A protein sequence fitness function for identifying natural and nonnatural proteins

The infinitesimally small sequence space naturally scouted in the millions of years of evolution suggests that the natural proteins are constrained by some functional prerequisites and should differ from randomly generated sequences. We have developed a protein sequence fitness scoring function that implements sequence and corresponding secondary structural information at tripeptide levels to differentiate natural and nonnatural proteins. The proposed fitness function is extensively validated on a dataset of about 210 000 natural and nonnatural protein sequences and benchmarked with existing methods for differentiating natural and nonnatural proteins. The high sensitivity, specificity, and percentage accuracy (0.81%, 0.95%, and 91% respectively) of the fitness function demonstrates its potential application for sampling the protein sequences with higher probability of mimicking natural proteins. Moreover, the four major classes of proteins (α proteins, β proteins, α/β proteins, and α + β proteins) are separately analyzed and β proteins are found to score slightly lower as compared to other classes. Further, an analysis of about 250 designed proteins (adopted from previously reported cases) helped to define the boundaries for sampling the ideal protein sequences. The protein sequence characterization aided by the proposed fitness function could facilitate the exploration of new perspectives in the design of novel functional proteins.     

Cell adhesion and the actin cytoskeleton of the enveloping layer in the zebrafish embryo during epiboly.

As the zebrafish embryo undergoes gastrulation and epiboly, the cells of the enveloping layer (EVL) expand, covering the entire yolk cell. During the epiboly process, the EVL cells move as a coherent layer, remaining tightly attached to each other and to the underlying yolk syncytial layer (YSL). In view of the central role of the actin cytoskeleton, in both cell motility and cell-cell adhesion, we have labeled these cells in situ with fluorescent phalloidin and anti-actin antibodies. We show that, throughout their migration, the EVL cells retain a conspicuous cortical actin cytoskeletal belt coinciding with cell surface cadherins. At the margins approaching the YSL, the EVL cells extend, from their apicolateral domains, actin-rich filopodial protrusions devoid of detectable cadherin. We have studied the role of the actin cytoskeleton in the maintenance of EVL cohesion during epiboly. Cytochalasin treatment of embryos induces EVL dissociation accompanied by general detachment of the rest of the embryonic cells. In the dissociating EVL cells, the cortical actin belt undergoes fragmentation with the formation of actin aggregates; cadherins, on the other hand, remain evenly distributed at the junctional cell surface. Removal of Ca2+ by ethyleneglycolbis (amino-ethyl-ether)-tetraacetic acid (EGTA) treatment also induces cell dissociation without visible disruption of the cortical actin belt. The protein kinase inhibitor (1-isoquinolinylsulfonyl)-2-methyl-piperazine dihydrochloride (H-7), which blocks acto-myosin contractility and disrupts actin cables in cultured cells, also potentiates cytochalasin-induced dissociation and promotes the projection of numerous actin-rich lamellipodial extensions. The fact that EVL cells produce microspike-like structures towards the YSL and are capable of lamellipodial activity lend further support to the suggestion (R.W. Keller and J.P. Trinkaus. 1987. Dev. Biol. 120: 12-24) that the EVL cells are not passively mobilized on the expanding YSL but actively participate in epiboly.     

Effects of metastasectomy and other factors on survival of patients with ovarian metastases from gastric cancer: a systematic review and meta-analysis

