Search results for "Sequence analysis"
showing 10 items of 1349 documents
Genome interdependence in insect-bacterium symbioses
2001
Symbioses between unicellular and multicellular organisms have contributed significantly to the evolution of life on Earth. As exemplified by several studies of bacterium-insect symbioses, modern genomic techniques are providing exciting new information about the molecular basis and the biological roles of these complex relationships, revealing for instance that symbionts have lost many genes for functions that are provided by the host, but that they can provide amino acids that the host cannot synthesize.
A novel putative insect chitinase with multiple catalytic domains: hormonal regulation during metamorphosis
2002
0264-6021 (Print) Journal Article Research Support, Non-U.S. Gov't; We have used differential display to identify genes that are regulated by juvenile hormone in the epidermis of the beetle Tenebrio molitor. One of the genes encodes T. molitor chitinase 5 (TmChit5), a chitinase possessing an unusual structure. Sequence analysis of TmChit5 identified five 'chitinase units' of approx. 480 amino acids with similarity to chitinase family 18. These units are separated by less conserved regions containing putative PEST (rich in proline, glutamic acid, serine and threonine) sequences, putative chitin-binding domains and mucin domains. Northern-blot analysis identified a single transcript of approx…
From phylogenetics to phylogenomics: the evolutionary relationships of insect endosymbiotic gamma-Proteobacteria as a test case.
2007
The increasing availability of complete genome sequences and the development of new, faster methods for phylogenetic reconstruction allow the exploration of the set of evolutionary trees for each gene in the genome of any species. This has led to the development of new phylogenomic methods. Here, we have compared different phylogenetic and phylogenomic methods in the analysis of the monophyletic origin of insect endosymbionts from the gamma-Proteobacteria, a hotly debated issue with several recent, conflicting reports. We have obtained the phylogenetic tree for each of the 579 identified protein-coding genes in the genome of the primary endosymbiont of carpenter ants, Blochmannia floridanus…
Artemisinin derivatives induce iron-dependent cell death (ferroptosis) in tumor cells
2015
Abstract Background Apoptosis and other forms of cell death have been intensively investigated in the past years to explain the mode of action of synthetic anticancer drugs and natural products. Recently, a new form of cell death emerged, which was termed ferroptosis, because it depends on intracellular iron. Here, the role of genes involved in iron metabolism and homeostasis for the cytotoxicity of ten artemisinin derivatives have been systematically investigated. Material and methods Log10IC50 values of 10 artemisinin derivatives (artesunate, artemether, arteether, artenimol, artemisitene, arteanuin B, another monomeric artemisinin derivative and three artemisinin dimer molecules) were co…
18S rRNA gene sequences and phylogenetic relationships of European hard-tick species (Acari: Ixodidae)
1998
The complete 18S rRNA gene sequences of the following six European hard-tick species were obtained by direct PCR cycle sequencing and silver-staining methods: Rhipicephalus pusillus, Boophilus annulatus, Dermacentor marginatus, Hyalomma lusitanicum, Haemaphysalis punctata, and Ixodes ricinus. Differences observed in the sequence alignment of these six species together with the 18S rRNA gene sequences of 13 other hard-tick species demonstrate that this gene is a good marker for supraspecific differentiation as well as genus grouping among hard ticks. Phylogenetic analyses strongly support that Hyalomma species share a common ancestor with Rhipicephalinae and, consequently, Hyalomminae should…
Keratinocytes Determine Th1 Immunity during Early Experimental Leishmaniasis
2010
Experimental leishmaniasis is an excellent model system for analyzing Th1/Th2 differentiation. Resistance to Leishmania (L.) major depends on the development of a L. major specific Th1 response, while Th2 differentiation results in susceptibility. There is growing evidence that the microenvironment of the early affected tissue delivers the initial triggers for Th-cell differentiation. To analyze this we studied differential gene expression in infected skin of resistant and susceptible mice 16h after parasite inoculation. Employing microarray technology, bioinformatics, laser-microdissection and in-situ-hybridization we found that the epidermis was the major source of immunomodulatory mediat…
Phylogeny and prevalence of kobuviruses in dogs and cats in the UK
2013
AbstractThe kobuviruses represent an emerging genus in the Picornaviridae. Here we have used next generation sequencing and conventional approaches to identify the first canine kobuvirus (CaKoV) from outside the USA. Phylogenetic analysis suggests that a single lineage genotype of CaKoV now exists in Europe and the USA with 94% nucleotide similarity in the coding region. CaKoV was only identified in a single case from a case–control study of canine diarrhoea, suggesting this virus was not a frequent cause of disease in this population. Attempts to grow CaKoV in cell culture failed. Sequence analysis suggested CaKoV was distinct from human Aichi virus (AiV), and unlikely to pose a significan…
Genome-Wide Association Analysis in Primary Sclerosing Cholangitis
2010
Background & Aims We aimed to characterize the genetic susceptibility to primary sclerosing cholangitis (PSC) by means of a genome-wide association analysis of single nucleotide polymorphism (SNP) markers. Methods A total of 443,816 SNPs on the Affymetrix SNP Array 5.0 (Affymetrix, Santa Clara, CA) were genotyped in 285 Norwegian PSC patients and 298 healthy controls. Associations detected in this discovery panel were re-examined in independent case-control panels from Scandinavia (137 PSC cases and 368 controls), Belgium/The Netherlands (229 PSC cases and 735 controls), and Germany (400 cases and 1832 controls). Results The strongest associations were detected near HLA-B at chromosome 6p21…
The differential diagnoses of uterine leiomyomas and leiomyosarcomas using DNA and RNA sequencing.
2019
BACKGROUND: Although uterine leiomyomas and leiomyosarcomas are considered biologically unrelated tumors, they share morphologic and histologic characteristics that complicate their differential diagnosis. The long-term therapeutic option for leiomyoma is laparoscopic myomectomy with morcellation, particularly for patients who wish to preserve their fertility. However, because of the potential dissemination of undiagnosed or hidden leiomyosarcoma from morcellation, there is a need to develop a preoperative assessment of malignancy risk. OBJECTIVE: Through an integrated comparative genomic and transcriptomic analysis, we aim to identify differential genetic targets in leiomyomas vs leiomyosa…
The Association between Cardiorespiratory Fitness and Gut Microbiota Composition in Premenopausal Women
2017
Abstract The aim of this study was to investigate the association between cardiorespiratory fitness and gut microbiota composition in premenopausal women. The participants consisted of 71 premenopausal Finnish women (aged 19–49 years). Gut microbiota were analyzed using flow cytometry, 16S rRNA gene hybridization and DNA-staining. Maximum oxygen uptake (VO₂ₘₐₓ) was assessed by respiratory gas analyzer and body composition by Bioimpdance. We found that participants with low VO₂ₘₐₓ had lower Bacteroides, but higher Eubacterium rectale-Clostridium coccoides than the high VO₂ₘₐₓ group (p < 0.05 for all). VO₂ₘₐₓ was inversely associated with EreC (r = −0.309, p = 0.01) but not with other bact…