Expanding understanding and scope of Pichia pastoris for secreted protein expression

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Capturing the ‘ome’ : the expanding molecular toolbox for RNA and DNA library construction

All sequencing experiments and most functional genomics screens rely on the generation of libraries to comprehensively capture pools of targeted sequences. In the past decade especially, driven by the progress in the field of massively parallel sequencing, numerous studies have comprehensively assessed the impact of particular manipulations on library complexity and quality, and characterized the activities and specificities of several key enzymes used in library construction. Fortunately, careful protocol design and reagent choice can substantially mitigate many of these biases, and enable reliable representation of sequences in libraries. This review aims to guide the reader through the vast expanse of literature on the subject to promote informed library generation, independent of the application

The potential of glycomics as prognostic biomarkers in liver disease and liver transplantation

The study of glycomics is a novel and fascinating approach for the development of biomarkers. It has become clear that in the field of liver disease specific glycomic patters are present in specific disease states, which has led to the development of diagnostic biomarkers. In this manuscript, we will describe two new applications of this technology for the development of prognostic biomarkers. The first biomarker is associated with the risk of hepatocellular carcinoma development in patients with compensated cirrhosis. The second biomarker is present in perfusate and is related to the risk of primary non function occurrence after liver transplantation. The technology used for these biomarkers could easily be implemented on routine capillary electrophoresis equipment

Human T cell glycosylation and implications on immune therapy for cancer

Glycosylation is an important post-translational modification, giving rise to a diverse and abundant repertoire of glycans on the cell surface, collectively known as the glycome. When focusing on immunity, glycans are indispensable in virtually all signaling and cell-cell interactions. More specifically, glycans have been shown to regulate key pathophysiological steps within T cell biology such as T cell development, thymocyte selection, T cell activity and signaling as well as T cell differentiation and proliferation. They are of major importance in determining the interaction of human T cells with tumor cells. In this review, we will describe the role of glycosylation of human T cells in more depth, elaborate on the importance of glycosylation in the interaction of human T cells with tumor cells and discuss the potential of cancer immunotherapies that are based on manipulating the glycome functions at the tumor immune interface

2D separation and profiling of complex oligosaccharide mixtures

Oligosaccharides present in various natural sources can contain different linkages, susbstitutions and building blocks with the same mass. Oligosaccharide mixtures often contain these isomeric and isobaric structures, which causes their complexity. These components are difficult to separate and analyze with conventional analytical methods. The technique described below was developed to obtain a higher resolution

Bacterial exchange in household washing machines

Household washing machines (WMs) launder soiled clothes and textiles, but do not sterilize them. We investigated the microbial exchange occurring in five household WMs. Samples from a new cotton T-shirt were laundered together with a normal laundry load. Analyses were performed on the influent water and the ingoing cotton samples, as well as the greywater and the washed cotton samples. The number of living bacteria was generally not lower in the WM effluent water as compared to the influent water. The laundering process caused a microbial exchange of influent water bacteria, skin-, and clothes related bacteria and biofilm-related bacteria in the WM. A variety of biofilm-producing bacteria were enriched in the effluent after laundering, although their presence in the cotton sample was low. Nearly all bacterial genera detected on the initial cotton sample were still present in the washed cotton samples. A selection for typical skin- and clothes related microbial species occurred in the cotton samples after laundering. Accordingly, malodour-causing microbial species might be further distributed to other clothes. The bacteria on the ingoing textiles contributed for a large part to the microbiome found in the textiles after laundering

A guide to Mycobacterium mutagenesis

The genus Mycobacterium includes several pathogens that cause severe disease in humans, like Mycobacterium tuberculosis (M. tb), the infectious agent causing tuberculosis. Genetic tools to engineer mycobacterial genomes, in a targeted or random fashion, have provided opportunities to investigate M. tb infection and pathogenesis. Furthermore, they have allowed the identification and validation of potential targets for the diagnosis, prevention, and treatment of tuberculosis. This review describes the various methods that are available for the generation of mutants in Mycobacterium species, focusing specifically on tools for altering slow-growing mycobacteria from the M. tb complex. Among others, it incorporates the recent new molecular biological technologies (e.g. ORBIT) to rapidly and/or genome-wide comprehensively obtain targeted mutants in mycobacteria. As such, this review can be used as a guide to select the appropriate genetic tools to generate mycobacterial mutants of interest, which can be used as tools to aid understanding of M. tb infection or to help developing TB intervention strategies

The impact of elevation of total bilirubin level and etiology of the liver disease on serum N-glycosylation patterns in mice and men

The GlycoFibroTest and GlycoCirrhoTest are noninvasive alternatives for liver biopsy that can be used as a follow-up tool for fibrosis patients and to diagnose cirrhotic patients, respectively. These tests are based on the altered N-glycosylation of total serum protein. Our aim was to investigate the impact of etiology on the alteration of N-glycosylation and whether other characteristics of liver patients could have an influence on N-glycosylation. In human liver patients, no specific alteration could be found to make a distinction according to etiological factor, although alcoholic patients had a significant higher mean value for the GlycoCirrhoTest. Undergalactosylation did not show a significantly different quantitative alteration in the cirrhotic and non-cirrhotic population of all etiologies. Importantly, patients with an elevation of total bilirubin level (>2 mg/dl) had a strong increase of glycans modified with alpha 1-6 fucose. The fucosylation index was therefore significantly higher in fibrosis/cirrhosis and hepatocellular carcinoma patients with elevated total bilirubin levels irrespective of etiology. Furthermore, in a multiple linear regression analysis, only markers for cholestasis significantly correlated with the fucosylation index. In mouse models of chronic liver disease, the fucosylation index was uniquely significantly increased in mice that were induced with a common bile duct ligation. Mice that were chronically injected with CCl4 did not show this increase. Apart from this difference, common changes characteristic to fibrosis development in mice were observed. Finally, mice induced with a partial portal vein ligation did not show biological relevant changes indicating that portal hypertension does not contribute to the alteration of N-glycosylation

Production, purification and crystallization of a trans-sialidase from Trypanosoma vivax

Sialidases and trans-sialidases play important roles in the life cycles of various microorganisms. These enzymes can serve nutritional purposes, act as virulence factors or mediate cellular interactions (cell evasion and invasion). In the case of the protozoan parasite Trypanosoma vivax, trans-sialidase activity has been suggested to be involved in infection-associated anaemia, which is the major pathology in the disease nagana. The physiological role of trypanosomal trans-sialidases in host-parasite interaction as well as their structures remain obscure. Here, the production, purification and crystallization of a recombinant version of T. vivaxtrans-sialidase 1 (rTvTS1) are described. The obtained rTvTS1 crystals diffracted to a resolution of 2.5 angstrom and belonged to the orthorhombic space group P2(1)2(1)2(1), with unit-cell parameters a = 57.3, b = 78.4, c = 209.0 angstrom