Mechanism of activation of human c-KIT kinase by internal tandem duplications of the juxtamembrane domain and point mutations at aspartic acid 816

The patients suffering from acidosis usually sign psychological deficits. The cerebral dysfunction is reportedly caused by an acid-induced functional impairment of GABAergic neurons; however, the role of pyramidal neurons in this process remains unclear. By using electrophysiological method and changing extracellular pH, we investigated the influence of acidic environment on pyramidal neurons in the cortical slices, such as their ability of firing spikes and response to synaptic inputs. A low pH of artificial cerebral spinal fluid elevates the responses of pyramidal neurons to excitatory synaptic inputs and their ability of encoding digital spikes, as well as reduces the signal transmission at GABAergic synapses. The elevated ability of neuronal spiking is associated with the decreases of refractory periods and threshold potentials. Therefore, acidosis deteriorates brain functions through making the activities between cortical pyramidal neurons and GABAergic neurons imbalanced toward the overexcitation of neural networks, a process similar to neural excitotoxicity.     

Biochemical functionalization of polymeric cell substrata can alter mechanical compliance

Biochemical functionalization of surfaces is an increasingly utilized mechanism to promote or inhibit adhesion of cells. To promote mammalian cell adhesion, one common functionalization approach is surface conjugation of adhesion peptide sequences such as Arg-Gly-Asp (RGD), a ligand of transmembrane integrin molecules. It is generally assumed that such functionalization does not alter the local mechanical properties of the functionalized surface, as is important to interpretations of macromolecular mechanotransduction in cells. Here, we examine this assumption systematically, through nanomechanical measurement of the nominal elastic modulus of polymer multilayer films of nanoscale thickness, functionalized with RGD through different processing routes. We find that the method of biochemical functionalization can significantly alter mechanical compliance of polymeric substrata such as weak polyelectrolyte multilayers (PEMs), increasingly utilized materials for such studies. In particular, immersed adsorption of intermediate functionalization reagents significantly decreases compliance of the PEMs considered herein, whereas polymer-on-polymer stamping of these same reagents does not alter compliance of weak PEMs. This finding points to the potential unintended alteration of mechanical properties via surface functionalization and also suggests functionalization methods by which chemical and mechanical properties of cell substrata can be controlled independently.     

Structure and function of the Gondwanian hemoglobin of Pseudaphritis urvillii, a primitive notothenioid fish of temperate latitudes

The suborder Notothenioidei dominates the Antarctic ichthyofauna. The non-Antarctic monotypic family Pseudaphritidae is one of the most primitive families. The characterization of the oxygen-transport system of euryhaline Pseudaphritis urvillii is herewith reported. Similar to most Antarctic notothenioids, this temperate species has a single major hemoglobin (Hb 1, over 95% of the total). Hb 1 has strong Bohr and Root effects. It shows two very uncommon features in oxygen binding: At high pH values, the oxygen affinity is exceptionally high compared to other notothenioids, and subunit cooperativity is modulated by pH in an unusual way, namely the curve of the Hill coefficient is bell-shaped, with values approaching 1 at both extremes of pH. Molecular modeling, electronic absorption and resonance Raman spectra have been used to characterize the heme environment of Hb 1 in an attempt to explain these features, particularly in view of some potentially important nonconservative replacements found in the primary structure. Compared to human HbA, no major changes were found in the structure of the proximal cavity of the alpha-chain of Hb 1, although an altered distal histidyl and heme position was identified in the models of the beta-chain, possibly facilitated by a more open heme pocket due to reduced steric constraints on the vinyl substituent groups. This conformation may lead to the hemichrome form identified by spectroscopy in the Met state, which likely fulfils a potentially important physiological role.     

A dynamic mass balance model for phosphorus fluxes and concentrations in coastal areas

This paper presents a general, process-based mass balance model (CoastMab) for total phosphorus (TP) in defined coastal areas (at the ecosystem scale). The model is based on ordinary differential equations and calculates inflow, outflow and internal fluxes on a monthly basis. It consists of four compartments: surface water, deep water, erosion/transportation areas for fine sediments and accumulation areas for fine sediments. The separation between surface water and deep water is not done based on water temperature, but on sedimentological criteria instead (from the theoretical wave base). There are algorithms for all major internal TP fluxes (sedimentation, resuspension, diffusion, mixing and burial). Validations were performed using data from 21 different Baltic coastal areas. The results show that the model predicts monthly TP in water and chlorophyll a very well (generally within the uncertainty bands of the empirical data). The model has also been put through sensitivity tests, which show that the most important factor regulating the predictions of the model is generally the TP concentration in the sea beyond the coast. The model is simple to apply, since all driving variables may be accessed from maps or monitoring programs. The driving variables include coastal area, section area (between the defined coastal area and the adjacent sea), mean and maximum depths, latitude (used to predict water temperatures, stratification and mixing), salinity and TP concentration in the sea. Many of the model structures are general and could be used for areas other than those included in this study, e.g., for open coasts, estuaries or tidal coasts, as well as for other substances than phosphorus.     

