Kaposi's sarcoma-associated herpesvirus OX2 glycoprotein activates myeloid-lineage cells to induce inflammatory cytokine production

Kaposi's sarcoma is an inflammatory cytokine-mediated angioproliferative disease which is triggered by infection by Kaposi's sarcoma-associated herpesvirus (KSHV). KSHV contains an open reading frame, K14, that has significant homology with cellular OX2, designated viral OX2 (vOX2). In this report, we demonstrate that vOX2 encodes a glycosylated cell surface protein with an apparent molecular mass of 55 kDa. Purified glycosylated vOX2 protein dramatically stimulated primary monocytes, macrophages, and dendritic cells to produce the inflammatory cytokines interleukin 1beta (IL-1beta), IL-6, monocyte chemoattractant protein 1, and TNF-alpha. Furthermore, expression of vOX2 on B lymphocytes stimulated monocytes to produce inflammatory cytokines in mixed culture. These results demonstrate that like its cellular counterpart, vOX2 targets myeloid-lineage cells, but unlike cellular OX2, which delivers a restrictive signal, KSHV vOX2 provides an activating signal, resulting in the production of inflammatory cytokines. Thus, this is a novel viral strategy where KSHV has acquired the cellular OX2 gene to induce inflammatory cytokine production, which potentially promotes the cytokine-mediated angiogenic proliferation of KSHV-infected cells.     

Minimalistic Predictor of Protein Binding Energy: Contribution of Solvation Factor to Protein Binding

It has long been known that solvation plays an important role in protein-protein interactions. Here, we use a minimalistic solvation-based model for predicting protein binding energy to estimate quantitatively the contribution of the solvation factor in protein binding. The factor is described by a simple linear combination of buried surface areas according to amino-acid types. Even without structural optimization, our minimalistic model demonstrates a predictive power comparable to more complex methods, making the proposed approach the basis for high throughput applications. Application of the model to a proteomic database shows that receptor-substrate complexes involved in signaling have lower affinities than enzyme-inhibitor and antibody-antigen complexes, and they differ by chemical compositions on interfaces. Also, we found that protein complexes with components that come from the same genes generally have lower affinities than complexes formed by proteins from different genes, but in this case the difference originates from different interface areas. The model was implemented in the software PYTHON, and the source code can be found on the Shakhnovich group webpage: http://faculty.chemistry.harvard.edu/shakhnovich/software.     

The genome of the marine medaka Oryzias melastigma

Marine medaka (Oryzias melastigma) is considered to be a useful fish model for marine and estuarine ecotoxicology studies and has good potential for field‐based population genomics because of its geographical distribution in Asian estuarine and coastal areas. In this study, we present the first whole‐genome draft of O. melastigma. The genome assembly consists of 8,602 scaffolds (N50 = 23.737 Mb) and a total genome length of 779.4 Mb. A total of 23,528 genes were predicted, and 12,670 gene families shared with three teleost species (Japanese medaka, mangrove killifish and zebrafish) were identified. Genome analyses revealed that the O. melastigma genome is highly heterozygous and contains a large number of repeat sequences. This assembly represents a useful genomic resource for fish scientists.     

Organization and assembly of the TRAPPII complex

Current models suggest that TRAPP tethering complexes exist in two forms. Whereas the seven-subunit TRAPPI complex mediates ER-to-Golgi transport, TRAPPII contains three additional subunits (Trs65, Trs120 and Trs130) and is required for distinct tethering events at Golgi membranes. It is not clear how TRAPPII assembly is regulated. Here, we show that Tca17 is a fourth TRAPPII-specific component, and that Trs65 and Tca17 interact with distinct domains of Trs130 and make different contributions to complex assembly. Whereas Tca17 promotes the stable association of TRAPPII-specific subunits with the core complex, Trs65 stabilizes TRAPPII in an oligomeric form. We show that Trs85, which was previously reported to be a subunit of both TRAPPI and TRAPPII, is not associated with the TRAPPII complex in yeast. However, we find that proteins related to Trs85, Trs65 and Tca17 are part of the same TRAPP complex in mammalian cells. These findings have implications for models of TRAPP complex formation and suggest that TRAPP complexes may be organized differently in yeast and mammals.     

