scholarly journals Differences in firing efficiency, chromatin and transcription underlie the developmental plasticity of the Arabidopsis originome

2018 ◽  
Author(s):  
J. Sequeira-Mendes ◽  
Z. Vergara ◽  
R. Peiró ◽  
J. Morata ◽  
I. Aragüez ◽  
...  
Keyword(s):  
Developmental Plasticity ◽  
Developmental Stages ◽  
Gc Content ◽  
Postembryonic Development ◽  
Genome Replication ◽  
Development Environment ◽  
Firing Strength ◽  
Dna Replication Origins ◽  
Firing Efficiency ◽  
Two Stages

AbstractEukaryotic genome replication depends on thousands of DNA replication origins (ORIs) that constitute the originome. A major challenge is to learn ORI biology in multicellular organisms in the context of growing organs to understand their developmental plasticity. We have determined the originome and chromatin landscape of Arabidopsis thaliana at two stages of postembryonic development. ORIs associate with multiple chromatin signatures including TSS but also regulatory regions and heterochromatin, where ORIs colocalize with retrotransposons. In addition, quantitative analysis of ORI activity led us to conclude that strong ORIs have high GC content and clusters of GGN trinucleotides. Development primarily influences ORI firing strength rather than ORI location. ORIs that preferentially fire at early developmental stages colocalize with GC-rich heterochromatin whereas at later stages with transcribed genes, perhaps as a consequence of changes in chromatin features associated with developmental processes. Our study provides the originome of an organism at the postembryo stage that should allow us to study ORI biology in response to development, environment and mutations with a quantitative approach. In a wider scope, the computational strategies developed here can be transferred to other eukaryotic systems.

scholarly journals Spatiotemporal coupling and decoupling of gene transcription with DNA replication origins during embryogenesis in C. elegans

eLife ◽  
2016 ◽  
Vol 5 ◽  
Author(s):  
Ehsan Pourkarimi ◽  
James M Bellush ◽  
Iestyn Whitehouse
Keyword(s):  
Dna Replication ◽  
Developmental Stages ◽  
Embryonic Cell ◽  
Genome Replication ◽  
Replication Origins ◽  
C Elegans ◽  
Cellular Changes ◽  
Zygotic Transcription ◽  
Close Proximity ◽  
Dna Replication Origins

The primary task of developing embryos is genome replication, yet how DNA replication is integrated with the profound cellular changes that occur through development is largely unknown. Using an approach to map DNA replication at high resolution in C. elegans, we show that replication origins are marked with specific histone modifications that define gene enhancers. We demonstrate that the level of enhancer associated modifications scale with the efficiency at which the origin is utilized. By mapping replication origins at different developmental stages, we show that the positions and activity of origins is largely invariant through embryogenesis. Contrary to expectation, we find that replication origins are specified prior to the broad onset of zygotic transcription, yet when transcription initiates it does so in close proximity to the pre-defined replication origins. Transcription and DNA replication origins are correlated, but the association breaks down when embryonic cell division ceases. Collectively, our data indicate that replication origins are fundamental organizers and regulators of gene activity through embryonic development.

scholarly journals Differences in firing efficiency, chromatin, and transcription underlie the developmental plasticity of the Arabidopsis DNA replication origins

2019 ◽  
Vol 29 (5) ◽  
pp. 784-797 ◽  
Author(s):  
Joana Sequeira-Mendes ◽  
Zaida Vergara ◽  
Ramon Peiró ◽  
Jordi Morata ◽  
Irene Aragüez ◽  
...  
Keyword(s):  
Dna Replication ◽  
Developmental Plasticity ◽  
Replication Origins ◽  
Dna Replication Origins ◽  
Firing Efficiency

scholarly journals Retrotransposons are specified as DNA replication origins in the gene-poor regions of Arabidopsis heterochromatin

