On the Hardness of the Strongly Dependent Decision Problem

We present necessary and sufficient conditions for solving the strongly dependent decision (SDD) problem in various distributed systems. Our main contribution is a novel characterization of the SDD problem based on point-set topology. For partially synchronous systems, we show that any algorithm that solves the SDD problem induces a set of executions that is closed with respect to the point-set topology. We also show that the SDD problem is not solvable in the asynchronous system augmented with any arbitrarily strong failure detectors.Comment: Appeared in ICDCN 201

Solving k-Set Agreement with Stable Skeleton Graphs

In this paper we consider the k-set agreement problem in distributed message-passing systems using a round-based approach: Both synchrony of communication and failures are captured just by means of the messages that arrive within a round, resulting in round-by-round communication graphs that can be characterized by simple communication predicates. We introduce the weak communication predicate PSources(k) and show that it is tight for k-set agreement, in the following sense: We (i) prove that there is no algorithm for solving (k-1)-set agreement in systems characterized by PSources(k), and (ii) present a novel distributed algorithm that achieves k-set agreement in runs where PSources(k) holds. Our algorithm uses local approximations of the stable skeleton graph, which reflects the underlying perpetual synchrony of a run. We prove that this approximation is correct in all runs, regardless of the communication predicate, and show that graph-theoretic properties of the stable skeleton graph can be used to solve k-set agreement if PSources(k) holds.Comment: to appear in 16th IEEE Workshop on Dependable Parallel, Distributed and Network-Centric System

Cellulose- and xylan-degrading yeasts: Enzymes, applications and biotechnological potential

Microbes and their carbohydrate-active enzymes are central for\ua0depolymerization\ua0of complex lignocellulosic\ua0polysaccharides\ua0in the global\ua0carbon cycle. Their unique abilities to degrade and ferment carbohydrates are also utilized in many industrial processes such as baking, brewing and production of biofuels and drugs. Effective degradation and utilization of cellulose and\ua0hemicelluloses\ua0is important for the shift towards green bioeconomy, and requires microbes equipped with proper sets of carbohydrate-active enzymes (CAZymes). Knowledge of cellulolytic and xylanolytic CAZymes has mainly been generated from bacteria and\ua0filamentous fungi, while yeasts have been largely overlooked and may represent an untapped resource in natural CAZymes with industrial relevance. Cellulose and xylan-degrading yeasts with the ability to ferment\ua0saccharides\ua0are also promising candidates for consolidated bioprocesses (CBPs), as they can degrade lignocellulose and utilize its constituents to produce desired products at the same time. Cellulolytic yeasts able to utilize insoluble crystalline cellulose are rare while xylanolytic yeasts are rather widespread in nature. The lack of particular enzymes in yeasts can be remediated by introducing the missing enzymes into strains having outstanding product-forming attributes.In this review, we provide a comprehensive overview of the cellulose- and xylan-degrading ascomycetous and basidiomycetous yeasts known to date. We describe how these yeasts can be identified through bioprospecting and\ua0bioinformatic\ua0approaches and summarize available growth and enzymatic assays for strain characterization. Known and predicted CAZymes are extensively analyzed, both in individual species and in a\ua0phylogenetic\ua0perspective. We also describe the strategies used for construction of recombinant cellulolytic and xylanolytic strains as well as current applications for polysaccharide-degrading yeasts. Finally, we discuss the great potential of these yeasts as industrial cell factories, identify open research questions and provide suggestions for future investigations

Phylogeny, classification and metagenomic bioprospecting of microbial acetyl xylan esterases

