Search results for "Sequencing"
showing 10 items of 1087 documents
Process understanding of a wastewater batch reactor with block-wise PLS
2007
In this work a systematic methodology ‘block-wise PLS’ has been applied to thoroughly analyse data from a sequencing batch reactor (SBR) operated for biological phosphorus removal from wastewater. The aim of this study was to diagnose process variables (collected by the inexpensive and low-maintenance sensors installed in the SBR) likely related to the main key indicator of process performance: the phosphorus removal efficiency (PRE), determined off-line in the quality control laboratory. In this way, it is intended to aid the process operators in the detection of abnormal values of these critical variables which would indicate undesirable process performance, so that, they could act on the…
Two hundred and fifty-four metagenome-assembled bacterial genomes from the bank vole gut microbiota.
2020
Abstract Vertebrate gut microbiota provide many essential services to their host. To better understand the diversity of such services provided by gut microbiota in wild rodents, we assembled metagenome shotgun sequence data from a small mammal, the bank vole Myodes glareolus (Rodentia, Cricetidae). We were able to identify 254 metagenome assembled genomes (MAGs) that were at least 50% ( n = 133 MAGs), 80% ( n = 77 MAGs) or 95% ( n = 44 MAGs) complete. As typical for a rodent gut microbiota, these MAGs are dominated by taxa assigned to the phyla Bacteroidetes ( n = 132 MAGs) and Firmicutes ( n = 80), with some Spirochaetes ( n = 15) and Proteobacteria ( n = 11). Based on coverage over…
Using Unfold-PCA for batch-to-batch start-up process understanding and steady-state identification in a sequencing batch reactor
2007
In chemical and biochemical processes, steady-state models are widely used for process assessment, control and optimisation. In these models, parameter adjustment requires data collected under nearly steady-state conditions. Several approaches have been developed for steady-state identification (SSID) in continuous processes, but no attempt has been made to adapt them to the singularities of batch processes. The main aim of this paper is to propose an automated method based on batch-wise unfolding of the three-way batch process data followed by a principal component analysis (Unfold-PCA) in combination with the methodology of Brown and Rhinehart 2 for SSID. A second goal of this paper is to…
Draft Genome Sequence of the Microbispora sp. Strain ATCC-PTA-5024, Producing the Lantibiotic NAI-107.
2014
ABSTRACT We report the draft genome sequence of Microbispora sp. strain ATCC-PTA-5024, a soil isolate that produces NAI-107, a new lantibiotic with the potential to treat life-threatening infections caused by multidrug-resistant Gram-positive pathogens. The draft genome of strain Microbispora sp. ATCC-PTA-5024 consists of 8,543,819 bp, with a 71.2% G+C content and 7,860 protein-coding genes.
ChIP-Seq from Limited Starting Material of K562 Cells and Drosophila Neuroblasts Using Tagmentation Assisted Fragmentation Approach
2019
Chromatin immunoprecipitation is extensively used to investigate the epigenetic profile and transcription factor binding sites in the genome. However, when the starting material is limited, the conventional ChIP-Seq approach cannot be implemented. This protocol describes a method that can be used to generate the chromatin profiles from as low as 100 human or 1,000 Drosophila cells. The method employs tagmentation to fragment the chromatin with concomitant addition of sequencing adaptors. The method generates datasets with high signal to noise ratio and can be subjected to standard tools for ChIP-Seq analysis.
Animal rennets as sources of dairy lactic acid bacteria
2014
ABSTRACT The microbial composition of artisan and industrial animal rennet pastes was studied by using both culture-dependent and -independent approaches. Pyrosequencing targeting the 16S rRNA gene allowed to identify 361 operational taxonomic units (OTUs) to the genus/species level. Among lactic acid bacteria (LAB), Streptococcus thermophilus and some lactobacilli, mainly Lactobacillus crispatus and Lactobacillus reuteri , were the most abundant species, with differences among the samples. Twelve groups of microorganisms were targeted by viable plate counts revealing a dominance of mesophilic cocci. All rennets were able to acidify ultrahigh-temperature-processed (UHT) milk as shown by pH …
The complete genome sequence of Lamium mild mosaic virus, a member of the genus Fabavirus
2013
Springer-Verlag Wien 2013 Abstract Lamium mild mosaic virus (LMMV) is the only one of the five members of the genus Fabavirus for which there are no nucleotide sequence data. In this study, the complete genome sequence of LMMV was determined and compared with the available complete genome sequences of other members of the genus Fabavirus. The genome was the largest of the genus but maintained the typical orga- nization, with RNA 1 of 6080 nucleotides (nt), RNA 2 of 4065 nt, and an unusually long 3 0 untranslated region in RNA 2 of 603 nt. Phylogenetic analysis of the amino acid sequences of the protease-polymerase (Pro-Pol) region and the two coat proteins confirmed that LMMV belongs to a d…
Pandemic influenza A/H1N1 virus in a swine farm house in Sicily, Italy.
2012
This report describes a pandemic A/H1N1 (H1N1 pdm) virus outbreak occurred in December, 2009 in a swine farm used as research facility (Istituto Mediterraneo Trapianti e Terapie ad Alta Specializzazione) for preclinical studies, located in Sicily, Italy. All the 13 pigs of the farm, showed cough, fever, inappetence and weakness. At the same time, an unvaccinated worker of the stabling showed influenza-like symptoms. RNAv extracted from two swabs collected from infected pigs resulted positive by Real Time RT-PCR for Influenza A virus. Furthermore, after growth on embryonated eggs, viral isolates were identified by Real Time RT-PCR specific for H1N1 pdm virus and characterized antigenically. …
Molecular study of porcine transmissible gastroenteritis virus after serial animal passages revealed point mutations in S protein
2010
Porcine respiratory coronavirus is related genetically to porcine transmissible gastroenteritis virus with a large deletion in S protein. The respiratory virus is a mutated form that may be a consequence of the gastroen- teritis virus's evolution. Intensive passages of the virus in its natural host may enhance the appearance of mutations and therefore may contribute to any attenuated form of the virus. The objective of this study was to characterize the porcine transmissible gastroenteritis virus TMK22 strain after passages in piglets from 1992 until 2007. A typical experimental infection, molecular characterization, and serological analysis were also carried out to further char- acterize a…
Direct RNA nanopore sequencing of SARS-CoV-2 extracted from critical material from swabs
2020
ABSTRACTBackgroundIn consideration of the increasing prevalence of COVID-19 cases in several countries and the resulting demand for unbiased sequencing approaches, we performed a direct RNA sequencing experiment using critical oropharyngeal swab samples collected from Italian patients infected with SARS-CoV-2 from the Palermo region in Sicily.MethodsHere, we identified the sequences SARS-CoV-2 directly in RNA extracted from critical samples using the Oxford Nanopore MinION technology without prior cDNA retro-transcription.ResultsUsing an appropriate bioinformatics pipeline, we could identify mutations in the nucleocapisid (N) gene, which have been reported previously in studies conducted in…