Complete mitochondrial genome of a forensically important muscid, Hydrotaea chalcogaster (Diptera: Muscidae), with notes on its phylogenetic position

Muscidae are a dipteran family which is important for forensic investigations. However, it has received limited attention in forensic entomological experiments as a reason of identification issues. It is hard to identify specimens by morphological methods, especially in developmental stages. Therefore, complete mitochondrial genome sequences can be important tool in forensic entomology for identifying species. In this study we sequenced and analyzed the first complete mitochondrial genome from a forensically important Muscidae species Hydrotaea (=Ophyra) chalcogaster by next-generation sequencing. The mitochondrial genome of the sequenced species is circular molecules of 17,076?bp which have the typical mitochondrial genome complement of 13 protein-coding genes, 22 tRNAs, two ribosomal RNA genes and a control region. Rearrangements of gene positions are identical with the ancestral insect genome. Furthermore, phylogenetic relationships of the family Muscidae were evaluated in regard to mitochondrial protein coding genes. The inferred trees indicate that the Muscidae is a paraphyletic family. These data provide additional information for molecular identification of muscid species.     

House dust mite extract activates apical Cl− channels through protease‐activated receptor 2 in human airway epithelia

Adequate fluid secretion from airway mucosa is essential for maintaining mucociliary clearance, and fluid hypersecretion is a prominent feature of inflammatory airway diseases such as allergic rhinitis. House dust mite extract (HDM) has been reported to activate protease‐activated receptors (PARs), which play various roles in airway epithelia. However, the role of HDM in regulating ion transporters and fluid secretion has not been investigated. We examined the effect of HDM on ion transport in human primary nasal epithelial cells. The Ca²⁺‐sensitive dye Fura2‐AM was used to determine intracellular Ca²⁺ concentration ([Ca²⁺]_i) by means of spectrofluorometry in human normal nasal epithelial cells (NHNE). Short‐circuit current (Isc) was measured using Ussing chambers. Fluid secretion from porcine airway mucosa was observed by optical measurement. HDM extract (10 µg/Ml) effectively cleaved the PAR‐2 peptide and induced an increase of [Ca²⁺]_i that was abolished by desensitization with trypsin, but not with thrombin. Apical application of HDM‐induced Isc sensitive to both a cystic fibrosis transmembrane conductance regulator (CFTR) inhibitor and a Ca²⁺‐activated Cl^? channel (CaCC) inhibitor. HDM extract also stimulated fluid secretion from porcine airway mucosa. HDM extract activated PAR‐2 and apical Cl^? secretion via CaCC and CFTR, and HDM‐induced fluid secretion in porcine airway mucosa. Our results suggest a role for PAR‐2 in mucociliary clearance and fluid hypersecretion of airway mucosa in response to air‐borne allergens such as HDM. J. Cell. Biochem. 109: 1254–1263, 2010. © 2010 Wiley‐Liss, Inc.     

Delayed herbivory by migratory geese increases summer‐long CO2 uptake in coastal western Alaska

The advancement of spring and the differential ability of organisms to respond to changes in plant phenology may lead to “phenological mismatches” as a result of climate change. One potential for considerable mismatch is between migratory birds and food availability in northern breeding ranges, and these mismatches may have consequences for ecosystem function. We conducted a three‐year experiment to examine the consequences for CO₂ exchange of advanced spring green‐up and altered timing of grazing by migratory Pacific black brant in a coastal wetland in western Alaska. Experimental treatments represent the variation in green‐up and timing of peak grazing intensity that currently exists in the system. Delayed grazing resulted in greater net ecosystem exchange (NEE) and gross primary productivity (GPP), while early grazing reduced CO₂ uptake with the potential of causing net ecosystem carbon (C) loss in late spring and early summer. Conversely, advancing the growing season only influenced ecosystem respiration (ER), resulting in a small increase in ER with no concomitant impact on GPP or NEE. The experimental treatment that represents the most likely future, with green‐up advancing more rapidly than arrival of migratory geese, results in NEE changing by 1.2 µmol m^?2 s^?1 toward a greater CO₂ sink in spring and summer. Increased sink strength, however, may be mitigated by early arrival of migratory geese, which would reduce CO₂ uptake. Importantly, while the direct effect of climate warming on phenology of green‐up has a minimal influence on NEE, the indirect effect of climate warming manifest through changes in the timing of peak grazing can have a significant impact on C balance in northern coastal wetlands. Furthermore, processes influencing the timing of goose migration in the winter range can significantly influence ecosystem function in summer habitats.