scholarly journals Insights into the neutral and adaptive processes shaping the spatial distribution of genomic variation in the economically important Moroccan locust ( Dociostaurus maroccanus )

2020 ◽  
Vol 10 (9) ◽  
pp. 3991-4008
Author(s):  
María José González‐Serna ◽  
Pedro J. Cordero ◽  
Joaquín Ortego
Keyword(s):  
Spatial Distribution ◽  
Genomic Variation ◽  
Adaptive Processes ◽  
Dociostaurus Maroccanus

FRANC: a unified framework for multi-way local ancestry deconvolution with high density SNP data

2019 ◽  
Vol 21 (5) ◽  
pp. 1837-1845
Author(s):  
Ephifania Geza ◽  
Nicola J Mulder ◽  
Emile R Chimusa ◽  
Gaston K Mazandu
Keyword(s):  
Phenotypic Variability ◽  
Modern Human ◽  
Genomic Variation ◽  
Unified Framework ◽  
Local Ancestry ◽  
Human Heredity ◽  
Snp Data ◽  
Variation Patterns ◽  
Adaptive Processes ◽  
Local Ancestry Inference

Abstract Several thousand genomes have been completed with millions of variants identified in the human deoxyribonucleic acid sequences. These genomic variations, especially those introduced by admixture, significantly contribute to a remarkable phenotypic variability with medical and/or evolutionary implications. Elucidating local ancestry estimates is necessary for a better understanding of genomic variation patterns throughout modern human evolution and adaptive processes, and consequences in human heredity and health. However, existing local ancestry deconvolution tools are accessible as individual scripts, each requiring input and producing output in its own complex format. This limits the user’s ability to retrieve local ancestry estimates. We introduce a unified framework for multi-way local ancestry inference, FRANC, integrating eight existing state-of-the-art local ancestry deconvolution tools. FRANC is an adaptable, expandable and portable tool that manipulates tool-specific inputs, deconvolutes ancestry and standardizes tool-specific results. To facilitate both medical and population genetics studies, FRANC requires convenient and easy to manipulate input files and allows users to choose output formats to ease their use in further potential local ancestry deconvolution applications.

scholarly journals Whole Genome Analysis of 132 Clinical Saccharomyces cerevisiae Strains Reveals Extensive Ploidy Variation

2016 ◽  
Author(s):  
Yuan O Zhu ◽  
Gavin J Sherlock ◽  
Dmitri A Petrov
Keyword(s):  
Large Scale ◽  
Genomic Variation ◽  
Whole Genome Analysis ◽  
Yeast Strains ◽  
Copy Numbers ◽  
Adaptive Processes ◽  
Chromosomal Copy ◽  
Commercial Sources ◽  
Ploidy Changes ◽  
Copy Number Changes

Budding yeast has undergone several independent transitions from commercial to clinical lifestyles. The frequency of such transitions suggests that clinical yeast strains are derived from environmentally available yeast populations, including commercial sources. However, despite their important role in adaptive evolution, the prevalence of polyploidy and aneuploidy has not extensively analyzed in clinical strains. In this study, we have looked for patterns governing the transition to clinical invasion in the largest screen of clinical yeast isolates to date. In particular, we have focused on the hypothesis that ploidy changes have influenced adaptive processes. We sequenced 145 yeast strains, 132 of which are clinical isolates. We found pervasive large-scale genomic variation in both overall ploidy (34% of strains identified as 3n/4n) and individual chromosomal copy numbers (36% of strains identified as aneuploid). We also found evidence for the highly dynamic nature of yeasts genomes, with 35 strains showing partial chromosomal copy number changes and 8 strains showing multiple independent chromosomal events. Intriguingly, a lineage identified to be baker/commercial derived with a unique damaging mutation in NDC80 was particularly prone to polyploidy, with 83% of its members being triploid or tetraploid. Polyploidy was in turn associated with a >2x increase in aneuploidy rates as compared to other lineages. This dataset provides a rich source of information of the genomics of clinical yeast strains and highlights the potential importance of large-scale genomic copy variation in yeast adaptation.

