scholarly journals Massive rhizobial genomic variations associated with partner quality in Lotus–Mesorhizobium symbiosis

2020 ◽  
Author(s):  
Masaru Bamba ◽  
Seishiro Aoki ◽  
Tadashi Kajita ◽  
Hiroaki Setoguchi ◽  
Yasuyuki Watano ◽  
...  
Keyword(s):  
Core Genome ◽  
De Novo ◽  
Lotus Japonicus ◽  
The Novel ◽  
Associated Bacteria ◽  
Association Analyses ◽  
Genomic Variations ◽  
The Core ◽  
Genome Variations

ABSTRACTIn diverse mutualistic relationships, genetic variations in impact on the growth of interacting partners—variations in partner quality—are common, despite the theoretical prediction that selection favoring high-quality partners should eliminate such variations. Here, we investigated how variations in partner quality could be maintained in the nitrogen-fixing mutualism between Lotus japonicus and Mesorhizobium bacteria. We reconstructed de novo assembled full-genome sequences from nine rhizobial symbionts, finding massive variations in the core genome and the contrastingly similar symbiotic islands, indicating recent horizontal gene transfer (HGT) of the symbiosis islands into diverse Mesorhizobium lineages. A cross-inoculation experiment using nine sequenced rhizobial symbionts and 15 L. japonicus accessions revealed extensive quality variations represented by plant growth phenotypes, including genotype-by-genotype interactions. Quality variations were not associated with the presence/absence variations of known symbiosis-related genes in the symbiosis island, but rather, showed significant correlations with the core genome variations, supported by SNP- and kinship matrix-based association analyses. These findings highlight the novel role of HGT of symbiosis islands, which indirectly supply mutations of core genomes into L. japonicus-associated bacteria, thereby contributing to the maintenance of variations in partner quality.

scholarly journals Massive rhizobial genomic variation associated with partner quality in Lotus–Mesorhizobium symbiosis

2020 ◽  
Vol 96 (12) ◽  
Author(s):  
Masaru Bamba ◽  
Seishiro Aoki ◽  
Tadashi Kajita ◽  
Hiroaki Setoguchi ◽  
Yasuyuki Watano ◽  
...  
Keyword(s):  
Core Genome ◽  
De Novo ◽  
Lotus Japonicus ◽  
Genomic Variation ◽  
The Novel ◽  
High Quality ◽  
Cooperative Relationships ◽  
The Core ◽  
Quality Variation

ABSTRACT Variation in partner quality is commonly observed in diverse cooperative relationships, despite the theoretical prediction that selection favoring high-quality partners should eliminate such variation. Here, we investigated how genetic variation in partner quality could be maintained in the nitrogen-fixing mutualism between Lotus japonicus and Mesorhizobium bacteria. We reconstructed de novo assembled full-genome sequences from nine rhizobial symbionts, finding massive variation in the core genome and the similar symbiotic islands, indicating recent horizontal gene transfer (HGT) of the symbiosis islands into diverse Mesorhizobium lineages. A cross-inoculation experiment using 9 sequenced rhizobial symbionts and 15 L. japonicus accessions revealed extensive quality variation represented by plant growth phenotypes, including genotype-by-genotype interactions. Variation in quality was not associated with the presence/absence variation in known symbiosis-related genes in the symbiosis island; rather, it showed significant correlation with the core genome variation. Given the recurrent HGT of the symbiosis islands into diverse Mesorhizobium strains, local Mesorhizobium communities could serve as a major source of variation for core genomes, which might prevent variation in partner quality from fixing, even in the presence of selection favoring high-quality partners. These findings highlight the novel role of HGT of symbiosis islands in maintaining partner quality variation in the legume–rhizobia symbiosis.

scholarly journals A novel hybrid of Hypericum undulatum (Wavy-leaved St. John’s-wort, Hypericaceae) and its subsequent dispersal

