Carboxypeptidase E, a prohormone sorting receptor, is anchored to secretory granules via a C-terminal transmembrane insertion.

Carboxypeptidase E (CPE) is a sorting receptor that directs the prohormone pro-opiomelanocortin (POMC) to the regulated secretory pathway, and is also a prohormone processing enzyme in neuro/endocrine cells. It has been suggested that the 25 C-terminal amino acids are necessary for the binding of CPE to secretory granule membranes, but its orientation in the membrane is not known. In this study, we examined the structure and orientation of the membrane-binding domain at the C-terminus of CPE. In vitro experiments using model membranes demonstrated that the last 22 amino acids of CPE (CP peptide) insert in a shallow orientation into lipid bilayers at low pH. Circular dichroism analysis indicated that the CP peptide adopts a partial alpha-helical configuration at low pH, and helix content increases when it is bound to lipid. Protease protection experiments, immunolabeling, and immunoisolation of intact secretory granules with a C-terminal antibody revealed a cytoplasmic domain in CPE, consistent with a transmembrane orientation of this protein. We conclude that the membrane-binding domain of CPE must adopt an alpha-helical configuration to bind to lipids, and that CPE may require another integral membrane "chaperone" protein to insert through the lipid bilayer in a transmembrane fashion.     

Recovery after mass extinction: evolutionary assembly in large-scale biosphere dynamics

Biotic recoveries following mass extinctions are characterized by a process in which whole ecologies are reconstructed from low-diversity systems, often characterized by opportunistic groups. The recovery process provides an unexpected window to ecosystem dynamics. In many aspects, recovery is very similar to ecological succession, but important differences are also apparently linked to the innovative patterns of niche construction observed in the fossil record. In this paper, we analyse the similarities and differences between ecological succession and evolutionary recovery to provide a preliminary ecological theory of recoveries. A simple evolutionary model with three trophic levels is presented, and its properties (closely resembling those observed in the fossil record) are compared with characteristic patterns of ecological response to disturbances in continuous models of three-level ecosystems.     

PvuII-endonuclease induces structural alterations at the scissile phosphate group of its cognate DNA

We investigated the PvuII endonuclease with its cognate DNA by means of molecular dynamics simulations. Comparing the complexed DNA with a reference simulation of free DNA, we saw structural changes at the scissile phosphodiester bond. At this GpC step, the enzyme induces the highest twist and axial rise, inclination is increased and the minor groove widened. The distance between the scissile phosphate group and the phosphate group of the following thymine base is shortened significantly, indicating a substrate-assisted catalysis. A feasible reason for this vicinity is the catalytically important amino acid residue lysine 70, which bridges the free oxygen atoms of the successive phosphate groups. Due to this geometry, a compact reaction pocket is formed where a water molecule can be held, thus bringing the reaction partners for hydrolysis into contact. The O1-P-O2 angle of the scissile nucleotide is decreased, probably due to a complexation of the negative oxygen atoms through protein and solvent contacts.     

Role of lipopolysaccharide-binding protein in early alcohol-induced liver injury in mice

Cellular responses to endotoxins are enhanced markedly by LPS-binding protein (LBP). Furthermore, it has been demonstrated that endotoxins and proinflammatory cytokines such as TNF-alpha participate in early alcohol-induced liver injury. Therefore, in this study, a long-term intragastric ethanol feeding model was used to test the hypothesis that LBP is involved in alcoholic hepatitis by comparing LBP knockout and wild-type mice. Two-month-old female mice were fed a high-fat liquid diet with either ethanol or isocaloric maltose-dextrin as control continuously for 4 wk. There was no difference in mean urine alcohol concentrations between the groups fed ethanol. Dietary alcohol significantly increased liver to body weight ratios and serum alanine aminotransferase levels in wild-type mice (189 +/- 31 U/L) over high-fat controls (24 +/- 7 U/L), effects which were blunted significantly in LBP knockout mice (60 +/- 17 U/L). Although no significant pathological changes were observed in high-fat controls, 4 wk of dietary ethanol caused steatosis, mild inflammation, and focal necrosis in wild-type animals as expected (pathology score, 5.9 +/- 0.5). These pathological changes were reduced significantly in LBP knockout mice fed ethanol (score, 2.6 +/- 0.5). Endotoxin levels in the portal vein were increased significantly after 4 wk in both groups fed ethanol. Moreover, ethanol increased TNF-alpha mRNA expression in wild-type, but not in LBP knockout mice. These data are consistent with the hypothesis that LBP plays an important role in early alcohol-induced liver injury by enhancing LPS-induced signal transduction, most likely in Kupffer cells.     

