scholarly journals Quantitative Approach to Fish Cytogenetics in the Context of Vertebrate Genome Evolution

Genes ◽  
2021 ◽  
Vol 12 (2) ◽  
pp. 312
Author(s):  
Veronika Borůvková ◽  
W. Mike Howell ◽  
Dominik Matoulek ◽  
Radka Symonová
Keyword(s):  
Large Scale ◽  
Open Space ◽  
Repetitive Sequences ◽  
Gc Content ◽  
Chromosome Size ◽  
Vertebrate Genome ◽  
Fish Cytogenetics ◽  
Large Variability ◽  
The Relationship ◽  
Chromosome Level

Our novel Python-based tool EVANGELIST allows the visualization of GC and repeats percentages along chromosomes in sequenced genomes and has enabled us to perform quantitative large-scale analyses on the chromosome level in fish and other vertebrates. This is a different approach from the prevailing analyses, i.e., analyses of GC% in the coding sequences that make up not more than 2% in human. We identified GC content (GC%) elevations in microchromosomes in ancient fish lineages similar to avian microchromosomes and a large variability in the relationship between the chromosome size and their GC% across fish lineages. This raises the question as to what extent does the chromosome size drive GC% as posited by the currently accepted explanation based on the recombination rate. We ascribe the differences found across fishes to varying GC% of repetitive sequences. Generally, our results suggest that the GC% of repeats and proportion of repeats are independent of the chromosome size. This leaves an open space for another mechanism driving the GC evolution in vertebrates.

scholarly journals The effects of chromosome fusions on genetic diversity and evolutionary turnover of functional loci consistently depends on chromosome size

2021 ◽  
Author(s):  
Francesco Cicconardi ◽  
James J Lewis ◽  
Simon Henry Martin ◽  
Robert D. Reed ◽  
Charles G Danko ◽  
...  
Keyword(s):  
Chromosomal Rearrangements ◽  
Gc Content ◽  
Population Level ◽  
Chromosome Length ◽  
Adaptive Divergence ◽  
Chromosome Size ◽  
Turnover Rates ◽  
Chromosome Fusion ◽  
Chromosome Fusions ◽  
Chromosome Level

Major changes in chromosome number and structure are linked to a series of evolutionary phenomena, including intrinsic barriers to gene flow or suppression of recombination due to chromosomal rearrangements. However, chromosome rearrangements can also affect the fundamental dynamics of molecular evolution within populations by changing relationships between linked loci and altering rates of recombination. Here, we build chromosome-level assembly Eueides isabella and, together with the chromosome-level assembly of Dryas iulia, examine the evolutionary consequences of multiple chromosome fusions in Heliconius butterflies. These assemblies pinpoint fusion points on 10 of the 21 autosomal chromosomes and reveal striking differences in the characteristics of fused and unfused chromosomes. The ten smallest autosomes in D. iulia and E. isabella, which have each fused to a longer chromosome in Heliconius, have higher repeat and GC content, and longer introns than predicted by their chromosome length. Following fusion, these characteristics change to become more in line with chromosome length. The fusions also led to reduced diversity, which likely reflects increased background selection and selection against introgression between diverging populations, following a reduction in per-base recombination rate. We further show that chromosome size and fusion impact turnover rates of functional loci at a macroevolutionary scale. Together these results provide further evidence that chromosome fusion in Heliconius likely had dramatic effects on population level processes shaping rates of neutral and adaptive divergence. These effects may have impacted patterns of diversification in Heliconius, a classic example of an adaptive radiation.

Squamate Chromosome Size and GC Content Assessed by Flow Karyotyping

2019 ◽  
Vol 157 (1-2) ◽  
pp. 46-52 ◽  
Author(s):  
Fumio Kasai ◽  
Patricia C.M. O'Brien ◽  
Malcolm A. Ferguson-Smith
Keyword(s):  
Gene Mapping ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Chromosome Painting ◽  
Karyotype Evolution ◽  
Gc Content ◽  
Whole Genome ◽  
Chromosome Size ◽  
The Relationship ◽  
Reptilian Species

Chromosome homologies in reptiles have been investigated extensively by gene mapping and chromosome painting. Relative chromosome size can be estimated roughly from conventional karyotypes, but chromosome GC content cannot be evaluated by any of these approaches. However, GC content can be obtained by whole-genome sequencing, although complete data are available only for a limited number of reptilian species. Chromosomes can be characterized by size and GC content in bivariate flow karyotypes, in which the distribution of peaks represents the differences. We have analysed flow karyotypes from 9 representative squamate species and show chromosome profiles for each species based on the relationship between size and GC content. Our results reveal that the GC content of macrochromosomes is invariable in the 9 species. A higher GC content was found in microchromosomes, similar to profiles previously determined in crocodile, turtle, and chicken. The findings suggest that karyotype evolution in reptiles is characterized by unique features of chromosome GC content.

