Open Source Software Acquisition: Beyond the Business Case

Lately we have seen a growing interest from both public and private organisations to adopt Open Source Software (OSS), not only for a few, specific applications but also on a more general level throughout the organisation. As a consequence, the organisations’ decisions on adoption of OSS are becoming increasingly more important and complex. We present three perspectives organisations can employ in their decisions: seeing OSS acquisition as a business case, as COTS acquisition, and as architectural change within a governance framework. We present case studies of decisions on OSS adoption, and categorise the decision criteria we have found. Our results indicate that for large-scale adoption of OSS, focus will be on architectural considerations: enterprise-wide architectures will at first be a barrier, but in the long term OSS’s support of open standards can be a major enabler for OSS adoption. In contrast, in smaller organisations and in small-scale adoption of OSS, the cheap price of OSS is a major enabler, as it provides a good opportunity for experiments and short-term economic benefits. For small organisations these experiments can lead to development of a common IT-architecture, and in larger organisations OSS can be adopted in niche-areas, without significantly violating an existing IT-architecture

The natural catalytic function of <i>CuG</i>E glucuronoyl esterase in hydrolysis of genuine lignin-carbohydrate complexes from birch

Abstract Background Glucuronoyl esterases belong to carbohydrate esterase family 15 and catalyze de-esterification. Their natural function is presumed to be cleavage of ester linkages in lignin–carbohydrate complexes particularly those linking lignin and glucuronoyl residues in xylans in hardwood. Results Here, we show for the first time a detailed product profile of aldouronic acids released from birchwood lignin by a glucuronoyl esterase from the white-rot fungus Cerrena unicolor (CuGE). CuGE releases substrate for GH10 endo-xylanase which results in significantly increased product release compared to the action of endo-xylanase alone. CuGE also releases neutral xylo-oligosaccharides that can be ascribed to the enzymes feruloyl esterase side activity as demonstrated by release of ferulic acid from insoluble wheat arabinoxylan. Conclusion The data verify the enzyme’s unique ability to catalyze removal of all glucuronoxylan associated with lignin and we propose that this is a direct result of enzymatic cleavage of the ester bonds connecting glucuronoxylan to lignin via 4-O-methyl glucuronoyl-ester linkages. This function appears important for the fungal organism’s ability to effectively utilize all available carbohydrates in lignocellulosic substrates. In bioprocess perspectives, this enzyme is a clear candidate for polishing lignin for residual carbohydrates to achieve pure, native lignin fractions after minimal pretreatment

Identifying Business Barriers and Enablers for the Adoption of Open Source Software

The main research interest in Open Source Software (OSS) has been in answering the questions of why individuals and organizations without economic compensation contribute to OSS projects and how these projects are organized. In this paper we instead focus on managerial decisions for acquisition of OSS and discuss potential barriers for widespread use of OSS. Based on existing literature and a small case study, we develop and discuss the hypothesis that a major barrier may be the "customer" organizations’ uncertainty and unfamiliarity with the relationships with OSS "vendors". To develop viable models for these relationships is an important challenge, which we will deal with in a research project, of which this paper should be seen as a first step

Increased trans-glycosylation activity of hexosaminidases for synthesis of human milk oligosaccharides

It is well known that the composition of human breast milk differs significantly from the one of ordinary bovine milk. Especially the presence of sialylated and fucosylated oligosaccharides contributes to its health and development promoting features for newborn infants. [1] Nevertheless, not all newborns and especially premature infants sometimes cannot be breast fed for different reasons. For those children it is important that they receive a proper balanced formula product containing the above mentioned human milk oligosaccharides (HMOs). With respect to this we are developing new enzymatic routes for synthesis of sialylated and fucosylated oligosaccharides, which can be used as functional ingredient for infant formula. In a previous work two candidate hexoasaminidases (both belonging to the GH20 family) were identified from a metagenomic library, which were able to synthesize the basic HMO backbone structure, Lacto-N-triose II, from chitobiose and lactose by trans-glycosylation. [2] Since the yields using these enzymes were low (2% for hex1 and 8% for hex2 based on the donor substrate chitobiose) we wanted to increase their trans-glycosylation activity to increase their applicability for a feasible process. It was decided to follow a rational design approach first to keep the screening effort low. Therefore peptide pattern recognition (PPR) [3] analysis was performed on the whole GH20 CAZy family (approx. 3000 sequences) to identify other enzymes with potential trans-glycosylation activity based on relatedness. By phylogenetic analysis of the group containing the two known enzymes (approx. 1000 sequences) and subsequent alignment of the closely related sequences a loop insertion close to the active site was identified. Homology modelling revealed that introduction of this loop structure into hex1 and hex2 would lead to a significantly narrower active site and therefore contribute to exclusion of water from the active site, which is a well-known strategy to increase trans-glycosylation activity. The proposed loop mutants were then expressed, purified and characterized towards trans-glycosylation activity. For hex2 it turned out that none of the loop mutants showed an improved trans-glycosylation activity compared to the wild-type. But for hex1 three out of four showed an up to seven-fold improved trans-glycosylation activity compared to the wild-type, which refers even to a higher trans-glycosylation activity than previously observed for the hex2 wild-type. [4] In conclusion we succeeded in engineering an enzyme towards increased trans-glycosylation activity using a custom-made rational approach utilizing available sequence analysis methods. [1] L. Bode, Glycobiology 2012, 22, 1147–1162. [2] C. Nyffenegger, R. T. Nordvang, B. Zeuner, M. Łężyk, E. Difilippo, M. J. Logtenberg, H. A. Schols, A. S. Meyer, J. D. Mikkelsen, Appl. Microbiol. Biotechnol. 2015, 99, 7997–8009. [3] P. K. Busk, L. Lange, Appl. Environ. Microbiol. 2013, 79, 3380–3391. [4] S. B. Jamek, J. Muschiol, J. Holck, P. K. Busk, L. Lange, J. D. Mikkelsen, A. S. Meyer, 2017, manuscript submitted

It All Starts with a Sandwich: Identification of Sialidases with Trans-Glycosylation Activity

Sialidases (3.2.1.18) may exhibit trans-sialidase activity to catalyze sialylation of lactose if the active site topology is congruent with that of the Trypanosoma cruzi trans-sialidase (EC 2.4.1.-). The present work was undertaken to test the hypothesis that a particular aromatic sandwich structure of two amino acids proximal to the active site of the T. cruzi trans-sialidase infers trans-sialidase activity. On this basis, four enzymes with putative trans-sialidase activity were identified through an iterative alignment from 2909 native sialidases available in GenBank, which were cloned and expressed in Escherichia coli. Of these, one enzyme, SialH, derived from Haemophilus parasuis had an aromatic sandwich structure on the protein surface facing the end of the catalytic site (Phe168; Trp366), and was indeed found to exhibit trans-sialidase activity. SialH catalyzed production of the human milk oligosaccharide 3'-sialyllactose as well as the novel trans-sialylation product 3-sialyllactose using casein glycomacropeptide as sialyl donor and lactose as acceptor. The findings corroborated that Tyr119 and Trp312 in the T. cruzi trans-sialidase are part of an aromatic sandwich structure that confers trans-sialylation activity for lactose sialylation. The in silico identification of trans-glycosidase activity by rational active site topology alignment thus proved to be a quick tool for selecting putative trans-sialidases amongst a large group of glycosyl hydrolases. The approach moreover provided data that help understand structure-function relations of trans-sialidases