Search results for "genomics"
showing 10 items of 1255 documents
Effect of somatic cell count level on functional longevity in Valle del Belice dairy sheep assessed using survival analysis.
2009
The objectives of this study were to evaluate the effect of somatic cell count (SCC) on functional longevity and to estimate the heritability of functional longevity using survival analysis in Valle del Belice dairy sheep. A total of 4,880 lactations of 2,190 ewes from 11 flocks were used. In this study, SCC was considered as an indication of subclinical mastitis. In case of clinical cases, identified by the technicians at milking time, test-day weights and milk samples of those ewes were not considered. Somatic cells were analyzed as counts, without any transformation, and were grouped in 3 classes based on the observed SCC maximum (mxSCC). The mxSCC classes, expressed as 103 cells/mL, wer…
Time-to-event analysis of mastitis at first-lactation in Valle del Belice ewes
2007
A time-to-event study for mastitis at first-lactation in Valle del Belice ewes was conducted, using survival analysis with an animal model. The goals were to evaluate the effect of lambing season and level of milk production on the time from lambing to the day when a ewe experienced a test-day with a recorded SCC greater than or equal to 750,000 cells/ml, and to estimate, for this trait, its heritability and the percentage of variation explained by the flock-year of lambing effect. A dataset with 2468 first-lactation records, collected from 1998 to 2003 in Valle del Belice ewes allocated in 17 flocks, was used. The Cox model used included lambing season and total milk yield adjusted for lac…
Molecular docking and pharmacogenomics of vinca alkaloids and their monomeric precursors, vindoline and catharanthine.
2011
International audience; Vinblastine and vincristine are dimeric indole alkaloids derived from (formerly: ). Their monomeric precursor molecules are vindoline and catharanthine. While vinblastine and vincristine are well-known mitotic spindle poisons, not much is known about vindoline and catharanthine. Vindoline and catharanthine showed weak cytotoxicity, while vinblastine, vincristine, and the semisynthetic vindesine and vinorelbine revealed high cytotoxicity towards cancer cells. This may reflect a general biological principle of poisonous plants. Highly toxic compounds are not only active towards predators, but also towards plant tissues. Hence, plants need mechanisms to protect themselv…
In-Depth Characterization of Viral Isolates from Plasma and Cells Compared with Plasma Circulating Quasispecies in Early HIV-1 Infection
2012
Background The use of in vitro models to unravel the phenotypic characteristics of circulating viral variants is key to understanding HIV-1 pathogenesis but limited by the availability of primary viral isolates from biological samples. However, overall in vivo genetic variability of HIV-1 within a subject may not be reflected in the viable viral population obtained after isolation. Although several studies have tried to determine whether viral populations expanded in vitro are representative of in vivo findings, the answer remains unclear due to the reduced number of clonal sequences analyzed or samples compared. In order to overcome previous experimental limitations, here we applied Deep P…
PML nuclear body-residing proteins sequentially associate with HPV genome after infectious nuclear delivery.
2019
Subnuclear promyelocytic leukemia (PML) nuclear bodies (NBs) are targeted by many DNA viruses after nuclear delivery. PML protein is essential for formation of PML NBs. Sp100 and Small Ubiquitin-Like Modifier (SUMO) are also permanently residing within PML NBs. Often, large DNA viruses disassemble and reorganize PML NBs to counteract their intrinsic antiviral activity and support establishment of infection. However, human papillomavirus (HPV) requires PML protein to retain incoming viral DNA in the nucleus for subsequent efficient transcription. In contrast, Sp100 was identified as a restriction factor for HPV. These findings suggested that PML NBs are important regulators of early stages o…
Fragmentation and Coverage Variation in Viral Metagenome Assemblies, and Their Effect in Diversity Calculations
2015
Metagenomic libraries consist of DNA fragments from diverse species, with varying genome size and abundance. High-throughput sequencing platforms produce large volumes of reads from these libraries, which may be assembled into contigs, ideally resembling the original larger genomic sequences. The uneven species distribution, along with the stochasticity in sample processing and sequencing bias, impacts the success of accurate sequence assembly. Several assemblers enable the processing of viral metagenomic data de novo, generally using overlap layout consensus or de Bruijn graph approaches for contig assembly. The success of viral genomic reconstruction in these datasets is limited by the de…
Transcriptional Upregulation of Genes Related to Virulence Activation in Entamoeba histolytica
2007
Background To understand the molecular basis of virulence variability in Entamoeba histolytica , this study presents results about differential gene expression induced by E. histolytica trophozoites in liver of hamsters in order to produce experimental amebic liver abscess (ALA) and consequently reactivate its virulence. Methods Amebic cultures were studied before (BALA) and after (AALA) inoculation in hamster peritoneal cavity. Markers of pathogenicity such as the rate of erythrophagocytosis, hemolytic activity, and cytotoxic effects on MDCK cell monolayers were evaluated in order to correlate these phenotypic characteristics to differential gene expression between virulent and non-virulen…
Microbiome of the Black Sea Water Column Analyzed by Genome Centric Metagenomics  
2020
Abstract Background: The Black Sea is the largest brackish water body in the world, although it is connected to the Mediterranean Sea and presents an upper water layer similar to some regions of the former albeit with lower salinity and (mostly) temperature. In spite of its well-known hydrology and physico chemistry, this enormous water mass remains poorly studied at the microbial genomics level. Results: We have sampled its different water masses and analyzed the microbiome by classic and genome-resolved metagenomics generating a large number of metagenome-assembled genomes (MAGs) from them. The oxic zone presents many similarities to the global ocean while the euxinic water mass has simil…
Comprehensive dataset of shotgun metagenomes from oxygen stratified freshwater lakes and ponds
2021
Stratified lakes and ponds featuring steep oxygen gradients are significant net sources of greenhouse gases and hotspots in the carbon cycle. Despite their significant biogeochemical roles, the microbial communities, especially in the oxygen depleted compartments, are poorly known. Here, we present a comprehensive dataset including 267 shotgun metagenomes from 41 stratified lakes and ponds mainly located in the boreal and subarctic regions, but also including one tropical reservoir and one temperate lake. For most lakes and ponds, the data includes a vertical sample set spanning from the oxic surface to the anoxic bottom layer. The majority of the samples were collected during the open wate…
Chryseobacterium potabilaquae sp. nov., Chryseobacterium aquaeductus sp. nov. and Chryseobacterium fistulae sp. nov., from drinking water systems
2021
A polyphasic taxonomic study was conducted on three strains isolated from drinking water systems that had previously been deposited as Chryseobacterium species at the Spanish Type Culture Collection in order to complete their classification. Strains CECT 9293T, CECT 9390T and CECT 9393T were isolated from sites in Barcelona, Spain, in the framework of a project aimed at generating the first MALDI-TOF database specific for bacteria present in water for human consumption. Their partial 16S rRNA sequences showed that their closest relatives among the type strains of Chryseobacterium exhibited 98 % similarity or less, supporting their taxonomic novelty. At the same time, comparison between them…