scholarly journals A Reappraisal of the Evolutionary and Developmental Pathway of Apomixis and Its Genetic Control in Angiosperms

Genes ◽  
2020 ◽  
Vol 11 (8) ◽  
pp. 859 ◽  
Author(s):  
Gianni Barcaccia ◽  
Fabio Palumbo ◽  
Sergio Sgorbati ◽  
Emidio Albertini ◽  
Fulvio Pupilli
Keyword(s):  
Genetic Control ◽  
Unsolved Problem ◽  
Sensu Stricto ◽  
Developmental Pathways ◽  
Basal Angiosperm ◽  
Loss Of Function ◽  
Developmental Pathway ◽  
Model Species ◽  
Angiosperm Evolution ◽  
Recent Developments

Apomixis sensu stricto (agamospermy) is asexual reproduction by seed. In angiosperms it represents an easy byway of life cycle renewal through gamete-like cells that give rise to maternal embryos without ploidy reduction (meiosis) and ploidy restitution (syngamy). The origin of apomixis still represents an unsolved problem, as it may be either evolved from sex or the other way around. This review deals with a reappraisal of the origin of apomixis in order to deepen knowledge on such asexual mode of reproduction which seems mainly lacking in the most basal angiosperm orders (i.e., Amborellales, Nymphaeales and Austrobaileyales, also known as ANA-grade), while it clearly occurs in different forms and variants in many unrelated families of monocots and eudicots. Overall findings strengthen the hypothesis that apomixis as a whole may have evolved multiple times in angiosperm evolution following different developmental pathways deviating to different extents from sexuality. Recent developments on the genetic control of apomixis in model species are also presented and adequately discussed in order to shed additional light on the antagonist theories of gain- and loss-of-function over sexuality.

scholarly journals Fossil evidence for low gas exchange capacities for Early Cretaceous angiosperm leaves

Paleobiology ◽  
2011 ◽  
Vol 37 (2) ◽  
pp. 195-213 ◽  
Author(s):  
Taylor S. Feild ◽  
Garland R. Upchurch ◽  
David S. Chatelet ◽  
Timothy J. Brodribb ◽  
Kunsiri C. Grubbs ◽  
...  
Keyword(s):  
Gas Exchange ◽  
Early Cretaceous ◽  
Leaf Gas Exchange ◽  
Exchange Capacity ◽  
Basal Angiosperm ◽  
Photosynthetic Gas Exchange ◽  
Angiosperm Evolution ◽  
Early Angiosperm ◽  
Fossil Evidence ◽  
Functional Analyses

The photosynthetic gas exchange capacities of early angiosperms remain enigmatic. Nevertheless, many hypotheses about the causes of early angiosperm success and how angiosperms influenced Mesozoic ecosystem function hinge on understanding the maximum capacity for early angiosperm metabolism. We applied structure-functional analyses of leaf veins and stomatal pore geometry to determine the hydraulic and diffusive gas exchange capacities of Early Cretaceous fossil leaves. All of the late Aptian—early Albian angiosperms measured possessed low vein density and low maximal stomatal pore area, indicating low leaf gas exchange capacities in comparison to modern ecologically dominant angiosperms. Gas exchange capacities for Early Cretaceous angiosperms were equivalent or lower than ferns and gymnosperms. Fossil leaf taxa from Aptian to Paleocene sediments previously identified as putative stem-lineages to Austrobaileyales and Chloranthales had the same gas exchange capacities and possibly leaf water relations of their living relatives. Our results provide fossil evidence for the hypothesis that high leaf gas exchange capacity is a derived feature of later angiosperm evolution. In addition, the leaf gas exchange functions of austrobaileyoid and chloranthoid fossils support the hypothesis that comparative research on the biology of living basal angiosperm lineages reveals genuine signals of Early Cretaceous angiosperm ecophysiology.

