Pushing context-awareness down to the core: moreflexibility for the PerLa language

Information technology is increasingly pervading our envi- ronment, making real Mark Weiser’s vision of a “disappear- ing technology”. The work described in this paper focuses on using context to enable pervasive system personaliza- tion, allowing context-aware sensor-data tailoring. Since sensor networks, besides data collection, are also able to pro- duce active behaviours, the tailoring capabilities are also ex- tended to these, thus applying context-awareness to generic system operations. Moreover, because the number of pos- sible context can grow rapidly with the complexity of the application, the design phase is also supported by the possi- bility to speed-up and modularize the definition of the data and operations associated with each specific context, pro- ducing a support tool that eases the job of the designers of modern context-aware pervasive systems

Towards autonomic pervasive systems: the PerLa context language

The property of context-awareness, inherent to a Pervasive System, requires a clear definition of context and of how the context parameter values must be extracted from the real world. Since often the same variables are common to the operational system and to the context it operates into, the usage of the same language to manage both the application and the context can lead to substantial savings in application development time and costs. In this paper we propose a context-management extension to the PerLa language and middleware that allows for declarative gathering of context data from the environment, feeding this data to the internal context model and, once a context is active, acting on the relevant resources of the pervasive system, according to the chosen contextual policy

Fecal metaproteomic analysis reveals unique changes of the gut microbiome functions after consumption of sourdough Carasau bread

Sourdough-leavened bread (SB) is acknowledged for its great variety of valuable effects on consumer's metabolism and health, including a low glycemic index and a reduced content of the possible carcinogen acrylamide. Here, we aimed to investigate how these effects influence the gut microbiota composition and functions. Therefore, we subjected rats to a diet supplemented with SB, baker's yeast leavened bread (BB), or unsupplemented diet (chow), and, after 4 weeks of treatment, their gut microbiota was analyzed using a metaproteogenomic approach. As a result, diet supplementation with SB led to a reduction of specific members of the intestinal microbiota previously associated to low protein diets, namely Alistipes and Mucispirillum, or known as intestinal pathobionts, i.e., Mycoplasma. Concerning functions, asparaginases expressed by Bacteroides were observed as more abundant in SB-fed rats, leading to hypothesize that in their colonic microbiota the enzyme substrate, asparagine, was available in higher amounts than in BB- and chow-fed rats. Another group of protein families, expressed by Clostridium, was detected as more abundant in animal fed SB-supplemented diet. Of these, manganese catalase, small acid-soluble proteins (SASP), Ser/Thr kinase PrkA, and V-ATPase proteolipid subunit have been all reported to take part in Clostridium sporulation, strongly suggesting that the diet supplementation with SB might promote environmental conditions inducing metabolic dormancy of Clostridium spp. within the gut microbiota. In conclusion, our data describe the effects of SB consumption on the intestinal microbiota taxonomy and functions in rats. Moreover, our results suggest that a metaproteogenomic approach can provide evidence of the interplay between metabolites deriving from bread digestion and microbial metabolism

The Role and Relevance of Experimentation in Informatics

Informatics is a relatively young eld within sci- ence and engineering. Its research and develop- ment methodologies build on the scientic and de- sign methodologies in the classical areas, often with new elements to it. We take an in-depth look at one of the less well-understood methodologies in infor- matics, namely experimentation. What does it mean to do experiments in in- formatics? Does it make sense to `import' tradi- tional principles of experimentation from classical disciplines into the eld of computing and informa- tion processing? How should experiments be docu- mented? These are some of the questions that are treated. The report argues for the key role of empiri- cal research and experimentation in contemporary Informatics. Many IT systems, large and small, can only be designed sensibly with the help of experiments. We recommend that professionals and students alike are well-educated in the prin- ciples of sound experimentation in Informatics. We also recommend that experimentation protocols are used and standardized as part of the experimental method in Informatic

A human gut metaproteomic dataset from stool samples pretreated or not by differential centrifugation

We present a human gut metaproteomic dataset deposited in the ProteomeXchange Consortium via the PRIDE partner repository with the dataset identifier PXD001573. Ten aliquots of a single stool sample collected from a healthy human volunteer were either pretreated by differential centrifugation (DC; N=5) or not centrifuged (NC; N=5). Protein extracts were then processed by filter-aided sample preparation, single-run liquid chromatography and high-resolution mass spectrometry, and peptide identification was carried out using Sequest-HT as search engine within the Proteome Discoverer informatic platform. The dataset described here is also related to the research article entitled "Enrichment or depletion? The impact of stool pretreatment on metaproteomic characterization of the human gut microbiota" published in Proteomics (Tanca et al., 2015), [1]

