PABS: An online platform to assist BAC-by-BAC sequencing projects

Genome sequencing projects are either based on whole genome shotgun (WGS) or on a BAC-by-BAC strategy. Although WGS is in most cases the preferred choice, sometimes the BAC-by-BAC approach may be better because it requires a much simpler assembly process. Furthermore, when the study is limited to specific regions of the genome, the WGS would require an unjustified effort, making the BAC-by-BAC the only feasible strategy. In this paper we describe an informatics pipeline called PABS (Platform Assisted BAC-by-BAC Sequencing) that we developed to provide a tool to optimize the BAC-by-BAC sequencing strategy. PABS has two main functions: (i) PABS-Select, to choose suitable overlapping clones; and (ii) PABS-Validate, to verify whether a BAC under analysis is actually overlapping the neighboring BAC

Turismo em tempos de COVID-19: ensaios sobre casos na Argentina, Brasil, Moçambique e Portugal

É de notoriedade global que o turismo tem sido um dos setores mais afetados pela pandemia da Covid-19. Não sem menos, os danos causados possuem nuances em todas as dimensões: econômicas, políticas, sociais e geográficas, as quais, pela força do impacto, merecem ser desveladas. Em tempos de negação à ciência e obscurantismos diversos, iluminar as distintas e contraditórias formas pelas quais a pandemia afeta o turismo no Brasil e outras partes do mundo, considerando a imbricada relação entre diferentes escalas geográficas, é certamente a mais importante contribuição que esse grupo de pesquisadores e estudantes de graduação e pós-graduação de universidades e outras instituições públicas têm a compartilhar com a sociedade em geral.info:eu-repo/semantics/publishedVersio

Association of kidney disease measures with risk of renal function worsening in patients with type 1 diabetes

Background: Albuminuria has been classically considered a marker of kidney damage progression in diabetic patients and it is routinely assessed to monitor kidney function. However, the role of a mild GFR reduction on the development of stage 653 CKD has been less explored in type 1 diabetes mellitus (T1DM) patients. Aim of the present study was to evaluate the prognostic role of kidney disease measures, namely albuminuria and reduced GFR, on the development of stage 653 CKD in a large cohort of patients affected by T1DM. Methods: A total of 4284 patients affected by T1DM followed-up at 76 diabetes centers participating to the Italian Association of Clinical Diabetologists (Associazione Medici Diabetologi, AMD) initiative constitutes the study population. Urinary albumin excretion (ACR) and estimated GFR (eGFR) were retrieved and analyzed. The incidence of stage 653 CKD (eGFR < 60 mL/min/1.73 m2) or eGFR reduction > 30% from baseline was evaluated. Results: The mean estimated GFR was 98 \ub1 17 mL/min/1.73m2 and the proportion of patients with albuminuria was 15.3% (n = 654) at baseline. About 8% (n = 337) of patients developed one of the two renal endpoints during the 4-year follow-up period. Age, albuminuria (micro or macro) and baseline eGFR < 90 ml/min/m2 were independent risk factors for stage 653 CKD and renal function worsening. When compared to patients with eGFR > 90 ml/min/1.73m2 and normoalbuminuria, those with albuminuria at baseline had a 1.69 greater risk of reaching stage 3 CKD, while patients with mild eGFR reduction (i.e. eGFR between 90 and 60 mL/min/1.73 m2) show a 3.81 greater risk that rose to 8.24 for those patients with albuminuria and mild eGFR reduction at baseline. Conclusions: Albuminuria and eGFR reduction represent independent risk factors for incident stage 653 CKD in T1DM patients. The simultaneous occurrence of reduced eGFR and albuminuria have a synergistic effect on renal function worsening