scholarly journals Epigenomic regulation of heart failure: integrating histone marks, long noncoding RNAs, and chromatin architecture

F1000Research ◽  
2018 ◽  
Vol 7 ◽  
pp. 1713 ◽  
Author(s):  
Timothy A. McKinsey ◽  
Thomas M. Vondriska ◽  
Yibin Wang
Keyword(s):  
Heart Failure ◽  
Therapeutic Potential ◽  
Noncoding Rnas ◽  
Loss Of Function ◽  
Sequencing Technologies ◽  
Recent Developments ◽  
Non Coding Rnas ◽  
Epigenomic Regulation ◽  
Generation Sequencing ◽  
Epigenetic Processes

Epigenetic processes are known to have powerful roles in organ development across biology. It has recently been found that some of the chromatin modulatory machinery essential for proper development plays a previously unappreciated role in the pathogenesis of cardiac disease in adults. Investigations using genetic and pharmacologic gain- and loss-of-function approaches have interrogated the function of distinct epigenetic regulators, while the increased deployment of the suite of next-generation sequencing technologies have fundamentally altered our understanding of the genomic targets of these chromatin modifiers. Here, we review recent developments in basic and translational research that have provided tantalizing clues that may be used to unlock the therapeutic potential of the epigenome in heart failure. Additionally, we provide a hypothesis to explain how signal-induced crosstalk between histone tail modifications and long non-coding RNAs triggers chromatin architectural remodeling and culminates in cardiac hypertrophy and fibrosis.

The COP9 signalosome influences the epigenetic landscape of Arabidopsis thaliana

2018 ◽  
Vol 35 (16) ◽  
pp. 2718-2723 ◽  
Author(s):  
Tamir Tuller ◽  
Alon Diament ◽  
Avital Yahalom ◽  
Assaf Zemach ◽  
Shimshi Atar ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Methylation ◽  
Arabidopsis Thaliana ◽  
Gene Expression Regulation ◽  
Developmental Pathways ◽  
Cop9 Signalosome ◽  
Supplementary Information ◽  
Loss Of Function ◽  
Genome Wide ◽  
High Level

Abstract Motivation The COP9 signalosome is a highly conserved multi-protein complex consisting of eight subunits, which influences key developmental pathways through its regulation of protein stability and transcription. In Arabidopsis thaliana, mutations in the COP9 signalosome exhibit a number of diverse pleiotropic phenotypes. Total or partial loss of COP9 signalosome function in Arabidopsis leads to misregulation of a number of genes involved in DNA methylation, suggesting that part of the pleiotropic phenotype is due to global effects on DNA methylation. Results We determined and analyzed the methylomes and transcriptomes of both partial- and total-loss-of-function Arabidopsis mutants of the COP9 signalosome. Our results support the hypothesis that the COP9 signalosome has a global genome-wide effect on methylation and that this effect is at least partially encoded in the DNA. Our analyses suggest that COP9 signalosome-dependent methylation is related to gene expression regulation in various ways. Differentially methylated regions tend to be closer in the 3D conformation of the genome to differentially expressed genes. These results suggest that the COP9 signalosome has a more comprehensive effect on gene expression than thought before, and this is partially related to regulation of methylation. The high level of COP9 signalosome conservation among eukaryotes may also suggest that COP9 signalosome regulates methylation not only in plants but also in other eukaryotes, including humans. Supplementary information Supplementary data are available at Bioinformatics online.