2016 ◽  
Author(s):  
Zaida Vergara ◽  
Joana Sequeira-Mendes ◽  
Jordi Morata ◽  
Elizabeth Hénaff ◽  
Ramón Peiró ◽  
...  
Keyword(s):  
Dna Replication ◽  
Gc Content ◽  
Genomic Stability ◽  
Genome Replication ◽  
Replication Origins ◽  
Entire Genome ◽  
Genome Wide ◽  
Concerted Activity ◽  
Dna Replication Origins ◽  
Multicellular Organisms

AbstractGenomic stability depends on faithful genome replication. This is achieved by the concerted activity of thousands of DNA replication origins (ORIs) scattered throughout the genome. In spite of multiple efforts, the DNA and chromatin features that determine ORI specification are not presently known. We have generated a high-resolution genome-wide map of ORIs in cultured Arabidopsis thaliana cells that rendered a collection of 3230 ORIs. In this study we focused on defining the features associated with ORIs in heterochromatin. We found that while ORIs tend to colocalize with genes in euchromatic gene-rich regions, they frequently colocalize with transposable elements (TEs) in pericentromeric gene-poor domains. Interestingly, ORIs in TEs associate almost exclusively with retrotransposons, in particular, of the Gypsy family. ORI activity in retrotransposons occurs independently of TE expression and while maintaining high levels of H3K9me2 and H3K27me1, typical marks of repressed heterochromatin. ORI-TEs largely colocalize with chromatin signatures defining GC-rich heterochromatin. Importantly, TEs with active ORIs contain a local GC content higher than the TEs lacking them. Our results lead us to conclude that ORI colocalization with TEs is largely limited to retrotransposons, which are defined by their transposition mechanisms based on transcription, and they occur in a specific chromatin landscape. Our detailed analysis of ORIs responsible for heterochromatin replication has also implications on the mechanisms of ORI specification in other multicellular organisms in which retrotransposons are major components of heterochromatin as well as of the entire genome.

scholarly journals Mining of Brassica-Specific Genes (BSGs) and Their Induction in Different Developmental Stages and under Plasmodiophora brassicae Stress in Brassica rapa

2018 ◽  
Vol 19 (7) ◽  
pp. 2064 ◽  
Author(s):  
Mingliang Jiang ◽  
Xiangshu Dong ◽  
Hong Lang ◽  
Wenxing Pang ◽  
Zongxiang Zhan ◽  
...  
Keyword(s):  
Gene Expression ◽  
Brassica Rapa ◽  
Developmental Stages ◽  
Plasmodiophora Brassicae ◽  
Expression Patterns ◽  
Gc Content ◽  
Biological Information ◽  
Lower Percentage ◽  
Orphan Genes ◽  
Conserved Genes

Orphan genes, also called lineage-specific genes (LSGs), are important for responses to biotic and abiotic stresses, and are associated with lineage-specific structures and biological functions. To date, there have been no studies investigating gene number, gene features, or gene expression patterns of orphan genes in Brassica rapa. In this study, 1540 Brassica-specific genes (BSGs) and 1824 Cruciferae-specific genes (CSGs) were identified based on the genome of Brassica rapa. The genic features analysis indicated that BSGs and CSGs possessed a lower percentage of multi-exon genes, higher GC content, and shorter gene length than evolutionary-conserved genes (ECGs). In addition, five types of BSGs were obtained and 145 out of 529 real A subgenome-specific BSGs were verified by PCR in 51 species. In silico and semi-qPCR, gene expression analysis of BSGs suggested that BSGs are expressed in various tissue and can be induced by Plasmodiophora brassicae. Moreover, an A/C subgenome-specific BSG, BSGs1, was specifically expressed during the heading stage, indicating that the gene might be associated with leafy head formation. Our results provide valuable biological information for studying the molecular function of BSGs for Brassica-specific phenotypes and biotic stress in B. rapa.