Ovarian metastasis from gastric cancer (Krukenberg tumor [KT]) has no consensus treatment and the role of surgical treatment is still controversial. Identifying prognostic factors for KT could help guide the management of this tumor. We used a meta-analysis to evaluate the prognostic value of metastasectomy and other factors in patients with KT to develop a treatment plan. We searched literature in PubMed, Cochrane library and EMBASE. We analyzed hazard ratios (HR) and 95% confidence intervals (CI) with respect to overall survival (OS). The meta-analysis included 12 cohort studies with 1,031 patients associated with longer OS following metastasectomy (HR = 0.41; 95% CI = 0.32–0.53; P < 0.001), R0 resection (HR = 0.37; 95% CI = 0.26–0.53; P < 0.001), metachronous ovarian metastasis (HR = 0.74; 95% CI = 0.58–0.93; P = 0.012), size of KT (<5 cm) (HR = 0.74; 95% CI = 0.58–0.95; P = 0.019), ECOG PS (Eastern Cooperative Oncology Group performance status) 0 to 1 (HR = 0.48; 95% CI = 0.29–0.80; P = 0.004), tumor confined to ovary (HR = 0.40; 95% CI = 0.16–0.99; P = 0.047), and tumor confined to pelvic cavity (HR = 0.36; 95% CI = 0.14–0.92; P = 0.033). Shorter OS was associated with peritoneal carcinomatosis (HR = 2.00; 95% CI = 1.25–3.21; P = 0.004), ascites (HR = 1.66; 95% CI = 1.19–2.31; P = 0.003) and positive CEA (HR = 1.41; 95% CI = 1.10–1.82; P = 0.007). Gastrectomy led to a slight improvement in OS, but without statistical significance (HR = 0.69; 95% CI = 0.47–1.02; P = 0.061). No significant difference in OS was observed in patients with signet-ring cells (HR = 1.17; 95% CI = 0.91–1.51; P = 0.226), bilateral ovarian metastasis (HR = 0.87; 95% CI = 0.70–1.08; P = 0.212), age ≥ 50 years (HR = 0.93; 95% CI = 0.71–1.22; P = 0.619), positive CA19-9 (HR = 1.01; 95% CI = 0.75–1.35; P = 0.960), and positive CA-125 (HR = 0.98; 95% CI = 0.73–1.33; P = 0.915). Various factors affect OS in patients with KT.     

Growth of Musca domestica (Diptera: Muscidae) and Sarcophaga dux (Diptera: Sarcophagidae) larvae in poultry and livestock manures: Implication for animal waste management

Natural diets commonly exploited by the flies are animal manures including production from the poultry and livestock facilities. The larvae of the common filth flies such as Musca domestica and Sarcophaga dux are known as voracious feeders and may thus be used to convert manures into non-polluted residue. This study was conducted to observe the impact on flies' growth rate and capability of the larvae to process animal manures using chicken, goat and cow manures. One hundred newly hatched larvae of M. domestica and S. dux were introduced separately into 150?g manures under laboratory conditions. The initial wet mass and larvae length were recorded while mortality rate and dry mass were measured after the larvae were placed into the manures. The results showed that the manure types give significant effects (p?<?.05) on the growth of M. domestica and S. dux larvae. Cow manures and chicken manures contributed the highest growth for M. domestica and S. dux respectively. This result confirmed by the mean increment in wet mass and larvae length. In contrast, M. domestica greatly reduced 59.9?±?4% chicken manures while 25.0?±?1.8% goat manures reduced by S. dux. The potential of M. domestica and S. dux larvae to reduce animal waste products were further discussed in this study.     

Multiploid CD61+ Cells Are the Pre-Dominant Cell Lineage Infected during Acute Dengue Virus Infection in Bone Marrow

Depression of the peripheral blood platelet count during acute infection is a hallmark of dengue. This thrombocytopenia has been attributed, in part, to an insufficient level of platelet production by megakaryocytes that reside in the bone marrow (BM). Interestingly, it was observed that dengue patients experience BM suppression at the onset of fever. However, few studies focus on the interaction between dengue virus (DENV) and megakaryocytes and how this interaction can lead to a reduction in platelets. In the studies reported herein, BM cells from normal healthy rhesus monkeys (RM) and humans were utilized to identify the cell lineage(s) that were capable of supporting virus infection and replication. A number of techniques were employed in efforts to address this issue. These included the use of viral RNA quantification, nonstructural protein and infectivity assays, phenotypic studies utilizing immunohistochemical staining, anti-differentiation DEAB treatment, and electron microscopy. Cumulative results from these studies revealed that cells in the BM were indeed highly permissive for DENV infection, with human BM having higher levels of viral production compared to RM. DENV-like particles were predominantly observed in multi-nucleated cells that expressed CD61+. These data suggest that megakaryocytes are likely the predominant cell type infected by DENV in BM, which provides one explanation for the thrombocytopenia and the dysfunctional platelets characteristic of dengue virus infection.     

