scholarly journals Reconstructing the transcriptional ontogeny of maize and sorghum supports an inverse hourglass model of inflorescence development

2019 ◽  
Author(s):  
Samuel Leiboff ◽  
Sarah Hake
Keyword(s):  
Random Forest ◽  
Developmental Stages ◽  
List Type ◽  
Inflorescence Development ◽  
Closely Related Species ◽  
Developmental Age ◽  
Maize Tassel ◽  
Rapid Divergence ◽  
Hourglass Model ◽  
Developmental Reprogramming

AbstractAssembling meaningful comparisons between species is a major limitation in studying the evolution of organismal form. To understand development in maize and sorghum, closely-related species with architecturally distinct inflorescences, we collected RNAseq profiles encompassing inflorescence body plan specification in both species. We reconstructed molecular ontogenies from 40 B73 maize tassels and 47 BT×623 sorghum panicles and separated them into transcriptional stages. To discover new markers of inflorescence development, we used random forest machine learning to determine stage by RNAseq. We used two descriptions of transcriptional conservation to identify hourglass-like developmental stages. Despite short evolutionary ancestry of 12 million years, we found maize and sorghum inflorescences are most different during their hourglass-like stages of development, following an ‘inverse-hourglass’ model of development. We discuss if agricultural selection may account for the rapid divergence signatures in these species and the observed separation of evolutionary pressure and developmental reprogramming.HighlightsTranscript dynamics identify maize tassel and sorghum panicle developmental stagesRandom forest predicts developmental age by gene expression, providing molecular markers and an in silico staging applicationMaize and sorghum inflorescences are most similar when committing stem cells to a determinant fateExpression conservation identifies hourglass-like stage, but transcriptomes diverge, similar to ‘inverse hourglass’ observations in cross-phyla animal embryo comparisons

scholarly journals Enhancer-dependence of gene expression increases with developmental age

2019 ◽  
Author(s):  
Wenqing Cai ◽  
Jialiang Huang ◽  
Qian Zhu ◽  
Bin E. Li ◽  
Davide Seruggia ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Stages ◽  
Chromatin Accessibility ◽  
List Type ◽  
Primary Cells ◽  
Embryonic Cells ◽  
Human Origin ◽  
Chromatin Interactions ◽  
Developmental Age ◽  
Specific Control

SummaryHow overall principles of gene regulation (the “logic”) may change during ontogeny is largely unexplored. We compared transcriptomic, epigenomic and topological profiles in embryonic (EryP) and adult (EryD) erythroblasts. Despite reduced chromatin accessibility compared to EryP, distal chromatin of EryD is enriched in H3K27ac, Gata1 and Myb occupancy. In contrast to EryP-specific genes, which exhibit promoter-centric regulation through Gata1, EryD-specific genes employ distal enhancers for long-range regulation through enhancer-promoter looping, confirmed by Gata1 HiChIP. Genome editing demonstrated distal enhancers are required for gene expression in EryD but not in EryP. Applying a metric for enhancer-dependence of transcription, we observed a progressive reliance on enhancer control with increasing age of ontogeny among diverse primary cells and tissues of mouse and human origin. Our findings highlight fundamental and conserved differences in regulatory logic at distinct developmental stages, characterized by simpler promoter-centric regulation in embryonic cells and combinatorial enhancer-driven control in adult cells.HighlightsRegulation of embryonic-specific erythroid genes is promoter-centric through Gata1Adult-specific control is combinatorial enhancer-driven and requires MybAdult specific genes have increased enhancer-promoter chromatin interactionsEnhancer-dependence increases progressively with increasing developmental age

scholarly journals How Can Satellite DNA Divergence Cause Reproductive Isolation? Let Us Count the Chromosomal Ways

2012 ◽  
Vol 2012 ◽  
pp. 1-11 ◽  
Author(s):  
Patrick M. Ferree ◽  
Satyaki Prasad
Keyword(s):  
Reproductive Isolation ◽  
Developmental Stages ◽  
Rapid Evolution ◽  
Model Organisms ◽  
Cellular Mechanisms ◽  
Closely Related Species ◽  
Heterochromatin Formation ◽  
Interspecies Hybrids ◽  
Postzygotic Reproductive Isolation ◽  
And Function