Guwiyang Wurra–‘Fire Mouse’: a global gene knockout model for TSPO/PBR drug development, loss-of-function and mechanisms of compensation studies

2015 ◽  
Vol 43 (4) ◽  
pp. 553-558 ◽  
Author(s):  
Ryan J. Middleton ◽  
Guo-Jun Liu ◽  
Richard B. Banati
Keyword(s):  
Mitochondrial Permeability Transition ◽  
Gene Knockout ◽  
Physiological Role ◽  
Permeability Transition Pore ◽  
Permeability Transition ◽  
Benzodiazepine Receptor ◽  
Translocator Protein ◽  
Loss Of Function ◽  
Recent Developments

The highly conserved 18-kDa translocator protein (TSPO) or peripheral benzodiazepine receptor (PBR), is being investigated as a diagnostic and therapeutic target for disease conditions ranging from inflammation to neurodegeneration and behavioural illnesses. Many functions have been attributed to TSPO/PBR including a role in the mitochondrial permeability transition pore (MPTP), steroidogenesis and energy metabolism. In this review, we detail the recent developments in determining the physiological role of TSPO/PBR, specifically based on data obtained from the recently generated Tspo knockout mouse models. In addition to defining the role of TSPO/PBR, we also describe the value of Tspo knockout mice in determining the selectivity, specificity and presence of any off-target effects of TSPO/PBR ligands.

scholarly journals From genomes to function: haloarchaea as model organisms

Microbiology ◽  
2006 ◽  
Vol 152 (3) ◽  
pp. 585-590 ◽  
Author(s):  
Jörg Soppa
Keyword(s):  
High Efficiency ◽  
Biological Process ◽  
Molecular Genetic ◽  
High Salt ◽  
Halobacterium Salinarum ◽  
Model Organisms ◽  
Loss Of Function ◽  
Model Species ◽  
Chromosomal Genes ◽  
Biological Methods

Haloarchaea are adapted to high-salt environments and accumulate equally high salt concentrations in the cytoplasm. The genomes of representatives of six haloarchaeal genera have been fully or partially sequenced, allowing the analysis of haloarchaeal properties in silico. Transcriptome and proteome analyses have been established for Halobacterium salinarum and Haloferax volcanii. Genetic systems are available including methods that allow the fast in-frame deletion or modification of chromosomal genes. The high-efficiency transformation system of Hf. volcanii allows the isolation of genes essential for a biological process by complementation of loss-of-function mutants. For the analysis of haloarchaeal biology many molecular genetic, biochemical, structural and cell biological methods have been adapted to application at high salt concentrations. Recently it has become clear that several different mechanisms allow the adaptation of proteins to the high salt concentration of the cytoplasm. Taken together, the wealth of techniques available make haloarchaea excellent archaeal model species.

scholarly journals Postzygotic reproductive isolation established in the endosperm: mechanisms, drivers and relevance

2021 ◽  
Vol 376 (1826) ◽  
Author(s):  
Claudia Köhler ◽  
Katarzyna Dziasek ◽  
Gerardo Del Toro-De León
Keyword(s):  
Driving Forces ◽  
Diploid Species ◽  
Reproductive Function ◽  
Model Species ◽  
Angiosperm Evolution ◽  
Postzygotic Reproductive Isolation ◽  
Specific Manner ◽  
Parent Of Origin ◽  
Triploid Block ◽  
Epigenetic Processes

The endosperm is a developmental innovation of angiosperms that supports embryo growth and germination. Aside from this essential reproductive function, the endosperm fuels angiosperm evolution by rapidly establishing reproductive barriers between incipient species. Specifically, the endosperm prevents hybridization of newly formed polyploids with their non-polyploid progenitors, a phenomenon termed the triploid block. Furthermore, recently diverged diploid species are frequently reproductively isolated by endosperm-based hybridization barriers. Current genetic approaches have revealed a prominent role for epigenetic processes establishing these barriers. In particular, imprinted genes, which are expressed in a parent-of-origin-specific manner, underpin the interploidy barrier in the model species Arabidopsis . We will discuss the mechanisms establishing hybridization barriers in the endosperm, the driving forces for these barriers and their impact for angiosperm evolution. This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’

