Top 10 Biorxiv Papers Today in Developmental Biology


2.0 Mikeys
#1. Analysis of sea star larval regeneration reveals conserved processes of whole-body regeneration across the metazoa
Gregory Cary, Andrew Wolff, Olga Zueva, Joseph Pattinato, Veronica Hinman
Background: Metazoan lineages exhibit a wide range of regenerative capabilities that vary among developmental stage and tissue type. The most robust regenerative abilities are apparent in the phyla Cnidaria, Platyhelminthes, and Echinodermata, whose members are capable of whole-body regeneration (WBR). This phenomenon has been well-characterized in planarian and hydra models, but the molecular details of WBR are less established within echinoderms, or any other deuterostome system. Thus, it is not clear to what degree aspects of this regenerative ability are due to deeply conserved mechanisms. Results: We characterize regeneration in the larval stage of the Bat Star (Patiria miniata). Following bisection along the anterior-posterior axis, larvae progress through phases of wound healing and re-proportioning of larval tissues. The overall number of proliferating cells is reduced following bisection and we find evidence for a re-deployment of genes with known roles in embryonic axial patterning. Following axial re-specification, we...
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jpcleland: beautiful work by @veronica_hinman and co on whole-body regeneration in a deuterostome (seastar, not star fish!!!!): https://t.co/2mWYffYxg9
MaslyLab: Analysis of sea star larval regeneration reveals conserved processes of whole-body regeneration across the metazoa https://t.co/ywIUCDZQ9f
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Authors: 5
Total Words: 14347
Unqiue Words: 3809

1.997 Mikeys
#2. X Chromosome Dosage Modulates Multiple Molecular and Cellular Properties of Mouse Pluripotent Stem Cells Independently of Global DNA Methylation Levels
Juan Song, Adrian Janiszewski, Natalie De Geest, Lotte Vanheer, Irene Talon, Mouna El Bakkali, Taeho Oh, Vincent Pasque
During early mammalian development, the two X-chromosomes in female cells are active. Dosage compensation between XX female and XY male cells is then achieved by X-chromosome inactivation in female cells. Reprogramming female mouse somatic cells into induced pluripotent stem cells (iPSCs) leads to X-chromosome reactivation. The extent to which increased X-chromosome dosage (X-dosage) in female iPSCs leads to differences in the molecular and cellular properties of XX and XY iPSCs is still unclear. We show that chromatin accessibility in mouse iPSCs is modulated by X-dosage. Specific sets of transcriptional regulator motifs are enriched in chromatin with increased accessibility in XX or XY iPSCs. We show that the transcriptome, growth and pluripotency exit are also modulated by X-dosage in iPSCs. To understand the mechanisms by which increased X-dosage modulates the molecular and cellular properties of mouse pluripotent stem cells, we used heterozygous deletions of the X-linked gene Dusp9 in XX embryonic stem cells. We show that...
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Sample Sizes : [3, 3, 2, 2, 2, 3, 2, 3, 2]
Authors: 8
Total Words: 17852
Unqiue Words: 4003

1.996 Mikeys
#3. Body composition and growth in full-term small for gestational age and large for gestational age Swedish infants assessed with air displacement plethysmography at birth and at 3-4 months of age.
Elisabeth Olhager, Anna Larsson, Peter Ottosson, Caroline Törnqvist
Background: Being born small for gestational age (SGA) or large for gestational age (LGA) has short and long term metabolic consequences. There is a growing interest in the extent to which body composition, both in the short and the long term, differs in infants born at the extremes of these birth weights. Methods: Body composition in 25 SGA and 25 LGA infants were assessed during the first days of life and at 3-4 months of age using air displacement plethysmography. Results: SGA infants had significantly lower body fat (%) at birth compared to LGA infants. SGA infants increased their body weight and length at a significantly higher rate between birth and 3-4 months than LGA infants. Fat mass (g) in SGA infants increased 23 times between birth and 3-4 months of age compared to 2.8 times for LGA infants. At 3-4 months of age LGA infants reached a threshold in body fat (%) while SGA infants were still gaining body fat (%). Conclusion: Several significant differences have been identified between SGA and LGA infants, indicating that...
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Authors: 4
Total Words: 5355
Unqiue Words: 1449