Satellites are one of the most enigmatic parts of the eukaryotic genome. These highly repetitive, noncoding sequences make up as much as half or more of the genomic content and are known to play essential roles in chromosome segregation during meiosis and mitosis, yet they evolve rapidly between closely related species. Research over the last several decades has revealed that satellite divergence can serve as a formidable reproductive barrier between sibling species. Here we highlight several key studies on Drosophila and other model organisms demonstrating deleterious effects of satellites and their rapid evolution on the structure and function of chromosomes in interspecies hybrids. These studies demonstrate that satellites can impact chromosomes at a number of different developmental stages and through distinct cellular mechanisms, including heterochromatin formation. These findings have important implications for how loci that cause postzygotic reproductive isolation are viewed.

scholarly journals Song discrimination by nestling collared flycatchers during early development

2016 ◽  
Vol 12 (7) ◽  
pp. 20160234 ◽  
Author(s):  
S. Eryn McFarlane ◽  
Axel Söderberg ◽  
David Wheatcroft ◽  
Anna Qvarnström
Keyword(s):  
Metabolic Rate ◽  
Developmental Stages ◽  
Closely Related Species ◽  
Selective Learning ◽  
Collared Flycatcher ◽  
Song Perception ◽  
Song Discrimination ◽  
Novel Method ◽  
Species Specific ◽  
Early Developmental

Pre-zygotic isolation is often maintained by species-specific signals and preferences. However, in species where signals are learnt, as in songbirds, learning errors can lead to costly hybridization. Song discrimination expressed during early developmental stages may ensure selective learning later in life but can be difficult to demonstrate before behavioural responses are obvious. Here, we use a novel method, measuring changes in metabolic rate, to detect song perception and discrimination in collared flycatcher embryos and nestlings. We found that nestlings as early as 7 days old respond to song with increased metabolic rate, and, by 9 days old, have increased metabolic rate when listening to conspecific when compared with heterospecific song. This early discrimination between songs probably leads to fewer heterospecific matings, and thus higher fitness of collared flycatchers living in sympatry with closely related species.

scholarly journals Life cycle of Early Cambrian microalgae from theSkiagia-plexus acritarchs

2010 ◽  
Vol 84 (2) ◽  
pp. 216-230 ◽  
Author(s):  
Małgorzata Moczydłowska
Keyword(s):  
Life Cycle ◽  
Developmental Stages ◽  
Biological Species ◽  
Complex Life Cycle ◽  
Early Cambrian ◽  
Closely Related Species ◽  
Vegetative Cells ◽  
Depositional Settings ◽  
Sexual Generation ◽  
Sheath Structure

Light microscopy studies on new materials and museum collections of early Cambrian organic-walled microfossils, informally called acritarchs, provide the observations on phenetic features that permit a comparison to certain Modern microalgae and the recognition of various developmental stages in their life cycle. the microfossils derive from various depositional settings in Estonia, Australia, Greenland, Sweden, and Poland. the exceptionally preserved microfossils reveal the internal body within the vesicle, the endocyst, and the process of releasing the endocyst from the cyst. Vegetative cells, cysts, and endocysts are distinguished, and the hypothetical reconstruction of a complex life cycle with the alternation of sexual and asexual generations is proposed. Acritarchs from theSkiagia-plexus are cysts, and likely zygotes in the sexual generation, which periodically rested as “benthic plankton.” Some microfossils of theLeiosphaeridia-plexus that are inferred to be vegetative cells were planktonic and probably haplobiontic. These form-taxa may belong to a single biological species, or a few closely related species, and represent the developmental stages and alternating generations in a complex life cycle that is expressed by polymorphic, sphaero- and acanthomorphic acritarchs. the morphological resemblance and diagnostic cell wall ultrastructure with the trilaminar sheath structure known from earlier studies suggest that the early Cambrian microfossils are the ancestral representatives and/or early lineages to the Modern class Chlorophyceae and the orders Volvocales and Chlorococcales.