The bovine milk microbiota: insights and perspectives from -omics studies

Recent significant progress in culture-independent techniques, together with the parallel development of -omics technologies and data analysis capabilities, have led to a new perception of the milk microbiota as a complex microbial community with great diversity and multifaceted biological roles, living in an environment that was until recently believed to be sterile. In this review, we summarize and discuss the latest findings on the milk microbiota in dairy cows, with a focus on the role it plays in bovine physiology and health. Following an introduction on microbial communities and the importance of their study, we present an overview of the -omics methods currently available for their characterization, and outline the potential offered by a systems biology approach encompassing metatranscriptomics, metaproteomics, and metametabolomics. Then, we review the recent discoveries on the dairy cow milk microbiome enabled by the application of -omics approaches. Learning from studies in humans and in the mouse model, and after a description of the endogenous route hypothesis, we discuss the role of the milk microbiota in the physiology and health of both the mother and the offspring, and report how it can be changed by farming practices and during infection. In conclusion, we shortly outline the impact of the milk microbiota on the quality of milk and of dairy products

A first immunohistochemistry study of transketolase and transketolase-like 1 expression in canine hyperplastic and neoplastic mammary lesions

Background: Canine mammary tumors represent the most common neoplasm in female dogs, and the discovery of cancer biomarkers and their translation to clinical relevant assays is a key requirement in the war on cancer. Since the description of the 'Warburg effect', the reprogramming of metabolic pathways is considered a hallmark of pathological changes in cancer cells. In this study, we investigate the expression of two cancer-related metabolic enzymes, transketolase (TKT) and transketolase-like 1 (TKTL1), involved in the pentose phosphate pathway (PPP), an alternative metabolic pathway for glucose breakdown that could promote cancer by providing the precursors and energy required for rapidly growing cells. Results: TKT and TKTL1 protein expression was investigated by immunohistochemistry in canine normal (N = 6) and hyperplastic glands (N = 3), as well as in benign (N = 11) and malignant mammary tumors (N = 17). TKT expression was higher in hyperplastic lesions and in both benign and malignant tumors compared to the normal mammary gland, while TKTL1 levels were remarkably higher in hyperplastic lesions, simple adenomas and simple carcinomas than in the normal mammary glands (P < 0.05). Conclusions: This study reveals that the expression of a key PPP enzyme varies along the evolution of canine mammary neoplastic lesions, and supports a role of metabolic changes in the development of canine mammary tumors

Diversity and functions of the sheep faecal microbiota : A multi-omic characterization

Little is currently known on the microbial populations colonizing the sheep large intestine, despite their expected key role in host metabolism, physiology and immunity. This study reports the first characterization of the sheep faecal microbiota composition and functions, obtained through the application of a multi-omic strategy. An optimized protocol was first devised for DNA extraction and amplification from sheep stool samples. Then, 16S rDNA sequencing, shotgun metagenomics and shotgun metaproteomics were applied to unravel taxonomy, genetic potential and actively expressed functions and pathways respectively. Under a taxonomic perspective, the sheep faecal microbiota appeared globally comparable to that of other ruminants, with Firmicutes being the main phylum. In functional terms, we detected 2097 gene and 441 protein families, finding that the sheep faecal microbiota was primarily involved in catabolism. We investigated carbohydrate transport and degradation activities and identified phylum-specific pathways, such as methanogenesis for Euryarchaeota and acetogenesis for Firmicutes. Furthermore, our approach enabled the identification of proteins expressed by the eukaryotic component of the microbiota. Taken together, these findings unveil structure and role of the distal gut microbiota in sheep, and open the way to further studies aimed at elucidating its connections with management and dietary variables in sheep farming

Proteomic analysis of Rhodotorula mucilaginosa : dealing with the issues of a non-conventional yeast

Red yeasts ascribed to the species Rhodotorula mucilaginosa are gaining increasing attention, due to their numerous biotechnological applications, spanning carotenoid production, liquid bioremediation, heavy metal biotransformation and antifungal and plant growth-promoting actions, but also for their role as opportunistic pathogens. Nevertheless, their characterization at the 'omic' level is still scarce. Here, we applied different proteomic workflows to R. mucilaginosa with the aim of assessing their potential in generating information on proteins and functions of biotechnological interest, with a particular focus on the carotenogenic pathway. After optimization of protein extraction, we tested several gel-based (including 2D-DIGE) and gel-free sample preparation techniques, followed by tandem mass spectrometry analysis. Contextually, we evaluated different bioinformatic strategies for protein identification and interpretation of the biological significance of the dataset. When 2D-DIGE analysis was applied, not all spots returned a unambiguous identification and no carotenogenic enzymes were identified, even upon the application of different database search strategies. Then, the application of shotgun proteomic workflows with varying levels of sensitivity provided a picture of the information depth that can be reached with different analytical resources, and resulted in a plethora of information on R. mucilaginosa metabolism. However, also in these cases no proteins related to the carotenogenic pathway were identified, thus indicating that further improvements in sequence databases and functional annotations are strictly needed for increasing the outcome of proteomic analysis of this and other non-conventional yeasts