A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology

Genomic data allow the large-scale manual or semi-automated assembly of metabolic network reconstructions, which provide highly curated organism-specific knowledge bases. Although several genome-scale network reconstructions describe Saccharomyces cerevisiae metabolism, they differ in scope and content, and use different terminologies to describe the same chemical entities. This makes comparisons between them difficult and underscores the desirability of a consolidated metabolic network that collects and formalizes the 'community knowledge' of yeast metabolism. We describe how we have produced a consensus metabolic network reconstruction for S. cerevisiae. In drafting it, we placed special emphasis on referencing molecules to persistent databases or using database-independent forms, such as SMILES or InChI strings, as this permits their chemical structure to be represented unambiguously and in a manner that permits automated reasoning. The reconstruction is readily available via a publicly accessible database and in the Systems Biology Markup Language (http://www.comp-sys-bio.org/yeastnet). It can be maintained as a resource that serves as a common denominator for studying the systems biology of yeast. Similar strategies should benefit communities studying genome-scale metabolic networks of other organisms.     

Preparation and characteristics of moulded biodegradable cellulose fibers/MPU-20 composites (CFMCs) by steam injection technology

In this work, the moulded cellulose fibers/MPU-20 composites (CFMCs) with apparent specific gravity lower than 100 kg/m³ and thickness of 20–200 mm have been successfully manufactured using a new design of steam injection technology and equipment. It was found that the CFMCs have good cushioning properties, with a cushion factor lower than 4. Two yield deformation stages were observed in the compressive process. Compressive stress–strain and cushion factor-stain curves were measured as a function of steam injection pressure, transmission time, holding time, MPU-20 resin dosage and apparent specific gravity. Chemical groups, crystallinity, and thermal properties of samples were studied through the use of FTIR spectroscopy, X-ray diffraction (XRD), and DTA–TGA. In addition, the microstructure and morphology were investigated by scanning electron microscope (SEM) and atomic force microscope (AFM).     

Pro‐apoptotic Noxa is involved in ablative focal irradiation‐induced lung injury

Although lung injury including fibrosis is a well‐documented side effect of lung irradiation, the mechanisms underlying its pathology are poorly understood. X‐rays are known to cause apoptosis in the alveolar epithelial cells of irradiated lungs, which results in fibrosis due to the proliferation and differentiation of fibroblasts and the deposition of collagen. Apoptosis and BH3‐only pro‐apoptotic proteins have been implicated in the pathogenesis of pulmonary fibrosis. Recently, we have established a clinically analogous experimental model that reflects focal high‐dose irradiation of the ipsilateral lung. The goal of this study was to elucidate the mechanism underlying radiation‐induced lung injury based on this model. A radiation dose of 90 Gy was focally delivered to the left lung of C57BL/6 mice for 14 days. About 9 days after irradiation, the mice began to show increased levels of the pro‐apoptotic protein Noxa in the irradiated lung alongside increased apoptosis and fibrosis. Suppression of Noxa expression by small interfering RNA protected cells from radiation‐induced cell death and decreased expression of fibrogenic markers. Furthermore, we showed that reactive oxygen species participate in Noxa‐mediated, radiation‐induced cell death. Taken together, our results show that Noxa is involved in X‐ray‐induced lung injury.     

The adsorption of NO,NH<Subscript>3</Subscript>, N<Subscript>2</Subscript> on carbon surface: a density functional theory study

To explore the adsorption mechanism of NO, NH₃, N₂ on a carbon surface, and the effect of basic and acidic functional groups, density functional theory was employed to investigate the interactions between these molecules and carbon surfaces. Molecular electrostatic potential, Mulliken population analyses, reduced density gradient, and Mayer bond order analyses were used to clarify the adsorption mechanism. The results indicate that van der Waals interactions are responsible for N₂ physisorption, and N₂ is the least likely to adsorb on a carbon surface. Modification of carbon materials to decorate basic or acidic functional groups could enhance the NH₃ physisorption because of hydrogen bonding or electrostatic interactions, however, NO physisorption on a carbon surface is poor. Zig-zag sites are more reactive than armchair sites when these gas molecules absorb on the edge sites of carbon surface.

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Graphical abstract NH₃, N₂, NO adsortion on carbon surface

     

Immobilization of proline-specific endoprotease on nonporous silica nanoparticles functionalized with amino group

Enzyme immobilization is believed to provide an excellent base for increasing environmental tolerance of enzyme and considerable period of time. In this work, a kind of nonporous silica nanoparticles functionalized with amino group was synthesized to immobilize proline-specific endoprotease (PSEP). PSEP is known to specifically cleave peptides (or esters) at the carboxyl side of proline, thus can prevent the formation of haze and prolong the shelf life of beer. After immobilization, the environmental tolerance (temperature and pH, respectively) was obviously improved, and the immobilized enzyme can retain above 90 % of its original activity after 6 uses. Moreover, the immobilized enzyme can effectively prevent the formation of chill-haze using fresh beer fermentation liquid.     

Characterization and high‐yield production of non‐N‐glycosylated recombinant human BCMA‐Fc in Pichia pastoris

B‐cell maturation antigen (BCMA) fused at the C‐terminus to the Fc portion of human IgG1 (BCMA‐Fc) blocks B‐cell activating factor (BAFF) and proliferation‐inducing ligand (APRIL)‐mediated B‐cell activation, leading to immune disorders. The fusion protein has been cloned and produced by several engineering cell lines. To reduce cost and enhance production, we attempted to express recombinant human BCMA‐Fc (rhBCMA‐Fc) in Pichia pastoris under the control of the AOX1 methanol‐inducible promoter. To produce the target protein with uniform molecular weight and reduced immunogenicity, we mutated two predicted N‐linked glycosylation sites. The secretory yield was improved by codon optimization of the target gene sequence. After fed‐batch fermentation under optimized conditions, the highest yield (207 mg/L) of rhBCMA‐Fc was obtained with high productivity (3.45 mg/L/h). The purified functional rhBCMA‐Fc possessed high‐binding affinity to APRIL and dose‐dependent inhibition of APRIL‐induced proliferative activity in vitro through three‐step purification. Thus, this yeast‐derived expression method could be a low‐cost and effective alternative to the production of rhBCMA‐Fc in mammalian cell lines.     

Enhancement of milk protein expression in mammary epithelial cells <Emphasis Type="Italic">via</Emphasis> co-culturing with preadipocyte cells

Mammary gland development is critically dependent on the interactions between its stromal and epithelial compartments. In this study, we established a co-culture of bovine mammary epithelial Mac-T cells and murine preadipocyte 3T3-L1 cells. Mac-T cells were co-cultured with 3T3-L1 cells for four days and production of milk proteins was induced for three days. After seven days of co-culturing, the number of alveolar-like colonies in the presence of 3T3-L1 cells was significantly higher than that in control group. Expression levels of αS1-casein and β-casein mRNAs were significantlyincreased by co-culturing with 3T3-L1 cells. In addition, casein protein production was significantly higher in the co-culture of Mac-T cells with 3T3-L1 cells than in control Mac-T cells. Substances that induced casein production in Mac-T cells also stimulated adipogenesis in 3T3-L1 cells. We suggest that a co-culture system of bovine mammary epithelial cells and preadipocyte cells is an efficient method for in vitro milk protein production.