Large-scale profiling of Rab GTPase trafficking networks: the membrome

Rab GTPases and SNARE fusion proteins direct cargo trafficking through the exocytic and endocytic pathways of eukaryotic cells. We have used steady state mRNA expression profiling and computational hierarchical clustering methods to generate a global overview of the distribution of Rabs, SNAREs, and coat machinery components, as well as their respective adaptors, effectors, and regulators in 79 human and 61 mouse nonredundant tissues. We now show that this systems biology approach can be used to define building blocks for membrane trafficking based on Rab-centric protein activity hubs. These Rab-regulated hubs provide a framework for an integrated coding system, the membrome network, which regulates the dynamics of the specialized membrane architecture of differentiated cells. The distribution of Rab-regulated hubs illustrates a number of facets that guides the overall organization of subcellular compartments of cells and tissues through the activity of dynamic protein interaction networks. An interactive website for exploring datasets comprising components of the Rab-regulated hubs that define the membrome of different cell and organ systems in both human and mouse is available at http://www.membrome.org/.     

Effects of dietary combination of chromium and biotin on growth performance, carcass characteristics, and oxidative stress markers in heat-distressed Japanese quail

Environmental stress causes adverse effects in performance and antioxidant status of poultry. Dietary chromium supplementation promotes the growth rate and feed efficiency of growing poultry and these beneficial effects of chromium appear to be greater under stress. Biotin, a member of the vitamin B complex, is involved in the metabolism of carbohydrates, fats, and proteins. In a previous experiment, we examined the effects of chromium picolinate (CrPic) as a chromium source in birds subjected to high environmental temperature and the data showed that supplementation with CrPic ameliorated the deletorious effect of stress. The study was conducted to determine the effects of a supplementation of combination of CrPic and biotin (Diachrome^TM) on performance, carcass characteristics, levels of oxidative stress markers, serum cholesterol, and glucose concentrations in Japanese quail (Coturnix coturnix japonica) exposed to high ambient temperature of 34°C. Two hundred forty Japanese quail (10 d old) were randomly assigned to 8 treatment groups consisting of 10 replicates of 3 birds. The birds were kept in a temperature-controlled room at 22°C (thermo-neutral [TN] groups) or 34°C (for 8h/d; 09.00 am to 05.00 pm; heat-stress [HS] groups). Birds were fed either a basal (control) diet (TN and HS) or the basal diet supplemented with either 1, 2 or 4 mg of Diachrome/kg of diet. Heat exposure decreased performance when the basal diet was fed (p=0.001). Diachrome supplementation increased feed intake (p=0.001), body weight (p=0.05), feed efficiency (p=0.01), and carcass traits (p≤0.05) variables linearly in birds reared under HS conditions. Serum vitamin C (p=0.05) and vitamin E (p=0.03) concentrations increased, whereas malondialdehyde (MDA) levels in serum and the liver (p=0.01), thigh muscle (p=0.05), and serum cholesterol and glucose concentrations (p=0.05) decreased in supplemented birds reared at a high temperature. It should be noted that when birds were kept at the thermo-neutral temperature, Diachrome supplementation did not affect (p>0.05) the variables measured, with the exception of a reduction in serum cholesterol and glucose. Results of the present study suggest that Diachrome can be considered a protective dietary supplement by reducing the negative effects of high environment temperature on performance and oxidative stress in quail.     

Relationship among levels of leptin and zinc,copper, and zinc/copper ratio in plasma of patients with essential hypertension and healthy normotensive subjects

Obesity is among the main contributing factors in the etiology of essential hypertension (EHT). Leptin, the product of the ob gene, is expressed mainly in adipose tissue. We examined the relationship between two trace elements, zinc (Zn) and copper (Cu), and leptin in patients with EHT (n=35) and normotensive (NT) controls (n=50) because leptin as well as Zn and Cu were reported to be associated with the pathophysiology of EHT. Plasma leptin levels were determined with a commercial enzyme-linked immunosorbent assay (ELISA) kit. Atomic absorption spectrophotometry was utilized to determine plasma Zn and Cu levels. There was a negative correlation between leptin and Zn, and the Zn/Cu ratio (r=−0.359, p<0.05; r=0.361, p<0.05, respectively) in pooled subjects. When subjects were divided based on the presence or absence of hypertension, there was a negative correlation between leptin and Zn (r=−0.375, p<0.05) as well as leptin and Zn/Cu ratio (r=−0.398, p<0.05) in NT subjects. Similar trends were observed when leptin/BMI (body mass index) levels were utilized. There was no significant correlations between levels of Cu and leptin or leptin/BMI. In conclusion, in addition to high leptin levels, Zn and the Zn/Cu ratio were lower in patients with EHT compared to NT controls.     