scholarly journals The role of neutral and adaptive genomic variation in population diversification and speciation in two ground squirrel species of conservation concern

2021 ◽  
Author(s):  
Soraia Barbosa ◽  
Kimberly Andrews ◽  
Amanda Goldberg ◽  
Digpal Gour ◽  
Paul Hohenlohe ◽  
...  
Keyword(s):  
Ground Squirrels ◽  
Genomic Variation ◽  
Nucleotide Polymorphisms ◽  
Environmental Pressures ◽  
Specific Level ◽  
Conservation Implications ◽  
Species Of Conservation Concern ◽  
Adaptive Processes ◽  
Conservation Concern ◽  
Adaptive Differentiation

Understanding the neutral (demographic) and adaptive processes leading to the differentiation of species and populations is a critical component of evolutionary and conservation biology. In this context, recently diverged taxa represent a unique opportunity to study the process of genetic differentiation. Northern and southern Idaho ground squirrels (Urocitellus brunneus – NIDGS, and U. endemicus - SIDGS, respectively) are a recently diverged pair of sister species that have undergone dramatic declines in the last 50 years and are currently found in metapopulations across restricted spatial areas with distinct environmental pressures. Here we genotyped single-nucleotide polymorphisms (SNPs) from buccal swabs with restriction site-associated DNA sequencing (RADseq). With these data we evaluated neutral genetic structure at both the inter- and intra-specific level, and identified putatively adaptive SNPs using population structure outlier and genotype-environment association (GEA) analyses. At the interspecific level, we found a clear separation between NIDGS and SIDGS, and evidence for adaptive differentiation relating to differences in hibernation. At the intraspecific level, we identified 3 Evolutionarily Significant Units for NIDGS and 2 for SIDGS plus multiple Management and Adaptive Units. Elevation appears to be the main driver of adaptive differentiation in NIDGS, while neutral variation patterns match and extend that identified in previous studies using microsatellite markers. For SIDGS, neutral substructure generally reflected the effect of natural geographic barriers, while adaptive variation reflected differences in land cover and temperature. These results clearly highlight the roles of neutral and adaptive processes for understanding species and population differentiation, which can have important conservation implications in threatened species.

scholarly journals Chromosomal fusion and life history-associated genomic variation contribute to within-river local adaptation of Atlantic salmon

2018 ◽  
Author(s):  
Kyle Wellband ◽  
Claire Mérot ◽  
Tommi Linnansaari ◽  
J. A. K. Elliott ◽  
R. Allen Curry ◽  
...  
Keyword(s):  
Population Structure ◽  
Atlantic Salmon ◽  
Local Adaptation ◽  
Spatial Scales ◽  
Genetic Relationships ◽  
Snp Array ◽  
Summer Precipitation ◽  
Genomic Variation ◽  
Chromosome 9 ◽  
Adaptive Processes

AbstractChromosomal inversions have been implicated in facilitating adaptation in the face of high levels of gene flow, but whether chromosomal fusions also have similar potential remains poorly understood. Atlantic salmon are usually characterized by population structure at multiple spatial scales; however, this is not the case for tributaries of the Miramichi River in North America. To resolve genetic relationships between populations in this system and the potential for known chromosomal fusions to contribute to adaptation we genotyped 728 juvenile salmon using a 50K SNP array. Consistent with previous work, we report extremely weak overall population structuring (Global FST = 0.004) and failed to support hierarchical structure between the river’s two main branches. We provide the first genomic characterization of a previously described polymorphic fusion between chromosomes 8 and 29. Fusion genomic characteristics included high LD, reduced heterozygosity in the fused homokaryotes, and strong divergence between the fused and the unfused rearrangement. Population structure based on fusion karyotype was five times stronger than neutral variation (FST = 0.019) and the frequency of the fusion was associated with summer precipitation supporting a hypothesis that this rearrangement may contribute local adaptation despite weak neutral differentiation. Additionally, both outlier variation among populations and a polygenic framework for characterizing adaptive variation in relation to climate identified a 250 Kb region of chromosome 9, including the gene six6 that has previously been linked to age-at-maturity and run-timing for this species. Overall our results indicate that adaptive processes, independent of major river branching, are more important than neutral processes for structuring these populations.

