Search results for " Sequencing"
showing 6 items of 976 documents
Grazing intensity in subarctic tundra affects the temperature adaptation of soil microbial communities
2015
Abstract Grazing by large ungulates, such as reindeer (Rangifer tarandus L.), in subarctic tundra exerts a considerable effect on the soil microclimate. Because of higher insulation by the aboveground vegetation in light versus heavily grazed areas, soil temperatures during the growing season are considerably higher under heavy grazing. Here, we hypothesized that these grazer-induced changes in soil microclimate affect the temperature sensitivity of soil microbial activity. To test this hypothesis, we conducted soil incubations at different temperatures (4 °C, 9 °C and 14 °C) for six weeks using soils from sites with contrasting long-term grazing intensities. Microbial respiration at low te…
Variants of human CLDN9 cause mild to profound hearing loss
2021
Hereditary deafness is clinically and genetically heterogeneous. We investigated deafness segregating as a recessive trait in two families. Audiological examinations revealed an asymmetric mild to profound hearing loss with childhood or adolescent onset. Exome sequencing of probands identified a homozygous c.475G>A;p.(Glu159Lys) variant of CLDN9 (NM_020982.4) in one family and a homozygous c.370_372dupATC;p.(Ile124dup) CLDN9 variant in an affected individual of a second family. Claudin 9 (CLDN9) is an integral membrane protein and constituent of epithelial bicellular tight junctions that form semi-permeable, paracellular barriers between inner ear perilymphatic and endolymphatic compartment…
Experimental Evolution Reveals a Genetic Basis for Membrane-Associated Virus Release
2021
Many animal viruses replicate and are released from cells in close association to membranes. However, whether this is a passive process or is controlled by the virus remains poorly understood. Importantly, the genetic basis and evolvability of membrane-associated viral shedding have not been investigated. To address this, we performed a directed evolution experiment using coxsackievirus B3, a model enterovirus, in which we repeatedly selected the free-virion or the fast-sedimenting membrane-associated viral subpopulations. The virus responded to this selection regime by reproducibly fixing a series of mutations that altered the extent of membrane-associated viral shedding, as revealed by fu…
Extracellular vesicle DNA from human melanoma tissues contains cancer-specific mutations
2022
Liquid biopsies are promising tools for early diagnosis and residual disease monitoring in patients with cancer, and circulating tumor DNA isolated from plasma has been extensively studied as it has been shown to contain tumor-specific mutations. Extracellular vesicles (EVs) present in tumor tissues carry tumor-derived molecules such as proteins and nucleic acids, and thus EVs can potentially represent a source of cancer-specific DNA. Here we identified the presence of tumor-specific DNA mutations in EVs isolated from six human melanoma metastatic tissues and compared the results with tumor tissue DNA and plasma DNA. Tumor tissue EVs were isolated using enzymatic treatment followed by ultra…
Molecular Characterization of a Variant of Bacillus anthracis-Specific Phage AP50 with Improved Bacteriolytic Activity▿ †
2008
ABSTRACT The genome sequence of a Bacillus anthracis -specific clear plaque mutant phage, AP50c, contains 31 open reading frames spanning 14,398 bp, has two mutations compared to wild-type AP50t, and has a colinear genome architecture highly similar to that of gram-positive Tectiviridae phages. Spontaneous AP50c-resistant B. anthracis mutants exhibit a mucoid colony phenotype.
A New Phylogenetic Framework for the Animal-Adapted
2018
Tuberculosis (TB) affects humans and other animals and is caused by bacteria from the Mycobacterium tuberculosis complex (MTBC). Previous studies have shown that there are at least nine members of the MTBC infecting animals other than humans; these have also been referred to as ecotypes. However, the ecology and the evolution of these animal-adapted MTBC ecotypes are poorly understood. Here we screened 12,886 publicly available MTBC genomes and newly sequenced 17 animal-adapted MTBC strains, gathering a total of 529 genomes of animal-adapted MTBC strains. Phylogenomic and comparative analyses confirm that the animal-adapted MTBC members are paraphyletic with some members more closely relate…