Serum proinflammatory mediators at different periods of therapy in patients with multiple myeloma

Multiple myeloma (MM) is a malignant disease characterized by the clonal proliferation of plasma cells within the bone marrow. Several cytokines have been demonstrated to be involved in the control of growth, progression, and dissemination of MM. We determined serum levels of interleukin-1beta (IL-1beta), soluble interleukin-2 receptor (sIL-2R), interleukin-6 (IL-6), interleukin-8 (IL-8), tumor necrosis factor-alpha (TNF-alpha), and C-reactive protein (CRP) in 14 newly diagnosed MM patients. The median age of the patients was 63.4 +/- 10.8 years and all of the patients were stage III (classified according to the Durie-Salmon classification). The same parameters were measured in 15 healthy controls. In addition, we also examined the effects of vincristine-adriamycin-dexamethasone (VAD) therapy on the same parameters and mediators as well as the relationship among the parameters in the same patient groups. The serum concentrations of TNF-alpha, IL-1beta, sIL-2R, IL-6, IL-8, and CRP (18.6 +/- 3.7 pg/mL, 10.1 +/- 2.8 pg/mL, 730 +/- 220 U/mL, 11.4 +/- 3.3 pg/mL, 23.9 +/- 8.3 pg/mL, and 49.9 +/- 19.5 mg/dL, resp) were significantly higher in newly diagnosed MM patients than in healthy controls (P < .0001). All of the parameters were found to be significantly reduced after chemotherapy. In conclusion, we found that after the VAD therapy, the level of these cytokines which are thought to play an important role in the pathogenesis of MM was significantly suppressed. This is the first study demonstrating strong impact of VAD treatment on circulating mediators of sIL-2R and IL-8 levels parameters.     

Hypoxic Induction of Vasorin Regulates Notch1 Turnover to Maintain Glioma Stem-like Cells

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Combined computational design of a zinc‐binding site and a protein–protein interaction: One open zinc coordination site was not a robust hotspot for de novo ubiquitin binding

We computationally designed a de novo protein–protein interaction between wild‐type ubiquitin and a redesigned scaffold. Our strategy was to incorporate zinc at the designed interface to promote affinity and orientation specificity. A large set of monomeric scaffold surfaces were computationally engineered with three‐residue zinc coordination sites, and the ubiquitin residue H68 was docked to the open coordination site to complete a tetrahedral zinc site. This single coordination bond was intended as a hotspot and polar interaction for ubiquitin binding, and surrounding residues on the scaffold were optimized primarily as hydrophobic residues using a rotamer‐based sequence design protocol in Rosetta. From thousands of independent design simulations, four sequences were selected for experimental characterization. The best performing design, called Spelter, binds tightly to zinc (K_d < 10 nM) and binds ubiquitin with a K_d of 20 µM in the presence of zinc and 68 µM in the absence of zinc. Mutagenesis studies and nuclear magnetic resonance chemical shift perturbation experiments indicate that Spelter interacts with H68 and the target surface on ubiquitin; however, H68 does not form a hotspot as intended. Instead, mutation of H68 to alanine results in tighter binding. Although a 3/1 zinc coordination arrangement at an interface cannot be ruled out as a means to improve affinity, our study led us to conclude that 2/2 coordination arrangements or multiple‐zinc designs are more likely to promote high‐affinity protein interactions. Proteins 2013; 81:1245–1255. © 2013 Wiley Periodicals, Inc.     

Vavien: an algorithm for prioritizing candidate disease genes based on topological similarity of proteins in interaction networks

Genome-wide linkage and association studies have demonstrated promise in identifying genetic factors that influence health and disease. An important challenge is to narrow down the set of candidate genes that are implicated by these analyses. Protein-protein interaction (PPI) networks are useful in extracting the functional relationships between known disease and candidate genes, based on the principle that products of genes implicated in similar diseases are likely to exhibit significant connectivity/proximity. Information flow?based methods are shown to be very effective in prioritizing candidate disease genes. In this article, we utilize the topology of PPI networks to infer functional information in the context of disease association. Our approach is based on the assumption that PPI networks are organized into recurrent schemes that underlie the mechanisms of cooperation among different proteins. We hypothesize that proteins associated with similar diseases would exhibit similar topological characteristics in PPI networks. Utilizing the location of a protein in the network with respect to other proteins (i.e., the "topological profile" of the proteins), we develop a novel measure to assess the topological similarity of proteins in a PPI network. We then use this measure to prioritize candidate disease genes based on the topological similarity of their products and the products of known disease genes. We test the resulting algorithm, Vavien, via systematic experimental studies using an integrated human PPI network and the Online Mendelian Inheritance in Man (OMIM) database. Vavien outperforms other network-based prioritization algorithms as shown in the results and is available at www.diseasegenes.org.     

Living bacterial sacrificial porogens to engineer decellularized porous scaffolds

Decellularization and cellularization of organs have emerged as disruptive methods in tissue engineering and regenerative medicine. Porous hydrogel scaffolds have widespread applications in tissue engineering, regenerative medicine and drug discovery as viable tissue mimics. However, the existing hydrogel fabrication techniques suffer from limited control over pore interconnectivity, density and size, which leads to inefficient nutrient and oxygen transport to cells embedded in the scaffolds. Here, we demonstrated an innovative approach to develop a new platform for tissue engineered constructs using live bacteria as sacrificial porogens. E.coli were patterned and cultured in an interconnected three-dimensional (3D) hydrogel network. The growing bacteria created interconnected micropores and microchannels. Then, the scafold was decellularized, and bacteria were eliminated from the scaffold through lysing and washing steps. This 3D porous network method combined with bioprinting has the potential to be broadly applicable and compatible with tissue specific applications allowing seeding of stem cells and other cell types.