Relationship between total plasma homocysteine and the risk of aneurysms – a meta-analysis

VASA ◽  
2020 ◽  
pp. 1-6
Author(s):  
Hanji Zhang ◽  
Dexin Yin ◽  
Yue Zhao ◽  
Yezhou Li ◽  
Dejiang Yao ◽  
...  
Keyword(s):  
Large Scale ◽  
Meta Analysis ◽  
Single Species ◽  
Total Plasma ◽  
Control Groups ◽  
Randomized Controlled ◽  
Randomized Controlled Studies ◽  
The Difference ◽  
The Relationship ◽  
Healthy Participants

Summary: Our meta-analysis focused on the relationship between homocysteine (Hcy) level and the incidence of aneurysms and looked at the relationship between smoking, hypertension and aneurysms. A systematic literature search of Pubmed, Web of Science, and Embase databases (up to March 31, 2020) resulted in the identification of 19 studies, including 2,629 aneurysm patients and 6,497 healthy participants. Combined analysis of the included studies showed that number of smoking, hypertension and hyperhomocysteinemia (HHcy) in aneurysm patients was higher than that in the control groups, and the total plasma Hcy level in aneurysm patients was also higher. These findings suggest that smoking, hypertension and HHcy may be risk factors for the development and progression of aneurysms. Although the heterogeneity of meta-analysis was significant, it was found that the heterogeneity might come from the difference between race and disease species through subgroup analysis. Large-scale randomized controlled studies of single species and single disease species are needed in the future to supplement the accuracy of the results.

New ''Cold War''

2020 ◽  
pp. 27-34
Author(s):  
Vladimir Batiuk
Keyword(s):  
Cold War ◽  
Nuclear Weapons ◽  
Armed Conflict ◽  
Large Scale ◽  
Arms Race ◽  
Ideological Struggle ◽  
Nuclear Arms Race ◽  
The Cold War ◽  
The Relationship ◽  
Nuclear Arms

In this article, the ''Cold War'' is understood as a situation where the relationship between the leading States is determined by ideological confrontation and, at the same time, the presence of nuclear weapons precludes the development of this confrontation into a large-scale armed conflict. Such a situation has developed in the years 1945–1989, during the first Cold War. We see that something similar is repeated in our time-with all the new nuances in the ideological struggle and in the nuclear arms race.

Investigating Diseases and Chemicals in COVID-19 Literature with Text Mining (Preprint)

2020 ◽  
Author(s):  
Amir Karami ◽  
Brandon Bookstaver ◽  
Melissa Nolan
Keyword(s):  
Text Mining ◽  
Literature Review ◽  
Topic Modeling ◽  
Large Scale ◽  
Clinical Manifestations ◽  
International Health ◽  
Research Papers ◽  
Strategic Plans ◽  
Funding Agencies ◽  
The Relationship

BACKGROUND The COVID-19 pandemic has impacted nearly all aspects of life and has posed significant threats to international health and the economy. Given the rapidly unfolding nature of the current pandemic, there is an urgent need to streamline literature synthesis of the growing scientific research to elucidate targeted solutions. While traditional systematic literature review studies provide valuable insights, these studies have restrictions, including analyzing a limited number of papers, having various biases, being time-consuming and labor-intensive, focusing on a few topics, incapable of trend analysis, and lack of data-driven tools. OBJECTIVE This study fills the mentioned restrictions in the literature and practice by analyzing two biomedical concepts, clinical manifestations of disease and therapeutic chemical compounds, with text mining methods in a corpus containing COVID-19 research papers and find associations between the two biomedical concepts. METHODS This research has collected papers representing COVID-19 pre-prints and peer-reviewed research published in 2020. We used frequency analysis to find highly frequent manifestations and therapeutic chemicals, representing the importance of the two biomedical concepts. This study also applied topic modeling to find the relationship between the two biomedical concepts. RESULTS We analyzed 9,298 research papers published through May 5, 2020 and found 3,645 disease-related and 2,434 chemical-related articles. The most frequent clinical manifestations of disease terminology included COVID-19, SARS, cancer, pneumonia, fever, and cough. The most frequent chemical-related terminology included Lopinavir, Ritonavir, Oxygen, Chloroquine, Remdesivir, and water. Topic modeling provided 25 categories showing relationships between our two overarching categories. These categories represent statistically significant associations between multiple aspects of each category, some connections of which were novel and not previously identified by the scientific community. CONCLUSIONS Appreciation of this context is vital due to the lack of a systematic large-scale literature review survey and the importance of fast literature review during the current COVID-19 pandemic for developing treatments. This study is beneficial to researchers for obtaining a macro-level picture of literature, to educators for knowing the scope of literature, to journals for exploring most discussed disease symptoms and pharmaceutical targets, and to policymakers and funding agencies for creating scientific strategic plans regarding COVID-19.

