scholarly journals Analytical limits of hybrid identification using genetic markers: an empirical and simulation study in Hippolais warblers

2015 ◽  
Author(s):  
Jan O Engler ◽  
Soenke Twietmeyer ◽  
Jean Secondi ◽  
Ortwin Elle ◽  
Axel Hochkirch
Keyword(s):  
Genetic Markers ◽  
Ssr Markers ◽  
Simulation Study ◽  
Aflp Markers ◽  
F1 Hybrids ◽  
Rapid Loss ◽  
Natural Systems ◽  
Wide Range ◽  
Assignment Probability

Hybridization is known to occur in a wide range of avian species, yet the rate and persistence of hybridization on populations is often hard to assess. Genotyping using variable genetic marker sets has become a common tool to identify hybrid individuals, however assignment outputs can differ depending on the marker set used. Here, we study hybrid assignment in two sibling Hippolais warblers, where hybrid assignment has shown to differ between SSR and AFLP markers. Simulation of heterospecific individuals as well as backcrosses (typed using SSR markers) reveals a rapid loss of assignment probability in higher backcross generations. However, the characterization of F1 hybrids was clearly distinguished from both parental taxa. The differences in marker sets are not contradictory but complementary. The rate of hybridization is lower than previously expected with AFLP markers but introgression might be long-lasting. This could be either due to differences in power of the marker systems used or due to non-neutral variation covered by AFLP but not SSR markers. We call for more attention to be paid regarding the potential limits of classical marker systems to investigate hybridization and its persistence in natural systems.

scholarly journals Analyses of genetic diversity and population structure of anchote (Coccinia abyssinica (Lam.) Cogn.) using newly developed EST-SSR markers

2021 ◽  
Author(s):  
Bekele Serbessa Tolera ◽  
Kifle Dagne Woldegebriel ◽  
Abel Teshome Gari ◽  
Mulatu Geleta Dida ◽  
Kassahun Tesfaye Geletu
Keyword(s):  
Genetic Diversity ◽  
Population Structure ◽  
Ssr Markers ◽  
Polymorphic Information Content ◽  
Citrullus Lanatus ◽  
Wide Range ◽  
Minor Crop ◽  
Ssrs Markers ◽  
Expressed Sequence

AbstractAnchote (Coccinia abyssinica (Lam.) Cogn.) is a perennial root crop belonging to Cucurbitaceae family. It is endemic to Ethiopia and distributed over wide range of agro-ecologies. For further improvement and efficient conservation of this crop, characterization of its genetic diversity and its pattern of distribution is a vitally important step. Expressed sequence tags-simple sequence repeats (EST-SSRs) markers were developed from publicly available watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai] ESTs in the GenBank database. Among those novel markers, eight were polymorphic and subsequently used for genetic diversity and population structure analyses of 30 anchote accessions collected from western Ethiopia. A total of 24 alleles were obtained across the eight polymorphic loci and 30 accessions that revealed moderate level of genetic diversity in this minor crop. Among the eight loci, locus CA_06 was the most informative with six alleles and polymorphic information content (PIC) of 0.76. The accessions showed about threefold variation in terms of genetic diversity, with expected heterozygosity (He) ranging from 0.15 (accession An) to 0.44 (accession Dg). Other accessions with higher genetic diversity include Ar and Gu (He = 0.43 and 0.41, respectively). Analysis of molecular variance (AMOVA) revealed that the variation within accessions and among accessions accounted for 84.7% and 15.3% of the total variation, respectively. The study revealed low but significant population differentiation in this crop with no clear pattern of population structure. The EST-SSR markers developed in this study are the first of their kind for anchote and can be used for characterization of its wider genetic resources for conservation and breeding purposes.

Polymer Chemistry

2004 ◽  
Keyword(s):  
Conducting Polymers ◽  
Liquid Crystalline ◽  
Polymer Chemistry ◽  
Chain Growth ◽  
Crystalline Polymers ◽  
Wide Range ◽  
Cyclic Oligomers ◽  
Step Growth

Polymer Chemistry: A Practical Approach in Chemistry has been designed for both chemists working in and new to the area of polymer synthesis. It contains detailed instructions for preparation of a wide-range of polymers by a wide variety of different techniques, and describes how this synthetic methodology can be applied to the development of new materials. It includes details of well-established techniques, e.g. chain-growth or step-growth processes together with more up-to-date examples using methods such as atom-transfer radical polymerization. Less well-known procedures are also included, e.g. electrochemical synthesis of conducting polymers and the preparation of liquid crystalline elastomers with highly ordered structures. Other topics covered include general polymerization methodology, controlled/"living" polymerization methods, the formation of cyclic oligomers during step-growth polymerization, the synthesis of conducting polymers based on heterocyclic compounds, dendrimers, the preparation of imprinted polymers and liquid crystalline polymers. The main bulk of the text is preceded by an introductory chapter detailing some of the techniques available to the scientist for the characterization of polymers, both in terms of their chemical composition and in terms of their properties as materials. The book is intended not only for the specialist in polymer chemistry, but also for the organic chemist with little experience who requires a practical introduction to the field.

