Search results for " Sequencing"

Complete sequence, genotyping and comparative analysis of Pepino mosaic virus discovered isolates from Italy

2011

Pepino mosaic virus (PepMV) causes economic damage to the tomato industry worldwide. In Italy, the virus is endemic in Sicily, an important tomato-production region, and a new outbreak has been recorded in Sardinia after the first PepMV appearance in 2001. Italian PepMV isolates from these two geographically distant regions were molecularly characterized and the complete nucleotide sequence of four isolates was determined by walking primer strategy. The complete nucleotide and deduced amino acid sequences were analyzed and compared with published PepMV sequences. Italian isolates belong to the PepMV-Ch2 strain and had 97.2% to 98.5% identity with those of the reference PepMV-Ch2 deposited i…

Temporal dynamic of biofilms enhances the settlement of the central-1 Mediterranean reef2 builder Dendropoma cristatum (Biondi, 1859)

2021

Research on marine invertebrate settlement provides baseline knowledge for restoration technique implementation, especially for biogenic engineers with limited dispersion ability. Previously, we determined that the maturity of a biofilm strongly enhances the settlement of the vermetid reef-builder Dendropoma cristatum . In order to elucidate which biofilm features support a higher settlement of this species, we analyse the structure and composition of a marine biofilm over time, through microscopic observations, eukaryotic and prokaryotic fingerprinting analyses and 16S rDNA Illumina sequencing. The vermetid settlement temporal increase matched with the higher biofilm extent on the substrat…

Aerobic granular sludge: State of the art, applications, and new perspectives.

2018

The aerobic granular sludge (AGS) process has attracted significant interest over the last decade and is one of the most promising wastewater treatment technologies. AGS offers several advantages over conventional activated sludge (CAS) including excellent settling, and higher volumetric loading capacity. Because of porosity, concentration gradients develop and stratified aerobic, anoxic, and anaerobic layers develop throughout granule depth. This is the reason for simultaneous nutrient removal in a single tank. Aerobic granulation is influenced by many parameters including wastewater characteristics and operating conditions. Among these, the anaerobic upflow feeding strategy and a properly…

Taxidermal Preparations of an Extinct Sicilian Wolf Population (Canis lupus Linnaeus, 1758): Biological Studies and Restoration

2022

In last decades, biotechnologies have enabled a deep development of knowledge in all fields of life sciences, allowing the collection of a wide range of data. Furthermore, the relationship between scientific investigations and conservation actions of cultural heritage is increasingly consolidated and now it is one of the peculiar points both for sustainable restoration and use of the cultural asset, also evaluating the cultural assets as source of biological information. In this study, Sicilian wolf (Canis lupus) specimens conserved in Sicilian Natural Museums, become a source of biological information on Sicilian biodiversity, establishing specific conservative protocol developed cooperati…

DETECTION OF NEW GENES RESPONSIBLE OF FAMILIAL RECESSIVE HYPERCHOLESTEROLEMIA: PRELIMINARY DATA FROM AN EXOME SEQUENCING APPROACH

2014

Mucosal Neuroma Syndrome without mutations of the RET-protooncogene: A histologic study on a case, supported by molecular genetic analysis.

2010

Mucosal neuromas are nerve hamartomas of the digestive tract and larynx, usually observed in the setting of Multiple Endocrine Neoplasia type 2B (MEN2B), i.e. in the presence of typical mutations and in association with medullary thyroid carcinoma, pheochromocytoma and marfanoid habitus. Exceptionally, they arise without the accompanying mutations and endocrine tumors, and in this paper we are reporting a histologic study on a case lacking the specific mutations. The patient was an adolescent girl with marfanoid habitus, with a left-sided epidermal nevus of the neck, and a bulging left upper lip and cheek. The left side of her tongue was considerably enlarged and studded with multiple protr…

High-Quality Whole-Genome Sequence of an Estradiol-Degrading Strain, Novosphingobium tardaugens NBRC 16725

2019

In this work we report the complete sequence and assembly of the estradiol-degrading bacterium Novosphingobium tardaugens NBRC 16725 genome into a single contig using the Pacific Biosciences RS II system.

Construction of Metatranscriptomic Libraries for 5′ End Sequencing of rRNAs for Microbiome Research

2021

Metatranscriptomic sequencing enables studying community-wide gene expression profiles of microbial samples and getting functional insight on their up- or downregulated pathways. However, shotgun sequencing is not the most efficient way to study expression of ribosomal RNA genes or to compare lot of samples in experimental setups. Here we describe an efficient primer-independent method for processing and barcoding libraries for directional sequencing of the 5' end region of the RNA. When applying size selection of the original RNA, the method forms an optimal solution for the simultaneous analysis of bacterial, archaeal, and eukaryotic rRNA diversity.

Structure, organization and expression of two clustered cuticle protein genes during the metamorphosis of an insect, Tenebrio molitor.

1998

A 4-kb DNA segment of Tenebrio molitor (Insecta, Coleoptera) genomic DNA containing two larval-pupal cuticular genes has been cloned and sequenced. These genes, transcribed in opposite directions, are related in DNA sequence and the proteins encoded are very similar. Each of them contains a single intron located inside the sequence encoding the signal peptide, and a conserved sequence at -200 bp from the mRNA start position. These similarities in sequence suggest that these genes have evolved by duplication followed by diversification and that they are members of a family of genes with a common ancestry. They are the first example of clustered genes in Tenebrio molitor.

unitas: the universal tool for annotation of small RNAs

2017

AbstractBackgroundNext generation sequencing is a key technique in small RNA biology research that has led to the discovery of functionally different classes of small non-coding RNAs in the past years. However, reliable annotation of the extensive amounts of small non-coding RNA data produced by high-throughput sequencing is time-consuming and requires robust bioinformatics expertise. Moreover, existing tools have a number of shortcomings including a lack of sensitivity under certain conditions, limited number of supported species or detectable sub-classes of small RNAs.ResultsHere we introduce unitas, an out-of-the-box ready software for complete annotation of small RNA sequence datasets, …