2020 ◽  
Vol 2 (3) ◽  
Author(s):  
Andrew Jones ◽  
Fred Rumsey
Keyword(s):  
De Novo ◽  
Parental Species ◽  
Species Range ◽  
The Novel ◽  
The Core ◽  
St John’S Wort ◽  
St John's Wort ◽  
Core Site

The novel hybrid Hypericum undulatum Schousb. ex. Willd. x H. perforatum L. is described from Cardiganshire (v.c.46) and given the name H. x cereticae R.A. Jones, F.J. Rumsey & N. Robson.  Despite reduced fertility it shows indications of ongoing introgression and signs of recent dispersal up to 5 km from the core site. The hybrid has arisen recently at the northern extremes of the rarer (H. undulatum) parental species’ range, although at neither site are the parents currently sympatric and in the outlying population both are absent, supporting the belief that here it has not arisen de novo but has colonised through unknown agencies.

scholarly journals CGT-seq: epigenome-guided de novo assembly of the core genome for divergent populations with large genome

2018 ◽  
Vol 46 (18) ◽  
pp. e107-e107 ◽  
Author(s):  
Meifang Qi ◽  
Zijuan Li ◽  
Chunmei Liu ◽  
Wenyan Hu ◽  
Luhuan Ye ◽  
...  
Keyword(s):  
De Novo Assembly ◽  
Core Genome ◽  
De Novo ◽  
Large Genome ◽  
The Core

scholarly journals Rare and de novo variants in 827 congenital diaphragmatic hernia probands implicate LONP1 and ALYREF as new candidate risk genes

2021 ◽  
Author(s):  
Lu Qiao ◽  
Le Xu ◽  
Lan Yu ◽  
Julia Wynn ◽  
Rebecca Hernan ◽  
...  
Keyword(s):  
Congenital Diaphragmatic Hernia ◽  
Diaphragmatic Hernia ◽  
Rare Variants ◽  
De Novo ◽  
Disease Genes ◽  
Risk Genes ◽  
Association Analyses ◽  
Significant Enrichment ◽  
Coding Variants

Congenital diaphragmatic hernia (CDH) is a severe congenital anomaly that is often accompanied by other anomalies. Although the role of genetics in the pathogenesis of CDH has been established, only a small number of disease genes have been identified. To further investigate the genetics of CDH, we analyzed de novo coding variants in 827 proband-parent trios and confirmed an overall significant enrichment of damaging de novo variants, especially in constrained genes. We identified LONP1 (Lon Peptidase 1, Mitochondrial) and ALYREF (Aly/REF Export Factor) as novel candidate CDH genes based on de novo variants at a false discovery rate below 0.05. We also performed ultra-rare variant association analyses in 748 cases and 11,220 ancestry-matched population controls and identified LONP1 as a risk gene contributing to CDH through both de novo and ultra-rare inherited largely heterozygous variants clustered in the core of the domains and segregating with CDH in familial cases. Approximately 3% of our CDH cohort was heterozygous with ultra-rare predicted damaging variants in LONP1 who have a range of clinical phenotypes including other anomalies in some individuals and higher mortality and requirement for extracorporeal membrane oxygenation. Mice with lung epithelium specific deletion of Lonp1 die immediately after birth and have reduced lung growth and branching that may at least partially explain the high mortality in humans. Our findings of both de novo and inherited rare variants in the same gene may have implications in the design and analysis for other genetic studies of congenital anomalies.

scholarly journals Animation in the Core of Dystopia: Ari Folman’s The Congress

Animation ◽  
2019 ◽  
Vol 14 (3) ◽  
pp. 222-234
Author(s):  
María Lorenzo Hernández
Keyword(s):  
Virtual Reality ◽  
Augmented Reality ◽  
Production System ◽  
Film Industry ◽  
The Novel ◽  
Star System ◽  
The Core ◽  
Human Thought ◽  
Changing Role