Per una ricostruzione teorico-generale del concetto di abuso del diritto

This work examines the notion of abuse of rights. It is a choice solicited by the ascertainment of its vitality and of the increasing interest shown towards it by the elaborations of the doctrine as well as by jurisprudential applications. It is, moreover, a notion arisen from the doctrine and the jurisprudence. Only some legal systems, not our own, have absorbed it as a prescriptive rule, and there is no doubt that this circumstance represents a peculiar matter of interest. The perspective of investigation chosen, and considered most helpful for the purpose of understanding the abuse of rights, certainly involves dedicating space to the elaboration of the doctrine and to the jurisprudential cases that have made use of this instrument. Nonetheless, this does not mean to engage once more again (several have been the monographs dedicated to the abuse of rights by now) in an as most complete reconstruction as possible of its systematic traits and of its conditions of use. This work rather wants to be a reflection on the general theory of law. As a matter of fact, the notion of abuse of rights calls the attention of the expert to numerous and structural issues, which question the instruments that in the positivist and formalist vision of the regulations of inter-subjective relations still predominant today, constitute its protagonists (the rules, and the subjective rights meant as expressions of the same rules); the role of the interpreter and the jurist; finally, it questions in a particularly perceptive way about the function and the methods of the theoretical understanding of juridical phenomena and of the role of juridical science. It appears possible to reasonably assert that the notion of abuse of rights - beyond its practical function and its concrete application to many situations that emerge in the progress of relations and do not find any other adequate solutions - is especially relevant in this last perspective, that is to say in pointing out the function that the juridical science fulfils and must fulfil in interpreting, understanding and directing the solution of questions that involve the ratio and the structure itself of the juridical system. More explicitly, the thesis that this work means to prove is that the category of abuse of rights, which arises and then exists as an operative instrument of the interpreter and the jurist in order to satisfy well determined needs of the juridical system (and historically, in reaction to well determined conceptions of the juridical system), may be usefully, and perhaps especially considered and investigated as an instrument of the juridical science, that is as a "juridical concept" by means of which the jurist approaches the understanding, the interpretation and theorisation of the juridical experience. To this end the structure of this work has been arranged in three parts. The first part intends to define the boundaries and the structural significance of the notion of abuse of rights. This implies, first of all, that the conceptual categories that contribute to reconstruct the notion are to be accounted for: the category of subjective rights (in that the notion of abuse of rights originates in reaction to its strictly individualist foundation, and a control of the exercise of rights is proposed) and that of offence. Traditionally, the abuse of rights is considered as a tertium genus between the prospect of acting in accordance with a right and acting unlawfully. The abuse of rights as a concept defines itself necessarily in relationship with these other two concepts. On the other hand the thorough understanding of the conceptual autonomy of the abuse of rights demands to account for some instruments - of a former origin, that is widely elaborated and used in other legal systems - which share the same ratio of the prohibition of abuse and with it contribute to the identification and sanction of unlawful occurrences. These are the notions of exceptio doli generalis, the prohibition of venire contra factum proprium and the institution of the Verwirkung. The second part of the work directly deals with the questions relating to abuse through the investigation of the standpoints of the doctrine and the jurisprudence. Ample space is dedicated to the analysis of the most representative elaborations of the doctrine, both Italian and French. This survey leads to the identification of a significant line of development that starting from the first standpoints that deal with abuse as an issue of exclusively moral or ideological nature, rather evolves in the direction of an increasing awareness of the conceptual autonomy and of the utter juridical essence of the notion of abuse. Likewise significant appears to be the examination of jurisprudential verdicts, whilst the awareness of the conceptual and systematic significance of the notion of abuse undoubtedly proves to be inferior. Nonetheless, the reference to it is more and more frequent and reveals to be an instrument necessary to highlight crucial requirements of the system of inter-subjective relations. The last part is concerned with explaining precisely these conclusions suggested and justified by the analysis of the discipline and the jurisprudence. Moreover, in the light of the starting thesis, according to which the abuse of rights may be considered as a juridical concept and thus the lines of its development may represent the path of formation of a juridical concept, this last part also wants to account for the acquisitions of the philosophy of law and of the general theory of law on the theme of juridical concepts. Thus the standpoints of the famous controversy of the years 1935-1945, which had as its protagonists particularly Pugliatti, Jemolo, Cesarini Sforza and Calogero, are dealt with as well as the standpoints elaborated with regard to juridical concepts pertaining to the analytical philosophy, in a particular way in Scarpelli's and Pintore's works. Besides, the examination of these authors' beliefs leads to the ascertainment of the inadequacy of the reading keys that they propose in order to understand what a juridical concept is, how it is born and what power of understanding it grants. In the yet big differences of presuppositions and attitude that characterize these authors, however, they do not actually diverge form the epistemological horizon that asserts the conventional and operative nature of concepts and their inevitable dependence on the positive datum. Therefore, the answer to the hypothesis that the examined question of abuse lets perceive still remains open: that of a concept which delineates itself as such not from a prescriptive provision but from a real, substantial need of "ordering" of inter-subjective relations that is progressively received, elaborated, "systematised" by the work of the doctrine and the jurisprudence

