scholarly journals Visualization of Genome Signatures of Eukaryote Genomes by Batch-Learning Self-Organizing Map with a Special Emphasis onDrosophilaGenomes

2014 ◽  
Vol 2014 ◽  
pp. 1-8 ◽  
Author(s):  
Takashi Abe ◽  
Yuta Hamano ◽  
Toshimichi Ikemura
Keyword(s):  
Detailed Examination ◽  
Self Organizing Map ◽  
Genome Sequences ◽  
Alignment Free ◽  
Wide Range ◽  
Evolutionary Studies ◽  
High Throughput Dna Sequencing ◽  
Species Specific ◽  
Sequence Characteristics ◽  
Remarkable Progress

A strategy of evolutionary studies that can compare vast numbers of genome sequences is becoming increasingly important with the remarkable progress of high-throughput DNA sequencing methods. We previously established a sequence alignment-free clustering method “BLSOM” for di-, tri-, and tetranucleotide compositions in genome sequences, which can characterize sequence characteristics (genome signatures) of a wide range of species. In the present study, we generated BLSOMs for tetra- and pentanucleotide compositions in approximately one million sequence fragments derived from 101 eukaryotes, for which almost complete genome sequences were available. BLSOM recognized phylotype-specific characteristics (e.g., key combinations of oligonucleotide frequencies) in the genome sequences, permitting phylotype-specific clustering of the sequences without any information regarding the species. In our detailed examination of 12Drosophilaspecies, the correlation between their phylogenetic classification and the classification on the BLSOMs was observed to visualize oligonucleotides diagnostic for species-specific clustering.

scholarly journals Homoploid hybridization signals due to ancestral subdivision: a case study on the D lineage in wheat

2019 ◽  
Author(s):  
Yunfeng Jiang ◽  
Zhongwei Yuan ◽  
Haiyan Hu ◽  
Xueling Ye ◽  
Zhi Zheng ◽  
...  
Keyword(s):  
Hybrid Speciation ◽  
Genome Sequences ◽  
False Detection ◽  
Statistical Framework ◽  
Homoploid Hybridization ◽  
Wide Range ◽  
Evolutionary Studies ◽  
Homoploid Hybrid

AbstractHomoploid hybrid speciation has been reported in a wide range of species since the exploitation of genome sequences in evolutionary studies. However, the interference of ancestral subdivision has not been adequately considered in many such investigations. Using the D lineage in wheat as an example, we showed clearly that ancestral subdivision has led to false detection of homoploid hybridization signals. We develop a novel statistical framework by examining the changes in shared ancestral variations and infer on the likelihood of speciation due to genuine homoploid hybridization or ancestral subdivisions. Applying this to wheat data, we found that homoploid hybridization was not involved in the origin of the D lineage contrary to the now widely held belief. This example indicates that the significance of homoploid hybrid speciation is likely exaggerated. The underlying methodology developed in this study should be valuable for clarifying whether homoploid hybridization has contributed to the speciation of many other species.

Self-Organizing Map (SOM) unveils and visualizes hidden sequence characteristics of a wide range of eukaryote genomes

Gene ◽  
2006 ◽  
Vol 365 ◽  
pp. 27-34 ◽  
Author(s):  
Takashi Abe ◽  
Hideaki Sugawara ◽  
Shigehiko Kanaya ◽  
Makoto Kinouchi ◽  
Toshimichi Ikemura
Keyword(s):  
Self Organizing Map ◽  
Wide Range ◽  
Sequence Characteristics ◽  
Self Organizing

scholarly journals A Novel Bioinformatics Method for Efficient Knowledge Discovery by BLSOM from Big Genomic Sequence Data

2014 ◽  
Vol 2014 ◽  
pp. 1-11
Author(s):  
Yu Bai ◽  
Yuki Iwasaki ◽  
Shigehiko Kanaya ◽  
Yue Zhao ◽  
Toshimichi Ikemura
Keyword(s):  
Genomic Sequence ◽  
Sequence Data ◽  
Self Organizing Map ◽  
Genome Signature ◽  
A Genome ◽  
Wide Range ◽  
Oligonucleotide Composition ◽  
Species Specific