Ari Folman’s The Congress (2013) borrows freely from Stanisław Lem’s dystopian view in his Sci-fi novel The Futurological Congress (1971) to propose the gradual dissolution of the human into an artificial form, which is animation. By moving the action of the novel from a hypothetical future to contemporary Hollywood, Ari Folman gives CGI animation the role of catalyst for changes not only in the production system, but for human thought and, therefore, for society. This way, the film ponders the changing role of performers at the time of their digitalization, as well as on the progressive dematerialization of the film industry, considering a dystopian future where simulation fatally displaces reality, which invites relating The Congress with Jean Baudrillard’s and Alan Cholodenko’s theses on how animating technologies have resulted in the culture of erasing. Moreover, this article highlights how Lem’s metaphor of the manipulation of information in the Soviet era is transformed in the second part of The Congress into a vision of cinema as a collective addiction, relating it to Alexander Dovzhenko’s and Edgar Morin’s speculative theories of total film – which come close to the potentialities of today’s Virtual Reality and Augmented Reality. In addition, although The Congress is a disturbing view of film industry and animating technologies, its vision of film is nostalgically retro as it vindicates an entire tradition of Golden Age animation that transformed the star system into cartoons, suggesting the fictionalization of their lives and establishing a postmodern continuum between animation and film.

scholarly journals Leon Petrażycki on Norms and Their Logical Study

Studia Humana ◽  
2018 ◽  
Vol 7 (4) ◽  
pp. 30-38 ◽  
Author(s):  
Elena Lisanyuk ◽  
Evelina Barbashina
Keyword(s):  
Legal Theory ◽  
The Novel ◽  
The Core ◽  
Logical Study ◽  
Normative Relation

Abstract In this paper we discuss L. Petrażycki’s idea of norm as a normative relation and show its repercussions in two perspectives connected to each other, in the legal theory in the framework of which it was originally introduced and where its role was straightforward, and in logic where it played a shadowy role of a fresh idea which in his expectation would have been the core of the novel logical theories capable of modelling reasoning in law and morals. We pay attention to the scholarly environment in which Petrażycki has proposed those ideas and to the unlucky fate of his academic legacy which is now being rediscovered.

scholarly journals Evidence of Extensive Homologous Recombination in the Core Genome ofRickettsia

2009 ◽  
Vol 2009 ◽  
pp. 1-5 ◽  
Author(s):  
Jinyu Wu ◽  
Tonghai Yu ◽  
Qiyu Bao ◽  
Fangqing Zhao
Keyword(s):  
Homologous Recombination ◽  
Pathogenic Bacteria ◽  
Core Genome ◽  
Phylogenetic Network ◽  
Genomic Analysis ◽  
Intracellular Bacteria ◽  
The Core ◽  
Evolutionary Genomic ◽  
The Impact

The important role of homologous recombination has been extensively demonstrated to be fundamental for genetic variation in bacterial genomes. In contrast to extracellular or facultative intracellular bacteria, obligate intracellular bacteria are considered to be less prone to recombination, especially for their core genomes. InRickettsia, only antigen-related genes were identified to have experienced homologous recombination. In this study, we employed evolutionary genomic approaches to investigate the impact of recombination on the core genome ofRickettsia. Phylogenetic network and phylogenetic compatibility matrix analyses are clearly consistent with the hypothesis that recombination has occurred frequently duringRickettsiaevolution. 28% ofRickettsiacore genes (194 out of 690) are found to present the evidence of recombination under four independent statistical methods. Further functional classification shows that these recombination events occur across all functional categories, with a significant overrepresentation in the cell wall/membrane/envelope biogenesis, which may provide a molecular basis for the parasite adaptation to host immunity. This evolutionary genomic analysis provides insight into the substantial role of recombination in the evolution of the intracellular pathogenic bacteriaRickettsia.

scholarly journals Feminist dystopian consciousness in margaret atwood’s the handmaid's tale

2018 ◽  
Vol 4 (4) ◽  
pp. 1-9
Author(s):  
Fatima Zahra El Arbaoui
Keyword(s):  
Women's Rights ◽  
Female Gender ◽  
Feminist Movement ◽  
Women’S Rights ◽  
The Novel ◽  
The Core ◽  
Feminist Consciousness ◽  
Rights Issue