Tomato (Solanum lycopersicum) genome: sequencing and analysis of chromosome 12

The Solanaceae family includes a number of closely related plant species with diverse phenotypes that have been exploited for agronomic, pharmaceutical and ornamental purposes. In 2003 'The International Solanaceae Genome Project' (SOL) launched the initiative to sequence the 220 Mb of euchromatin of the tomato (Solanum lycopersicum) genome as the central part of a wider project aiming to increase our knowledge about diversity and adaptation in crop species (http://www.sgn.cornell.edu/solanaceae-project/). The sequencing proceeds on a BAC-by-BAC basis with the 12 chromosomes divided over several genomic laboratories of ten different countries. As a member of the project, the Italian research team is involved in the sequencing of the euchromatin portions of chromosome 12. During my PhD project, I had the opportunity to face this challenging project from different points of view including molecular, cytogenetic and bioinformatic analysis. A large part of my effort was focused in setting up a sequencing pipeline and starting the construction of a minimal subset of BAC clones covering the chromosome 12 euchromatin with minimal overlaps. The progress can be viewed through the development of the TPF and AGP files, available from the SGN repository (http://www.sgn.cornell.edu/). A key step for the success of the sequencing project is the identification of a reliable minimal tiling path of neighbouring BAC clones. To improve this process, I contributed to the development of a informatics pipeline called PABS (Platform Assisted BAC-by-BAC Sequencing), freely available to the community at our web site (http://tomato.cribi.unipd.it/files/bioinformatics.html) (Todesco S. et al., 2008). PABS has been specifically designed to minimize the negative impact of genomic repeats, considering that a repeat element can connect non-contiguous regions of the genome, leading to misalignment of BACs and possible "jumps" along the genome. PABS has two main functions: 1) PABS-Select, to choose suitable overlapping clones for the sequencing walk; 2) PABS-Validate to verify whether a BAC under analysis is actually overlapping the preceding BAC. A BAC-based physical map is a fundamental tool to further assist the sequencing work but also to connect the minimal tiling path of BACs. In my study, I improved the molecular combing technique (Lebofsky R. et al., 2003; Monier K et al., 2001; Allemand JF et al., 1997) for producing multicolour FISH on stretched genomic DNA molecules. This technique allows accurate mapping of BAC clones and precise measurement of physical distances between contigs with a spatial resolution of 1 to 5 kb. Finally, to explore the data generated by the BAC-by-BAC sequencing I contributed to a preliminary annotation of the tomato BACs sequences. As a result of this analysis, we outlined some features of the gene organization in the tomato genome

eDNA Metabarcoding Analysis as Tool to Assess the Presence of Non-Indigenous Species (NIS): A Case Study in the Bilge Water

One of the most important causes of biodiversity loss are non-indigenous species (NIS), in particular invasive ones. The dispersion of NIS mainly depends on anthropogenic activities such as maritime traffic, which account for almost half of the total NIS introduction in the European seas, as reported by the European Environmental Agency. For this reason, NIS management measures are mainly focused on commercial ports (i.e., ballast water management and Marine Strategy Framework Directive monitoring), underestimating the role of marinas and tourist harbors; these host small vessels (Salmo salar). Excluding food contamination species, twelve of these found in the bilge waters were already known as NIS in the Mediterranean Sea, belonging to algae, mollusks, crustaceans, annelids, echinoderms, and fishes. Nine of these species are new to Italian waters. The results obtained in the present work support the importance of NIS monitoring in marinas and small harbors, particularly in the bilge waters, through eDNA metabarcoding, having detected several potential NIS that otherwise would not have been discovered