Comparison of slow larval and fast adult muscle innervated by the same motor neurone

1980 ◽  
Vol 84 (1) ◽  
pp. 103-118
Author(s):  
M. B. Rheuben ◽  
A. E. Kammer
Keyword(s):  
Developmental Stages ◽  
Neuromuscular Junctions ◽  
Motor Nerve ◽  
Thick Filament ◽  
Motor Neurone ◽  
Muscle Fibre Types ◽  
Thin Filaments ◽  
Adult Muscle ◽  
Motor Neurones ◽  
Two Stages

1. Muscles innervated by an identified set of motor neurones were compared between larval and adult stages. 2. The structure of the larval muscle is typically tonic: long sarcomeres, irregular Z-bands, and 10-12 thin filaments around each thick filament. The structure of the adult muscle is phasic: 3-4 micrometers sarcomeres, regular Z-bands, 6-8 thin filaments around each thick filament, and large mitochondrial volume. 3. The tensions produced by these muscles were correspondingly different. The larval twitch was about 7 times slower and the tetanus/twitch ratio 10 times greater than those of the adult. 4. No structural or physiological differences were observed in the neuromuscular junctions of the two stages. 5. The relatively unchanging functional relationship of a single motor neurone with two different muscle fibre types during two developmental stages is compared with the converse situation in which it has been reported that implantation of a different type of motor nerve into a muscle modifies contractile properties.

Flatworms (Schmidtea nova) prey upon embryos of the common frog (Rana temporaria) and induce minor developmental acceleration

2015 ◽  
Vol 36 (2) ◽  
pp. 155-163 ◽  
Author(s):  
Ori Segev ◽  
Ariel Rodríguez ◽  
Susanne Hauswaldt ◽  
Karen Hugemann ◽  
Miguel Vences
Keyword(s):  
Developmental Plasticity ◽  
Developmental Stages ◽  
Rana Temporaria ◽  
Common Frog ◽  
Predator Species ◽  
Positive Effects ◽  
Hatching Time ◽  
Risk Of Predation ◽  
Frog Rana Temporaria ◽  
Indirect Cues

Amphibians vary in the degree of pre-metamorphic developmental plasticity in response to risk of predation. Changes in hatching time and development rate can increase egg or tadpole survival respectively by shortening the duration of the more vulnerable stages. The intensity of predator induced developmental response and its direction, i.e. delayed, accelerated, or none, varies considerably between amphibian and predator species. We surveyed freshly deposited clutches of the European common frog Rana temporaria in a population in Braunschweig, Germany and found that 62% (N = 20) of the clutches contained planarians (Schmidtea nova), with an average of 3.94 ± 0.79 and a maximum of 13 planarians per clutch. A laboratory predation experiment confirmed that this planaria preys on R. temporaria eggs and early embryos. We further exposed freshly laid egg masses to either free, caged, or no planarians treatments using floating containers within a breeding pond where the two species co-occur. After 10 days exposure, embryos showed developmental stages 14-25 along the Gosner scale with statistically significant positive effects of both predator treatments. The observed effect was rather slight as predator-exposed individuals showed an increase by a single Gosner stage relative to those raised without planarians. The detected trend suggests that direct and indirect cues from flatworms, rarely considered as anuran predators, might induce a developmental response in R. temporaria early developmental stages.

scholarly journals Postembryonic development of tapeworms — source of novel phylogenetic characters for analysis of cestode evolution: comparative TEM studies

2007 ◽  
Vol 44 (3) ◽  
pp. 130-136 ◽  
Author(s):  
Z. Świderski
Keyword(s):  
Developmental Stages ◽  
Early Stage ◽  
Thick Layer ◽  
Cell Types ◽  
Postembryonic Development ◽  
Current Data ◽  
The Body ◽  
Ultrastructural Studies ◽  
Calcareous Corpuscle ◽  
Parenchymal Cells

