Search results for "GENOME"
showing 10 items of 1913 documents
Optimization of anti-proliferative activity using a screening approach with a series of bis-heterocyclic G-quadruplex ligands
2013
Abstract Using a phenotypic screening and SAR optimization approach, a phenyl-bis-oxazole derivative has been identified with anti-proliferative activity, optimized with the use of a panel of cancer cell lines. The lead compound was synthesized by means of a short and effective two-step synthesis using Pd-catalyzed direct arylation. The compound stabilizes several quadruplex DNA sequences including a human telomeric DNA and one from the promoter of the HSP90 gene, although the structure–activity relationships of the series are not obviously related to the quadruplex binding.
Gene therapy and editing in the treatment of hereditary blood disorders: Medical and ethical aspects
2021
Gene therapy and gene editing are revolutionising the treatment of genetic diseases, most notably haematological disorders. This paper evaluates the use of both techniques in hereditary blood disorders. Many studies have been conducted in this field, especially with gene therapy, with very promising results in diseases such as haemophilia, certain haemoglobinopathies and Fanconi anaemia. The application of these techniques in clinical practice and the foreseeable development of these approaches in the coming years suggest that it might be useful to evaluate the results achieved thus far. It is also essential to reflect on the possible bioethical concerns raised by the use of both technique…
Shedding light on biogas: Phototrophic biofilms in anaerobic digesters hold potential for improved biogas production
2019
Conventional anaerobic digesters intended for the production of biogas usually operate in complete darkness. Therefore, little is known about the effect of light on their microbial communities. In the present work, 16S rRNA gene amplicon Nanopore sequencing and shotgun metagenomic sequencing were used to study the taxonomic and functional structure of the microbial community forming a biofilm on the inner wall of a laboratory-scale transparent anaerobic biodigester illuminated with natural sunlight. The biofilm was composed of microorganisms involved in the four metabolic processes needed for biogas production, and it was surprisingly rich in Rhodopseudomonas faecalis, a versatile bacterium…
Chloroplast DNA evidence for introgression and long distance dispersal in the desert annualSenecio flavus (Asteraceae)
1995
Phylogenetic analysis of chloroplast DNA (cpDNA) restriction site variation supports a close genetic relationship between the Southwest AsianSenecio flavus subsp.breviflorus and the North AmericanS. mohavensis. The intercontinental disjunct distribution of these two desert annuals may have originated via long distance dispersal. The chloroplast genomes of the Southern and North AfricanS. flavus subsp.flavus and subsp.breviflorus differ by at least ten restriction sites, while at most two restriction sites differentiate the cpDNA genomes of subsp.breviflorus and the outgroupS. squalidus. This suggests that the cpDNA genome ofS. flavus subsp.breviflorus may have resulted from introgression an…
Complete Genome Sequence of Acidaminococcus intestini RYC-MR95, a Gram-Negative Bacterium from the Phylum Firmicutes
2011
ABSTRACT Acidaminococcus intestini belongs to the family Acidaminococcaceae , order Selenomonadales , class Negativicutes , phylum Firmicutes . Negativicutes show the double-membrane system of Gram-negative bacteria, although their chromosomal backbone is closely related to that of Gram-positive bacteria of the phylum Firmicutes . The complete genome of a clinical A. intestini strain is here presented.
Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs
2018
Background: Transcription factors (TFs) bind to gene promoters or distal regulatory elements that interact with the promoter via chromatin looping. While the TF binding sites themselves are detected genome-wide by ChIP-seq experiments, it is difficult to associate them regulated genes without information of chromatin looping. Recent experimental techniques such as Hi-C or ChIA-PET measure long-range interactions genome-wide but are experimentally elaborate and have limited resolution. Here, we present Computational Chromosome Conformation Capture by Correlation of ChIP-seq at CTCF motifs (7C). Results: While ChIP-seq was not designed to detect contacts, the formaldehyde treatment in the ChI…
A new gene superfamily of pathogen-response (repat) genes in Lepidoptera: Classification and expression analysis
2012
Repat (REsponse to PAThogens) genes were first identified in the midgut of Spodoptera exigua (Lepidoptera: Noctuidae) in response to Bacillus thuringiensis and baculovirus exposure. Since then, additional repat gene homologs have been identified in different studies. In this study the comprehensive larval transcriptome from S. exigua was analyzed for the presence of novel repat-homolog sequences. These analyses revealed the presence of at least 46 repat genes in S. exigua, establishing a new gene superfamily in this species. Phylogenetic analysis and studies of conserved motifs in these hypothetical proteins have allowed their classification in two main classes, αREPAT and βREPAT. Studies o…
Paratransgenic manipulation of a tsetse microRNA alters the physiological homeostasis of the fly’s midgut environment
2021
Tsetse flies are vectors of parasitic African trypanosomes, the etiological agents of human and animal African trypanosomoses. Current disease control methods include fly-repelling pesticides, fly trapping, and chemotherapeutic treatment of infected people and animals. Inhibiting tsetse’s ability to transmit trypanosomes by strengthening the fly’s natural barriers can serve as an alternative approach to reduce disease. The peritrophic matrix (PM) is a chitinous and proteinaceous barrier that lines the insect midgut and serves as a protective barrier that inhibits infection with pathogens. African trypanosomes must cross tsetse’s PM in order to establish an infection in the fly, and PM struc…
Deploying Genome Editing Tools for Dissecting the Biology of Nut Trees
2019
Walnuts are among the most important nut crops grown in temperate regions of the world. Commercial production in California, and increasingly worldwide, relies on only few clonally grafted scion genotypes, particularly “Chandler,” and more recently clonally propagated disease-resistant rootstocks. Diseases, nematodes, insect pests, abiotic stresses, and other nutritional and environmental factors, can reduce walnut productivity and quality, affecting grower profitability. The California Walnut Breeding Program at UC Davis has developed and released scion cultivars and rootstocks to help address some of these problems. Sequencing of the walnut genome is expected to speed walnut breeding by f…
Real-time Fluorescence Measurement of Enterovirus Uncoating
2019
Viruses need to open, i.e., uncoat, in order to release their genomes for efficient replication and translation. Especially for non-enveloped viruses, such as enteroviruses, the cues leading to uncoating are less well known. The status of the virus has previously been observed mainly by transmission electron microscopy using negative staining, cryo electron microscopy, X-ray crystallography or gradient separation (reviewed in Tuthill et al., 2010, Myllynen et al., 2016, Ruokolainen et al., 2019). However, monitoring of uncoating has been limited by the lack of methods detecting dynamic changes of the virions. Here, we present a real-time fluorescence based protocol, which detects the viral …