Logic based methods for SNPs tagging and reconstruction

SNPs are positions of the DNA sequences where the differences among individuals are embedded. The knowledge of such SNPs is crucial for disease association studies, but even if the number of such positions is low (about 1% of the entire sequence), the cost to extract the complete information is actually very high. Recent studies have shown that DNA sequences are structured into blocks of positions, that are conserved during evolution, where there is strong correlation among values (alleles) of different loci. To reduce the cost of extracting SNPs information, the block structure of the DNA has suggested to limit the process to a subset of SNPs, the so-called Tag SNPs, that are able to maintain the most of the information contained in the whole sequence. In this paper, we apply a technique for feature selection based on integer programming to the problem of Tag SNP selection. Moreover, to test the quality of our approach, we consider also the problem of SNPs reconstruction, i.e. the problem of deriving unknown SNPs from the value of Tag SNPs and propose two reconstruction methods, one based on a majority vote and the other on a machine learning approach. We test our algorithm on two public data sets of different nature, providing results that are, when comparable, in line with the related literature. One of the interesting aspects of the proposed method is to be found in its capability to deal simultaneously with very large SNPs sets, and, in addition, to provide highly informative reconstruction rules in the form of logic formulas.     

Antioxidant activity of phenolic and phenylethanoid glycosides from Teucrium polium L

In the present study, the chemical composition and antioxidant activities of Teucrium polium L. (Lamiaceae) were assessed. Fractionation of methanol extract obtained from the aerial parts of T. polium yielded one new phenylethanoid glycoside, named poliumoside B, together with four known flavonoids, two iridoid glycosides and a known poliumoside. The structures of all of these compounds were elucidated on the basis of spectroscopic data from 1D and 2D NMR experiments and MS spectral analyses. The antioxidant activities of the crude extracts and of the isolated compounds were evaluated through tests such as DPPH radical-scavenging capability, reducing power, xanthine oxidase inhibitory effect and inhibition of linoleic acid peroxidation. The highest antioxidant activity was found in the n-butanol extract, which also contained active polyphenols, thus suggesting that this plant could be used as a source of natural molecules, to provide safe antioxidant additives and nutraceuticals. The structure–activity relationships of the isolated compounds are also discussed.     

The carbohydrate recognition domain of surfactant protein A mediates binding to the major surface glycoprotein of Pneumocystis carinii

Pneumocystis carinii is a common cause of life-threatening pneumonia in immunodeficient patients. Pulmonary surfactant protein A (SP-A), an alveolar glycoprotein containing collagen-like and carbohydrate recognition domains (CRD), binds P. carinii and enhances adherence to alveolar macrophages. In this study, we examined the structural basis of the interaction between SP-A and the major surface glycoprotein of P. carinii (MSG). Rat SP-A bound to purified rat P. carinii-derived MSG in a saturable and calcium-dependent manner, which was partially reversible by coincubation with excess monosaccharides, or pretreatment of MSG with N-glycanase. Mutant recombinant SP-As with neutral amino acid substitutions for the predicted calcium- and carbohydrate-coordinating residues of the CRD were synthesized in insect cells using baculovirus vectors and tested for binding to MSG. Substitutions of negatively charged (Glu195, Glu202, and Asp215) and polar residues (Asn214) of the CRD with alanine but not substitution of the Arg197 with glycine reduced the binding of SP-A to mannose-Sepharose beads and to MSG. Deletion of the N-linked oligosaccharides from SP-A by mutagenesis of the consensus sequences for glycosylation had no effect on binding. We conclude that the CRD mediates the binding of SP-A to oligosaccharides attached to MSG.     

Physiopathology of pneumoperitoneum

INTRODUCTION: Laparoscopic surgery contributes to many clinical advantages, but pneumoperitoneum in human body has new physiopathological consequences. MATERIALS AND METHODS: The aim of this study was to review recent literature about the effects of pneumoperitoneum. Cardiovascular, pulmonary and liver functions were examinated after pneumoperitoneum. RESULTS: There is a correlation between the increase in intra-abdominal pressure and properties of gas chosen (CO2 vs helium). There is a correlation between serum level modifications of liver functionality in postoperative laparoscopic surgery. CONCLUSIONS: Laparoscopic surgery has contributed to many clinical advantages (postoperative pain reduction, swift resumption, etc.), but pneumoperitoneum modifies physiological function. The aim of our next work will be the assessment of postoperative liver function, without clinical symptoms.     

