Genome conformation and transcription regulation: methods and applications

The 3D organization of chromatin within the nucleus is crucial for genome functionality. This is true at multiple levels of resolution: on a large scale, with chromosomes occupying distinct volumes (chromosome territories), at the level of individual chromatin fibers, organized in compartmentalized domains (as the Topologically Associating Domains, TADs), and down to the formation of short range chromatin interactions (as enhancer-promoter loops). The widespread adoption of high-throughput techniques derived from Chromosome Conformation Capture (3C) has been instrumental in advancing the knowledge of chromatin nuclear organization. In particular, Hi-C has the potential to achieve the most comprehensive characterization of chromatin 3D interactions, as in principle it can detect any pair of restriction fragments connected as a result of ligation by proximity. The analysis of the enormous amount of genomic data produced by Hi-C required the development of ad hoc algorithms and computational procedures. Despite the increasing number of available bioinformatics pipelines, no consensus on the optimal approach to analyze Hi-C data has been reached yet. Therefore, we quantitatively compared several Hi-C data analysis methods for the identification of multi-scale chromatin structures to highlight strengths and weaknesses of the various methods and propose application guidelines and good practices. Specifically, we compared different computational approaches (6 for the characterization of chromatin loops and 7 to identify TADs) using publicly available Hi-C datasets, comprising data from different species and cell lines, Hi-C protocol variations and data resolution. Additionally, the algorithms were tested on simulated Hi-C data to assess sensitivity and precision of each method. The tools differed in terms of implemented analysis steps and strategies adopted for alignment, filtering, normalization, and feature identification (global or local looping interactions calling and single-scale or multi-scale TAD discovery). Results of this comparison indicate that performances of the methods considerably vary, both in quantitative and qualitative terms, and that the tools need extensive optimization of the parameters in order to work properly. Despite, in general, TAD callers resulted riper than algorithms to call interactions, still most of them are characterized by crucial limitations, as for instance the inability to investigate how the 3D organization of chromatin structures evolves over time (as e.g., during differentiation). Although the molecular mechanisms underlying TADs formation are still debated, it is evident that distinct interaction patterns can be observed within individual TADs. In particular, some domains appear to have a very compact structure, while others have a less uniform or weaker interaction frequency within the domain, while showing a strong interaction between the borders. To address these limitations, I developed TAD-AH (TADs Advanced Hierarchy), a four-step sequential procedure coded in R, for the characterization of both static and dynamically changing chromatin domains. As a case study, I analyzed Hi-C data generated prior and post human fibroblasts (IMR90) trans-differentiation into skeletal muscle cells (myoblasts, and, when put in differentiation media, myotubes) by overexpression of muscle stem cells master regulator MyoD. I integrated Hi-C with epigenomic and transcriptomic data from the same conditions and confirmed that the identified genomic features are consistent with the biological scenario under scrutiny

Parental and Child Time Investments and the Cognitive Development of Adolescents

While a large literature has focused on the impact of parental investments on child cognitive development, very little is known about the role of the child’s own investments alongside that of the parents. By using the Child Development Supplement of the Panel Study of Income Dynamics, we model the cognitive production function for adolescents using an augmented value-added model and adopt an estimation method that takes account of unobserved child characteristics. We find that a child’s own investments made during adolescence matter more than the mother’s. Our empirical results appear to be robust to several sensitivity checks

Self investments of adolescents and their cognitive development

While a large literature has focused on the impact of parental investments on child cognitive development, very little is known about the role of child's own investments. Information on how children invest their time separately from parents is probably little informative for babies and toddlers, but it becomes more and more important in later stages of life, such as adolescence, when children start to take decisions independently. By using the Child Development Supplement of the PSID (Panel Study of Income Dynamics), we model the production of cognitive ability of adolescents and extend the set of inputs to include the child's own time investments. Looking at investments during adolescence, we find that child's investments matter more than mother's investments. On the contrary, looking at investments during childhood, it is the mother's investments that are more important. Our results are obtained accounting for potential unobserved child's and family's endowments and are robust across several specifications and samples, e.g. considering and not considering father's investments and non-intact families

Natural history of patients with non cirrhotic portal hypertension: Comparison with patients with compensated cirrhosis

Background. The knowledge of natural history of patients with portal hypertension (PH) not due to cirrhosis is less well known than that of cirrhotic patients. Aim. To describe the clinical presentation and the outcomes of 89 patients with non-cirrhotic PH (25 with non-cirrhotic portal hypertension, INCPH, and 64 with chronic portal vein thrombosis, PVT) in comparison with 77 patients with Child A cirrhosis. Methods. The patients were submitted to a standardized clinical, laboratory, ultrasonographic and endoscopic follow-up. Variceal progression, incidence of variceal bleeding, portal vein thrombosis, ascites and survival were recorded. Results. At presentation, the prevalence of varices, variceal bleeding and ascites was similar in the 3 groups. During follow-up, the rate of progression to varices at risk of bleeding (p<0.0001) and the incidence of first variceal bleeding (p=0.02) were significantly higher in non-cirrhotic then in cirrhotic patients. A PVT developed in 32% of INCPH patients and in 18% of cirrhotics (p=0.02). Conclusions. In the patients with non–cirrhotic PH variceal progression is more rapid and bleeding more frequent than in cirrhotics. Patients with INCPH are particularly prompt to develop PVT. This observational study suggests that the management of patients with non-cirrhotic PH should take into consideration the natural history of portal hypertension in these patients and cannot be simply derived by the observation of cirrhotic patients

Analysis of Multi-ingredient Food Supplements by Fingerprint HPTLC Approach

The increase of import/export of every kind of herbal products calls urgently for adequate controls. Analysis of herbal food supplement (botanicals) is a difficult task, like in the composition determination of a multi-ingredient product, where several botanical drugs were used. Actually, this is an important argument in consideration of health security. The authors reported the results of an analytical approach based on HPTLC (high performance thin layer chromatography) fingerprints comparison and tailored to determine the composition of marketed multi-ingredient botanicals. The method gave positive data in case of the presence of 3-5 species, whereas difficulties were recorded when the number of plants is increased

The Stat3-Fam3a axis promotes muscle stem cell myogenic lineage progression by inducing mitochondrial respiration.