Lithography below 100 nm

1983 ◽  
Vol 41 ◽  
pp. 96-99
Author(s):  
L. D. Jackel
Keyword(s):  
Spatial Distribution ◽  
Electron Beam ◽  
Electron Scattering ◽  
Electron Beam Lithography ◽  
Substrate Material ◽  
Local Electron ◽  
Electron Dose ◽  
Positive Resist ◽  
Exposure Process

Most production electron beam lithography systems can pattern minimum features a few tenths of a micron across. Linewidth in these systems is usually limited by the quality of the exposing beam and by electron scattering in the resist and substrate. By using a smaller spot along with exposure techniques that minimize scattering and its effects, laboratory e-beam lithography systems can now make features hundredths of a micron wide on standard substrate material. This talk will outline sane of these high- resolution e-beam lithography techniques.We first consider parameters of the exposure process that limit resolution in organic resists. For concreteness suppose that we have a “positive” resist in which exposing electrons break bonds in the resist molecules thus increasing the exposed resist's solubility in a developer. Ihe attainable resolution is obviously limited by the overall width of the exposing beam, but the spatial distribution of the beam intensity, the beam “profile” , also contributes to the resolution. Depending on the local electron dose, more or less resist bonds are broken resulting in slower or faster dissolution in the developer.

SEM evaluation of the TEM cold-stage double-film specimen

1984 ◽  
Vol 42 ◽  
pp. 272-273
Author(s):  
Jayesh Bellare
Keyword(s):  
Spatial Distribution ◽  
Sample Preparation ◽  
Sample Thickness ◽  
Specimen Preparation ◽  
Preparation Technique ◽  
Liquid Sample ◽  
Thin Specimen ◽  
Sample Preparation Technique ◽  
Cold Stage ◽  
Film Specimen

Seeing is believing, but only after the sample preparation technique has received a systematic study and a full record is made of the treatment the sample gets.For microstructured liquids and suspensions, fast-freeze thermal fixation and cold-stage microscopy is perhaps the least artifact-laden technique. In the double-film specimen preparation technique, a layer of liquid sample is trapped between 100- and 400-mesh polymer (polyimide, PI) coated grids. Blotting against filter paper drains excess liquid and provides a thin specimen, which is fast-frozen by plunging into liquid nitrogen. This frozen sandwich (Fig. 1) is mounted in a cooling holder and viewed in TEM.Though extremely promising for visualization of liquid microstructures, this double-film technique suffers from a) ireproducibility and nonuniformity of sample thickness, b) low yield of imageable grid squares and c) nonuniform spatial distribution of particulates, which results in fewer being imaged.

Macroprobe Mode for the Study of Segregation in Steels

1990 ◽  
Vol 48 (2) ◽  
pp. 260-261
Author(s):  
Auclair Gilles ◽  
Benoit Danièle
Keyword(s):  
Mechanical Properties ◽  
Spatial Distribution ◽  
High Performance ◽  
Volume Fraction ◽  
Sheet Steel ◽  
Acquisition Time ◽  
Chemical Information ◽  
X Ray ◽  
Accurate Quantitative Analysis ◽  
Optical Micrographs

During these last 10 years, high performance correction procedures have been developed for classical EPMA, and it is nowadays possible to obtain accurate quantitative analysis even for soft X-ray radiations. It is also possible to perform EPMA by adapting this accurate quantitative procedures to unusual applications such as the measurement of the segregation on wide areas in as-cast and sheet steel products.The main objection for analysis of segregation in steel by means of a line-scan mode is that it requires a very heavy sampling plan to make sure that the most significant points are analyzed. Moreover only local chemical information is obtained whereas mechanical properties are also dependant on the volume fraction and the spatial distribution of highly segregated zones. For these reasons we have chosen to systematically acquire X-ray calibrated mappings which give pictures similar to optical micrographs. Although mapping requires lengthy acquisition time there is a corresponding increase in the information given by image anlysis.

