptide complexes on the surface of β cells and receptors (TCRs) on T cells. Those CTLs with high affinity TCRs (also called high avidity T cells) cause most of the harm, while those with low affinity TCRs (also called low avidity T cells) play a more mysterious role. Recent experimental evidence suggests that low avidity T cells accumulate as memory T cells during the disease and may be protective in NOD mice (a strain prone to developing T1D), delaying disease progression. It has been hypothesized that such low avidity T cells afford disease protection either by crowding the islets of Langerhans, where β cells reside, or by killing antigen presenting cells (APCs).In this paper, we explore the hypothesized mechanisms for this protective effect in the context of a series of models for (1) the interactions of low and high avidity T cells, (2) the effect of APCs and (3) the feedback from β cell killing to autoantigen-induced T cell proliferation. We analyze properties of these models, noting consistency of predictions with observed behaviour. We then use the models to examine the influence of various treatment strategies on the progression of the disease. The model reveals that progressive accumulation of memory low avidity autoreactive T cells during disease progression makes treatments aimed at expanding these protective T cell types more effective close to, or at the onset of clinical disease. It also provides evidence for the hypothesis that low avidity T cells kill APCs (rather than the alternate hypothesis that they crowd the islets).