scholarly journals Cis-directed cleavage and nonstoichiometric abundances of 21-nt reproductive phasiRNAs in grasses

2018 ◽  
Author(s):  
Saleh Tamim ◽  
Zhaoxia Cai ◽  
Sandra Mathioni ◽  
Jixian Zhai ◽  
Chong Teng ◽  
...  
Keyword(s):  
Computational Analysis ◽  
Developmental Stages ◽  
Transcriptional Gene Silencing ◽  
List Type ◽  
Small Interfering Rnas ◽  
Regulatory Activity ◽  
Sequence Composition ◽  
Post Transcriptional Gene Silencing ◽  
Non Coding Rnas ◽  
Weak Accumulation

SummaryPost-transcriptional gene silencing in plants results from independent activities of diverse small RNA types. In anthers of grasses, hundreds of loci yield non-coding RNAs that are processed into 21- and 24-nt phased small interfering RNAs (phasiRNAs); these are triggered by miR2118 and miR2275.We characterized these “reproductive phasiRNAs” from rice panicles and anthers across seven developmental stages. Our computational analysis identified characteristics of the 21-nt reproductive phasiRNAs that impact their biogenesis, stability, and potential functions.We demonstrate that 21-nt reproductive phasiRNAs can function in cis to target their own precursors. We observed evidence of this cis regulatory activity in both rice (Oryza sativa) and maize (Zea mays). We validated this activity with evidence of cleavage and a resulting shift in the pattern of phasiRNA production.We characterize biases in phasiRNA biogenesis, demonstrating that the Pol II-derived “top” strand phasiRNAs are consistently higher abundance than the bottom strand. The first phasiRNA from each precursor overlaps the miR2118 target site, and this impacts phasiRNA accumulation or stability, evident in the weak accumulation of this phasiRNA position. Additional influences on this first phasiRNA duplex include the sequence composition and length, and we show that these factors impact Argonaute loading.

scholarly journals Science Map of Cochrane Systematic Reviews Receiving the Most Altmetric Attention: Network Visualization and Machine Learning Perspective

2019 ◽  
Author(s):  
Jafar Kolahi ◽  
Saber Khazaei ◽  
Elham Bidram ◽  
Roya Kelishadi ◽  
Pedram Iranmanesh ◽  
...  
Keyword(s):  
Random Forest ◽  
Network Analysis ◽  
Systematic Reviews ◽  
Citation Network ◽  
Random Forest Model ◽  
List Type ◽  
Policy Document ◽  
Forest Model ◽  
University Of Oxford ◽  
Citation Network Analysis

AbstractWe aimed to analyze and visualize the science map of Cochrane systematic reviews (CSR) with high Altmetric attention scores (AAS). On 10 May 2019, the Altmetric data of the CSR Database were obtained from the Altmetric database (Altmetric LLP, London, UK). Bibliometric data of the top 5% of CSR were extracted from the Web of Science. Keyword co-occurrence, co-authorship, and co-citation network analysis were then employed using VOSviewer software. A Random forest model was used to analyze the citation patterns. A total of 12016 CSR with AAS were found (Total mentions: 259968) with Twitter being the most popular Altmetric resource. Consequently, the top 5% (607 articles, mean AAS: 171.2, 95% confidence level (CL): 14.4, mean citations: 42.1, 95%CL: 1.3) with the highest AAS were included in the study. Keyword co-occurrence network analysis revealed female, adult, and child as the most popular keywords. Helen V. Worthington (University of Manchester, Manchester, UK), and the University of Oxford and UK had the greatest impact on the network at the author, organization and country levels respectively. The co-citation network analysis revealed that The Lancet and CSR database had the most influence on the network. However, AAS were not correlated with citations (r=0.15) although they were correlated with policy document mentions (r=0.61). The results of random forest model confirmed the importance of policy document mentions. Despite the popularity of CSR in the Twittersphere, disappointingly, they were rarely shared and discussed within the new academic tools that are emerging, such as F1000 prime, Publons, and PubPeer.Article HighlightsThe CSR database was most mentioned in Twitter.Twitter and News act as the greatest prominent issues regarding altmetric scores.