Molecular architecture of a eukaryotic DNA transposase

Mobile elements and their inactive remnants account for large proportions of most eukaryotic genomes, where they have had central roles in genome evolution. Over 50 years ago, McClintock reported a form of stress-induced genome instability in maize in which discrete DNA segments move between chromosomal locations. Our current mechanistic understanding of enzymes catalyzing transposition is largely limited to prokaryotic transposases. The Hermes transposon from the housefly is part of the eukaryotic hAT superfamily that includes hobo from Drosophila, McClintock's maize Activator and Tam3 from snapdragon. We report here the three-dimensional structure of a functionally active form of the transposase from Hermes at 2.1-A resolution. The Hermes protein has some structural features of prokaryotic transposases, including a domain with a retroviral integrase fold. However, this domain is disrupted by the insertion of an additional domain. Finally, transposition is observed only when Hermes assembles into a hexamer.     

Structural basis for ligand recognition and discrimination of a quorum-quenching antibody

In the postantibiotic era, available treatment options for severe bacterial infections caused by methicillin-resistant Staphylococcus aureus have become limited. Therefore, new and innovative approaches are needed to combat such life-threatening infections. Virulence factor expression in S. aureus is regulated in a cell density-dependent manner using “quorum sensing,” which involves generation and secretion of autoinducing peptides (AIPs) into the surrounding environment to activate a bacterial sensor kinase at a particular threshold concentration. Mouse monoclonal antibody AP4-24H11 was shown previously to blunt quorum sensing-mediated changes in gene expression in vitro and protect mice from a lethal dose of S. aureus by sequestering the AIP signal. We have elucidated the crystal structure of the AP4-24H11 Fab in complex with AIP-4 at 2.5 Å resolution to determine its mechanism of ligand recognition. A key Glu^H95 provides much of the binding specificity through formation of hydrogen bonds with each of the four amide nitrogens in the AIP-4 macrocyclic ring. Importantly, these structural data give clues as to the interactions between the cognate staphylococcal AIP receptors AgrC and the AIPs, as AP4-24H11·AIP-4 binding recapitulates features that have been proposed for AgrC-AIP recognition. Additionally, these structural insights may enable the engineering of AIP cross-reactive antibodies or quorum quenching vaccines for use in active or passive immunotherapy for prevention or treatment of S. aureus infections.     

Multivariate meta-analysis of proteomics data from human prostate and colon tumours

Background  

There is a vast need to find clinically applicable protein biomarkers as support in cancer diagnosis and tumour classification. In proteomics research, a number of methods can be used to obtain systemic information on protein and pathway level on cells and tissues. One fundamental tool in analysing protein expression has been two-dimensional gel electrophoresis (2DE). Several cancer 2DE studies have reported partially redundant lists of differently expressed proteins. To be able to further extract valuable information from existing 2DE data, the power of a multivariate meta-analysis will be evaluated in this work.     

The stalk region of dynamin drives the constriction of dynamin tubes

The GTPase dynamin is essential for numerous vesiculation events including clathrin-mediated endocytosis. Upon GTP hydrolysis, dynamin constricts a lipid bilayer. Previously, a three-dimensional structure of mutant dynamin in the constricted state was determined by helical reconstruction methods. We solved the nonconstricted state by a single-particle approach and show that the stalk region of dynamin undergoes a large conformational change that drives tube constriction.     

Biodegradable films of partly branched poly(l-lactide)-co-poly(epsilon-caprolactone) copolymer: modulation of phase morphology, plasticization properties and thermal depolymerization

We report on the modulation of phase morphology, plasticization properties, and thermal stability of films of partly branched poly(l-lactide)-co-poly(epsilon-caprolactone) copolymer (PLLA-co-PCL) with additions of low molecular weight compounds, namely, triethyl citrate ester, diethyl phthalate, diepoxy polyether (poly(propylene glycol) diglycidyl ether), and with epoxidized soybean oil (ESO). The PLLA-co-PCL/polyether films showed significant stability against thermal depolymerization, high film flexibility, and good plasticizing properties, probably due to cross-linking and chain branching formation between diepoxy groups with both the end carboxyl and hydroxyl groups of the PLLA copolymer (initially present or generated during the degradation process) to produce primary ester and ether bonds, respectively. Diethyl phthalate and triethyl citrate ester were found to be efficient plasticizers for PLLA copolymer in terms of glass transition and mechanical properties, but the more water-soluble plasticizer triethyl citrate induced a dramatic loss in the molecular weight of the copolymer. Although ESO cannot play the role of a plasticizer, it substantially stabilizes and retards thermal depolymerization of the PLLA copolymer matrix, possibly because of a reaction between epoxy groups with the end carboxyl and hydroxyl groups of the PLLA copolymer. The presence of ESO in PLLA-co-PCL/ESO/triethyl citrate blends enhanced the compatibility and miscibility of the plasticizer with the PLLA copolymer matrix, considerably improved the mechanical properties (elongation at break), and substantially stabilized the copolymer against thermal depolymerization. It seems likely that the epoxy groups interact not only with the end hydroxyl and carboxyl group of the copolymer but as well with the hydroxyl group of triethyl citrate plasticizer to produce a new ether bond (C-O-C) as the cross-linking unit. On the other hand, for PLLA-co-PCL/ESO/polyether blends, (80/10/10) epoxidized oil distorts the compactness of the blend by diminishing the proposed entanglements between carboxyl, hydroxyl, and diepoxy groups of polyether and reduces the high elongation properties otherwise observed in the PLLA-co-PCL/polyether films. The multicomponent approach toward modulating poly(l-lactide)-co-poly(epsilon-caprolactone) copolymer films using epoxy compounds and plasticizers and the insight into the nature of various PLLA matrixes presented here offer advantages to a broad engineering of PLLA copolymer films having desirable physical properties and multiphase behavior for efficient uses in future technical applications.