scholarly journals Cytogenetic Analysis and Chromosomal Mapping of Repetitive DNA in Melipona Species (Hymenoptera, Meliponini)

2019 ◽  
Vol 158 (4) ◽  
pp. 213-224 ◽  
Author(s):  
Natália M. Travenzoli ◽  
Bárbara A. Lima ◽  
Danon C. Cardoso ◽  
Jorge A. Dergam ◽  
Tânia M. Fernandes-Salomão ◽  
...  
Keyword(s):  
Stingless Bees ◽  
Chromosome Evolution ◽  
Repetitive Sequences ◽  
Sensu Stricto ◽  
Chromosomal Mapping ◽  
Evolutionary Constraints ◽  
Rdna Sites ◽  
Melipona Species ◽  
The Relationship ◽  
Evolutionary Lineages

Stingless bees of the genus Melipona are subdivided into 4 subgenera called Eomelipona, Melikerria, Melipona sensu stricto, and Michmelia according to species morphology. Cytogenetically, the species of the genus Melipona show variation in the amount and distribution of heterochromatin along their chromosomes and can be separated into 2 groups: the first with low content of heterochromatin and the second with high content of heterochromatin. These heterochromatin patterns and the number of chromosomes are characteristics exclusive to Melipona karyotypes that distinguish them from the other genera of the Meliponini. To better understand the karyotype organization in Melipona and the relationship among the subgenera, we mapped repetitive sequences and analyzed previously reported cytogenetic data with the aim to identify cytogenetic markers to be used for investigating the phylogenetic relationships and chromosome evolution in the genus. In general, Melipona species have 2n = 18 chromosomes, and the species of each subgenus share the same characteristics in relation to heterochromatin regions, DAPI/CMA3 fluorophores, and the number and distribution of 18S rDNA sites. Microsatellites were observed only in euchromatin regions, whereas the (TTAGG)6 repeats were found at telomeric sites in both groups. Our data indicate that in addition to the chromosome number, the karyotypes in Melipona could be separated into 2 groups that are characterized by conserved cytogenetic features and patterns that generally are shared by species within each subgenus, which may reflect evolutionary constraints. Our results agree with the morphological separation of the Melipona into 4 subgenera, suggesting that they must be independent evolutionary lineages.

scholarly journals Large-Scale, High-Throughput Validation of Short Hairpin RNA Sequences for RNA Interference

2006 ◽  
Vol 11 (3) ◽  
pp. 236-246 ◽  
Author(s):  
Laurence H. Lamarcq ◽  
Bradley J. Scherer ◽  
Michael L. Phelan ◽  
Nikolai N. Kalnine ◽  
Yen H. Nguyen ◽  
...  
Keyword(s):  
High Throughput ◽  
Large Scale ◽  
Strong Support ◽  
Gc Content ◽  
Rapid Identification ◽  
Hairpin Rna ◽  
Rna Sequences ◽  
Short Hairpin ◽  
Short Hairpin Rnas ◽  
Interfering Rna

A method for high-throughput cloning and analysis of short hairpin RNAs (shRNAs) is described. Using this approach, 464 shRNAs against 116 different genes were screened for knockdown efficacy, enabling rapid identification of effective shRNAs against 74 genes. Statistical analysis of the effects of various criteria on the activity of the shRNAs confirmed that some of the rules thought to govern small interfering RNA (siRNA) activity also apply to shRNAs. These include moderate GC content, absence of internal hairpins, and asymmetric thermal stability. However, the authors did not find strong support for positionspecific rules. In addition, analysis of the data suggests that not all genes are equally susceptible to RNAinterference (RNAi).

scholarly journals Strategic resources and smallholder performance at the bottom of the pyramid

