Algorithm for predicting functionally equivalent proteins from BLAST and HMMER searches

In order to predict biologically significant attributes such as function from protein sequences, searching against large databases for homologous proteins is a common practice. In particular, BLAST and HMMER are widely used in a variety of biological fields. However, sequencehomologous proteins determined by BLAST and proteins having the same domains predicted by HMMER are not always functionally equivalent, even though their sequences are aligning with high similarity. Thus, accurate assignment of functionally equivalent proteins from aligned sequences remains a challenge in bioinformatics. We have developed the FEP-BH algorithm to predict functionally equivalent proteins from protein-protein pairs identified by BLAST and from protein-domain pairs predicted by HMMER. When examined against domain classes of the Pfam-A seed database, FEP-BH showed 71.53% accuracy, whereas BLAST and HMMER were 57.72% and 36.62%, respectively. We expect that the FEP-BH algorithm will be effective in predicting functionally equivalent proteins from BLAST and HMMER outputs and will also suit biologists who want to search out functionally equivalent proteins from among sequence-homologous proteins.     

Functional expression and characterization of recombinant NADPH-P450 reductase from Malassezia globosa

Malassezia globosa is a common pathogenic fungus that causes skin diseases including dandruff and seborrheic dermatitis in humans. Analysis of its genome identified a gene (MGL_1677) coding for a putative NADPH-P450 reductase (NPR) to support the fungal cytochrome P450 enzymes. The heterologously expressed recombinant M. globosa NPR protein was purified, and its functional features were characterized. The purified protein generated a single band on SDS-PAGE at 80.74 kDa and had an absorption maximum at 452 nm, indicating its possible function as an oxidized flavin cofactor. It evidenced NADPH-dependent reducing activity for cytochrome c or nitroblue tetrazolium. Human P450 1A2 and 2A6 were able to successfully catalyze the O-deethylation of 7- ethoxyresorufin and the 7-hydroxylation of coumarin, respectively, with the support of the purified NPR. These results demonstrate that purified NPR is an orthologous reductase protein that supports cytochrome P450 enzymes in M. globosa.     

Construction of healthy arteries using computed tomography and virtual histology intravascular ultrasound

Vessel geometry for numerical analysis is generally obtained by computed tomography (CT) or magnetic resonance imaging (MRI) and intravascular ultrasound (IVUS). Most medical imaging is obtained from patients for hemodynamic analysis due to the properties of vascular disease and the difficulties in angiography. To predict the site where plaque occurs and understand the progression of the lesion, however, it is necessary to take into consideration not only the diseased artery, but also the blood flow characteristics of healthy artery. In order to simulate healthy vessels prior to lesion formation, we performed CT and virtual histology intravascular ultrasound (VH-IVUS) on three actual patients and this data was used to develop criteria for healthy vessel construction, a method that virtually removes all intravascular plaque. The lumen of a vessel generated by CT and the lumen from VH-IVUS were compared, and the cross-sectional areas of plaque components (fibrous, fibrofatty, dense calcium, and necrotic) and the lumen from VH-IVUS were analyzed. Geometric differences in the healthy vessel and diseased vessel were analyzed, and flow characteristics of the healthy vessel and diseased vessel were compared through computational fluid dynamics simulation. Low average wall shear stress (AWSS) was distributed in the site where plaque was removed from the healthy vessel, and a high oscillatory shear index (OSI) was observed in the region proximal to the site where plaque previously existed. Low AWSS and high OSI are widely accepted indicators of plaque formation or the direction of plaque progression. A numerical model that effectively predicts lesion forming sites was also generated based on the healthy vessel construction method presented in this study.     

Phospholipase C Activator m-3M3FBS Protects against Morbidity and Mortality Associated with Sepsis

Although phospholipase C (PLC) is a crucial enzyme required for effective signal transduction and leukocyte activation, the role of PLC in polymicrobial sepsis remains unclear. In this study, we show that the direct PLC activator m-3M3FBS treatment significantly attenuates vital organ inflammation, widespread immune cell apoptosis, and mortality in a mouse sepsis model induced by lethal cecal ligation and puncture challenge. Mechanistically, m-3M3FBS-dependent protection was largely abolished by pretreatment of mice with the PLC-selective inhibitor U-73122, thus confirming PLC agonism by m-3M3FBS in vivo. PLC activation enhanced the bactericidal activity and hydrogen peroxide production of mouse neutrophils, and it also enhanced the production of IFN-γ and IL-12 while inhibiting proseptic TNF-α and IL-1β production in cecal ligation and puncture mice. In a second model of sepsis, PLC activation also inhibited the production of TNF-α and IL-1β following systemic LPS challenge. In conclusion, we show that agonizing the central signal transducing enzyme PLC by m-3M3FBS can reverse the progression of toxic shock by triggering multiple protective downstream signaling pathways to maintain organ function, leukocyte survival, and to enhance microbial killing.     