Prevention of experimental autoimmune encephalomyelitis in common marmosets using an anti-IL-12p40 monoclonal antibody

The experimental autoimmune encephalomyelitis (EAE) model in the common marmoset approximates recognized features of the human disease multiple sclerosis (MS) with regard to its clinical presentation as well as neuropathological and radiological aspects of the lesions in brain and spinal cord. IL-12 is a proinflammatory cytokine that is produced by APC and promotes differentiation of Th1 effector cells. IL-12 is produced in the developing lesions of patients with MS as well as in EAE-affected animals. Previously it was shown that interference in IL-12 pathways effectively prevents EAE in rodents. In this study we report that in vivo neutralization of IL-12p40 using a novel Ab has beneficial effects in the myelin-induced EAE model in common marmosets. The Ab was injected i.v. at 7-day intervals starting well after immunization (day 14) and was continued until the end of the study (day 86). Stable levels of the Ab were measured 3 days after each injection throughout the study period. During this period anti-Ab responses could not be detected. We demonstrate that anti-IL-12p40 treatment has a protective effect on the neurological dysfunction as well as on neuropathological changes normally observed in the brain and spinal cord of EAE-affected individuals.     

Spatial distribution of leaf nitrogen and photosynthetic capacity within the foliage of individual trees: disentangling the effects of local light quality,leaf irradiance,and transpiration

There is presently no consensus about the factor(s) driving photosynthetic acclimation and the intra-canopy distribution of leaf characteristics under natural conditions. The impact was tested of local (i) light quality (red/far red ratio), (ii) leaf irradiance (PPFD(i)), and (iii) transpiration rate (E) on total non-structural carbohydrates per leaf area (TNC(a)), TNC-free leaf mass-to-area ratio (LMA), total leaf nitrogen per leaf area (N(a)), photosynthetic capacity (maximum carboxylation rate and light-saturated electron transport rate), and leaf N partitioning between carboxylation and bioenergetics within the foliage of young walnut trees grown outdoors. Light environment (quantity and quality) was controlled by placing individual branches under neutral or green screens during spring growth, and air vapour pressure deficit (VPD) was prescribed and leaf transpiration and photosynthesis measured at branch level by a branch bag technique. Under similar levels of leaf irradiance, low air vapour pressure deficit decreased transpiration rate but did not influence leaf characteristics. Close linear relationships were detected between leaf irradiance and leaf N(a), LMA or photosynthetic capacity, and low R/FR ratio decreased leaf N(a), LMA and photosynthetic capacity. Irradiance and R/FR also influenced the partitioning of leaf nitrogen into carboxylation and electron light transport. Thus, local light level and quality are the major factors driving photosynthetic acclimation and intra-canopy distribution of leaf characteristics, whereas local transpiration rate is of less importance.     

The sensitivity of ABI2 to hydrogen peroxide links the abscisic acid-response regulator to redox signalling

ABI1 and ABI2 are two protein serine/threonine phosphatases of type 2C (EC 3.1.3.16) that act as key regulators in the responses of Arabidopsis thaliana (L.) Heynh. to abscisic acid (ABA). They are involved in the control of ABA-mediated seed dormancy, stomatal closure and vegetative growth inhibition. Analysis of the enzymatic properties of ABI2 revealed high sensitivities towards protons and unsaturated fatty acids. Furthermore, the protein phosphatase activity of ABI2 is very sensitive to H2O2, which has recently emerged as a secondary messenger of ABA signalling. Upon H2O2 challenge, ABI2 is rapidly inactivated with an IC50 value of 50 microM in the presence of reduced glutathione. Inhibitor studies with phenylarsine oxide and manipulation of the redox status of ABI2 in vitro indicate that oxidation of critical cysteine residue(s) is responsible for inactivation. The levels of the major cellular thiol compounds cysteine and glutathione in leaves and seedlings of A. thaliana are compatible with a physiological role of H2O2 in regulating ABI2 activity. ABI2 is considered to exert negative regulation on ABA action. Thus, transient inactivation of this protein phosphatase by H2O2 would allow or enhance the ABA-dependent signalling process. In conclusion, ABI2 represents a likely target for redox-regulation of a hormonal signalling pathway in higher plants.     

The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective

Background

Transposable elements are found in the genomes of nearly all eukaryotes. The recent completion of the Release 3 euchromatic genomic sequence of Drosophila melanogaster by the Berkeley Drosophila Genome Project has provided precise sequence for the repetitive elements in the Drosophila euchromatin. We have used this genomic sequence to describe the euchromatic transposable elements in the sequenced strain of this species.

Results

We identified 85 known and eight novel families of transposable element varying in copy number from one to 146. A total of 1,572 full and partial transposable elements were identified, comprising 3.86% of the sequence. More than two-thirds of the transposable elements are partial. The density of transposable elements increases an average of 4.7 times in the centromere-proximal regions of each of the major chromosome arms. We found that transposable elements are preferentially found outside genes; only 436 of 1,572 transposable elements are contained within the 61.4 Mb of sequence that is annotated as being transcribed. A large proportion of transposable elements is found nested within other elements of the same or different classes. Lastly, an analysis of structural variation from different families reveals distinct patterns of deletion for elements belonging to different classes.

Conclusions

This analysis represents an initial characterization of the transposable elements in the Release 3 euchromatic genomic sequence of D. melanogaster for which comparison to the transposable elements of other organisms can begin to be made. These data have been made available on the Berkeley Drosophila Genome Project website for future analyses.