AbstractUltrastructural features of juvenile cestodes (metacestodes) can provide useful characters for phylogenetic and evolutionary analyses. Until now, however, they have been relatively little utilised (Beveridge 2001, Chervy 2002). The postembryonic development and structure of fully formed metacestodes were examined in two cyclophyllideans: Taenia parva Baer, 1926 (Taeniidae); and Sobolevitaenia verulamii (Mettrick, 1958) Korniushin, 1972 (Dilepididae). In T. parva, three developmental stages were recognized: (1) an early stage of exogenous budding at the surface of the central vesicle; (2) a stage of polycephalic cyst development accompanied by segmentation of the growing metacestode strobila and an obvious decrease in the size of the central vesicle; (3) a fully formed metacestode of the strobilocercus type with 14–24 invaginated scoleces. The tegument, scolex, subtegumental musculature of the strobilar segments, protonephridial system, calcareous corpuscles and medullary parenchyma of larvae exhibit general similarity to the same structures in adults at both LM and TEM levels. The morphogenesis of the metacestode of T. parva is compared with that of polycephalic metacestodes of other Taenia spp. (T. krepkogorski, T. twitchelli and T. endothoracica) and with other asexually multiplying metacestodes (Mesocestoides vogae, hymenolepidids and dilepidids). In S. verulamii, the body of the cysticercoid with invaginated scolex armed with a double crown of rostellar hooks was completely surrounded by the cercomer, which appears to be separated from the cyst and scolex. The surface of the suckers is covered with a thick layer of glycocalyx. Five cell types were distinguished in the sections: (1) perikarya of metacestode tegument; (2) glycolgen-storing parenchymal cells; (3) glandular-type cells with large, electron-dense secretory-like granules; (4) flame cells; and (5) calcareous corpuscle-forming cells. The surface of the cercomer is covered by elongated microvilli, which evidently differ from characteristic microtriches covering all other parts of the metacestode surface. The ultrastructure of S. verulamii evidently differs from that of the other dilepidid cestode examined to date, Lateriporus geographicus, the cyst wall of which more resembles cysticercoids of Hymenolepididae than those of Dilepididae. Concluding remarks: Ultrastructural studies on metacestodes have considerable promise for providing important new characters for phylogenetic analysis. New TEM data on a great variety of cestode species are urgently needed. Until now, this field has not been exploited in a systematic fashion. Until more comprehensive studies become available, the current data are not yet amenable to analysis.

A quantitative analysis of exopodite beating in the larvae of the lobster Homarus gammarus (L.)

1976 ◽  
Vol 274 (929) ◽  
pp. 69-85 ◽  
Keyword(s):  
Quantitative Analysis ◽  
Developmental Stages ◽  
Phase Relations ◽  
Computer Assisted ◽  
Cycle Duration ◽  
Raw Data ◽  
Homarus Gammarus ◽  
Larval Stages ◽  
Three Stages ◽  
Two Stages

Raw data on exopodite beating in the first three developmental stages of the lobster Homarus gammarus were collected and analysed for key beating parameters. The analysis was computer assisted and the main procedures used are described. Beating patterns are the same in all three stages and are usually very regular although perturbations do occur (figures 1, 2). When beating stops the deceleration and subsequent re-acceleration is very rapid (figure 1) and limb movement sequences usually start posteriorly and move forwards (figures 1, 2 d ). Ipsilateral phase relations are generally maintained at 0.4- 0.6 (figures 3, 4) and while the coupling between adjacent exopodites is usually stronger than for those further apart various deviations from this are occasionally seen (figure 5). No significant correlation between the ipsilateral phase relations of adjacent exopodites and base cycle duration was detected for any of the stages (figure 6). Contralateral phase relations undergo a constant progression (figures 7, 9) and this was found to be due to a heterodyne effect (figure 8) also described as gliding coordination. The powerstroke/returnstroke ratio for all stages was approximately 0.5 (figure 10) and no significant correlation was found with cycle duration (figure 11). The only substantial difference between the three larval stages which was noted was that of cycle duration, the cycles of stage III being shorter than those of the first two stages. The exopodite beating pattern was discussed in context with other metachronously cycling systems in arthropods and the implications of the present study discussed.