2019 ◽  
Vol 22 (3) ◽  
pp. 365-380 ◽  
Author(s):  
Matthias Olthaar ◽  
Wilfred Dolfsma ◽  
Clemens Lutz ◽  
Florian Noseleit
Keyword(s):  
Large Scale ◽  
Business Environment ◽  
Agricultural Economics ◽  
Local Market ◽  
Bottom Of The Pyramid ◽  
Fine Grained ◽  
Strategic Resources ◽  
Relative Contribution ◽  
The Relationship ◽  
Resource Based Theory

In a competitive business environment at the Bottom of the Pyramid smallholders supplying global value chains may be thought to be at the whims of downstream large-scale players and local market forces, leaving no room for strategic entrepreneurial behavior. In such a context we test the relationship between the use of strategic resources and firm performance. We adopt the Resource Based Theory and show that seemingly homogenous smallholders deploy resources differently and, consequently, some do outperform others. We argue that the ‘resource-based theory’ results in a more fine-grained understanding of smallholder performance than approaches generally applied in agricultural economics. We develop a mixed-method approach that allows one to pinpoint relevant, industry-specific resources, and allows for empirical identification of the relative contribution of each resource to competitive advantage. The results show that proper use of quality labor, storage facilities, time of selling, and availability of animals are key capabilities.

scholarly journals Lack of an association between gallstone disease and bilirubin levels with risk of colorectal cancer: a Mendelian randomisation analysis

2021 ◽  
Author(s):  
Richard Culliford ◽  
Alex J. Cornish ◽  
Philip J. Law ◽  
Susan M. Farrington ◽  
Kimmo Palin ◽  
...  
Keyword(s):  
Colorectal Cancer ◽  
Large Scale ◽  
Causal Effect ◽  
Gallstone Disease ◽  
Epidemiological Studies ◽  
Mendelian Randomisation ◽  
Linear Relationships ◽  
Potential Risk Factors ◽  
The Relationship ◽  
Circulating Levels

Abstract Background Epidemiological studies of the relationship between gallstone disease and circulating levels of bilirubin with risk of developing colorectal cancer (CRC) have been inconsistent. To address possible confounding and reverse causation, we examine the relationship between these potential risk factors and CRC using Mendelian randomisation (MR). Methods We used two-sample MR to examine the relationship between genetic liability to gallstone disease and circulating levels of bilirubin with CRC in 26,397 patients and 41,481 controls. We calculated the odds ratio per genetically predicted SD unit increase in log bilirubin levels (ORSD) for CRC and tested for a non-zero causal effect of gallstones on CRC. Sensitivity analysis was applied to identify violations of estimator assumptions. Results No association between either gallstone disease (P value = 0.60) or circulating levels of bilirubin (ORSD = 1.00, 95% confidence interval (CI) = 0.96–1.03, P value = 0.90) with CRC was shown. Conclusions Despite the large scale of this study, we found no evidence for a causal relationship between either circulating levels of bilirubin or gallstone disease with risk of developing CRC. While the magnitude of effect suggested by some observational studies can confidently be excluded, we cannot exclude the possibility of smaller effect sizes and non-linear relationships.

scholarly journals The Evolution of Isochores: Evidence From SNP Frequency Distributions

Genetics ◽  
2002 ◽  
Vol 162 (4) ◽  
pp. 1805-1810 ◽  
Author(s):  
Martin J Lercher ◽  
Nick G C Smith ◽  
Adam Eyre-Walker ◽  
Laurence D Hurst
Keyword(s):  
Population Genetics ◽  
Large Scale ◽  
Gc Content ◽  
Nucleotide Composition ◽  
Compositional Variation ◽  
Mutation Bias ◽  
Single Nucleotide ◽  
Frequency Distributions ◽  
Noncoding Regions ◽  
Standard Population

AbstractThe large-scale systematic variation in nucleotide composition along mammalian and avian genomes has been a focus of the debate between neutralist and selectionist views of molecular evolution. Here we test whether the compositional variation is due to mutation bias using two new tests, which do not assume compositional equilibrium. In the first test we assume a standard population genetics model, but in the second we make no assumptions about the underlying population genetics. We apply the tests to single-nucleotide polymorphism data from noncoding regions of the human genome. Both models of neutral mutation bias fit the frequency distributions of SNPs segregating in low- and medium-GC-content regions of the genome adequately, although both suggest compositional nonequilibrium. However, neither model fits the frequency distribution of SNPs from the high-GC-content regions. In contrast, a simple population genetics model that incorporates selection or biased gene conversion cannot be rejected. The results suggest that mutation biases are not solely responsible for the compositional biases found in noncoding regions.

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