Nonlinearity arising from noncooperative transcription factor binding enhances negative feedback and promotes genetic oscillations

We study the effects of multiple binding sites in the promoter of a genetic oscillator. We evaluate the regulatory function of a promoter with multiple binding sites in the absence of cooperative binding, and consider different hypotheses for how the number of bound repressors affects transcription rate. Effective Hill exponents of the resulting regulatory functions reveal an increase in the nonlinearity of the feedback with the number of binding sites. We identify optimal configurations that maximize the nonlinearity of the feedback. We use a generic model of a biochemical oscillator to show that this increased nonlinearity is reflected in enhanced oscillations, with larger amplitudes over wider oscillatory ranges. Although the study is motivated by genetic oscillations in the zebrafish segmentation clock, our findings may reveal a general principle for gene regulation.Comment: 11 pages, 8 figure

Undeclared animal species in dry and wet novel and hydrolyzed protein diets for dogs and cats detected by microarray analysis

Abstract Background Although the European Pet Food Industry Federation (FEDIAF) stated that labels must be accurate and provide detailed information on the ingredients, mislabeling of pet food has been documented by several authors. This phenomenon is of particular concern when related to products used as elimination diets for the diagnosis of adverse food reaction (AFR) in dogs and cats because the presence of undeclared ingredients may negatively interfere with the trial and prevent the veterinarian from making an appropriate diagnosis. The aim of this study was to shed light upon the problem of contamination and mislabeling in both dry and wet novel protein diets (NPDs) and hydrolyzed protein diets (HPDs) using a microarray-based commercial kit which tests for the presence of 19 animal species. Results Of the 40 analyzed products (9 dry NPDs, 22 wet NPDs, 6 dry HPDs and 3 wet HPDs), ten presented a content that correctly matched the label, while five did not contain the declared animal species, twenty-three revealed the presence of undeclared animal species, and two had a vague label that did not allow the evaluation of its accuracy. The most frequently contaminants identified in both dry and wet pet foods were pork, chicken and turkey. The presence of undeclared animal species was higher in dry than wet pet foods; furthermore, a lower number of contaminating animal species was identified in HPDs than NPDs (4 vs 10), and a lower number of contaminated HPDs (6 out of 9, 67%) than contaminated NPDs was detected (24 out of 31, 77%). Thirteen out of 14 brands tested presented at least one mislabeled product. Conclusions Mislabeling seems to be a widespread issue in pet foods used as elimination diets. Contamination can occur in all types of products used for the purpose, although dry NPDs are the main issue. Due to the high risk of contamination, particular attention should be given to both the selection of raw material suppliers and the production process

C-reactive protein level predicts mortality in COPD: a systematic review and meta-analysis

The prognostic role of baseline C-reactive protein (CRP) in chronic obstructive pulmonary disease (COPD) is controversial. In order to clarify this issue, we performed a systematic review and meta-analysis to assess the predictive effect of baseline CRP level in COPD patients. 15 eligible articles focusing on late mortality in COPD were included in our study. We performed a random-effects meta-analysis, and assessed heterogeneity and publication bias. We pooled hazard ratio (HR) estimates and their 95% confidence intervals on mortality for the comparison between the study-specific highest category of CRP levelversusthe lowest category. In overall analysis, elevated baseline CRP levels were significantly associated with higher mortality (HR 1.53, 95% CI 1.32–1.77,I2=68.7%, p<0.001). Similar results were observed across subgroups. However, higher mortality risk was reported in studies using a cut-off value of 3 mg·L−1(HR 1.61, 95% CI 1.12–2.30) and in those enrolling an Asiatic population (HR 3.51, 95% CI 1.69–7.31). Our analysis indicates that baseline high CRP level is significantly associated with higher late mortality in patients with COPD. Further prospective controlled studies are needed to confirm these data

Validation of an Eco-Friendly Automated Method for the Determination of Glucose and Fructose in Wines

Fermentable sugar dosage helps oenologists to establish a harvest’s moment and control the fermentation process of the musts. The official analyses recommended for their determination are long, laborious, and must be carried out by specialized personnel. On the contrary, instrumental analysis automation limits human errors, increases precision, and reduces the time and cost of the analyses. In the food production sector, to use methods other than those recommended by supranational bodies in official reports, it is necessary to validate the analytical processes to establish the conformity of the results between the new methods and the reference ones. This work validated an automated enzymatic apparatus to determine the sum of glucose and fructose levels in wine samples. The validation was carried out on wine samples (dry red wine, dry white wine, moderately sweet wine, and sweet wine) containing different sugar concentrations by comparing data obtained using the OIV-MA-AS311-02 method performed by a specialized operator (reference method) and the same method performed by an automated apparatus. The difference between the results’ means obtained with the two procedures was significant. Nevertheless, the automated procedure was considered suitable for the intended use since the differences between the averages were lower than the measurement uncertainty at the same concentration, and the repeatability results were better for the automated procedure than the reference method

