scholarly journals Gigantic Genomes Can Provide Empirical Tests of TE Dynamics Models — An Example from Amphibians

2020 ◽  
Author(s):  
Jie Wang ◽  
Michael W. Itgen ◽  
Huiju Wang ◽  
Yuzhou Gong ◽  
Jianping Jiang ◽  
...  
Keyword(s):  
Genome Size ◽  
Evolutionary Dynamics ◽  
Diversity Indices ◽  
Anatomy And Physiology ◽  
A Genome ◽  
History Of ◽  
Empirical Tests ◽  
And Function ◽  
Dynamics Models

AbstractTransposable elements (TEs) are a major determinant of eukaryotic genome size. The collective properties of a genomic TE community reveal the history of TE/host evolutionary dynamics and impact present-day host structure and function, from genome to organism levels. In rare cases, TE community/genome size has greatly expanded in animals, associated with increased cell size and altered anatomy and physiology. We characterize the TE landscape of the genome and transcriptome in an amphibian with a giant genome — the caecilian Ichthyophis bannanicus, which we show has a genome size of 12.2 Gb. Amphibians are an important model system because the clade includes independent cases of genomic gigantism. The I. bannanicus genome differs compositionally from other giant amphibian genomes, but shares a low rate of ectopic-recombination-mediated deletion. We examine TE activity using expression and divergence plots; TEs account for 15% of somatic transcription, and most superfamilies appear active. We quantify TE diversity in the caecilian, as well as other vertebrates with a range of genome sizes, using diversity indices commonly applied in community ecology. We synthesize previous models integrating TE abundance, diversity, and activity, and we test whether the caecilian meets model predictions for genomes with high TE abundance. We propose thorough, consistent characterization of TEs to strengthen future comparative analyses. Such analyses will ultimately be required to reveal whether the divergent TE assemblages found across convergent gigantic genomes reflect fundamental shared features of TE/host genome evolutionary dynamics.

Microarray-Based Characterization of Microbial Community Functional Structure and Heterogeneity Associated with Acid Mine Drainages

2015 ◽  
Vol 1130 ◽  
pp. 40-44 ◽  
Author(s):  
Li Shen ◽  
Hua Qun Yin ◽  
Qi Hu ◽  
Xue Duan Liu ◽  
Guan Zhou Qiu
Keyword(s):  
Microbial Communities ◽  
Geographic Distribution ◽  
Mine Drainage ◽  
Diversity Indices ◽  
Aquatic Life ◽  
Acid Mine ◽  
Composition And Structure ◽  
Composition Structure ◽  
And Function

Acid mine drainage (AMD) presents numerous problems to the aquatic life and surrounding ecosystems. However, little is known about the geographic distribution, diversity, composition, structure and function of AMD microbial communities. In this study, an AMD-specific microarray was used to analyze nine AMD microbial communities, and showed that those nine AMD microbial communities had high variations measured by the number of detected genes, overlapping genes between samples, unique genes, and diversity indices. Statistical analyses indicated that the concentrations of Fe, S, Ca, Mg, Zn, Cu and pH had strong impacts on both phylogenetic and functional diversity, composition, and structure of AMD microbial communities. This study provides insights into our understanding of the geographic distribution, diversity, composition, structure and functional potential of AMD microbial communities and key environmental factors shaping them.

scholarly journals Partial Characterization of Bacteriophages from Indonesia and its Potency as Biocontrol of Xanthomonas oryzae pv. oryzae

2021 ◽  
Vol 25 (01) ◽  
pp. 75-80
Author(s):  
Desi Rejeki
Keyword(s):  
Biological Control ◽  
Genome Size ◽  
Crop Production ◽  
Xanthomonas Oryzae ◽  
Biological Control Agents ◽  
Vitro Assay ◽  
Resistant Varieties ◽  
A Genome

Bacterial leaf blight (BLB) is a disease caused by Xanthomonas oryzae pv. oryzae (Xoo) of rice in rice-producing countries including Indonesia and attack rice in all stages of growth. In the advanced, crop production will be decreased by up to 50–70%. Recently, the practical efforts to overcome the problem by using resistant varieties, antibiotics, and sanitation; however, the ability of the pathogen to forms the new virulent pathotypes is noteworthy. Alternatively, the pathogen could be environmental-friendly controlled by utilizing bacteriophages as biological control agents because of their specific characteristics to their bacterial hosts. This research aimed to obtain information about the characteristic of the first isolated bacteriophages from Indonesia. The result showed that two bacteriophages had been isolated from soil in Arjasa Jember and soil in Gadingan Situbondo, namely phage XooX1IDN and phage XooX2IDN, respectively. The two phages were inactivated at 80ºC and stable at pH within the range of 6 to 8. The phage XooX1IDN has a genome size of approximately 39 kb, while phage XooX2IDN had a genome size 38 kb. Morphologically, both phages possessed the family of Myoviridae. Phage biocontrol in vitro assay showed that both phages significantly reduced the growth of BLB pathogen, indicating that both phages potentially, as biological control agents for BLB disease in rice. © 2021 Friends Science Publishers

