Search results for " sequencing"
showing 10 items of 976 documents
Metagenomic, microbiological, chemical and sensory profiling of Caciocavallo Podolico Lucano cheese
2023
In this study, Caciocavallo Podolico Lucano (CPL) cheese was deeply characterized for its bacterial community, chemical composition and sensory aspects. The entire cheese making process (from milk collection to ripened cheese) was performed by strictly applying the traditional protocol for CPL production in four dairy factories (A–D) representative of the production area. The vat made of wood represents the main transformation tool for CPL cheese production and the biofilms hosted onto the internal surfaces of all vats analyzed in this study were dominated by lactic acid bacteria. Total mesophilic microorganisms present in bulk milk (4.7–5.0 log CFU/ml) increased consistently after contact …
Next-Generation Sequencing-Based RiboMethSeq Protocol for Analysis of tRNA 2'-O-Methylation.
2016
Analysis of RNA modifications by traditional physico-chemical approaches is labor intensive, requires substantial amounts of input material and only allows site-by-site measurements. The recent development of qualitative and quantitative approaches based on next-generation sequencing (NGS) opens new perspectives for the analysis of various cellular RNA species. The Illumina sequencing-based RiboMethSeq protocol was initially developed and successfully applied for mapping of ribosomal RNA (rRNA) 2'-O-methylations. This method also gives excellent results in the quantitative analysis of rRNA modifications in different species and under varying growth condi…
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…
The sequencing of the complete genome of a Tomato black ring virus (TBRV) and of the RNA2 of three Grapevine chrome mosaic virus (GCMV) isolates from…
2014
The complete genome of a Tomato black ring virus isolate (TBRV-Mirs) (RNA1, 7,366 nt and RNA2, 4,640 nt) and the RNA2 sequences (4,437; 4,445; and 4,442 nts) of three Grapevine chrome mosaic virus isolates (GCMV-H6, -H15, and -H27) were determined. All RNAs contained a single open reading frame encoding polyproteins of 254 kDa (p1) and 149 kDa (p2) for TBRV-Mirs RNA1 and RNA2, respectively, and 146 kDa for GCMV RNA2. p1 of TBRV-Mirs showed the highest identity with TBRV-MJ (94 %), Beet ringspot virus (BRSV, 82 %), and Grapevine Anatolian ringspot virus (GARSV, 66 %), while p2 showed the highest identity with TBRV isolates MJ (89 %) and ED (85 %), followed by BRSV (65 %), GCMV (58 %), and GA…
Whole-Genome Sequence of Stenotrophomonas maltophilia D457, a Clinical Isolate and a Model Strain
2012
ABSTRACT Stenotrophomonas maltophilia is an opportunistic pathogen with an environmental origin, and it is an increasingly relevant cause of nosocomial infections. Here we present the whole-genome sequence of S. maltophilia strain D457, a clinical isolate that is being used as a model for studying antibiotic resistance in this bacterial species.
Lightweight BWT Construction for Very Large String Collections
2011
A modern DNA sequencing machine can generate a billion or more sequence fragments in a matter of days. The many uses of the BWT in compression and indexing are well known, but the computational demands of creating the BWT of datasets this large have prevented its applications from being widely explored in this context. We address this obstacle by presenting two algorithms capable of computing the BWT of very large string collections. The algorithms are lightweight in that the first needs O(m log m) bits of memory to process m strings and the memory requirements of the second are constant with respect to m. We evaluate our algorithms on collections of up to 1 billion strings and compare thei…
Lightweight algorithms for constructing and inverting the BWT of string collections
2013
Recent progress in the field of \{DNA\} sequencing motivates us to consider the problem of computing the Burrows‚ÄìWheeler transform (BWT) of a collection of strings. A human genome sequencing experiment might yield a billion or more sequences, each 100 characters in length. Such a dataset can now be generated in just a few days on a single sequencing machine. Many algorithms and data structures for compression and indexing of text have the \{BWT\} at their heart, and it would be of great interest to explore their applications to sequence collections such as these. However, computing the \{BWT\} for 100 billion characters or more of data remains a computational challenge. In this work we ad…
The DrosDel Collection
2004
Abstract We describe a collection of P-element insertions that have considerable utility for generating custom chromosomal aberrations in Drosophila melanogaster. We have mobilized a pair of engineered P elements, p{RS3} and p{RS5}, to collect 3243 lines unambiguously mapped to the Drosophila genome sequence. The collection contains, on average, an element every 35 kb. We demonstrate the utility of the collection for generating custom chromosomal deletions that have their end points mapped, with base-pair resolution, to the genome sequence. The collection was generated in an isogenic strain, thus affording a uniform background for screens where sensitivity to genetic background is high. The…
INVESTIGATION OF BIOTIC STRESS RESPONSES IN FRUIT TREE CROPS USING META-ANALYTICAL TECHNIQUES.
2020
In recent years, RNA sequencing and analysis using Next Generation Sequencing (NGS) methods have enabled to understand the gene expression pertaining to plant biotic and abiotic stress conditions in both quantitative and qualitative manner. The large number of transcriptomic works published in plants requires more meta-analysis studies that would identify common and specific features in relation of the high number of objective studies performed at different developmental and environmental conditions. Meta-analysis of transcriptomic data will identify commonalities and differences between differentially regulated gene lists and will allow screen which genes are key players in gene-gene and p…