The Second Edition of the Integrative Levels Classification: Evolution of a KOS

AbstractPurposeThis paper informs about the publication of the second edition of the Integrative Levels Classification (ILC2), a freely-faceted knowledge organization system (KOS), and reviews the main changes that have been introduced as compared to its first edition (ILC1).Design/methodology/approachThe most relevant changes are illustrated, with special reference to those of interest to general classification theory, by means of examples of notation for individual classes and combinations of them.FindingsChanges introduced in ILC2 include: the names and order of some main classes; the development of subclasses for various phenomena, especially quantities and algebraic structures; the order of facet categories and the new category of Disorder; notation for special facets; distinction of the semantical function of facets (attributes) from their syntactic function. The system can be freely accessed online through a PHP browser as well as in SKOS format.Research limitationsOnly a selection of changed classes is discussed for space reasons.Practical implicationsILC1 has been previously applied to the BARTOC directory of KOSs. Update of BARTOC data to ILC2 and application of ILC2 to further information systems are envisaged. Possible methods for reclassifying BARTOC with ILC2 are discussed.OriginalityILC is a newly developed classification system, based on phenomena instead of traditional disciplines and featuring various innovative devices. This paper is an original account of its most recent evolution

High CTLA-4 expression correlates with poor prognosis in thymoma patients

Thymomas, tumors that arise from epithelial cells of the thymus gland, are the most common neoplasms of the anterior mediastinum, with an incidence rate of approximately 2.5 per million/year. Cytotoxic T Lymphocyte Antigen 4 (CTLA-4 or CD152) exerts inhibitory activity on T cells, and since its oncogenic role in the progression of different types of tumors, it has emerged as a potential therapeutic target in cancer patients. In this study, we assessed the expression of CTLA-4 both at mRNA and protein levels in paraffin embedded-tissues from patients with thymomas. Furthermore, we evaluated the relationship between CTLA-4 expression and the clinical-pathologic characteristics and prognosis in patients with thymomas. Sixty-eight patients with median age corresponding to 62 years were included in this analysis. Thymomas were classified accordingly to the WHO and Masaoka-Koga for histochemical analysis and for prognostic significance. A statistical difference was found between CTLA-4 mRNA levels in human normal thymus compared with thymoma specimens. CTLA-4 expression was statistically found to progressively increase in A, B1, B2, AB and it was maximal in B3 thymomas. According to Masaoka-Koga pathological classification, CTLA-4 expression was lower in I, IIA and IIB, and higher in invasive III and IV stages. By confocal microscopy analysis we identified the expression of CTLA-4 both in tumor cells and in CD45+ tumor-infiltrating leukocytes, mainly in B3 and AB thymomas. Finally, CTLA-4 overexpression significantly correlates with reduced overall survival in thymoma patients and in atypical thymoma subgroup, suggesting that it represents a negative prognostic factor

Role of the Metal Center in the Modulation of the Aggregation Process of Amyloid Model Systems by Square Planar Complexes Bearing 2-(2'-pyridyl)benzimidazole Ligands

The effect of analogue Pd(II)-, Pt(II)-, and Au(III) compounds featuring 2-(2'-pyridyl)benzimidazole on the aggregation propensity of amyloid-like peptides derived from Aβ and from the C-terminal domain of nucleophosmin 1 was investigated. Kinetic profiles of aggregation were evaluated using thioflavin binding assays, whereas the interactions of the compounds with the peptides were studied by UV-Vis absorption spectroscopy and electrospray ionization mass spectrometry. The results indicate that the compounds modulate the aggregation of the investigated peptides using different mechanisms, suggesting that the reactivity of the metal center and the physicochemical properties of the metals (rather than those of the ligands and the geometry of the metal compounds) play a crucial role in determining the anti-aggregation properties

Obesity and common pathways of cancer and cardiovascular disease

Abstract Obesity is constantly increasing worldwide due to the progressive globalization of sedentary lifestyle and diet rich in lipids and processed food. Cardiovascular complications and cancer are the two most fearsome long-term sequelae of obesity that justify the recent definition of this threaten as 'obesity epidemic'. Shared biological pathways can be recognized for obesity-induced cardiovascular and oncological complications that might prompt targeted interventions with potentially double beneficial effect. The present review aims at summarizing main common biological pathways linking obesity with cardiovascular diseases and cancer in order to provide a research framework within which therapeutic strategies might have at the same time cardiovascular-protective and cancer-preventive effects