scholarly journals Organelle Genetics in Plants

2021 ◽  
Vol 22 (4) ◽  
pp. 2104
Author(s):  
Pedro Robles ◽  
Víctor Quesada
Keyword(s):  
Rna Editing ◽  
Posttranscriptional Regulation ◽  
Genome Engineering ◽  
Plant Mitochondria ◽  
Plastid Dna ◽  
Chloroplast Genomes ◽  
Wide Range ◽  
Organelle Genetics ◽  
Selection Of

Eleven published articles (4 reviews, 7 research papers) are collected in the Special Issue entitled “Organelle Genetics in Plants.” This selection of papers covers a wide range of topics related to chloroplasts and plant mitochondria research: (i) organellar gene expression (OGE) and, more specifically, chloroplast RNA editing in soybean, mitochondria RNA editing, and intron splicing in soybean during nodulation, as well as the study of the roles of transcriptional and posttranscriptional regulation of OGE in plant adaptation to environmental stress; (ii) analysis of the nuclear integrants of mitochondrial DNA (NUMTs) or plastid DNA (NUPTs); (iii) sequencing and characterization of mitochondrial and chloroplast genomes; (iv) recent advances in plastid genome engineering. Here we summarize the main findings of these works, which represent the latest research on the genetics, genomics, and biotechnology of chloroplasts and mitochondria.

scholarly journals Characterization of a Novel CaCO3-Forming Alkali-Tolerant Rhodococcus erythreus S26 as a Filling Agent for Repairing Concrete Cracks

Molecules ◽  
2021 ◽  
Vol 26 (10) ◽  
pp. 2967
Author(s):  
Seunghoon Choi ◽  
Sungjin Park ◽  
Minjoo Park ◽  
Yerin Kim ◽  
Kwang Min Lee ◽  
...  
Keyword(s):  
Building Materials ◽  
Culture Fluid ◽  
Natural Phenomenon ◽  
Environment Friendly ◽  
Wide Range ◽  
Filling Agent ◽  
Calcium Source ◽  
Alkali Tolerance ◽  
High Alkali

Biomineralization, a well-known natural phenomenon associated with various microbial species, is being studied to protect and strengthen building materials such as concrete. We characterized Rhodococcus erythreus S26, a novel urease-producing bacterium exhibiting CaCO3-forming activity, and investigated its ability in repairing concrete cracks for the development of environment-friendly sealants. Strain S26 grown in solid medium formed spherical and polygonal CaCO3 crystals. The S26 cells grown in a urea-containing liquid medium caused culture fluid alkalinization and increased CaCO3 levels, indicating that ureolysis was responsible for CaCO3 formation. Urease activity and CaCO3 formation increased with incubation time, reaching a maximum of 2054 U/min/mL and 3.83 g/L, respectively, at day four. The maximum CaCO3 formation was achieved when calcium lactate was used as the calcium source, followed by calcium gluconate. Although cell growth was observed after the induction period at pH 10.5, strain S26 could grow at a wide range of pH 4–10.5, showing its high alkali tolerance. FESEM showed rhombohedral crystals of 20–60 µm in size. EDX analysis indicated the presence of calcium, carbon, and oxygen in the crystals. XRD confirmed these crystals as CaCO3 containing calcite and vaterite. Furthermore, R. erythreus S26 successfully repaired the artificially induced large cracks of 0.4–0.6 mm width.

scholarly journals Isolation and Characterization of Strain Exiguobacterium sp. KRL4, a Producer of Bioactive Secondary Metabolites from a Tibetan Glacier

2021 ◽  
Vol 9 (5) ◽  
pp. 890
Author(s):  
Pietro Tedesco ◽  
Fortunato Palma Esposito ◽  
Antonio Masino ◽  
Giovanni Andrea Vitale ◽  
Emiliana Tortorella ◽  
...  
Keyword(s):  
Phenotypic Analysis ◽  
Biological Assays ◽  
C Elegans ◽  
Isolation And Characterization ◽  
Wide Range ◽  
Protein Encoding ◽  
Nematocidal Activity ◽  
Extremophilic Microorganisms ◽  
Unique Source