scholarly journals Hypoxia-inducible factor-1 mediates adaptive developmental plasticity of hypoxia tolerance in zebrafish, Danio rerio

2014 ◽  
Vol 281 (1786) ◽  
pp. 20140637 ◽  
Author(s):  
Cayleih E. Robertson ◽  
Patricia A. Wright ◽  
Louise Köblitz ◽  
Nicholas J. Bernier
Keyword(s):  
Danio Rerio ◽  
Cellular Response ◽  
Developmental Plasticity ◽  
Developmental Stages ◽  
Critical Role ◽  
Hypoxia Inducible Factor ◽  
Hypoxia Tolerance ◽  
Anthropogenic Factors ◽  
Critical Window ◽  
Hypoxia Inducible Factor 1

In recent years, natural and anthropogenic factors have increased aquatic hypoxia the world over. In most organisms, the cellular response to hypoxia is mediated by the master regulator hypoxia-inducible factor-1 (HIF-1). HIF-1 also plays a critical role in the normal development of the cardiovascular system of vertebrates. We tested the hypothesis that hypoxia exposures which resulted in HIF-1 induction during embryogenesis would be associated with enhanced hypoxia tolerance in subsequent developmental stages. We exposed zebrafish ( Danio rerio ) embryos to just 4 h of severe hypoxia or total anoxia at 18, 24 and 36 h post-fertilization (hpf). Of these, exposure to hypoxia at 24 and 36 hpf as well as anoxia at 36 hpf activated the HIF-1 cellular pathway. Zebrafish embryos that acutely upregulated the HIF-1 pathway had an increased hypoxia tolerance as larvae. The critical window for hypoxia sensitivity and HIF-1 signalling was 24 hpf. Adult male fish had a lower critical oxygen tension ( P crit ) compared with females. Early induction of HIF-1 correlated directly with an increased proportion of males in the population. We conclude that mounting a HIF-1 response during embryogenesis is associated with long-term impacts on the phenotype of later stages which could influence both individual hypoxia tolerance and population dynamics.

scholarly journals A comparative genetical study on DDT resistance in adults and larvae of the mosquito Aedes aegypti L

1967 ◽  
Vol 10 (3) ◽  
pp. 219-228 ◽  
Author(s):  
R. J. Wood
Keyword(s):  
Linkage Group ◽  
Developmental Stages ◽  
Major Gene ◽  
Group Iii ◽  
Group I ◽  
Fourth Larval Stage ◽  
Ddt Resistance ◽  
Group Ii ◽  
The Difference ◽  
Two Stages

Inheritance of DDT resistance has been studied in crosses between the highly resistant ‘T’ strain of A. aegypti (constituted by inbreeding from the TRINIDAD DDT-resistant stock) and the ‘64’ susceptible strain.Larval DDT resistance derives from a major gene RDDT1 on linkage group II, the order being RDDT1–s–y. Linkage group III may also contribute to larval resistance. Linkage group I makes no contribution.Adult DDT resistance derives from a major gene RDDT2, 18·2 ± 2·1 units from the market blt on linkage group III. Linkage group II has no influence on adult resistance.Selection with DDT to retain only RDDT1/+ segregants in larvae of backcrosses RDDT1/+×+/+ did not increase resistance in resulting adults, confirming the difference in genetic mechanism at the two stages.The F1 progenies from reciprocal crosses between ‘T’ and ‘64’ differed slightly but significantly in larval resistance, modifying the influence of the major gene RDDT1 in the heterozygote.The early developmental stages of the RDDT1/+ phenotype (up to the fourth larval stage) were more viable than the +/+ phenotype in backcross segregation. The difference in mortality probably exceeded 30%.

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