Search results for "Sequence databases"
showing 10 items of 13 documents
MiasDB: A Database of Molecular Interactions Associated with Alternative Splicing of Human Pre-mRNAs.
2016
Alternative splicing (AS) is pervasive in human multi-exon genes and is a major contributor to expansion of the transcriptome and proteome diversity. The accurate recognition of alternative splice sites is regulated by information contained in networks of protein-protein and protein-RNA interactions. However, the mechanisms leading to splice site selection are not fully understood. Although numerous databases have been built to describe AS, molecular interaction databases associated with AS have only recently emerged. In this study, we present a new database, MiasDB, that provides a description of molecular interactions associated with human AS events. This database covers 938 interactions …
Genetic Diversity of O-Antigens in Hafnia alvei and the Development of a Suspension Array for Serotype Detection.
2016
Hafnia alvei is a facultative and rod-shaped gram-negative bacterium that belongs to the Enterobacteriaceae family. Although it has been more than 50 years since the genus was identified, very little is known about variations among Hafnia species. Diversity in O-antigens (O-polysaccharide, OPS) is thought to be a major factor in bacterial adaptation to different hosts and situations and variability in the environment. Antigenic variation is also an important factor in pathogenicity that has been used to define clones within a number of species. The genes that are required to synthesize OPS are always clustered within the bacterial chromosome. A serotyping scheme including 39 O-serotypes has…
Sentinel hospital-based surveillance for norovirus infection in children with gastroenteritis between 2015 and 2016 in Italy
2018
Noroviruses are one of the leading causes of gastro-enteric diseases worldwide in all age groups. Novel epidemic noroviruses with GII.P16 polymerase and GII.2 or GII.4 capsid type have emerged worldwide in late 2015 and in 2016. We performed a molecular epidemiological study of the noroviruses circulating in Italy to investigate the emergence of new norovirus strains. Sentinel hospital-based surveillance, in three different Italian regions, revealed increased prevalence of norovirus infection in children (<15 years) in 2016 (14.4% versus 9.8% in 2015) and the emergence of GII.P16 strains in late 2016, which accounted for 23.0% of norovirus infections. The majority of the strains with a GII.…
Characterization of Bacillus thuringiensis isolates by their insecticidal activity and their production of Cry and Vip3 proteins.
2018
WOS: 000449027600099 PubMed ID: 30383811 Bacillus thuringiensis (Bt) constitutes the active ingredient of many successful bioinsecticides used in agriculture. In the present study, the genetic diversity and toxicity of Bt isolates was investigated by characterization of native isolates originating from soil, fig leaves and fruits from a Turkish collection. Among a total of 80 Bt isolates, 18 of them were found carrying a vip3 gene (in 23% of total), which were further selected. Insecticidal activity of spore/crystal mixtures and their supernatants showed that some of the Bt isolates had significantly more toxicity against some lepidopteran species than the HD1 reference strain. Five isolate…
The shell of the invasive bivalve species Dreissena polymorpha: biochemical, elemental and textural Investigations.
2016
28 pages; International audience; The zebra mussel Dreissena polymorpha is a well-established invasive model organism. Although extensively used in environmental sciences, virtually nothing is known of the molecular process of its shell calcification. By describing the microstructure, geochemistry and biochemistry/proteomics of the shell, the present study aims at promoting this species as a model organism in biomineralization studies, in order to establish a bridge with ecotoxicology, while sketching evolutionary conclusions. The shell of D. polymorpha exhibits the classical crossed-lamellar/complex crossed lamellar combination found in several heterodont bivalves, in addition to an extern…
Unexpected associated microalgal diversity in the lichen Ramalina farinacea is uncovered by pyrosequencing analyses
2017
The current literature reveals that the intrathalline coexistence of multiple microalgal taxa in lichens is more common than previously thought, and additional complexity is supported by the coexistence of bacteria and basidiomycete yeasts in lichen thalli. This replaces the old paradigm that lichen symbiosis occurs between a fungus and a single photobiont. The lichen Ramalina farinacea has proven to be a suitable model to study the multiplicity of microalgae in lichen thalli due to the constant coexistence of Trebouxia sp. TR9 and T. jamesii in long-distance populations. To date, studies involving phycobiont diversity within entire thalli are based on Sanger sequencing, but this method see…
Stimulated and unstimulated saliva samples have significantly different bacterial profiles
2018
Epidemiological studies use saliva on a regular basis as a non-invasive and easy-to-take sample, which is assumed to be a microbial representative of the oral cavity ecosystem. However, comparative studies between different kinds of saliva samples normally used in microbial studies are scarce. The aim of the current study was to compare oral microbiota composition between two different saliva samples collected simultaneously: non-stimulated saliva with paper points and stimulated saliva collected after chewing paraffin gum. DNA was extracted from saliva samples of ten individuals, then analyzed by 16S rRNA pyrosequencing to describe bacterial diversity. The results demonstrate significant d…
Spatial Distribution of Fungal Communities in an Arable Soil.
2015
Fungi are prominent drivers of ecological processes in soils, so that fungal communities across different soil ecosystems have been well investigated. However, for arable soils taxonomically resolved fine-scale studies including vertical itemization of fungal communities are still missing. Here, we combined a cloning/Sanger sequencing approach of the ITS/LSU region as marker for general fungi and of the partial SSU region for arbuscular mycorrhizal fungi (AMF) to characterize the microbiome in different maize soil habitats. Four compartments were analyzed over two annual cycles 2009 and 2010: a) ploughed soil in 0-10 cm, b) rooted soil in 40-50 cm, c) root-free soil in 60-70 cm soil depth a…
Functional Metagenomics of the Bronchial Microbiome in COPD
2015
Altres ajuts: Sociedad Catalana de Neumología; Fundació Catalana de Neumología; Fundació Parc Tauli; Marató de TV3; Sociedad Española de Neumología y Cirugía Torácica; Fundación Menarini; Generalitat Valenciana (Spain) [Prometeo/2009/092] i Centro de Investigación Biomédica en Red de Enfermedades Respiratorias (CIBERES) The course of chronic obstructive pulmonary disease (COPD) is frequently aggravated by exacerbations, and changes in the composition and activity of the microbiome may be implicated in their appearance. The aim of this study was to analyse the composition and the gene content of the microbial community in bronchial secretions of COPD patients in both stability and exacerbati…
New insights into the gut microbiome in loggerhead sea turtles Caretta caretta stranded on the Mediterranean coast
2019
Caretta caretta is the most common sea turtle species in the Mediterranean Sea. The species is threatened by anthropomorphic activity that causes thousands of deaths and hundreds of strandings along the Mediterranean coast. Stranded turtles are often cared for in rehabilitation centres until they recover or die. The objective of this study was to characterize the gut microbiome of nine sea turtles stranded along the Sicilian coast of the Mediterranean Sea using high-throughput sequencing analysis targeting V3–V4 regions of the bacterial 16S rRNA gene. Stool samples were collected from eight specimens hosted in the recovery centre after a few days of hospitalization (under 7) and from one ho…