Antibacterial activity and interaction mechanism of electrospun zinc-doped titania nanofibers

In this study, a biological evaluation of the antimicrobial activity of Zn-doped titania nanofibers was carried out using Escherichia coli ATCC 52922 (Gram negative) and Staphylococcus aureus ATCC 29231 (Gram positive) as model organisms. The utilized Zn-doped titania nanofibers were prepared by the electrospinning of a sol–gel composed of zinc nitrate, titanium isopropoxide, and polyvinyl acetate; the obtained electrospun nanofibers were vacuum dried at 80°C and then calcined at 600°C. The physicochemical properties of the synthesized nanofibers were determined by X-ray diffraction pattern, field emission scanning electron microscopy, energy-dispersive X-ray spectroscopy, electron probe microanalysis, thermogravimetry, and transmission electron microscopy (TEM). The antibacterial activity and the acting mechanism of Zn-doped titania nanofibers against bacteria were investigated by calculation of minimum inhibitory concentration and analyzing the morphology of the bacterial cells following the treatment with nanofibers solution. Our investigations reveal that the lowest concentration of Zn-doped titania nanofibers solution inhibiting the growth of S. aureus ATCC 29231 and E. coli ATCC 52922 strains is found to be 0.4 and 1.6 μg/ml, respectively. Furthermore, Bio-TEM analysis demonstrated that the exposure of the selected microbial strains to the nanofibers led to disruption of the cell membranes and leakage of the cytoplasm. In conclusion, the combined results suggested doping promotes antimicrobial effect; synthesized nanofibers possess a very large surface-to-volume ratio and may damage the structure of the bacterial cell membrane, as well as depress the activity of the membranous enzymes which cause bacteria to die in due course.     

Serum CA19–9, cathepsin D,and matrix metalloproteinase‐7 as a diagnostic panel for pancreatic ductal adenocarcinoma

Pancreatic ductal adenocarcinoma (PDAC) accounts for 95% of pancreatic cancers. CA19‐9 is not widely used for screening PDAC due to its low sensitivity. Here, we studied the clinical usefulness of cathepsin D, matrix metalloproteinases (MMPs), and tissue inhibitors of MMPs (TIMPs) for screening patients with PDAC. A total of 248 patients with PDAC and 216 control subjects were recruited (109 PDAC patients and 70 controls in the training set and 139 PDAC patients and 146 controls in the validation set). We measured serum levels of cathepsin D, TIMPs (?1, ?3, and ?4), and MMPs (?1, ?7, ?8, and ?9) using Fluorokine MAP multiplex kits. The concentrations of cathepsin D and MMP‐7 were significantly higher in PDAC subjects than control subjects. In the training set, the diagnostic sensitivity and AUC of the panel of CA19‐9, cathepsin D, and MMP‐7 for PDAC were increased to 88% and 0.900, compared to 74% and 0.835 of CA19‐9 single marker at 80% specificity. The sensitivity using cut‐off value of biomarker panel was significantly increased in the validation set as well as training set. Our findings indicate that a serum biomarker panel consisting of CA19‐9, cathepsin D, and MMP‐7 may provide the most effective screening test currently feasible for PDAC.     

Dynamic modulation of the kv2.1 channel by SRC-dependent tyrosine phosphorylation

The voltage-gated K(+) channel Kv2.1 is expressed as a highly phosphorylated protein in most central neurons, where it plays a key role in regulating neuronal membrane excitability. Previous studies have shown that Kv2.1 channel activity is upregulated by Src-mediated phosphorylation through an unknown mechanism. However, a systematic analysis of the molecular mechanism of Kv2.1 channel phosphorylation by Src is lacking. Here, we show that tyrosine phosphorylation by Src plays a fundamental role in regulating Kv2.1-mediated K(+) current enhancement. We found that the level of expression of the Kv2.1 protein is increased by Src kinase. Using mass spectrometric proteomic techniques, we identified two novel phosphotyrosine sites, Y686 and Y810, in the cytoplasmic domains of Kv2.1. We found that Src-dependent phosphorylation at these sites affects Kv2.1 through distinct regulatory mechanisms. Whereas phosphorylation at Y686 regulates Kv2.1 activity similarly to the known site Y124, phosphorylation at Y810 plays a significant role in regulating the intracellular trafficking of Kv2.1 channels. Our results show that these two novel tyrosine phosphorylation sites of Kv2.1 are crucial to regulating diverse aspects of Kv2.1 channel function and provide novel insights into molecular mechanisms for the regulation of Src-dependent modulation of Kv2.1 channels.     

