Functional Inactivation of Orthologs Causes Genomic Instability and Oxidative Stress in a Fly Model of MODY-2.

Maturity-onset diabetes of the young (MODY) type 2 is caused by heterozygous inactivating mutations in the gene encoding glucokinase (GCK), a pivotal enzyme for glucose homeostasis. In the pancreas GCK regulates insulin secretion, while in the liver it promotes glucose utilization and storage. We showed that silencing the orthologs and results in a MODY-2-like hyperglycemia.

Somatic Deletion in Exon 10 of Aryl Hydrocarbon Receptor Gene in Human GH-Secreting Pituitary Tumors.

Objective/purpose: The aryl hydrocarbon receptor (AHR) pathway plays a critical role in the biology of Growth Hormone (GH)-secreting pituitary tumor (somatotropinoma). Germline rs2066853 variant was found to be more frequent among acromegaly patients and associated with a more severe disease with larger invasive somatropinoma, and with resistance to somatostatin analogs treatment in patients living in polluted areas. However, no somatic changes in gene have been reported so far in acromegaly patients.

Signaling through estrogen receptors modulates long non-coding RNAs in prostate cancer.

Prostate cancer (PCa) is a sex-steroid hormone-dependent cancer in which estrogens play a critical role in both initiation and progression. Recently, several long non-coding RNAs (lncRNAs) have been associated with PCa and are supposedly playing a pivotal role in the biology and progression of this type of cancer. In this review, we focused on some lncRNAs that are known for their androgen and estrogen transcriptional responsiveness in PCa.

Fading of remote synchronization in tree networks of Stuart-Landau oscillators.

Remote synchronization (RS) is characterized by the appearance of phase coherence between oscillators that do not directly interact through a structural link in a network but exclusively through other units that are not synchronized or more weakly synchronized with them. This form of phase synchronization was observed initially in starlike motifs and later in random networks. In this paper, we report on an experimental setup for the analysis of RS in networks of Stuart-Landau oscillators and in particular investigate the behavior of tree structures focusing on the path to synchronization, that is, on the analysis of how synchronization emerges as the coupling strength increases from zero.

Interplay Between Long Noncoding RNAs and MicroRNAs in Cancer.

In the last decade noncoding RNAs (ncRNAs) have been extensively studied in several biological processes and human diseases including cancer. microRNAs (miRNAs) are the best-known class of ncRNAs. miRNAs are small ncRNAs of around 20-22 nucleotides (nt) and are crucial posttranscriptional regulators of protein coding genes.

CamurWeb: a classification software and a large knowledge base for gene expression data of cancer.

Background: The high growth of Next Generation Sequencing data currently demands new knowledge extraction methods. In particular, the RNA sequencing gene expression experimental technique stands out for case-control studies on cancer, which can be addressed with supervised machine learning techniques able to extract human interpretable models composed of genes, and their relation to the investigated disease. State of the art rule-based classifiers are designed to extract a single classification model, possibly composed of few relevant genes.

A feature-based integrated scoring scheme for cell cycle-regulated genes prioritization.

Prioritization of cell cycle-regulated genes from expression time-profiles is still an open problem. The point at issue is the surprisingly poor overlap among ranked lists obtained from different experimental protocols. Instead of developing a general-purpose computational methodology for detecting periodic signals, we focus on the budding yeast mitotic cell cycle.

Combining EEG signal processing with supervised methods for Alzheimer's patients classification.

Background: Alzheimer's Disease (AD) is a neurodegenaritive disorder characterized by a progressive dementia, for which actually no cure is known. An early detection of patients affected by AD can be obtained by analyzing their electroencephalography (EEG) signals, which show a reduction of the complexity, a perturbation of the synchrony, and a slowing down of the rhythms.

Methods: In this work, we apply a procedure that exploits feature extraction and classification techniques to EEG signals, whose aim is to distinguish patient affected by AD from the ones affected by Mild Cognitive Impairment (MCI) and healthy control (HC) samples.

TCGA2BED: extracting, extending, integrating, and querying The Cancer Genome Atlas.

Background: Data extraction and integration methods are becoming essential to effectively access and take advantage of the huge amounts of heterogeneous genomics and clinical data increasingly available. In this work, we focus on The Cancer Genome Atlas, a comprehensive archive of tumoral data containing the results of high-throughout experiments, mainly Next Generation Sequencing, for more than 30 cancer types.

Results: We propose TCGA2BED a software tool to search and retrieve TCGA data, and convert them in the structured BED format for their seamless use and integration.

MISSEL: a method to identify a large number of small species-specific genomic subsequences and its application to viruses classification.

Background: Continuous improvements in next generation sequencing technologies led to ever-increasing collections of genomic sequences, which have not been easily characterized by biologists, and whose analysis requires huge computational effort. The classification of species emerged as one of the main applications of DNA analysis and has been addressed with several approaches, e.g.