1,720,969 research outputs found
Functional and comparative characterization of Saccharomyces cerevisiae RVB1 and RVB2 genes with bacterial Ruv homologues
Full text linkExpression of yeast RuvB-like gene analogues of bacterial RuvB is self-regulated, as episomal overexpression of RVB1 and RVB2 decreases the expression of their chromosomal copies by 85%. Heterozygosity for either gene correlates with lower double-strand break repair of inverted-repeat DNA and decreased survival after UV irradiation, suggesting their haploinsufficiency, while overexpression of the bacterial RuvAB complex improves UV survival in yeast. Rvb2p preferentially binds artificial DNA Holiday junctions like the bacterial RuvAB complex, whereas Rvb1p binds to duplex or cruciform DNA. As both proteins also interact with chromatin, their role in recombination and repair through chromatin remodelling, and their evolutionary relationship to the bacterial homologue, is discussed.Fil: Radovic, Slobodanka. Yeast Molecular Genetics Group; ItaliaFil: Rapisarda, Viviana Andrea. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - Tucumán. Instituto Superior de Investigaciones Biológicas. Universidad Nacional de Tucumán. Instituto Superior de Investigaciones Biológicas; Argentina. Yeast Molecular Genetics Group; ItaliaFil: Tosato, Valentina. Yeast Molecular Genetics Group; ItaliaFil: Bruschi, Carlo V.. Yeast Molecular Genetics Group; Itali
Exome capture with heterologous enrichment in pig (Sus scrofa)
Full text linkThe discovery of new protein-coding DNA variants related to carcass traits is very important
for the Italian pig industry, which requires heavy pigs with higher thickness of subcutaneous
fat for Protected Designation of Origin (PDO) productions. Exome capture techniques offer
the opportunity to focus on the regions of DNA potentially related to the gene and protein
expression. In this research a human commercial target enrichment kit was used to evaluate
its performances for pig exome capture and for the identification of DNA variants suitable
for comparative analysis. Two pools of 30 pigs each, crosses of Italian Duroc X Large
White (DU) and Commercial hybrid X Large White (HY), were used and NGS libraries were
prepared with the SureSelectXT Target Enrichment System for Illumina Paired-End
Sequencing Library (Agilent). A total of 140.2 M and 162.5 M of raw reads were generated
for DU and HY, respectively. Average coverage of all the exonic regions for Sus scrofa
(ENSEMBL Sus_scrofa.Sscrofa10.2.73.gtf) was 89.33X for DU and 97.56X for HY; and
35% of aligned bases uniquely mapped to off-target regions. Comparison of sequencing
data with the Sscrofa10.2 reference genome, after applying hard filtering criteria, revealed a
total of 232,530 single nucleotide variants (SNVs) of which 20.6%mapped in exonic regions
and 49.5% within intronic regions. The comparison of allele frequencies of 213 randomly
selected SNVs from exome sequencing and the same SNVs analyzed with a Sequenom
MassARRAY1 system confirms that this “human-on-pig” approach offers new potentiality
for the identification of DNA variants in protein-coding genes.
Introduction
For PDO (Protected Designation of Origin) ham production, the Italian pig industry requires
heavy pigs, reared for 9 months and slaughtered at 160 kg live weight and with a carcass lean
percentage ranging from 40% to 55%. According to the production guidelines (EC No:
IT-PDO-0117-01149) [1], pigs must belong to the Large White and Landrace breeds, as
approved by the Italian Genealogical Register, and Duroc crossbreeds. Italian pig industry for
PDO hams requires heavy animals selected to have a higher amount of fat in comparison to
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Growth fitness, heme uptake and genomic variants in mutants of oxygen-tolerant Lacticaseibacillus casei and Lactiplantibacillus plantarum strains
No full textAdaptive Laboratory Evolution (ALE) is a powerful tool to improve the fitness of industrially relevant microorganisms, because it circumvents some of the problems related to the use of genetically modified strains. In this study, we used an ALE strategy involving serial batch cultivations in aerobic and respiratory conditions to generate spontaneous mutants from the respiration-competent strain Lacticaseibacillus casei N87. Genotypic changes in selected mutants were investigated using whole genome sequencing (WGS). The O2-tolerant Lactiplantibacillus plantarum C17 and its mutant C17-m58 (obtained from a previous ALE study) were included in heme uptake experiments and in WGS and variant calling analyses. Several Lcb. casei N87 mutants cultivated under aerobic and respiratory conditions showed improved biomass production, O2 uptake and oxidative stress tolerance compared to the parental strain. Mutants of Lcb. casei and Lpb. plantarum differed from the parental strains in the ability to use heme and menaquinone. High heme concentrations (> 10 mg/L), however, were toxic for all strains. Single nucleotide modifications (SNPs) were detected in some genes encoding for proteins and transcriptional regulators involved in carbon metabolism, oxidative stress, redox balance, and cell wall properties, but their role in the evolved phenotypes needs further investigations. We conclude that prolonged adaptation to aerobic and respiratory life-style may be used as natural strategy to generate strains with improved O2-consuming ability and oxidative stress tolerance, two important features to develop robust cultures and to reduce oxidative processes in foods
