Search results for " assignment"
showing 10 items of 65 documents
Can we rely on selected genetic markers for population identification? Evidence from coastal Atlantic cod
2018
Abstract The use of genetic markers under putative selection in population studies carries the potential for erroneous identification of populations and misassignment of individuals to population of origin. Selected markers are nevertheless attractive, especially in marine organisms that are characterized by weak population structure at neutral loci. Highly fecund species may tolerate the cost of strong selective mortality during early life stages, potentially leading to a shift in offspring genotypes away from the parental proportions. In Atlantic cod, recent genetic studies have uncovered different genotype clusters apparently representing phenotypically cryptic populations that coexist i…
Interbreeding between local and translocated populations of a cleaner fish in an experimental mesocosm predicts risk of disrupted local adaptation
2019
Source at https://doi.org/10.1002/ece3.5246. Translocation of organisms within or outside its native range carries the risk of modifying the community of the recipient ecosystems and induces gene flow between locally adapted populations or closely related species. In this study, we evaluated the genetic consequences of large‐scale translocation of cleaner wrasses that has become a common practice within the salmon aquaculture industry in northern Europe to combat sea lice infestation. A major concern with this practice is the potential for hybridization of escaped organisms with the local, recipient wrasse population, and thus potentially introduce exogenous alleles and breaking down coadap…
A molecular-based identification resource for the arthropods of Finland
2022
Publisher Copyright: © 2021 The Authors. Molecular Ecology Resources published by John Wiley & Sons Ltd. To associate specimens identified by molecular characters to other biological knowledge, we need reference sequences annotated by Linnaean taxonomy. In this study, we (1) report the creation of a comprehensive reference library of DNA barcodes for the arthropods of an entire country (Finland), (2) publish this library, and (3) deliver a new identification tool for insects and spiders, as based on this resource. The reference library contains mtDNA COI barcodes for 11,275 (43%) of 26,437 arthropod species known from Finland, including 10,811 (45%) of 23,956 insect species. To quantify the…
Oxygen and carbon isoscapes for the Baltic Sea : Testing their applicability in fish migration studies
2017
Conventional tags applied to individuals have been used to investigate animal movement, but these methods require tagged individuals be recaptured. Maps of regional isotopic variability known as “isoscapes” offer potential for various applications in migration research without tagging wherein isotope values of tissues are compared to environmental isotope values. In this study, we present the spatial variability in oxygen (δ18OH2O) and dissolved inorganic carbon (δ13CDIC) isotope values of Baltic Sea water. We also provide an example of how these isoscapes can reveal locations of individual animal via spatial probability surface maps, using the high-resolution salmon otolith isotope data fr…
Preselection statistics and Random Forest classification identify population informative single nucleotide polymorphisms in cosmopolitan and autochth…
2018
Commercial single nucleotide polymorphism (SNP) arrays have been recently developed for several species and can be used to identify informative markers to differentiate breeds or populations for several downstream applications. To identify the most discriminating genetic markers among thousands of genotyped SNPs, a few statistical approaches have been proposed. In this work, we compared several methods of SNPs preselection (Delta, F st and principal component analyses (PCA)) in addition to Random Forest classifications to analyse SNP data from six dairy cattle breeds, including cosmopolitan (Holstein, Brown and Simmental) and autochthonous Italian breeds raised in two different regions and …
Accelerating metagenomic read classification on CUDA-enabled GPUs.
2016
Metagenomic sequencing studies are becoming increasingly popular with prominent examples including the sequencing of human microbiomes and diverse environments. A fundamental computational problem in this context is read classification; i.e. the assignment of each read to a taxonomic label. Due to the large number of reads produced by modern high-throughput sequencing technologies and the rapidly increasing number of available reference genomes software tools for fast and accurate metagenomic read classification are urgently needed. We present cuCLARK, a read-level classifier for CUDA-enabled GPUs, based on the fast and accurate classification of metagenomic sequences using reduced k-mers (…
Dispersion from Cα or NH: 4D experiments for backbone resonance assignment of intrinsically disordered proteins
2020
AbstractResonance assignment of intrinsically disordered proteins is remarkably challenging due to scant chemical shift dispersion arising from conformational heterogeneity. The challenge is even greater if repeating segments are present in the amino acid sequence. To forward unambiguous resonance assignment of intrinsically disordered proteins, we present iHACANCO, HACACON and (HACA)CONCAHA, three Hα-detected 4D experiments with Cα as an additional dimension. In addition, we present (HACA)CON(CA)NH and (HACA)N(CA)CONH, new 4D Hα-start, HN-detect experiments which have two NH dimensions to enhance peak dispersion in a sequential walk through C′, NH and HN, and provide more accurate NH/HN ch…
1H, 13C, and 15N NMR chemical shift assignment of the complex formed by the first EPEC EspF repeat and N-WASP GTPase binding domain
2021
AbstractLEE-encoded effector EspF (EspF) is an effector protein part of enteropathogenic Escherichia coli’s (EPEC’s) arsenal for intestinal infection. This intrinsically disordered protein contains three highly conserved repeats which together compose over half of the protein’s complete amino acid sequence. EPEC uses EspF to hijack host proteins in order to promote infection. In the attack EspF is translocated, together with other effector proteins, to host cell via type III secretion system. Inside host EspF stimulates actin polymerization by interacting with Neural Wiskott-Aldrich syndrome protein (N-WASP), a regulator in actin polymerization machinery. It is presumed that EspF acts by di…
Prospective assessment of post-extraction gingival closure with bone substitute and calcium sulphate
2009
Introduction: The closure of post extraction gingival defects has not been studied in depth, although their achievement is of great importance in certain situations, such as prior to radiotherapy treatment in patients with oral cancer. The aim of this study is to assess the influence of bone substitutes on the time of closure of post extraction gingival defects. Materials and Methods: 22 patients underwent two symmetrical dental extractions. Using a split mouth model, with random assignment to one or other group, one was considered a control group (no filling with any type of material post extraction), whereas the other was considered the experimental group (filling with bone substitute and…
Linear and cyclic radio k-labelings of trees
2007
International audience; Motivated by problems in radio channel assignments, we consider radio k-labelings of graphs. For a connected graph G and an integer k ≥ 1, a linear radio k-labeling of G is an assignment f of nonnegative integers to the vertices of G such that |f(x)−f(y)| ≥ k+1−dG(x,y), for any two distinct vertices x and y, where dG(x,y) is the distance between x and y in G. A cyclic k-labeling of G is defined analogously by using the cyclic metric on the labels. In both cases, we are interested in minimizing the span of the labeling. The linear (cyclic, respectively) radio k-labeling number of G is the minimum span of a linear (cyclic, respectively) radio k-labeling of G. In this p…