Ultrastructural analysis of the spatial distribution of MRNA

1992 ◽  
Vol 50 (1) ◽  
pp. 552-553
Author(s):  
Gary Bassell ◽  
Robert H. Singer
Keyword(s):  
Electron Microscopy ◽  
Spatial Distribution ◽  
In Situ Hybridization ◽  
High Resolution ◽  
Nucleic Acids ◽  
Colloidal Gold ◽  
Dna Probe ◽  
Nucleotide Analogs ◽  
Gold Particles

We have been investigating the spatial distribution of nucleic acids intracellularly using in situ hybridization. The use of non-isotopic nucleotide analogs incorporated into the DNA probe allows the detection of the probe at its site of hybridization within the cell. This approach therefore is compatible with the high resolution available by electron microscopy. Biotinated or digoxigenated probe can be detected by antibodies conjugated to colloidal gold. Because mRNA serves as a template for the probe fragments, the colloidal gold particles are detected as arrays which allow it to be unequivocally distinguished from background.

Membrane microdomains: lessons from microscopy

1995 ◽  
Vol 53 ◽  
pp. 776-777
Author(s):  
J.M. Robinson ◽  
J.M Oliver
Keyword(s):  
Spatial Distribution ◽  
Plasma Membrane ◽  
Epithelial Cells ◽  
Plasma Membranes ◽  
Cell Types ◽  
Imaging Modalities ◽  
Membrane Microdomains ◽  
Membrane Domains ◽  
Lateral Heterogeneity ◽  
Functional Importance

Specialized regions of plasma membranes displaying lateral heterogeneity are the focus of this Symposium. Specialized membrane domains are known for certain cell types such as differentiated epithelial cells where lateral heterogeneity in lipids and proteins exists between the apical and basolateral portions of the plasma membrane. Lateral heterogeneity and the presence of microdomains in membranes that are uniform in appearance have been more difficult to establish. Nonetheless a number of studies have provided evidence for membrane microdomains and indicated a functional importance for these structures.This symposium will focus on the use of various imaging modalities and related approaches to define membrane microdomains in a number of cell types. The importance of existing as well as emerging imaging technologies for use in the elucidation of membrane microdomains will be highlighted. The organization of membrane microdomains in terms of dimensions and spatial distribution is of considerable interest and will be addressed in this Symposium.

An analytical microscopic study of metals in fluidized catalytic cracking catalyst

1986 ◽  
Vol 44 ◽  
pp. 854-855
Author(s):  
Clifford S. Rainey
Keyword(s):  
Electron Microscopy ◽  
Spatial Distribution ◽  
Catalytic Cracking ◽  
Catalyst Deactivation ◽  
Coke Formation ◽  
Acid Sites ◽  
Y Zeolite ◽  
Fcc Catalyst ◽  
Fluidized Catalytic Cracking ◽  
High Regeneration

The spatial distribution of V and Ni deposited within fluidized catalytic cracking (FCC) catalyst is studied because these metals contribute to catalyst deactivation. Y zeolite in FCC microspheres are high SiO2 aluminosilicates with molecular-sized channels that contain a mixture of lanthanoids. They must withstand high regeneration temperatures and retain acid sites needed for cracking of hydrocarbons, a process essential for efficient gasoline production. Zeolite in combination with V to form vanadates, or less diffusion in the channels due to coke formation, may deactivate catalyst. Other factors such as metal "skins", microsphere sintering, and attrition may also be involved. SEM of FCC fracture surfaces, AEM of Y zeolite, and electron microscopy of this work are developed to better understand and minimize catalyst deactivation.

Sign in / Sign up

Export Citation Format

Share Document