High level expression and characterization of the cyclophilin B gene from the anaerobic fungus Orpinomyces sp. strain PC-2

Cyclophilins are an evolutionarily conserved family of peptidyl-prolyl cis-trans isomerases (PPIases). A cyclophilin B (cypB) gene from the anaerobic fungus Orpinomyces sp. strain PC-2 was cloned and overexpressed in Escherichia coli. It was expressed as an amino-terminal 6 x His-tagged recombinant protein to facilitate purification. Highly purified protein (26.5 kDa) was isolated by two chromatographic steps involving affinity and gel filtration for biochemical studies of the enzyme. The recombinant CypB displayed PPIase activity with a k(cat)/K(m) of 8.9 x 10(6) M(-1) s(-1) at 10 degrees C and pH 7.8. It was inhibited by cyclosporin A (CsA) with an IC(50) of 23.5 nM, similar to those of the native protein and other cyclophilin B enzymes from animals. Genomic DNA analysis of cypB revealed that it was present as a single copy in Orpinomyces PC-2 and contained two introns, indicating it has a eukaryotic origin. It is one of the most heavily interrupted genes with intron sequences found in anaerobic fungi. The three-dimensional model of Orpinomyces PC-2 CypB was predicted with a homology modeling approach using the Swiss-Model Protein Modeling Server and three dimensional structure of human CypB as a template. The overall architecture of the CypB molecule is very similar to that of human CypB.     

Proteomic analysis of tumor establishment and growth in the B16-F10 mouse melanoma model

The B16-F10 mouse model of melanoma is a widely used model to study many aspects of cancer biology and therapeutics in a solid tumor. Melanomas aggressively progress within a dynamic microenvironment containing in addition to tumor cells, stroma cells and components such as fibroblasts, immune cells, vascular cells, extracellular matrix (ECM) and extracellular molecules. The goal of this study was to elucidate the processes of tumor progression by identifying differentially expressed proteins in the tumor mass during specific stages of tumor growth. A comparative proteome analysis was performed on B16-F10 derived tumors in C57BL/6 mice at days 3, 5, 7, and 10. Statistical approaches were used to determine quantitative differential protein expression at each tumor time stage. Hierarchical clustering of 44 protein spots (p < 0.01) revealed a progressive change in the tumor mass when all 4 time stages were classified together, but there was a clear switch in expression of these proteins between the day 5 and the day 7 tumors. A trend analysis showed 53 protein spots (p < 0.001) following 6 predominant kinetic paths of expression as the tumor progressed. The protein spots were then identified using MALDI-TOF mass spectrometry. Proteins involved in glycolysis, inflammation, wounding, superoxide metabolism, and chemotaxis increased during tumorigenesis. From day 3 to day 7 VEGF and active cathepsin D were induced 7-fold and 4-fold, respectively. Proteins involved in electron transport, protein folding, blood coagulation, and transport decreased during tumorigenesis. This work illustrates changes in the biology of the B16-F10 tumor mass during tumor progression.     

The crystal structure of a high affinity RNA stem-loop complexed with the bacteriophage MS2 capsid: further challenges in the modeling of ligand-RNA interactions

We have determined the structure to 2.8 A of an RNA aptamer (F5), containing 2'-deoxy-2-aminopurine (2AP) at the -10 position, complexed with MS2 coat protein by soaking the RNA into precrystallised MS2 capsids. The -10 position of the RNA is an important determinant of binding affinity for coat protein. Adenine at this position in other RNA stem-loops makes three hydrogen bonds to protein functional groups. Substituting 2AP for the -10 adenine in the F5 aptamer yields an RNA with the highest yet reported affinity for coat protein. The refined X-ray structure shows that the 2AP base makes an additional hydrogen bond to the protein compared to adenine that is presumably the principal origin of the increased affinity. There are also slight changes in phosphate backbone positions compared to unmodified F5 that probably also contribute to affinity. Such phosphate movements are common in structures of RNAs bound to the MS2 T = 3 protein shell and highlight problems for de novo design of RNA binding ligands.     

Growth and protection against oxidative stress in young clones and mature spruce trees (Picea abies L.) at high altitudes

Clones of Norway spruce (Picea abies L.) were grown for several years on an altitudinal gradient (1750 m, 1150 m and 800 m above sea level) to study the effects of environmental × genetic interactions on growth and foliar metabolites (protein, pigments, antioxidants). Clones at the tree line showed 4.3-fold lower growth rates and contained 60% less chlorophyll (per gram of dry matter) than those at valley level. The extent of growth reduction was clone-dependent. The mortality of the clones was low and not altitude-dependent. At valley level, but not at high altitude, needles of mature spruce trees showed lower pigment and protein concentrations than clones. In general, antioxidative systems in needles of the mature trees and young clones did not increase with increasing altitude. Needles of all trees at high altitude showed higher concentrations of dehydroascorbate than at lower altitudes, indicating higher oxidative stress. In one clone, previously identified as sensitive to acute ozone doses, this increase was significantly higher and the growth reduction was stronger than in the other genotypes. This clone also displayed a significant reduction in glutathione reductase activity at high altitude. These results suggest that induction of antioxidative systems is apparently not a general prerequisite to cope with altitude in clones whose mother plants originated from higher altitudes (about 650–1100 m above sea level, Hercycnic-Carpathian distribution area), but that the genetic constitution for maintenance of high antioxidative protection is important for stress compensation at the tree line. Received: 13 October 1998 / Accepted: 22 June 1999     