scholarly journals Evolutionary transition in accessible chromatin landscapes during vertebrate embryogenesis

2018 ◽  
Author(s):  
Masahiro Uesaka ◽  
Shigeru Kuratani ◽  
Hiroyuki Takeda ◽  
Naoki Irie
Keyword(s):  
Evolutionary Biology ◽  
Developmental Stages ◽  
Expression Profiles ◽  
Gene Expression Profiles ◽  
Molecular Evidence ◽  
Regulatory Regions ◽  
Evolutionary Origins ◽  
A Genome ◽  
Hourglass Model ◽  
Accessible Chromatin

The relationship between development and evolution is a central topic in evolutionary biology1,2. Recent transcriptome-based studies support the developmental hourglass model, which predicts that the animal embryogenetic program is most strongly conserved at mid-embryonic stages3-9. This model does not necessarily contradict the classical hypothesis10,11 that animal development recapitulates its evolutionary history after the mid-embryonic stages2,12. However, to date there is no molecular evidence supporting the hypothesis that gene-expression profiles that are more evolutionarily derived appear sequentially in late development. Here, by estimating activated genomic regions and their evolutionary origins, we show that the recapitulative pattern appears during late embryonic stages. We made a genome-wide assessment of accessible chromatin regions throughout embryogenesis in three vertebrate species (mouse, chicken, and medaka) and determined the phylogenetic range at which these regions were shared. In all three species, sequential activation of putative regulatory regions that were more derived occurred later in embryogenesis, whereas ancestral ones tended to be activated early. Our results clarify the chronologic changes in accessible chromatin landscapes and reveal a phylogenetic hierarchy in the evolutionary origins of putative regulatory regions that parallels developmental stages of activation. This relationship may explain, at least in part, the background for morphological observations of recapitulative events during embryogenesis.

scholarly journals Tripartite Inhibition of SRC-WNT-PKC Signalling Consolidates Human Naïve Pluripotency

2020 ◽  
Author(s):  
Jonathan Bayerl ◽  
Muneef Ayyash ◽  
Tom Shani ◽  
Yair Manor ◽  
Ohad Gafni ◽  
...  
Keyword(s):  
Pluripotent Stem Cells ◽  
Developmental Stages ◽  
List Type ◽  
Functional Screening ◽  
Dna Hypomethylation ◽  
Differentiation Potential ◽  
Reporter Systems ◽  
Simultaneous Inhibition ◽  
Functional Features ◽  
Erk Inhibition

AbstractDifferent conditions have been devised to isolate MEK/ERK signalling independent human naïve pluripotent stem cells (PSCs) that are distinct from conventional primed PSCs and better correspond to pre-implantation developmental stages. While the naïve conditions described thus far endow human PSCs with different extents of naivety features, isolating human pluripotent cells that retain characteristics of ground state pluripotency while maintaining differentiation potential and genetic integrity, remains a major challenge. Here we engineer reporter systems that allow functional screening for conditions that can endow both the molecular and functional features expected from human naive pluripotency. We establish that simultaneous inhibition of SRC-NFκB, WNT/ßCATENIN and PKC signalling pathways is essential for enabling expansion of teratoma competent fully naïve human PSCs in defined or xeno-free conditions. Divergent signalling and transcriptional requirements for maintaining naïve pluripotency were found between mouse and human. Finally, we establish alternative naïve conditions in which MEK/ERK inhibition is substituted with inhibition for NOTCH/RBPj signalling, which allow obtaining alternative human naïve PSCs with diminished risk for loss of imprinting and deleterious global DNA hypomethylation. Our findings set a framework for the signalling foundations of human naïve pluripotency and may advance its utilization in future translational applications.Highlights of key findingsCombined inhibition of SRC, WNT and PKC signaling consolidates human naïve pluripotencyStable expansion of DNA/RNA methylation-independent and TGF/ACTIVIN-independent human naïve PSCsOpposing roles for ACTIVIN and WNT/ßCATENIN signaling on mouse vs. human naive pluripotency2i and MEK/ERKi independent alternative human naïve PSC conditions via inhibiting NOTCH/RBPj signaling

scholarly journals Improved computational analysis of ribosome dynamics from 5’P degradome data using fivepeseq