With remarkable increase of genomic sequence data of a wide range of species, novel tools are needed for comprehensive analyses of the big sequence data. Self-Organizing Map (SOM) is an effective tool for clustering and visualizing high-dimensional data such as oligonucleotide composition on one map. By modifying the conventional SOM, we have previously developed Batch-Learning SOM (BLSOM), which allows classification of sequence fragments according to species, solely depending on the oligonucleotide composition. In the present study, we introduce the oligonucleotide BLSOM used for characterization of vertebrate genome sequences. We first analyzed pentanucleotide compositions in 100 kb sequences derived from a wide range of vertebrate genomes and then the compositions in the human and mouse genomes in order to investigate an efficient method for detecting differences between the closely related genomes. BLSOM can recognize the species-specific key combination of oligonucleotide frequencies in each genome, which is called a “genome signature,” and the specific regions specifically enriched in transcription-factor-binding sequences. Because the classification and visualization power is very high, BLSOM is an efficient powerful tool for extracting a wide range of information from massive amounts of genomic sequences (i.e., big sequence data).

scholarly journals Adherence to Ketogenic and Mediterranean Study Diets in a Crossover Trial: The Keto–Med Randomized Trial

Nutrients ◽  
2021 ◽  
Vol 13 (3) ◽  
pp. 967
Author(s):  
Matthew J. Landry ◽  
Anthony Crimarco ◽  
Dalia Perelman ◽  
Lindsay R. Durand ◽  
Christina Petlura ◽  
...  
Keyword(s):  
Randomized Trial ◽  
Randomized Clinical Trials ◽  
Secondary Analysis ◽  
Critical Factor ◽  
Detailed Examination ◽  
Diet Patterns ◽  
Time Points ◽  
Study Results ◽  
Wide Range ◽  
Diet Pattern

Adherence is a critical factor to consider when interpreting study results from randomized clinical trials (RCTs) comparing one diet to another, but it is frequently not reported by researchers. The purpose of this secondary analysis of the Keto–Med randomized trial was to provide a detailed examination and comparison of the adherence to the two study diets (Well Formulated Ketogenic Diet (WFKD) and Mediterranean Plus (Med-Plus)) under the two conditions: all food being provided (delivered) and all food being obtained by individual participants (self-provided). Diet was assessed at six time points including baseline (x1), week 4 of each phase when participants were receiving food deliveries (x2), week 12 of each phase when participants were preparing and providing food on their own (x2), and 12 weeks after participants completed both diet phases and were free to choose their own diet pattern (x1). The adherence scores for WFKD and Med-Plus were developed specifically for this study. Average adherence to the two diet patterns was very similar during both on-study time points of the intervention. Throughout the study, a wide range of adherence was observed among participants—for both diet types and during both the delivery phase and self-provided phase. Insight from this assessment of adherence may aid other researchers when answering the important question of how to improve behavioral adherence during dietary trials. This study is registered at clinicaltrials.gov NCT03810378.

scholarly journals Developmental perspectives on personality: implications for ecological and evolutionary studies of individual differences

2010 ◽  
Vol 365 (1560) ◽  
pp. 4029-4041 ◽  
Author(s):  
Judy A. Stamps ◽  
Ton G. G. Groothuis
Keyword(s):  
Developmental Plasticity ◽  
Niche Construction ◽  
Prior Experience ◽  
Life Stage ◽  
Animal Personality ◽  
Temporal Consistency ◽  
Developmental Processes ◽  
Wide Range ◽  
Evolutionary Studies ◽  
Research Programmes

Developmental processes can have major impacts on the correlations in behaviour across contexts (contextual generality) and across time (temporal consistency) that are the hallmarks of animal personality. Personality can and does change: at any given age or life stage it is contingent upon a wide range of experiential factors that occurred earlier in life, from prior to conception through adulthood. We show how developmental reaction norms that describe the effects of prior experience on a given behaviour can be used to determine whether the effects of a given experience at a given age will affect contextual generality at a later age, and to illustrate how variation within individuals in developmental plasticity leads to variation in contextual generality across individuals as a function of experience. We also show why niche-picking and niche-construction, behavioural processes which allow individuals to affect their own developmental environment, can affect the contextual generality and the temporal consistency of personality. We conclude by discussing how an appreciation of developmental processes can alert behavioural ecologists studying animal personality to critical, untested assumptions that underlie their own research programmes, and outline situations in which a developmental perspective can improve studies of the functional significance and evolution of animal personality.