A procedure to obtain average daily values of meteorological parameters from monthly averages

In this article, we suggest a new smoothing procedure that allows to reach two different goals: (1) obtaining a smooth trend during the year from meteorological parameters measured day by day in a number of years not large enough to obtain a regular average pattern and (2) obtaining expected daily values from the corresponding long-term monthly averages. In both cases the obtained daily sequence preserves the monthly averages.     

Polysplenia. Description of a case

A clinical and hemodynamic study of a case of polysplenia, with typical left bilateral symmetry, anomalies of systemic venous drainage and defect of the endocardial cushions. A brief revision of the literature is given and the embriological and clinical concept of the left bilateral symmetry is discussed.     

A biased‐randomized iterated local search for the distributed assembly permutation flow‐shop problem

Modern production systems require multiple manufacturing centers—usually distributed among different locations—where the outcomes of each center need to be assembled to generate the final product. This paper discusses the distributed assembly permutation flow‐shop scheduling problem, which consists of two stages: the first stage is composed of several production factories, each of them with a flow‐shop configuration; in the second stage, the outcomes of each flow‐shop are assembled into a final product. The goal here is to minimize the makespan of the entire manufacturing process. With this objective in mind, we present an efficient and parameter‐less algorithm that makes use of a biased‐randomized iterated local search metaheuristic. The efficiency of the proposed method is evaluated through the analysis of an extensive set of computational experiments. The results show that our algorithm offers excellent performance when compared with other state‐of‐the‐art approaches, obtaining several new best solutions.     

Serine Hydroxymethyltransferase from the Cold Adapted Microorganism Psychromonas ingrahamii: A Low Temperature Active Enzyme with Broad Substrate Specificity

Serine hydroxymethyltransferase from the psychrophilic microorganism Psychromonas ingrahamii was expressed in Escherichia coli and purified as a His-tag fusion protein. The enzyme was characterized with respect to its spectroscopic, catalytic, and thermodynamic properties. The properties of the psychrophilic enzyme have been contrasted with the characteristics of the homologous counterpart from E. coli, which has been structurally and functionally characterized in depth and with which it shares 75% sequence identity. Spectroscopic measures confirmed that the psychrophilic enzyme displays structural properties almost identical to those of the mesophilic counterpart. At variance, the P. ingrahamii enzyme showed decreased thermostability and high specific activity at low temperature, both of which are typical features of cold adapted enzymes. Furthermore, it was a more efficient biocatalyst compared to E. coli serine hydroxymethyltransferase (SHMT) particularly for side reactions. Many β-hydroxy-α-amino acids are SHMT substrates and represent important compounds in the synthesis of pharmaceuticals, agrochemicals and food additives. Thanks to these attractive properties, this enzyme could have a significant potential for biotechnological applications.     

Thyroid Hormones and Antioxidant Systems: Focus on Oxidative Stress in Cardiovascular and Pulmonary Diseases

In previous works we demonstrated an inverse correlation between plasma Coenzyme Q₁₀ (CoQ₁₀) and thyroid hormones; in fact, CoQ₁₀ levels in hyperthyroid patients were found among the lowest detected in human diseases. On the contrary, CoQ₁₀ is elevated in hypothyroid subjects, also in subclinical conditions, suggesting the usefulness of this index in assessing metabolic status in thyroid disorders. A Low-T3 syndrome is a condition observed in several chronic diseases: it is considered an adaptation mechanism, where there is a reduction in pro-hormone T4 conversion. Low T3-Syndrome is not usually considered to be corrected with replacement therapy. We review the role of thyroid hormones in regulation of antioxidant systems, also presenting data on total antioxidant capacity and Coenzyme Q₁₀. Published studies suggest that oxidative stress could be involved in the clinical course of different heart diseases; our data could support the rationale of replacement therapy in low-T3 conditions.