A synergistic approach to protein crystallization: Combination of a fixed‐arm carrier with surface entropy reduction

Protein crystallographers are often confronted with recalcitrant proteins not readily crystallizable, or which crystallize in problematic forms. A variety of techniques have been used to surmount such obstacles: crystallization using carrier proteins or antibody complexes, chemical modification, surface entropy reduction, proteolytic digestion, and additive screening. Here we present a synergistic approach for successful crystallization of proteins that do not form diffraction quality crystals using conventional methods. This approach combines favorable aspects of carrier‐driven crystallization with surface entropy reduction. We have generated a series of maltose binding protein (MBP) fusion constructs containing different surface mutations designed to reduce surface entropy and encourage crystal lattice formation. The MBP advantageously increases protein expression and solubility, and provides a streamlined purification protocol. Using this technique, we have successfully solved the structures of three unrelated proteins that were previously unattainable. This crystallization technique represents a valuable rescue strategy for protein structure solution when conventional methods fail.     

First record of the brachiopod Lingulella waptaensis with pedicle from the Middle Cambrian Burgess Shale

Pettersson Stolk, S., Holmer, L. E. and Caron, J ‐B. 2010. First record of the brachiopod Lingulella waptaensis with pedicle from the Middle Cambrian Burgess Shale. —Acta Zoologica (Stockholm) 91 : 150–162 The organophosphatic shells of linguloid brachiopods are a common component of normal Cambrian–Ordovician shelly assemblages. Preservation of linguloid soft‐part anatomy, however, is extremely rare, and restricted to a few species in Lower Cambrian Konservat Lagerstätten. Such remarkable occurrences provide unique insights into the biology and ecology of early linguloids that are not available from the study of shells alone. Based on its shells, Lingulella waptaensis Walcott, was originally described in 1924 from the Middle Cambrian Burgess Shale but despite the widespread occurrence of soft‐part preservation associated with fossils from the same levels, no preserved soft parts have been reported. Lingulella waptaensis is restudied herein based on 396 specimens collected by Royal Ontario Museum field parties from the Greater Phyllopod Bed (Walcott Quarry Shale Member, British Columbia). The new specimens, including three with exceptional preservation of the pedicle, were collected in situ in discrete obrution beds. Census counts show that L. waptaensis is rare but recurrent in the Greater Phyllopod Bed, suggesting that this species might have been generalist. The wrinkled pedicle protruded posteriorly between the valves, was composed of a central coelomic space, and was slender and flexible enough to be tightly folded, suggesting a thin chitinous cuticle and underlying muscular layers. The nearly circular shell and the long, slender and highly flexible pedicle suggest that L. waptaensis lived epifaunally, probably attached to the substrate. Vertical cross‐sections of the shells show that L. waptaensis possessed a virgose secondary layer, which has previously only been known from Devonian to Recent members of the Family Lingulidae.     

Animal behaviour: emotion in invertebrates?

Bees exposed to vigorous shaking designed to simulate a dangerous event judge ambiguous stimuli as predicting a negative outcome - a 'pessimistic' cognitive bias that is characteristic of anxious or depressed humans and other vertebrates in putative negative emotional states.     

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.     

Simultaneous EEG-fMRI during a Working Memory Task: Modulations in Low and High Frequency Bands

Background

EEG studies of working memory (WM) have demonstrated load dependent frequency band modulations. FMRI studies have localized load modulated activity to the dorsolateral prefrontal cortex (DLPFC), medial prefrontal cortex (MPFC), and posterior parietal cortex (PPC). Recently, an EEG-fMRI study found that low frequency band (theta and alpha) activity negatively correlated with the BOLD signal during the retention phase of a WM task. However, the coupling of higher (beta and gamma) frequencies with the BOLD signal during WM is unknown.

Methodology

In 16 healthy adult subjects, we first investigated EEG-BOLD signal correlations for theta (5–7 Hz), alpha1 (8–10), alpha2 (10–12 Hz), beta1 (13–20), beta2 (20–30 Hz), and gamma (30–40 Hz) during the retention period of a WM task with set size 2 and 5. Secondly, we investigated whether load sensitive brain regions are characterised by effects that relate frequency bands to BOLD signals effects.

Principal Findings

We found negative theta-BOLD signal correlations in the MPFC, PPC, and cingulate cortex (ACC and PCC). For alpha1 positive correlations with the BOLD signal were found in ACC, MPFC, and PCC; negative correlations were observed in DLPFC, PPC, and inferior frontal gyrus (IFG). Negative alpha2-BOLD signal correlations were observed in parieto-occipital regions. Beta1-BOLD signal correlations were positive in ACC and negative in precentral and superior temporal gyrus. Beta2 and gamma showed only positive correlations with BOLD, e.g., in DLPFC, MPFC (gamma) and IFG (beta2/gamma). The load analysis revealed that theta and—with one exception—beta and gamma demonstrated exclusively positive load effects, while alpha1 showed only negative effects.

Conclusions

We conclude that the directions of EEG-BOLD signal correlations vary across brain regions and EEG frequency bands. In addition, some brain regions show both load sensitive BOLD and frequency band effects. Our data indicate that lower as well as higher frequency brain oscillations are linked to neurovascular processes during WM.