Probiotic Bifidobacterium breve Induces IL-10-Producing Tr1 Cells in the Colon

Specific intestinal microbiota has been shown to induce Foxp3⁺ regulatory T cell development. However, it remains unclear how development of another regulatory T cell subset, Tr1 cells, is regulated in the intestine. Here, we analyzed the role of two probiotic strains of intestinal bacteria, Lactobacillus casei and Bifidobacterium breve in T cell development in the intestine. B. breve, but not L. casei, induced development of IL-10-producing Tr1 cells that express cMaf, IL-21, and Ahr in the large intestine. Intestinal CD103⁺ dendritic cells (DCs) mediated B. breve-induced development of IL-10-producing T cells. CD103⁺ DCs from Il10 ^−/−, Tlr2 ^−/−, and Myd88 ^−/− mice showed defective B. breve-induced Tr1 cell development. B. breve-treated CD103⁺ DCs failed to induce IL-10 production from co-cultured Il27ra ^−/− T cells. B. breve treatment of Tlr2 ^−/− mice did not increase IL-10-producing T cells in the colonic lamina propria. Thus, B. breve activates intestinal CD103⁺ DCs to produce IL-10 and IL-27 via the TLR2/MyD88 pathway thereby inducing IL-10-producing Tr1 cells in the large intestine. Oral B. breve administration ameliorated colitis in immunocompromised mice given naïve CD4⁺ T cells from wild-type mice, but not Il10 ^−/− mice. These findings demonstrate that B. breve prevents intestinal inflammation through the induction of intestinal IL-10-producing Tr1 cells.     

Delivered Biomass Costs of Honey Mesquite (Prosopis glandulosa) for Bioenergy Uses in the South Central USA

Honey mesquite (Prosopis glandulosa Torr.), a multistemmed tree that grows on grasslands and rangelands in the South Central USA (Texas, Oklahoma, and New Mexico), may have potential as a bioenergy feedstock due to a large amount of existing standing biomass and significant regrowth potential following initial harvest. The objective of this research was to determine the cost to harvest, store, and deliver mesquite biomass feedstock to a bioelectricity plant under the assumption that the rights to harvest mesquite could be acquired in long-term leases. The advantage of mesquite and similar rangeland shrubs as bioenergy feedstocks is that they do not grow on land better suited for growing food or fiber and thus will not impact agricultural food markets as corn grain ethanol has done. In addition, there are no cultivation costs. Results indicated that mesquite biomass density (Mg?ha^?1) and harvesting costs are major factors affecting cost of delivered biomass. Annual biomass consumption by the bioelectricity plant and percent of the total system area that contains biomass density that is suitable for harvest significantly affected land- related factors including total system area needed per bioelectricity plant and transport costs. Simulation results based on actual biomass density in Texas showed that higher and more spatially consistent biomass density would be an important factor in selecting a potential location for the bioelectricity plant. Harvesting mesquite has the potential for bioenergy feedstock given certain densities and total land areas since higher harvest and transport costs are offset by essentially no production costs.     

Anti-fibrotic effects of L-2-oxothiazolidine-4-carboxylic acid via modulation of nuclear factor erythroid 2-related factor 2 in rats

L-2-Oxothiazolidine-4-carboxylic acid (OTC) is a cysteine prodrug that maintains glutathione in tissues. The present study was designed to investigate anti-fibrotic and anti-oxidative effects of OTC via modulation of nuclear factor erythroid 2-related factor 2 (Nrf2) in an in vivo thioacetamide (TAA)-induced hepatic fibrosis model. Treatment with OTC (80 or 160 mg/kg) improved serum liver function parameters and significantly ameliorated liver fibrosis. The OTC treatment groups exhibited significantly lower expression of α-smooth muscle actin, transforming growth factor-β 1, and collagen α 1 mRNA than that in the TAA model group. Furthermore, the OTC treatment groups showed a significant decrease in hepatic malondialdehyde level compared to that in the TAA model group. Nrf2 and heme oxygenase-1 expression increased significantly in the OTC treatment groups compared with that in the TAA model group. Taken together, these results suggest that OTC restores the anti- oxidative system by upregulating Nrf2; thus, ameliorating liver injury and a fibrotic reaction.