Spinoza on Reason

2017 ◽  
Author(s):  
Michael LeBuffe
Keyword(s):  
Moral Theory ◽  
Historical Context ◽  
Human Mind ◽  
History Of Philosophy ◽  
History Of ◽  
And Function ◽  
Meaning And Function

In metaphysics, Spinoza associates reasons with causes or explanations. He contends that there is a reason for whatever exists and whatever does not exist. In his account of the human mind, Spinoza makes reason a peculiarly powerful kind of idea and the only source of our knowledge of objects in experience. In his moral theory, Spinoza introduces dictates of reason, which are action-guiding prescriptions. In politics, Spinoza suggests that reason, with religion, motivates cooperation in society. Reason shapes Spinoza’s philosophy, and central debates about Spinoza—including his place in the history of philosophy and in the European Enlightenment—turn upon our understanding of these claims. Spinoza on Reason starts with striking claims in each of these areas drawn from Spinoza’s two great works, the Ethics and the Theological Political Treatise; the book takes each characterization of reason on its own terms, explaining the claims and their historical context. While acknowledging the striking variety of reason’s roles, this work emphasizes the extent to which these different doctrines build upon one another. The result is a rich understanding of the meaning and function of each claim and, in the book’s conclusion, a detailed and accurate account of the contribution of reason to the systematic coherence of Spinoza’s philosophy.

A) Coagulation Proteins and Inhibitors: Cold-Insoluble Globulin (Clg), a Circulating Cell Surface Protein

1977 ◽  
Vol 38 (04) ◽  
pp. 0742-0750 ◽  
Author(s):  
Michael W. Mosesson
Keyword(s):  
Surface Protein ◽  
Cell Surface Protein ◽  
Cell Surfaces ◽  
Subsequent Growth ◽  
Coagulation Proteins ◽  
Growth Of Knowledge ◽  
History Of ◽  
Cold Insoluble Globulin ◽  
And Function

SummaryThe history of the discovery and characterization of the cold-insoluble globulin of plasma (Clg) is reviewed. Subsequent growth of knowledge relating to its structure and function in plasma, in tissues, and on cell surfaces is examined.

scholarly journals Caracterização de modelos sobre Tectónica de Placas em manuais escolares no ensino da Geologia

2019 ◽  
Vol 20 ◽  
pp. 265-274
Author(s):  
Paula Faustino ◽  
Pedro Callapez ◽  
Ana Rola ◽  
Elsa Gomes
Keyword(s):  
Higher Education ◽  
History Of Science ◽  
Scientific Literacy ◽  
Plate Tectonics ◽  
Teaching And Learning ◽  
Teaching Models ◽  
History Of ◽  
Constructivist Perspective ◽  
And Function

Resumo Neste estudo foi feita uma caracterização de modelos sobre a Tectónica de Placas, de acordo com a sua tipologia e função, presentes em manuais de Geologia, do ensino secundário e do 1.o ciclo do ensino superior, utilizados em Portugal. Os resultados indicam que, quanto à tipologia, os manuais apresentam poucos elementos sobre História da Ciência. No entanto, a diversidade de modelos presente nos manuais, relativamente à sua função, deve facilitar o ensino e aprendizagem da Tectónica de Placas, numa perspetiva holística e construtivista, contribuindo significativamente para a melhoria do nível de literacia científica do aluno. Palavras-chave: Modelos de ensino; Tipologia e função; Ensino secundário e superior.Abstract This study deals with the characterization of Plate Tectonics models according to their typology and function, from school textbooks of Geology used in secondary and higher education in Portugal. The results of a typological analysis suggest that all these textbooks contain few elements about History of Science. However, when their function is concerned, the diversity of models should facilitate the teaching and learning of Plate Tectonics in a holistic and constructivist perspective, being a significant contribute to improve the scientific literacy of the student. Keywords: Teaching models; Typology and function; Secondary and higher education.

scholarly journals Genome-wide features of introns are evolutionary decoupled among themselves and from genome size throughout Eukarya