Species-specific duplex PCR for the detection of Pratylenchus penetrans

Nematology ◽  
2009 ◽  
Vol 11 (6) ◽  
pp. 847-857 ◽  
Author(s):  
Lieven Waeyenberge ◽  
Nicole Viaene ◽  
Maurice Moens
Keyword(s):  
Internal Control ◽  
Dna Sequences ◽  
Rrna Gene ◽  
Duplex Pcr ◽  
Specific Primers ◽  
5.8S Rrna Gene ◽  
5.8S Rrna ◽  
Wide Range ◽  
Pcr Products ◽  
Species Specific

Abstract ITS1, the 5.8S rRNA gene and ITS2 of the rDNA region were sequenced from 20 different Pratylenchus species. Additionally, the same region was sequenced from seven populations of P. penetrans. After purifying, cloning and sequencing the PCR products, all sequences were aligned in order to find unique sites suitable for the design of species-specific primers for P. penetrans. Since ITS regions showed variability between and even within populations of P. penetrans, only three small DNA sequences were suitable for the construction of three potentially useful species-specific primers. New species-specific primers were paired with existing universal ITS primers and tested in all possible primer combinations. The best performing primer set, supplemented with a universal 28S rDNA primer set that served as an internal control, was tested in duplex PCR. The ideal annealing temperature, Mg2+ concentration and primer ratios were then determined for the most promising primer set. The optimised duplex PCR was subsequently tested on a wide range of different Pratylenchus spp. and 25 P. penetrans populations originating from all over the world. To test the sensitivity, the duplex PCR was conducted on DNA extracted from a single P. penetrans nematode mixed with varying amounts of nematodes belonging to another Pratylenchus species. Results showed that a reliable and sensitive P. penetrans species-specific duplex PCR was constructed.

The EU as an “enforcement patchwork”: the impact of national enforcement for compliance with EU water law in Spain and Britain

2013 ◽  
Vol 34 (2) ◽  
pp. 331-353 ◽  
Author(s):  
Mónica García Quesada
Keyword(s):  
Waste Water Treatment ◽  
National Level ◽  
State Level ◽  
Detailed Examination ◽  
Deterrent Effect ◽  
Eu Law ◽  
Wide Range ◽  
The Uk ◽  
The Impact ◽  
The Eu

AbstractFailures of compliance with European Union (EU) directives have revealed the EU as a political system capable of enacting laws in a wide range of different policy areas, but facing difficulties to ensure their actual implementation. Although the EU relies on national enforcement agencies to ensure compliance with the EU legislation, there is scarce analysis of the differential deterrent effect of national enforcement in EU law compliance. This article examines the enforcement of an EU water directive, the Urban Waste Water Treatment Directive, in Spain and the UK. It focuses on the existing national sanctions for disciplining actors in charge of complying with EU requirements, and on the actual use of punitive sanctions. The analysis shows that a more comprehensive and active disciplinary regime at the national level contributes to explain a higher degree of compliance with EU law. The article calls for a detailed examination of the national administrative and criminal sanction system for a more comprehensive understanding of the incentives and disincentives to comply with EU law at the national state level.

scholarly journals Community-curated and standardised metadata of published ancient metagenomic samples with AncientMetagenomeDir

2020 ◽  
Author(s):  
James A. Fellows Yates ◽  
Aida Andrades Valtueña ◽  
Ashild J. Vågene ◽  
Becky Cribdon ◽  
Irina M. Velsko ◽  
...  
Keyword(s):  
Large Scale ◽  
Genetic Data ◽  
Data Retrieval ◽  
Data Sources ◽  
Valuable Data ◽  
Dna And Rna ◽  
Wide Range ◽  
Evolutionary Studies ◽  
Meta Analyses ◽  
Microbial Samples

ABSTRACTAncient DNA and RNA are valuable data sources for a wide range of disciplines. Within the field of ancient metagenomics, the number of published genetic datasets has risen dramatically in recent years, and tracking this data for reuse is particularly important for large-scale ecological and evolutionary studies of individual microbial taxa, microbial communities, and metagenomic assemblages. AncientMetagenomeDir (archived at https://doi.org/10.5281/zenodo.3980833) is a collection of indices of published genetic data deriving from ancient microbial samples that provides basic, standardised metadata and accession numbers to allow rapid data retrieval from online repositories. These collections are community-curated and span multiple sub-disciplines in order to ensure adequate breadth and consensus in metadata definitions, as well as longevity of the database. Internal guidelines and automated checks to facilitate compatibility with established sequence-read archives and term-ontologies ensure consistency and interoperability for future meta-analyses. This collection will also assist in standardising metadata reporting for future ancient metagenomic studies.