2020 ◽  
Author(s):  
Lilit Nersisyan ◽  
Maria Ropat ◽  
Vicent Pelechano
Keyword(s):  
Computational Analysis ◽  
Developmental Stages ◽  
Biological Information ◽  
List Type ◽  
Computational Tools ◽  
Ribosome Stalling ◽  
Specific Analysis ◽  
Key Points ◽  
Reproducible Analysis

ABSTRACTIn eukaryotes, 5’-3’ co-translation degradation machinery follows the last translating ribosome providing an in vivo footprint of its position. Thus 5’P degradome sequencing, in addition to informing about RNA decay, also provides valuable information regarding ribosome dynamics. Multiple experimental methods have been developed to investigate the mRNA degradome, however computational tools for their reproducible analysis are lacking. Here we present fivepseq: an easy-to-use application for analysis and interactive visualization of 5’P degradome data. This tool performs both metagene and gene specific analysis, and allows to easily investigate codon specific ribosome pauses. To demonstrate its ability to provide new biological information, we investigate gene specific ribosome pauses in S. cerevisiae after eIF5A depletion. In addition to identifying pauses at expected codon motifs, we identify multiple genes with strain-specific frameshifts. To show its wide applicability, we investigate more complex 5’P degradome from A. thaliana and discover both motif-specific ribosome protection associated with particular developmental stages, as well as generally increased ribosome protection at termination level associated with age. Our work shows how the use of improved analysis tools for the study of 5’P degradome can significantly increase the biological information that can be derived from such datasets and facilitate its reproducible analysis.KEY POINTSAnalysis of 5’P degradome data with fivepseq informs about global and gene-specific translational features.Frameshifts in translation-related genes in S. cerevisiae may be linked to ribosome stalling.Ribosome protection at termination and codon motifs are linked to development in A. Thaliana.

scholarly journals Strong selective pressure by parasitoids mitigates the costs of consuming chemically defended plants

2021 ◽  
Author(s):  
Deidra J. Jacobsen
Keyword(s):  
Manduca Sexta ◽  
Natural Enemies ◽  
Developmental Stages ◽  
Parasitoid Wasp ◽  
Field Measurements ◽  
Secondary Compounds ◽  
List Type ◽  
Plant Secondary Compounds ◽  
Defensive Compounds ◽  
Cotesia Congregata

AbstractCo-evolutionary interactions between plants and herbivores have led to a range of plant defenses that minimize insect damage and a suite of counter-adaptations that allow herbivores to feed on defended plants. Consumption of plant secondary compounds results in herbivore growth and developmental costs but can be beneficial if eating these secondary compounds results in deterrence or harm to natural enemies.To test the role of secondary compounds on herbivore fitness in the context of natural enemies, I combined field measurements of the prevalence of a parasitoid wasp (Cotesia congregata) with detailed measurements of the costs of plant secondary compounds on growth, immune, and fitness traits across developmental stages in the herbivore Manduca sexta. When M. sexta larvae consume defended plants, Cotesia congregata are known to have reduced success. However, this anti-enemy benefit to the M. sexta host must be considered in relationship to parasitoid abundance and the type and strength of the fitness costs M. sexta incurs feeding on plant secondary compounds.I found that Cotesia congregata parasitoids exert large negative selective pressures, killing 31-57% of M. sexta larvae in the field. Manduca sexta developed fastest during the instars most at risk for parasitoid oviposition but growth was slowed by consumption of plant secondary compounds (nicotine and rutin). These negative size effects at the larval stage carried over to influence adult traits associated with flight and mating but there were no immune, survival, or fecundity costs of consuming plant defensive compounds as larvae.Synthesis. These results suggest that the developmental costs experienced by M. sexta herbivores consuming defensive compounds may be outweighed by a survival benefit in the face of abundant enemy pressures.

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