2018 ◽  
Author(s):  
Irma Lozada-Chávez ◽  
Peter F. Stadler ◽  
Sonja J. Prohaska
Keyword(s):  
Genome Size ◽  
Evolutionary Dynamics ◽  
Protein Coding ◽  
Specific Level ◽  
Spliceosomal Introns ◽  
Major Mechanism ◽  
Genome Wide ◽  
A Genome ◽  
Eukaryotic Gene ◽  
The Impact

AbstractThe impact of spliceosomal introns on genome and organismal evolution remains puzzling. Here, we investigated the correlative associations among genome-wide features of introns from protein-coding genes (e.g., size, density, genome-content, repeats), genome size and multicellular complexity on 461 eukaryotes. Thus, we formally distinguished simple from complex multicellular organisms (CMOs), and developed the program GenomeContent to systematically estimate genomic traits. We performed robust phylogenetic controlled analyses, by taking into account significant uncertainties in the tree of eukaryotes and variation in genome size estimates. We found that changes in the variation of some intron features (such as size and repeat composition) are only weakly, while other features measuring intron abundance (within and across genes) are not, scaling with changes in genome size at the broadest phylogenetic scale. Accordingly, the strength of these associations fluctuates at the lineage-specific level, and changes in the length and abundance of introns within a genome are found to be largely evolving independently throughout Eukarya. Thereby, our findings are in disagreement with previous estimations claiming a concerted evolution between genome size and introns across eukaryotes. We also observe that intron features vary homogeneously (with low repetitive composition) within fungi, plants and stramenophiles; but they vary dramatically (with higher repetitive composition) within holozoans, chlorophytes, alveolates and amoebozoans. We also found that CMOs and their closest ancestral relatives are characterized by high intron-richness, regardless their genome size. These patterns contrast the narrow distribution of exon features found across eukaryotes. Collectively, our findings unveil spliceosomal introns as a dynamically evolving non-coding DNA class and strongly argue against both, a particular intron feature as key determinant of eukaryotic gene architecture, as well as a major mechanism (adaptive or non-adaptive) behind the evolutionary dynamics of introns over a large phylogenetic scale. We hypothesize that intron-richness is a pre-condition to evolve complex multicellularity.

Quantitative and qualitative genomic characterization of cultivated Ilex L. species

2014 ◽  
Vol 13 (2) ◽  
pp. 142-152 ◽  
Author(s):  
Alexandra Marina Gottlieb ◽  
Lidia Poggio
Keyword(s):  
Genome Size ◽  
Repetitive Dna ◽  
Dna Sequences ◽  
Sequence Data ◽  
Repetitive Sequences ◽  
Representational Difference Analysis ◽  
Ilex Paraguariensis ◽  
Repetitive Dna Sequences ◽  
A Genome

The development of modern approaches to the genetic improvement of the tree crops Ilex paraguariensis (‘yerba mate’) and Ilex dumosa (‘yerba señorita’) is halted by the scarcity of basic genetic information. In this study, we characterized the implementation of low-cost methodologies such as representational difference analysis (RDA), single-strand conformation polymorphisms (SSCP), and reverse and direct dot-blot filter hybridization assays coupled with thorough bioinformatic characterization of sequence data for both species. Also, we estimated the genome size of each species using flow cytometry. This study contributes to the better understanding of the genetic differences between two cultivated species, by generating new quantitative and qualitative genome-level data. Using the RDA technique, we isolated a group of non-coding repetitive sequences, tentatively considered as Ilex-specific, which were 1.21- to 39.62-fold more abundant in the genome of I. paraguariensis. Another group of repetitive DNA sequences involved retrotransposons, which appeared 1.41- to 35.77-fold more abundantly in the genome of I. dumosa. The genomic DNA of each species showed different performances in filter hybridizations: while I. paraguariensis showed a high intraspecific affinity, I. dumosa exhibited a higher affinity for the genome of the former species (i.e. interspecific). These differences could be attributed to the occurrence of homologous but slightly divergent repetitive DNA sequences, highly amplified in the genome of I. paraguariensis but not in the genome of I. dumosa. Additionally, our hybridization outcomes suggest that the genomes of both species have less than 80% similarity. Moreover, for the first time, we report herein a genome size estimate of 1670 Mbp for I. paraguariensis and that of 1848 Mbp for I. dumosa.

scholarly journals The effect of population bottleneck size and selective regime on genetic diversity and evolvability in bacteria

2019 ◽  
Author(s):  
Tanita Wein ◽  
Tal Dagan
Keyword(s):  
Genetic Diversity ◽  
Evolutionary Dynamics ◽  
Natural Populations ◽  
Population Bottleneck ◽  
Population Bottlenecks ◽  
High Genetic Diversity ◽  
Temperature Regimes ◽  
Consequent Reduction ◽  
History Of