Metagenomic profiles of different types of Italian high-moisture Mozzarella cheese
Full text linkThe microbiota of different types of Italian high-moisture Mozzarella cheese produced using cow or buffalo milk, acidified with natural or selected cultures, and sampled at the dairy or at the mass market, was evaluated using a Next Generation Sequencing approach, in order to identify possible drivers of the bacterial diversity. Cow Mozzarella and buffalo Mozzarella acidified with commercial cultures were dominated by Streptococcus thermophilus, while buffalo samples acidified with natural whey cultures showed similar prevalence of L. delbrueckii subsp. bulgaricus, L. helveticus and S. thermophilus. Moreover, several species of non-starter lactic acid bacteria were frequently detected. The diversity in cow Mozzarella microbiota was much higher than that of water buffalo samples. Cluster analysis clearly separated cow's cheeses from buffalo's ones, the former having a higher prevalence of psychrophilic taxa, and the latter of Lactobacillus and Streptococcus. A higher prevalence of psychrophilic species and potential spoilers was observed in samples collected at the mass retail, suggesting that longer exposures to cooling temperatures and longer production-to-consumption times could significantly affect microbiota diversity. Our results could help in detecting some kind of thermal abuse during the production or storage of mozzarella cheese
Asymmetric allele-specific expression in relation to developmental variation and drought stress in barley hybrids
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Identification of tumorigenesis-related mRNAs associated with RNA-binding protein HuR in thyroid cancer cells
Full text linkRNA binding proteins (RBPs) play a central role in cell physiology and pathology. Among them, HuR is a nuclear RBP, which shuttles to the cytoplasm to allow its RNA targets processing. HuR over-expression and delocalization are often associated to cell transformation. Numerous cancers display increased HuR protein levels and its high cytoplasmic levels has been associated with a worse prognosis.In our study, we first evaluated HuR expression in normal and cancer thyroid tissues and then evaluated its function in thyroid cell lines. HuR is over-expressed in all thyroid tumor tissues; high cytoplasmic levels are detected in all thyroid carcinomas. HuR silencing decreased cell viability and determined apoptotic cell death, in a non-tumorigenic (Nthy-ori-3.1) and a tumorigenic (BCPAP) thyroid cell line. Global transcriptome analysis indicated that HuR silencing, though having similar biological effects, induces distinct gene expression modifications in the two cell lines. By using the RIP-seq approach, the HuR-bound RNA profiles of different thyroid cell lines were evaluated. We show that in distinct cell lines HuR-bound RNA profiles are different. A set of 114 HuR-bound RNAs distinguishing tumorigenic cell lines from the non-tumorigenic one was identified.Altogether, our data indicate that HuR plays a role in thyroid tumorigenesis. Moreover, our findings are a proof of concept that RBP targets differ between cells with the same origin but with distinct biological behavior
Going Beyond Counting First Authors in Author Co-citation Analysis
Full text linkThe present study examines one of the fundamental aspects of author co-citation analysis (ACA) - the way co-citation
counts are defined. Co-citation counting provides the data on which all subsequent statistical analyses and mappings
are based, and we compare ACA results based on two different types of co-citation counting - the traditional type that
only counts the first one among a cited work's authors on the one hand and a non-traditional type that takes into
account the first 5 authors of a cited work on the other hand. Results indicate that the picture produced through this non-traditional author co-citation counting contains more coherent author groups and is therefore considerably clearer. However, this picture represents fewer specialties in the research field being studied than that produced through the traditional first-author co-citation counting when the same number of top-ranked authors is selected and analyzed. Reasons for these effects are discussed
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