Occurrence and predictive utility of isochronal, equiproportional, and other types of development among arthropods

Mapping Intimacies ◽

10.1101/379164 ◽

2018 ◽

Author(s):

Brady K. Quinn

Keyword(s):

Developmental Stages ◽

List Type ◽

Alternative Development ◽

Decapod Crustaceans ◽

Predictive Utility ◽

Mixed Form ◽

Arthropod Development ◽

Juvenile Development

ABSTRACTIn isochronal (ICD) and equiproportional development (EPD), the proportion of total immature (egg, larval, and/or juvenile) development spent in each stage (developmental proportion) does not vary among stages or temperatures, respectively. ICD and EPD have mainly been reported in copepods, and whether they occur in other arthropods is not known. If they did, then rearing studies could be simplified because the durations of later developmental stages could be predicted based on those of earlier ones. The goal of this study was to test whether different taxa have ICD, EPD, or an alternative development type in which stage-specific proportions depend on temperature, termed ‘variable proportional’ development (VPD), and also how well each development type allowed later-stage durations to be predicted from earlier ones. Data for 71 arthropods (arachnids, copepod and decapod crustaceans, and insects) were tested, and most (85.9 %) species were concluded to have VPD, meaning that ICD and EPD do not occur generally. However, EPD predicted later-stage durations comparably well to VPD (within 19-23 %), and thus may still be useful. Interestingly, some species showed a ‘mixed’ form of development, where some stages’ developmental proportions varied with temperature while those of others did not, which should be further investigated.HighlightsWhether arthropod development is generally isochronal or equiproportional was testedDevelopmental proportions of most species’ stages varied with temperatureMany species had ‘mixed’ development between variable and equiproportional typesThe general occurrence of isochronal and equiproportional development was rejectedEquiproportional development did make reasonable predictions of stage durations

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

10.1101/243907 ◽

2018 ◽

Cited By ~ 2

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.

Enhancer-dependence of gene expression increases with developmental age

10.1101/678334 ◽

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

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

10.1101/2020.05.23.112433 ◽

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

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

10.1101/2020.01.22.915421 ◽

2020 ◽

Cited By ~ 3

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.

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

10.1101/2021.01.13.426617 ◽

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.

Gradual development of non-adjacent dependency learning during early childhood

10.1101/2020.09.01.277822 ◽

2020 ◽

Author(s):

Mariella Paul ◽

Claudia Männel ◽

Anne van der Kant ◽

Jutta L. Mueller ◽

Barbara Höhle ◽

...

Keyword(s):

Early Childhood ◽

Foreign Language ◽

Developmental Stages ◽

Event Related Potentials ◽

Gradual Transition ◽

List Type ◽

Passive Listening ◽

Gradual Development ◽

Related Potentials ◽

Syntactic Relations

AbstractIn order to become proficient native speakers, children have to learn the grammatical rules of their language. These grammatical rules can define morpho-syntactic relations between neighboring as well as distant elements of a sentence, so-called non-adjacent dependencies (NADs). Previous neurophysiological research suggests that NAD learning comprises different developmental stages during early childhood. Children up to 2 years of age show evidence of associative NAD learning under passive listening conditions, while children starting around the age of 3 to 4 years fail to show learning under passive listening, similarly to the pattern observed in adults. To test whether the transition between these developmental stages occurs in a gradual manner, we tested young children’s NADlearning in a foreign language using event-related potentials (ERPs). We found ERP evidence of NAD learning across the age of 1 to 3 years. However, the amplitude of the ERP effect indexing NAD learning decreased linearly with increasing age. These findings indicatea gradual transition in children’s ability to learn NADs associatively under passive listening during early childhood. Cognitively, this transition might be driven by children’s increasing morpho-syntactic knowledge in their native language, hindering NAD learning in novel linguistic contexts during passive listening. Neuroanatomically, changes in brain structure might play a crucial role, especially the maturation of the prefrontal cortex, which promotes top-down learning, as opposed to bottom-up, associative learning. In sum, our study provides evidence that NAD learning under passive listening conditions undergoes a gradual transition between different developmental stages during early childhood.Research HighlightsTransition between different developmental stages of non-adjacent dependency learning during early childhood evidenced by event-related brain potentialsChildren between 1 and 3 years of age showed learning of non-adjacent dependencies in a foreign language during passive listeningBrain responses revealed associative non-adjacent dependency learning across the tested age range, triggered by passive listeningGradual decrease of the strength of associative non-adjacent dependency learning, during early childhood

Essential Fatty Acid Requirements in Tropical and Cold-Water Marine Fish Larvae and Juveniles

Frontiers in Marine Science ◽

10.3389/fmars.2021.680003 ◽

2021 ◽

Vol 8 ◽

Author(s):

Sahar Chauffour Mejri ◽

Réjean Tremblay ◽

Céline Audet ◽

Paul S. Wills ◽

Marty Riche

Keyword(s):