143 GENOMIC ASSESSMENT ASSOCIATIONS OF THE PATERNAL EFFECT FOR DAUGHTER FERTILITY TRAITS IN HOLSTEIN CATTLE

2016 ◽  
Vol 28 (2) ◽  
pp. 201
Author(s):  
A. A. Sermyagin ◽  
E. A. Gladyr ◽  
O. S. Romanenkova ◽  
A. N. Ermilov ◽  
G. Brem ◽  
...  
Keyword(s):  
Genomic Variation ◽  
Gestation Length ◽  
Holstein Cattle ◽  
Ministry Of Education ◽  
Loss Of Function ◽  
Scientific Organizations ◽  
A Genome ◽  
Recent Developments ◽  
Estimated Breeding Values ◽  
Fertility Traits

A worldwide decline of fertility in Holsteins requires the reliable evaluation of fertility traits. Because of the low heritability of most fertility traits, the reliabilities of bull estimated breeding values (EBV) for these traits are usually low. Recent developments in molecular genetics have opened the possibilities of identifying and using genomic variation that can significantly boost the reliabilities of EBV. Furthermore, some of the fertility problems can be caused by embryonic lethality due to LoF (loss of function) mutations. The objective of our study was to identify loci associated with fertility-related traits in Russian Holstein cattle and to evaluate the distribution of several LoF mutations associated with fertility in the Russian Holstein bull population. A genome-wide scan was performed on 195 progeny-tested and 61 young bulls genotyped with the 50K Illumina BeadChip (Illumina Inc., San Diego, CA, USA). The analysis was carried out using EBV for gestation length (GL), calving interval (CI), conception rate (CR), and days to the first insemination (DI) calculated by best linear unbiased prediction (BLUP) SM methodology. To increase the prediction reliability of associations, genomic EBV (GEBV) for young bulls were obtained using an genomic BLUP (GBLUP) approach. Furthermore, the bulls were genotyped by PCR or PCR-RFLP for LoF mutations in FANCI, APAF1, and GART genes, which are associated with brachyspina (BY) and fertility haplotypes HH1 and HH3. The single nucleotide polymorphism (SNP) quality check and association analysis was performed using Plink (1.09) software. In total, 43 101 SNP passed quality control. The average number of daughters per sire was ~215. Bonferroni correction test for detection significant associations was applied as P < 1.2E × 10–6. The values for heritability were 0.036, 0.063, 0.035, and 0.068 for GL, CI, CR, and DI, respectively. Frequencies of the late abortions and stillbirths were 1.7 and 3.6% respectively. We identified some SNP with direct significant effects for fertility-related traits: BTA-31636-no-rs on BTA1 for GL (P = 1.2E × 10–6), Hapmap26774-BTA-163037 on BTA27 for CI (P = 1.1E × 10–6), and ARS-BFGL-NGS-89711 on BTA27 for CR (P = 2.1E × 10–7). One SNP (ARS-BFGL-NGS-92135) was found on BTA10 that was close to being significant for DI (P = 2.8E × 10–6). The direct EBV effect of SNP (R2) ranged from 8.4 to 9.0% of additive genetic variances. Genotyping bulls for LoF mutations revealed carrier frequencies of 2.0% for BY, 2.0% for HH1, and 4.3% for HH3. Our results will be useful to improve cow fertility traits in Holstein dairy herds in Russia. Furthermore, they allow selection of donor cows and bulls with more reliable EBV for fertility-related traits and that are free of LoF mutations associated with embryonic death for application in embryo transfer programs. The study was supported by the Federal Agency for Scientific Organizations and by the Russian Ministry of Education and Science, project no. RFMEFI60414X0062.