Extremophilic microorganisms represent a unique source of novel natural products. Among them, cold adapted bacteria and particularly alpine microorganisms are still underexplored. Here, we describe the isolation and characterization of a novel Gram-positive, aerobic rod-shaped alpine bacterium (KRL4), isolated from sediments from the Karuola glacier in Tibet, China. Complete phenotypic analysis was performed revealing the great adaptability of the strain to a wide range of temperatures (5–40 °C), pHs (5.5–8.5), and salinities (0–15% w/v NaCl). Genome sequencing identified KRL4 as a member of the placeholder genus Exiguobacterium_A and annotation revealed that only half of the protein-encoding genes (1522 of 3079) could be assigned a putative function. An analysis of the secondary metabolite clusters revealed the presence of two uncharacterized phytoene synthase containing pathways and a novel siderophore pathway. Biological assays confirmed that the strain produces molecules with antioxidant and siderophore activities. Furthermore, intracellular extracts showed nematocidal activity towards C. elegans, suggesting that strain KRL4 is a source of anthelmintic compounds.

scholarly journals Towards Reduced CNNs for De-Noising Phase Images Corrupted with Speckle Noise

Photonics ◽  
2021 ◽  
Vol 8 (7) ◽  
pp. 255
Author(s):  
Marie Tahon ◽  
Silvio Montresor ◽  
Pascal Picart
Keyword(s):  
Phase Error ◽  
Speckle Noise ◽  
Experimental Conditions ◽  
Benchmark Data ◽  
Wide Range ◽  
Phase Images ◽  
Different Depths ◽  
Phase Data ◽  
Do So

Digital holography is a very efficient technique for 3D imaging and the characterization of changes at the surfaces of objects. However, during the process of holographic interferometry, the reconstructed phase images suffer from speckle noise. In this paper, de-noising is addressed with phase images corrupted with speckle noise. To do so, DnCNN residual networks with different depths were built and trained with various holographic noisy phase data. The possibility of using a network pre-trained on natural images with Gaussian noise is also investigated. All models are evaluated in terms of phase error with HOLODEEP benchmark data and with three unseen images corresponding to different experimental conditions. The best results are obtained using a network with only four convolutional blocks and trained with a wide range of noisy phase patterns.

scholarly journals Raman Spectroscopy Investigation of Graphene Oxide Reduction by Laser Scribing

2021 ◽  
Vol 7 (2) ◽  
pp. 48
Author(s):  
Vittorio Scardaci ◽  
Giuseppe Compagnini
Keyword(s):  
Raman Spectroscopy ◽  
Graphene Oxide ◽  
Reduce Graphene Oxide ◽  
Oxide Reduction ◽  
Material Parameters ◽  
Laser Scribing ◽  
Wide Range ◽  
Scan Speed ◽  
Laser Reduction

Laser scribing has been proposed as a fast and easy tool to reduce graphene oxide (GO) for a wide range of applications. Here, we investigate laser reduction of GO under a range of processing and material parameters, such as laser scan speed, number of laser passes, and material coverage. We use Raman spectroscopy for the characterization of the obtained materials. We demonstrate that laser scan speed is the most influential parameter, as a slower scan speed yields poor GO reduction. The number of laser passes is influential where the material coverage is higher, producing a significant improvement of GO reduction on a second pass. Material coverage is the least influential parameter, as it affects GO reduction only under restricted conditions.

scholarly journals Characterization of Polysaccharidic Associations for Cosmetic Use: Rheology and Texture Analysis

Cosmetics ◽  
2021 ◽  
Vol 8 (3) ◽  
pp. 62
Author(s):  
Giovanni Tafuro ◽  
Alessia Costantini ◽  
Giovanni Baratto ◽  
Stefano Francescato ◽  
Laura Busata ◽  
...  
Keyword(s):  
Raw Materials ◽  
Immersion Test ◽  
High Viscosity ◽  
Natural Polymers ◽  
Public Attention ◽  
First Choice ◽  
Wide Range ◽  
Textural Parameters ◽  
Complementary Techniques

As public attention on sustainability is increasing, the use of polysaccharides as rheological modifiers in skin-care products is becoming the first choice. Polysaccharide associations can be used to increase the spreading properties of products and to optimize their sensorial profile. Since the choice of natural raw materials for cosmetics is wide, instrumental methodologies are useful for formulators to easily characterize the materials and to create mixtures with specific applicative properties. In this work, we performed rheological and texture analyses on samples formulated with binary and ternary associations of polysaccharides to investigate their structural and mechanical features as a function of the concentration ratios. The rheological measurements were conducted under continuous and oscillatory flow conditions using a rotational rheometer. An immersion/de-immersion test conducted with a texture analyzer allowed us to measure some textural parameters. Sclerotium gum and iota-carrageenan imparted high viscosity, elasticity, and firmness in the system; carob gum and pectin influenced the viscoelastic properties and determined high adhesiveness and cohesiveness. The results indicated that these natural polymers combined in appropriate ratios can provide a wide range of different textures and that the use of these two complementary techniques represents a valid pre-screening tool for the formulation of green products.

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