Metabolic reprogramming is an active regulator of stem cell fate choices, and successful stem cell differentiation in different compartments requires the induction of oxidative phosphorylation. However, the mechanisms that promote mitochondrial respiration during stem cell differentiation are poorly understood. Here we demonstrate that Stat3 promotes muscle stem cell myogenic lineage progression by stimulating mitochondrial respiration in mice. We identify Fam3a, a cytokine-like protein, as a major Stat3 downstream effector in muscle stem cells. We demonstrate that Fam3a is required for muscle stem cell commitment and skeletal muscle development. We show that myogenic cells secrete Fam3a, and exposure of Stat3-ablated muscle stem cells to recombinant Fam3a in vitro and in vivo rescues their defects in mitochondrial respiration and myogenic commitment. Together, these findings indicate that Fam3a is a Stat3-regulated secreted factor that promotes muscle stem cell oxidative metabolism and differentiation, and suggests that Fam3a is a potential tool to modulate cell fate choices

Larvicidal and ovideterrent properties of neem oil and fractions against the filariasis vector Aedes albopictus (Diptera: Culicidae): a bioactivity survey across production sites

Neem seed oil (NSO) of Azadirachta indica (Meliaceae) contains more than 100 determined biologically active compounds, and many formulations deriving from them showed toxicity, antifeedancy and repellence against a number of arthropod pests. However, it is widely known that botanical products can differ in their chemical composition and bioactivity, as function of the production site and production process. We used high-performance thin layer chromatography (HPTLC) to investigate differences in chemical constituents of NSOs from three production sites. HPTLC analyses showed several differences in chemical abundance and diversity among NSOs, with special reference to limonoids. Furthermore, the three NSOs and their fractions of increasing polarities [i.e. ethyl acetate (EA) fraction and butanol (BU) fraction] were evaluated for larvicidal toxicity and field oviposition deterrence against the Asian tiger mosquito, Aedes albopictus, currently the most invasive mosquito worldwide. Results from bioactivity experiments showed good toxicity of NSOs and EA fractions against A. albopictus fourth instarlarvae (with LC50 values ranging from 142.28 to 209.73 ppm), while little toxicity was exerted by BU fractions. A significant effect of the production site and dosage was also found and is probably linked to differences in abundance of constituents among samples, as highlighted by HPTLC analyses. NSOs and EAs were also able to deter A. albopictus oviposition in the field (effective repellence values ranging from 98.55 to 70.10 %), while little effectiveness of BU fractions was found. Concerning ovideterrent activity, no difference due to the production site was found. This is the first report concerning larvicidal toxicity of NSO against A. albopictus and ovideterrence against Culicidae in the field. The chance to use chemicals fromthe NSO EA fraction seems promising, since they are effective at lower doses, if compared to synthetic products currently marketed, and could be an advantageous alternative to build newer and safer mosquito control tools

Phenotypical Characterization and Clinical Outcome of Canine Burkitt-Like Lymphoma

In dogs, Burkitt-like lymphoma (B-LL) is rare tumor and it is classified as a high-grade B-cell malignancy. The diagnosis is challenging because of the similar histologic appearance with other histotypes, no defined phenotypical criteria and poorly described clinical aspects. The aim of the study was to provide a detailed description of clinical and morphological features, as well as immunophenotypical profile of B-LL in comparison with the human counterpart. Thirteen dogs with histologically proven B-LL, for which a complete staging and follow-up were available, were retrospectively selected. Immunohistochemical expression of CD20, PAX5, CD3, CD10, BCL2, BCL6, MYC, and caspase-3 was evaluated. Histologically, all B-LLs showed a diffuse architecture with medium to large-sized cells, high mitotic rate and diffuse starry sky appearance. B-phenotype of neoplastic cells was confirmed both by flow-cytometry and immunohistochemistry. Conversely, B-LLs were negative for BCL2 and MYC, whereas some cases co-expressed BCL6 and CD10, suggesting a germinal center B-cell origin. Disease stage was advanced in the majority of cases. All dogs received CHOP-based chemotherapy with or without immunotherapy. Despite treatment, prognosis was poor, with a median time to progression and survival of 130 and 228 days, respectively. Nevertheless, ~30% of dogs survived more than 1 year. An increased apoptotic index, a high turnover index and caspase-3 index correlated with shorter survival. In conclusion, canine B-LL shows phenotypical differences with the human counterpart along with features that might help to differentiate this entity from diffuse large B-cell lymphoma

Pedicularis L. Genus. Systematics, botany, phytochemistry, chemotaxonomy, ethnopharmacology, and other

In this review, the relevance of the plant species belonging to the Pedicularis L. genus has been considered from different points of view. Particular emphasis was given to phytochemistry and ethnopharmacology, since several classes of natural compounds have been reported within this genus and many of its species are well known to be employed in the traditional medicines of many Asian countries. Some important conclusions on the chemotaxonomic and chemosystematic aspects of the genus have also been provided for the first time. Actually, this work represents the first total comprehensive review on this genus