Margaret Atwood's famous dystopian novel, The Handmaid’s tale, was written in 1985 during the emergence of the opposition to the feminist movement. The struggle that occurred between both parties of the women's rights issue excited Atwood, as an active advocate of this movement, to write this novel to alert women of what the female gender may mislay if the feminist movement were defeated. She has attempted to warn her readers through the life of Offred; a handmaid who expresses her dystopian feminist consciousness by taking the role of a storyteller and being the narrator and controller of her own story. The core aim of this article would be to focus on how Offred combines her feminist consciousness, memories, and language as liberty instruments to detect her way towards freedom? How can this consciousness be the seed which grows into the sapling of self-expression she cultivates and nourishes through the novel?

scholarly journals Ecofeminism in Doris Lessing’s Mara and Dann: An Adventure

2017 ◽  
Author(s):  
AWEJ-tls for Translation & Literary Studies ◽  
Najla R. Aldeeb
Keyword(s):  
Global Warming ◽  
The Novel ◽  
Female Characters ◽  
The Core ◽  
The Future ◽  
Male Dominated ◽  
Liberal Culture

Doris Lessing's Mara and Dann: An Adventure (1999) is a fantasy novel with focus on nature. Lessing portrays a world in which oppression by a male-dominated society is at the root of countless problems. It depicts the effects of global warming in the future emphasizing that the domination of women is the core of all crises in the environment. The novel implies that women are able to lead as most of the female characters in the novel play the role of the leader starting from Daima, the woman who protects Mara and Dann as children, to Orphne the woman who heals Dann from addiction. Applying Greta Claire Gaard’s (1993) principles of ecofeminism to literature classifies and justifies the cause of the movement (p. 20). This paper sheds light on Gaard’s four types of ecofeminism in Lessing’s Rama and Dann: An Adventure: liberal, culture, social and socialist by discussing the apocalypses, patriarchal legacy, pathetic fallacy and radical orthodoxies as features of ecofeminism.

scholarly journals Ceramide metabolite, not intact ceramide molecule, may be responsible for cellular toxicity

2004 ◽  
Vol 380 (3) ◽  
pp. 715-722 ◽  
Author(s):  
Kou-Yi TSERNG ◽  
Ronda L. GRIFFIN
Keyword(s):  
De Novo ◽  
Solvent Mixture ◽  
Solvent Mixtures ◽  
Distribution Analysis ◽  
The Novel ◽  
Cell Toxicity ◽  
Stable Isotope Labelling ◽  
Mass Isotopomer Distribution Analysis ◽  
Hydrolysis Of

Ceramides, which are produced from the hydrolysis of sphingomyelin or synthesized from serine and palmitate in a de novo pathway, are regarded as important cellular signals for inducing apoptosis. However, controversy over this proposed role of ceramides exists. Using stable isotope labelling coupled with GC (gas chromatography)-MS and mass isotopomer distribution analysis, we have studied the metabolism of exogenous long-chain ceramides in HL60 cells. Our results do not support the concept of enhanced ceramide transport into cells induced by solvent mixtures of ethanol and hydrocarbons. In addition, cell toxicity does not correlate with the amount of intact ceramide in the cells. Our results are more consistent with a disturbance of sphingomyelin metabolism induced by the solvent mixture. The characteristics of this disturbed sphingolipid disposition are the inhibition of dihydroceramide desaturation and an enhanced degradation of sphingomyelin. As a consequence, dihydroceramides accumulate and the cellular sphingomyelin content decreases. Inhibition of these pathways is most likely to be induced by the increased production of novel ceramide metabolites instead of by intact ceramides. Octadecane-1,2-diol is identified as a possible mediator. Treatments that divert ceramide degradation to the novel pathway are potential strategies in cancer therapy for inducing cell toxicity.

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