Search results for "genomics"

Direct squencing from the minimal number of DNA molecules needed to fill a 454 picotiterplate

2014

Notice of Republication: This article was republished on June 17, 2014, to correct an error in the title. The publisher apologizes for the error. In addition, a typographical error was corrected in the Abstract. Please download this article again to view the correct version. The originally published, uncorrected article and the republished, corrected article are provided here for reference.

Mining virulence genes using metagenomics.

2011

When a bacterial genome is compared to the metagenome of an environment it inhabits, most genes recruit at high sequence identity. In free-living bacteria (for instance marine bacteria compared against the ocean metagenome) certain genomic regions are totally absent in recruitment plots, representing therefore genes unique to individual bacterial isolates. We show that these Metagenomic Islands (MIs) are also visible in bacteria living in human hosts when their genomes are compared to sequences from the human microbiome, despite the compartmentalized structure of human-related environments such as the gut. From an applied point of view, MIs of human pathogens (e.g. those identified in enter…

Inflammatory networks in ageing, age-related diseases and longevity

2006

Inflammation is considered a response set by the tissues in response to injury elicited by trauma or infection. It is a complex network of molecular and cellular interactions that facilitates a return to physiological homeostasis and tissue repair. The individual response against infection and trauma is also determined by gene variability. Ageing is accompanied by chronic low-grade inflammation state clearly showed by 2-4-fold increase in serum levels of inflammatory mediators. A wide range of factors has been claimed to contribute to this state; however, the most important role seems to be played by the chronic antigenic stress, which affects immune system thorough out life with a progress…

Npl3 stabilizes R-loops at telomeres to prevent accelerated replicative senescence.

2019

Abstract Telomere shortening rates must be regulated to prevent premature replicative senescence. TERRA R‐loops become stabilized at critically short telomeres to promote their elongation through homology‐directed repair (HDR), thereby counteracting senescence onset. Using a non‐bias proteomic approach to detect telomere binding factors, we identified Npl3, an RNA‐binding protein previously implicated in multiple RNA biogenesis processes. Using chromatin immunoprecipitation and RNA immunoprecipitation, we demonstrate that Npl3 interacts with TERRA and telomeres. Furthermore, we show that Npl3 associates with telomeres in an R‐loop‐dependent manner, as changes in R‐loop levels, for example, …

Compressive biological sequence analysis and archival in the era of high-throughput sequencing technologies

2013

High-throughput sequencing technologies produce large collections of data, mainly DNA sequences with additional information, requiring the design of efficient and effective methodologies for both their compression and storage. In this context, we first provide a classification of the main techniques that have been proposed, according to three specific research directions that have emerged from the literature and, for each, we provide an overview of the current techniques. Finally, to make this review useful to researchers and technicians applying the existing software and tools, we include a synopsis of the main characteristics of the described approaches, including details on their impleme…

Current bioinformatics tools in genomic biomedical research (Review).

2006

On the advent of a completely assembled human genome, modern biology and molecular medicine stepped into an era of increasingly rich sequence database information and high-throughput genomic analysis. However, as sequence entries in the major genomic databases currently rise exponentially, the gap between available, deposited sequence data and analysis by means of conventional molecular biology is rapidly widening, making new approaches of high-throughput genomic analysis necessary. At present, the only effective way to keep abreast of the dramatic increase in sequence and related information is to apply biocomputational approaches. Thus, over recent years, the field of bioinformatics has r…

Classification of Sequences with Deep Artificial Neural Networks: Representation and Architectural Issues

2021

DNA sequences are the basic data type that is processed to perform a generic study of biological data analysis. One key component of the biological analysis is represented by sequence classification, a methodology that is widely used to analyze sequential data of different nature. However, its application to DNA sequences requires a proper representation of such sequences, which is still an open research problem. Machine Learning (ML) methodologies have given a fundamental contribution to the solution of the problem. Among them, recently, also Deep Neural Network (DNN) models have shown strongly encouraging results. In this chapter, we deal with specific classification problems related to t…

MITOCONDRIAL DNA VARIATION IN ITALIAN BOS PRIMIGENIUS: NEW CLUES INTO THE CATTLE DOMESTICATION PROCESS.

2008

Comparative Genomics and Primate Radiation

2011

Nutraceuticals and Functional Foods. Experimental research as a means for the innovation of already existing products: reporting of a type case.

2023

Innovation and the creation of new products in a company, or in a food industry, is an expensive process and requires profound transformations of the production processes. For this reason, the governance of some businesses often gives up on the idea of innovating, especially if some of their products, driving the market, can ensure short and medium-term earnings security. It is also quite well known, however, that the long-term solidity of a company is ensured only by innovation: mediating between these two possibilities is very difficult but one sustainable possibility, today, may consist in functionalizing already existing food products, adding, in the industrial manufacturing process, bi…