Expression of Key Ion Transporters in the Gill and Esophageal-Gastrointestinal Tract of Euryhaline Mozambique Tilapia Oreochromis mossambicus Acclimated to Fresh Water,Seawater and Hypersaline Water

The ability of euryhaline Mozambique tilapia to tolerate extreme environmental salinities makes it an excellent model for investigating iono-regulation. This study aimed to characterize and fill important information gap of the expression levels of key ion transporters for Na⁺ and Cl⁻ in the gill and esophageal-gastrointestinal tract of Mozambique tilapia acclimated to freshwater (0 ppt), seawater (30 ppt) and hypersaline (70 ppt) environments. Among the seven genes studied, it was found that nkcc2, nkcc1a, cftr, nka-α1 and nka-α3, were more responsive to salinity challenge than nkcc1b and ncc within the investigated tissues. The ncc expression was restricted to gills of freshwater-acclimated fish while nkcc2 expression was restricted to intestinal segments irrespective of salinity challenge. Among the tissues investigated, gill and posterior intestine were found to be highly responsive to salinity changes, followed by anterior and middle intestine. Both esophagus and stomach displayed significant up-regulation of nka-α1 and nka-α3, but not nkcc isoforms and cftr, in hypersaline-acclimated fish suggesting a response to hypersalinity challenge and involvement of other forms of transporters in iono-regulation. Changes in gene expression levels were partly corroborated by immunohistochemical localization of transport proteins. Apical expression of Ncc was found in Nka-immunoreactive cells in freshwater-acclimated gills while Nkcc co-localized with Nka-immunoreactive cells expressing Cftr apically in seawater- and hypersaline-acclimated gills. In the intestine, Nkcc-stained apical brush border was found in Nka-immunoreactive cells at greater levels under hypersaline conditions. These findings provided new insights into the responsiveness of these genes and tissues under hypersalinity challenge, specifically the posterior intestine being vital for salt absorption and iono-osmoregulation in the Mozambique tilapia; its ability to survive in hypersalinity may be in part related to its ability to up-regulate key ion transporters in the posterior intestine. The findings pave the way for future iono-regulatory studies on the Mozambique tilapia esophageal-gastrointestinal tract.     

Crystal Structure of the Mp1p Ligand Binding Domain 2 Reveals Its Function as a Fatty Acid-binding Protein

Penicillium marneffei is a dimorphic, pathogenic fungus in Southeast Asia that mostly afflicts immunocompromised individuals. As the only dimorphic member of the genus, it goes through a phase transition from a mold to yeast form, which is believed to be a requisite for its pathogenicity. Mp1p, a cell wall antigenic mannoprotein existing widely in yeast, hyphae, and conidia of the fungus, plays a vital role in host immune response during infection. To understand the function of Mp1p, we have determined the x-ray crystal structure of its ligand binding domain 2 (LBD2) to 1.3 Å. The structure reveals a dimer between the two molecules. The dimer interface forms a ligand binding cavity, in which electron density was observed for a palmitic acid molecule interacting with LBD2 indirectly through hydrogen bonding networks via two structural water molecules. Isothermal titration calorimetry experiments measured the ligand binding affinity (K_d) of Mp1p at the micromolar level. Mutations of ligand-binding residues, namely S313A and S332A, resulted in a 9-fold suppression of ligand binding affinity. Analytical ultracentrifugation assays demonstrated that both LBD2 and Mp1p are mostly monomeric in vitro, no matter with or without ligand, and our dimeric crystal structure of LBD2 might be the result of crystal packing. Based on the conformation of the ligand-binding pocket in the dimer structure, a model for the closed, monomeric form of LBD2 is proposed. Further structural analysis indicated the biological importance of fatty acid binding of Mp1p for the survival and pathogenicity of the conditional pathogen.     