Toward a History of the "Soviet Language" (Sovyaz): Archival Documents, Electronic Sources, and the National Corpus

2015 ◽  
Vol 59 (2) ◽  
pp. 270-289
Author(s):  
Alexander Nakhimovsky
Keyword(s):  
Sensu Stricto ◽  
Russian Language ◽  
Soviet Period ◽  
Close Reading ◽  
Archival Documents ◽  
Recent Developments ◽  
History Of ◽  
New Research ◽  
Revolutionary Period ◽  
National Corpus

The subject matter of this paper is the "Soviet language" (SovYaz for short), a variety of Russian that was used in official contexts during the Soviet period. The use of the term "Soviet language" does not signify a commitment to viewing it as a language or a dialect in the linguistic sense. The question of whether SovYaz is, in fact, a social dialect sensu stricto, is beyond the scope of this paper and irrelevant to its purposes, although the materials presented here may help clarify the argument. This study of SovYaz seeks to utilize three relatively recent developments: newly opened archives with previously unimaginable sources of linguistic data; abundant searchable texts in electronic form; and a powerful new research tool, the National Corpus of the Russian Language (NCRL). The goal is methodological--to illustrate an approach to the study of SovYaz made possible by these new developments. The paper makes extensive use of the following procedure. First, a feature of SovYaz is identified in two documents selected for close reading, one a newspaper article, the other a top-secret NKVD report. That feature is then traced through other sources, including NCRL. The evolution of the feature is followed from the pre-revolutionary period to later times, sometimes all the way to the 21st century. Finally, the feature is described in some detail. In my experience, the emergence of the National Corpus makes possible a research methodology that transcends a close reading of selected documents but works well with it.

Multidimensional Developmental Pathways: A Proposal to Facilitate the Conceptualisation of ‘Family Diversity’

1986 ◽  
Vol 34 (3) ◽  
pp. 590-610 ◽  
Author(s):  
Jon Bernardes
Keyword(s):  
Life Course ◽  
Family Life ◽  
Developmental Pathways ◽  
Developmental Pathway ◽  
Central Type ◽  
Family Diversity ◽  
Starting Point ◽  
The Family ◽  
The Rich ◽  
The Life Course

This analysis takes Elder's work on the life-course as a starting point. Two proposals are made: (1) That the sociological use of the concept of ‘the family’ should be restricted to indicate only the occurrence of everyday usage; (2) That the notion of the ‘family life-course’ be replaced by the notion of individual life-courses coinciding upon developmental pathways. In this way the idea of a central type of ‘the family’ is made redundant and we are required, instead, to discover when and why participants refer to a particular developmental pathway as being ‘a family’. This approach not only facilitates the conceptualisation ‘family diversity’ but also compels researchers to engage the rich complexity of everyday life.

scholarly journals Fundamental Characteristics of Bat Interferon Systems

2020 ◽  
Vol 10 ◽  
Author(s):  
Emily Clayton ◽  
Muhammad Munir
Keyword(s):  
Innate Immunity ◽  
Immune System ◽  
Model Species ◽  
Novel Genes ◽  
Highly Pathogenic ◽  
Essential Component ◽  
Biological Features ◽  
Zoonotic Viruses ◽  
Recent Developments ◽  
Flying Fox

Interferons are an essential component of the innate arm of the immune system and are arguably one of the most important lines of defence against viruses. The human IFN system and its functionality has already been largely characterized and studied in detail. However, the IFN systems of bats have only been marginally examined to date up until the recent developments of the Bat1k project which have now opened new opportunities in research by identifying six new bat genomes to possess novel genes that are likely associated with viral tolerance exhibited in bats. Interestingly, bats have been hypothesized to possess the ability to establish a host-virus relationship where despite being infected, they exhibit limited signs of disease and still retain the ability to transmit the disease into other susceptible hosts. Bats are one of the most abundant and widespread vertebrates on the planet and host many zoonotic viruses that are highly pathogenic to humans. Several genomics, immunological, and biological features are thought to underlie novel antiviral mechanisms of bats. This review aims to explore the bat IFN system and developments in its diverse IFN features, focusing mainly on the model species, the Australian black flying fox (Pteropus alecto), while also highlighting bat innate immunity as an exciting and fruitful area of research to understand their ability to control viral-mediated pathogenesis.

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