NAMPT in drug-resistant melanoma: linking NAMPT-dependent metabolic reprogramming and immune regulation

Introduction Targeted-therapy and immune checkpoint inhibitors (ICIs) have notably improved the treatment of BRAF-mutated metastatic melanoma (MM) patients; however resistance to treatment dramatically impacts on the survival of patients. BRAF(i)nhibitors-resistant MM cells showed increased amounts of NAD, an essential redox cofactor, supporting their metabolic adaptations underlying the acquisition of drug resistance. This was obtained selectively overexpressing the rate-limiting NAD-biosynthetic enzyme nicotinamide phosphoribosyltransferase (NAMPT). NAMPT-NAD axis becomes a driver of melanoma progression and resistance to BRAFi, that it may be therapeutically targeted. Material and Method NAMPT-NAD axis was studied using biochemical, enzymatic, immunohistochemical assays. Immunoprecipitation of NAMPT following mass spectrometry (MS) analysis was used to define NAMPT interactome. In silico analysis using TCGA database, western blot analysis and RT-PCR were used to detect and confirm protein expression and signaling pathways activation. Results and discussion The BRAF oncogenic signaling and NAMPT expression are molecularly linked. We found that mutations in the BRAF oncogene positively correlate with NAMPT expression in TCGA melanoma cohort and in tissue from MM patients. The over-expression of NAMPT correlates with its gene amplification. Analyzing the nature of this genetic amplification we found a co-amplification of others genes including PIK3CG that we started to evaluate functionally. A second set of preliminary data revealed a significant increase in the nuclear localization of NAMPT in resistant cells, also as NAMPT nuclear fraction chromatin-bound. We performed NAMPT immunoprecipitation following MS in cellular extract to identify NAMPT-interacting proteins. Data showed enrichment of NAMPT-interacting nuclear proteins and proteins involved in RNA processing, translation, metabolic processes, cellular response to stress and immune response among others. Starting to analyze NAMPT-immune gene signature relationship we found in TCGA melanoma cohort a positive correlation between NAMPT expression and interferon signaling, including CD274, IRF1, STAT1 genes that will be further investigated. Conclusion The multiple roles of NAMPT as intracellular and soluble protein are known; here we speculate that NAMPT could have an essential and unknown function in the nucleus and in regulating immune responses, with a possible impact on ICIs activities

Histology of pediatric classic Hodgkin lymphoma: From diagnosis to prognostic stratification

Aims Classic Hodgkin lymphoma (cHL) is a common malignancy of the pediatric age. Although clinical-radiological features are routinely used for disease risk stratification, the role of tumor histology has yet to be defined. This study aimed to characterize the clinical-pathological features of a large cohort of pediatric cHL specifically investigating the relevance of tumor histology for the prognostic stratification of patients.Methods and results The study considered 96 clinically annotated cases of pediatric cHL treated according to the AIEOP-LH2004 protocol. The following histological parameters were considered: (i) cHL variant; (ii) grade of nodular sclerosis (NS); (iii) staining for Bcl2 and p53, and expression of B-cell (BCA) and T-cell antigens (TCA) by Hodgkin/Reed-Sternberg cells. The study population consisted of 51 males and 45 females (median age: 13.6 years) with five-year overall and progression-free survival of 94% and 81%, respectively. Most cases featured NS morphology (96%) with a prevalence of NS1 over NS2 grades. Two NS2 variants were recognized (sarcomatous/syncytial and fibrohistiocytic). A consistent subset of cases disclosed positivity for BCA (34%), TCA (26%), p53 (13%), and Bcl2 (19%). Clinical-pathological correlations showed a more aggressive clinical course for NS2 over NS1 cases. The NS2 fibrohistiocytic variant was associated with the worst outcome. No other histological features correlated with prognosis.Conclusions Pediatric cHL is a clinically and histologically heterogeneous neoplasm. The majority of cases disclose NS morphology and aberrant phenotypes are frequently encountered. In the pediatric population, NS grading and NS2 subtyping bear significant prognostic impact