TNF‐α induces matrix metalloproteinase‐9 expression in A549 cells: Role of TNFR1/TRAF2/PKCα‐dependent signaling pathways

Matrix metalloproteinases (MMPs), in particular MMP‐9, have been shown to be induced by cytokines, including TNF‐α and contributes to airway inflammation. However, the mechanisms underlying TNF‐α‐induced MMP‐9 expression in human A549 cells remain unclear. Here, we report that TNF‐α‐induced MMP‐9 gene expression was mediated through the TNFR1/TRAF2/PKCα‐dependent signaling pathways in A549 cells, determined by zymographic, RT‐PCR, and Western blotting analyses. TNF‐α‐induced MMP‐9 expression was reduced by pretreatment with a TNFR Ab. Furthermore, TNF‐α‐induced TNFR1 and TRAF2 complex formation was revealed by immunoprecipitation using an anti‐TNFR1 Ab followed by Western blot analysis against an anti‐TRAF2 or anti‐TNFR1 Ab. In addition, TNF‐α‐induced MMP‐9 expression was also reduced by pretreatment with the inhibitor of PKCα (Gö6983), c‐Src (PP1), EGFR (AG1478), or PI3K (LY294002) or transfection with siRNAs of PKCα, Src, EGFR, Akt, p65, p300, and c‐Jun. On the other hand, TNF‐α stimulated the phosphorylation of c‐Src, EGFR, Akt, JNK1/2, and c‐Jun, which were inhibited by pretreatment with Gö6983. We also showed that TNF‐α induced Akt translocation and the formation of an Akt/p65/p300 complex. Pretreatment with the inhibitor of JNK1/2 (SP600125) but not the inhibitor of MEK1/2 (U0126), p38 MAPK (SB202190), or PI3K (LY294002), markedly inhibited TNF‐α‐induced c‐Jun mRNA levels. Taken together, these data suggest that in A549 cells, TNF‐α induces MMP‐9 expression via the TNFR1/TRAF2/PKCα‐dependent JNK1/2/c‐Jun and c‐Src/EGFR/PI3K/Akt pathways. J. Cell. Physiol. 454–464, 2010. © 2010 Wiley‐Liss, Inc.     

Renal expression of arachidonic acid metabolizing enzymes and RhoA/Rho kinases in fructose insulin resistant hypertensive rats

Fructose feeding has been shown to induce insulin resistance and hypertension. Renal protein expression for the cytochrome P (CYP) 450 arachidonic acid metabolizing enzymes has been shown to be altered in other models of diet-induced hypertension. Of special interest is CYP4A, which produces the potent vasoconstrictor, 20-hydroxyeicosatetraenoic acid and CYP2C, which catalyzes the formation of the potent dilators epoxyeicosatrienoic acids as well as soluble epoxide hydrolase (sEH) which metabolizes the latter to dihydroxyeicosatrienoic acids. The RhoA/Rho kinase (ROCK) signaling pathway is downstream of arachidonic acid and is reported to mediate metabolic-cardio-renal dysfunctions in some experimental models of insulin resistance and diabetes. The aim of the present study was to determine the expression of CYP4A, CYP2C23, CYP2C11, sEH, RhoA, ROCK-1, ROCK-2, and phospho-Lin-11/Isl-1/Mec-3 kinase (LIMK) in kidneys of fructose-fed (F) rats. Male Wistar rats were fed a high fructose diet for 8 weeks. Body weight, systolic blood pressure, insulin sensitivity, and renal expression of the aforementioned proteins were assessed. No change was observed in the body weight of F rats; however, euglycemia and hyperinsulinemia implicating impaired glucose tolerance and significant elevation in systolic blood pressure were observed. Renal expression of CYP4A and CYP2C23 was significantly increased while that of CYP2C11 and sEH was not changed in F rats. Equal expression for RhoA in both control and F rats and an enhanced level of ROCK-1 and ROCK-2 constitutively activate 130 kDa cleavage fragments as well as phospho-LIMK. These data suggest that the kidneys could be actively participating in the pathogenesis of insulin resistance-induced hypertension through the arachidonic acid CYP 450-RhoA/Rho kinase pathway(s).