Fatty Acids ◽

Developmental Stages ◽

Cold Water ◽

Marine Species ◽

Warm Water ◽

Larvae And Juveniles ◽

Juvenile Stages ◽

Early Developmental ◽

Juvenile Development ◽

Water Species

To improve survival at early developmental stages (larvae and juveniles) of captive fish species, essential nutrients [i.e., essential fatty acids (EFA)] need to be identified. The physiological needs are likely to be different among species, particularly among those using different thermal habitats, because lipids are largely used to maintain cell membrane integrity (homeoviscous adaptation) in fishes. This review paper will focus on currently published research and the main results from our laboratories regarding optimum qualitative EFA requirements during larval and early juvenile stages in a warm-water marine species, the Florida pompano (Trachinotus carolinus), and a cold-water marine species, the winter flounder (Pseudopleuronectes americanus). To identify the qualitative optimal EFA requirements, we calculated the ratio of certain fatty acids (FA) in larval or early juvenile tissues to total FA present in the diet. This ratio indicates whether a specific FA from prey is selectively incorporated by larvae and juveniles. Overall, we found that young larvae from both cold- and warm-water species have greater demands for n-3 and n-6 highly unsaturated fatty acids (HUFA) than do larvae at weaning stages. However, the qualitative EFA requirements of the cold-water species at all early developmental stages were higher than those of the warm-water species. Enriched rotifer diets provided satisfactory amounts of omega 3 and omega 6 in Florida pompano, with small selective retention for docosahexaenoic acid (DHA), eicosapentaenoic acid (EPA), and arachidonic acid (ARA), suggesting a potential minor diet deficiency in these EFA. There were higher deficiencies in the cold-water species fed enriched rotifers, as demonstrated by the higher selective retentions of all EFA (DHA, EPA, and ARA), with the exception of larvae fed with copepods. The physiological needs in EFA for juvenile development seemed to be better met for both species when they were fed micro pellets. From the beginning of settlement and in young juveniles, qualitative values of 12% DHA, 10% EPA, 5% ARA, and 40% PUFA of total FA seem to be required for winter flounder juvenile development. In Florida pompano, these requirements could be met until larger juvenile stages, with 15% DHA, 3% EPA, 2% ARA, 2% DPA, and total PUFA below 30% of total FA. This review was done to aid future research aiming to develop nutritionally balanced microdiets or live-prey enrichment diets to satisfy the physiological requirements of captive tropical and cold-water marine fish species.

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

10.1101/616235 ◽

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

The UN Development Decades (1961-2000): Evolution of Appraisal Systems in the Context of Development Theories

Vestnik RUDN International Relations ◽

10.22363/2313-0660-2020-20-1-170-183 ◽

2020 ◽

Vol 20 (1) ◽

pp. 170-183

Author(s):

Marina Vladimirovna Larionova

Keyword(s):

Human Development ◽

Developmental Stages ◽

Academic Research ◽

Modernization Theory ◽

Alternative Development ◽

Development Indicators ◽

Development Decade ◽

Dependence Theory ◽

Development Concept ◽

Appraisal Systems

The article explores the review and appraisal systems’ dynamics in the period from the First to the Fourth UN Development Decades in the context of the dominant developmental theories’ evolution. To reveal possible interrelations the author uses the methods of comparative assessment and periodization. The overview draws on analysis on resolutions and documents of the UN General Assembly adopted in 1960-2000, expert materials, academic research and international institutions’ reports. Development concepts which emerged in 1960-2000 had an undoubted influence on cooperation for development and the review and appraisal parameters. Developmental stages theory and modernization theory defined the priorities and parameters of the First Development Decade’s (1961-1970). In 1970s, growing economic interdependence, detente and the outcomes of the First Decade’s which showed that development could not be driven exclusively by modernization, industrialization and economic growth, determined emergence of the dependence theory and the alternative development concept. The new thinking was reflected in the provisions of the Second Development Decade. The Third Development Decade (1981-1990) provisions were built on a compromise between the dependence theory, modernization theory and the alternative development concept. For the first time concrete parameters of social development, eradication of poverty and inequality were specified. The Fourth Development Decade provisions revealed the influence of the neoliberalism in its “post-Washington consensus” reincarnation and the sustainable development concept. In the nineties the human development discourse put equality, wellbeing and freedom at the core of the development, bringing a new focus on the social and human development indicators.

Heterotrimeric kinesin-2 motor subunit, KLP68D, localises Drosophila odour receptor coreceptor in the distal domain of the olfactory cilia

10.1101/2020.11.24.395905 ◽

2020 ◽

Author(s):

Swadhin C. Jana ◽

Akanksha Jain ◽

Priya Dutta ◽

Anjusha Singh ◽

Lavanya Adusumilli ◽

...

Keyword(s):

Sensory Neurons ◽

Outer Segment ◽

Developmental Stages ◽

Olfactory Sensory Neurons ◽

List Type ◽

Tail Domain ◽

Specific Domain ◽

Electrophysiological Response ◽

Olfactory Cilia ◽

Specific Regulation

AbstractCiliary localisation of the odour receptor coreceptor (Orco) is essential for insect olfaction. Here, we show that in the Drosophila antenna Orco enters the bipartite cilia expressed on the olfactory sensory neurons in two discrete, one-hour intervals after the adult eclosion. Genetic analyses suggest that the heterotrimeric kinesin-2 is essential for Orco transfer from the base into the cilium. Using in vitro pulldown assay, we show that Orco binds to the C-terminal tail domain of KLP68D, the β-subunit of kinesin-2. Reduced Orco enrichment decreases electrophysiological response to odours and loss of olfactory behaviour. Finally, we show that kinesin-2 function is necessary to compact Orco to an approximately four-micron stretch at the distal portion of the ciliary outer-segment bearing singlet microtubule filaments. Altogether, these results highlight an independent, tissue-specific regulation of Orco entry at specific developmental stages and its localisation to a ciliary subdomain by kinesin-2.Graphical AbstractAuthor SummaryJana, Jain, Dutta et al., show that the odour receptor coreceptor only enters the cilia expressed on olfactory sensory neurons at specified developmental stages requiring heterotrimeric kinesin-2. The motor also helps to localise the coreceptor in a compact, environment-exposed domain at the ciliary outer-segment.Highlights:Odorant receptor coreceptor (Orco) selectively enters the olfactory cilia.Orco localises in a specific domain at the distal segment of the olfactory cilium.Orco/ORx binds to the C-terminal tail domain of the kinesin-2β motor subunit.Orco entry across the transition zone and its positioning require Kinesin-2.