Abstract Population bottlenecks leading to a drastic reduction of the population size are common in the evolutionary dynamics of natural populations; their occurrence is known to have implications for genome evolution due to genetic drift, the consequent reduction in genetic diversity and the rate of adaptation. Nevertheless, an empirical characterization of the effect of population bottleneck size on evolutionary dynamics of bacteria is currently lacking. Here we show that selective conditions have a stronger effect on the evolutionary history of bacteria in comparison to population bottlenecks. We evolved Escherichia coli populations under three different population bottleneck sizes (small, medium, large) in two temperature regimes (37 °C and 20 °C). We find a high genetic diversity in the large in comparison to the small bottleneck size. Nonetheless, the cold temperature led to reduced genetic diversity regardless the bottleneck size, hence, the temperature has a stronger effect on the genetic diversity in comparison to the bottleneck size. A comparison of the fitness gain among the evolved populations reveals a similar pattern where the temperature has a significant effect on the fitness. Our study demonstrates that population bottlenecks are an important determinant of bacterial evolvability; their consequences depend on the selective conditions and are best understood via their effect on the standing genetic variation.

scholarly journals Characterization of the Heavy-Metal-Associated Isoprenylated Plant Protein (HIPP) Gene Family from Triticeae Species

2020 ◽  
Vol 21 (17) ◽  
pp. 6191 ◽  
Author(s):  
Heng Zhang ◽  
Xu Zhang ◽  
Jia Liu ◽  
Ying Niu ◽  
Yiming Chen ◽  
...  
Keyword(s):  
Heavy Metal ◽  
Root Growth Inhibition ◽  
Biotic Stresses ◽  
Cd Tolerance ◽  
Triticeae Species ◽  
Genome Wide ◽  
A Genome ◽  
Localization Analysis ◽  
And Function

Heavy-metal-associated (HMA) isoprenylated plant proteins (HIPPs) only exist in vascular plants. They play important roles in responses to biotic/abiotic stresses, heavy-metal homeostasis, and detoxification. However, research on the distribution, diversification, and function of HIPPs in Triticeae species is limited. In this study, a total of 278 HIPPs were identified from a database from five Triticeae species, and 13 were cloned from Haynaldia villosa. These genes were classified into five groups by phylogenetic analysis. Most HIPPs had one HMA domain, while 51 from Clade I had two, and all HIPPs had good collinear relationships between species or subgenomes. In silico expression profiling revealed that 44 of the 114 wheat HIPPs were dominantly expressed in roots, 43 were upregulated under biotic stresses, and 29 were upregulated upon drought or heat treatment. Subcellular localization analysis of the cloned HIPPs from H. villosa showed that they were expressed on the plasma membrane. HIPP1-V was upregulated in H. villosa after Cd treatment, and transgenic wheat plants overexpressing HIPP1-V showed enhanced Cd tolerance, as shown by the recovery of seed-germination and root-growth inhibition by supplementary Cd. This research provides a genome-wide overview of the Triticeae HIPP genes and proved that HIPP1-V positively regulates Cd tolerance in common wheat.

scholarly journals Genome-Wide Identification of TCP Transcription Factors Family in Sweet Potato Reveals Significant Roles of miR319-Targeted TCPs in Leaf Anatomical Morphology

2021 ◽  
Vol 12 ◽  
Author(s):  
Lei Ren ◽  
Haixia Wu ◽  
Tingting Zhang ◽  
Xinyu Ge ◽  
Tianlong Wang ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Sweet Potato ◽  
Binding Sites ◽  
Ipomoea Batatas ◽  
Expression Profiles ◽  
Submicroscopic Structure ◽  
Genome Wide ◽  
A Genome ◽  
And Function

Plant-specific TCP transcription factors play vital roles in the controlling of growth, development, and the stress response processes. Extensive researches have been carried out in numerous species, however, there hasn’t been any information available about TCP genes in sweet potato (Ipomoea batatas L.). In this study, a genome-wide analysis of TCP genes was carried out to explore the evolution and function in sweet potato. Altogether, 18 IbTCPs were identified and cloned. The expression profiles of the IbTCPs differed dramatically in different organs or different stages of leaf development. Furthermore, four CIN-clade IbTCP genes contained miR319-binding sites. Blocking IbmiR319 significantly increased the expression level of IbTCP11/17 and resulted in a decreased photosynthetic rate due to the change in leaf submicroscopic structure, indicating the significance of IbmiR319-targeted IbTCPs in leaf anatomical morphology. A systematic analyzation on the characterization of the IbTCPs together with the primary functions in leaf anatomical morphology were conducted to afford a basis for further study of the IbmiR319/IbTCP module in association with leaf anatomical morphology in sweet potato.

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