scholarly journals Mycorrhizal Communities and Isotope Signatures in Two Partially Mycoheterotrophic Orchids

2021 ◽  
Vol 12 ◽  
Author(s):  
Hans Jacquemyn ◽  
Rein Brys ◽  
Michael Waud ◽  
Alexandra Evans ◽  
Tomáš Figura ◽  
...  
Keyword(s):  
Isotopic Signatures ◽  
Carbon And Nitrogen ◽  
Wide Range ◽  
Terrestrial Orchids ◽  
Significant Enrichment ◽  
Mycoheterotrophic Plants ◽  
C And N ◽  
Species Specific ◽  
Epipactis Helleborine ◽  
Isotope Analyses

Partial mycoheterotrophy, the ability of plants to obtain carbon from fungi throughout their life cycle in combination with photosynthesis, appears to be more common within the Plant Kingdom than previously anticipated. Recent studies using stable isotope analyses have indicated that isotope signatures in partially mycoheterotrophic plants vary widely among species, but the relative contributions of family- or species-specific characteristics and the identity of the fungal symbionts to the observed differences remain unclear. Here, we investigated in detail mycorrhizal communities and isotopic signatures in four co-occurring terrestrial orchids (Platanthera chlorantha, Epipactis helleborine, E. neglecta and the mycoheterotrophic Neottia nidus-avis). All investigated species were mycorrhizal generalists (i.e., associated with a large number of fungi simultaneously), but mycorrhizal communities differed significantly between species. Mycorrhizal communities associating with the two Epipactis species consisted of a wide range of fungi belonging to different families, whereas P. chlorantha and N. nidus-avis associated mainly with Ceratobasidiaceae and Sebacinaceae species, respectively. Isotopic signatures differed significantly between both Epipactis species, with E. helleborine showing near autotrophic behavior and E. neglecta showing significant enrichment in both carbon and nitrogen. No significant differences in photosynthesis and stomatal conductance were observed between the two partially mycoheterotrophic orchids, despite significant differences in isotopic signatures. Our results demonstrate that partially mycoheterotrophic orchids of the genus Epipactis formed mycorrhizas with a wide diversity of fungi from different fungal families, but variation in mycorrhizal community composition was not related to isotope signatures and thus transfer of C and N to the plant. We conclude that the observed differences in isotope signatures between E. helleborine and E. neglecta cannot solely be explained by differences in mycorrhizal communities, but most likely reflect a combination of inherent physiological differences and differences in mycorrhizal communities.

scholarly journals A species-specific nucleosomal signature defines a periodic distribution of amino acids in proteins

Open Biology ◽  
2015 ◽  
Vol 5 (4) ◽  
pp. 140218 ◽  
Author(s):  
Luis Quintales ◽  
Ignacio Soriano ◽  
Enrique Vázquez ◽  
Mónica Segurado ◽  
Francisco Antequera
Keyword(s):  
Amino Acids ◽  
Protein Composition ◽  
Open Reading Frames ◽  
Yeast Genome ◽  
Relative Distribution ◽  
Periodic Distribution ◽  
Wide Range ◽  
Average Distribution ◽  
Species Specific ◽  
High Degree

Nucleosomes are the basic structural units of chromatin. Most of the yeast genome is organized in a pattern of positioned nucleosomes that is stably maintained under a wide range of physiological conditions. In this work, we have searched for sequence determinants associated with positioned nucleosomes in four species of fission and budding yeasts. We show that mononucleosomal DNA follows a highly structured base composition pattern, which differs among species despite the high degree of histone conservation. These nucleosomal signatures are present in transcribed and non-transcribed regions across the genome. In the case of open reading frames, they correctly predict the relative distribution of codons on mononucleosomal DNA, and they also determine a periodicity in the average distribution of amino acids along the proteins. These results establish a direct and species-specific connection between the position of each codon around the histone octamer and protein composition.

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