Acetyl xylan esterases (AcXEs), also termed xylan deacetylases, are broad specificity Carbohydrate-Active Enzymes (CAZymes) that hydrolyse ester bonds to liberate acetic acid from acetylated hemicellulose (typically polymeric xylan and xylooligosaccharides). They belong to eight families within the Carbohydrate Esterase (CE) class of the CAZy database. AcXE classification is largely based on sequence-dependent phylogenetic relationships, supported in some instances with substrate specificity data. However, some sequence-based predictions of AcXE-encoding gene identity have proved to be functionally incorrect. Such ambiguities can lead to mis-assignment of genes and enzymes during sequence data-mining, reinforcing the necessity for the experimental confirmation of the functional properties of putative AcXE-encoding gene products. Although one-third of all characterized CEs within CAZy families 1–7 and 16 are AcXEs, there is a need to expand the sequence database in order to strengthen the link between AcXE gene sequence and specificity. Currently, most AcXEs are derived from a limited range of (mostly microbial) sources and have been identified via culture-based bioprospecting methods, restricting current knowledge of AcXEs to data from relatively few microbial species. More recently, the successful identification of AcXEs via genome and metagenome mining has emphasised the huge potential of culture-independent bioprospecting strategies. We note, however, that the functional metagenomics approach is still hampered by screening bottlenecks. The most relevant recent reviews of AcXEs have focused primarily on the biochemical and functional properties of these enzymes. In this review, we focus on AcXE phylogeny, classification and the future of metagenomic bioprospecting for novel AcXEs.The South African Department of Science and Technology Biocatalysis Initiative, National Research Foundation (DAC, TPM), the University of Pretoria’s Genomics Research Institute (DAC) and Research Development Program (TPM). FAA was supported by funds from the Organisation for Women in Science in the Developing World (OWSD).http://www.elsevier.com/locate/emt2017-11-30hb2016Genetic

Recent progress in understanding mode of action of acetylxylan esterases

Acetylation is one of the main obstacles to the effective enzymatic conversion of hemicelluloses to fermentable sugars. In nature, the microbial degradation of hemicellulose involves the action of deacetylating esterases that act synergistically with glycoside hydrolases. In the industrial processing of lignocelluloses biomass, alkaline pretreatments remove acetyl groups by saponification, but other non-alkaline pretreatment methods generate acetylated hemicelluloses. Complete saccharification of plant hemicelluloses can’t be achieved without the deacetylating enzymes. Recent years have witnessed considerale progress in our understanding of the mode of acetylation of hemicellulose and mode of action of microbial polysaccharide deacetylases. In this article we focus on the diversity and role of acetylxylan esterases in the breakdown of acetylxylan, the most abundant hemicellulose in nature.This work was supported by grants from the Slovak Academy of Sciences grant agency VEGA 2/0037/14, by The Slovak Research and Development Agency under the contract No. APVV-0602-12, by grant 214613 from the Norwegian Research Council and by the FP7 project Waste2Go under contract 308363 with European Commission.https://www.jstage.jst.go.jp/browse/jagam201

Changes in the arabinoxylan fraction of wheat grain during 1 alcohol production

Laboratory produced DDGS samples were compared with commercial samples from a distillery and a biofuel plant. Changes in structure, solubility and content of arabinoxylan (AX) was determined. The distillation process results in a relative increase of AX content compared to the starting material. The heating and drying processes involved in the production of DDGS lead to an increased solubility and viscosity of water-extractable AX. Production of DDGS results in structural changes to the AX. There is a decrease in 2-and 3-linked arabinose oligosaccharides, that contributes to around a 50% reduction in arabinosylation in DDGS compared with the starting grains. The current study shows that laboratory-scale DDGS provide an accurate representation of the commercial scale and that the AX composition of DDGS is consistently uniform irrespective of starting material. The uniformity of DDGS and thin stillage makes them a good potential source of AX for production of prebiotics or other novel products

On the Hardness of the Strongly Dependent Decision Problem

We present necessary and sufficient conditions for solving the strongly dependent decision (SDD) problem in various distributed systems. Our main contribution is a novel characterization of the SDD problem based on point-set topology. For partially synchronous systems, we show that any algorithm that solves the SDD problem induces a set of executions that is closed with respect to the point-set topology. We also show that the SDD problem is not solvable in the asynchronous system augmented with any arbitrarily strong failure detectors