1.996 Mikeys
#4. Maintenance of spatial gene expression by Polycomb-mediated repression after formation of a vertebrate body plan
Julien Rougot, Naomi D Chrispijn, Marco Aben, Dei M Elurbe, Karolina M Andralojc, Patrick J Murphy, Pascal WTC Jansen, Michiel Vermeulen, Bradley R Cairns, Leonie M Kamminga
Polycomb group proteins are transcriptional repressors that are important regulators of cell fate during embryonic development. Among them, Ezh2 is responsible for catalyzing the epigenetic repressive mark H3K27me3 and is essential for animal development. The ability of zebrafish embryos lacking both maternal and zygotic ezh2 to form a normal body plan provides a unique model to comprehensively study Ezh2 function during early development in vertebrates. By using a multi-omics approach, we found that Ezh2 is required for the recruitment of H3K27me3 and Polycomb group protein Rnf2. However, in absence of Ezh2, only minor changes in global H3K4me3 levels and gene and protein expression occurred. These changes were mainly due to local deregulation of transcription factors outside their normal expression boundaries. Altogether, our results in zebrafish show that Polycomb-mediated gene repression is important only after the body plan is formed to maintain spatially restricted transcriptional profiles of Polycomb-targeted transcription factors.
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Sample Sizes : [2336, 11979, 1317]
Authors: 10
Total Words: 14802
Unqiue Words: 4496

1.995 Mikeys
#5. Reevaluation of the Role of ERK3 in Perinatal Survival and Post-Natal Growth Using New Genetically-Engineered Mouse Models
Mathilde Soulez, Marc K Saba-El-Leil, Benjamin Turgeon, Simon Mathien, Philippe Coulombe, Sonia Klinger, Justine Rousseau, Kim Lévesque, Sylvain Meloche
The physiological functions of the atypical MAP kinase ERK3 remain poorly characterized. Previous analysis of mice with a targeted insertion of the lacZ reporter in the Mapk6 locus (Mapk6lacZ) showed that inactivation of ERK3 in Mapk6lacZ mice leads to perinatal lethality associated with intrauterine growth restriction, defective lung maturation, and neuromuscular anomalies. To further explore the role of ERK3 in physiology and disease, we generated novel mouse models expressing a catalytically-inactive (Mapk6KD) or conditional (Mapk6D) allele of ERK3. Surprisingly, we found that mice devoid of ERK3 kinase activity or expression survive the perinatal period without any observable lung or neuromuscular phenotype. ERK3 mutant mice reached adulthood, were fertile and showed no apparent health problem. However, analysis of growth curves revealed that ERK3 kinase activity is ncessary for optimal post-natal growth. To gain insight into the genetic basis underlying the discrepancy in phenotypes of different Mapk6 mutant mouse models, we...
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Authors: 9
Total Words: 7814
Unqiue Words: 2630

0.0 Mikeys
#6. A cell cycle-coordinated nuclear compartment for Polymerase II transcription encompasses the earliest gene expression before global genome activation
Yavor Hadzhiev, Haseeb Qureshi, Lucy Wheatley, Ledean Cooper, Aleksandra Jasiulewicz, Huy Van Nguyen, Joseph Wragg, Divyasree Poovathumkadavil, Sacha Conic, Sarah Bajan, Attila Sik, Gyorgy Hutvagner, Laszlo Tora, Agnieszka Gambus, John S Fossey, Ferenc Mueller
Most metazoan embryos commence development with rapid cleavages without zygotic gene expression and their genome activation is delayed until the mid-blastula transition (MBT). However, a set of genes escape global repression during the extremely fast cell cycles, which lack gap phases and their transcription is activated before the MBT. Here we describe the formation and the spatio-temporal dynamics of a distinct transcription compartment, which encompasses the earliest detectable transcription during the first wave of genome activation. Simultaneous 4D imaging of expression of pri-miR430 and zinc finger genes by a novel, native transcription imaging approach reveals a pair of shared transcription compartments regulated by homolog chromosome organisation. These nuclear compartments carry the majority of nascent RNAs and transcriptionally active Polymerase II, are depleted of compact chromatin and represent the main sites for detectable transcription before MBT. We demonstrate that transcription occurs in the S-phase of the...
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jonmoulton: A cell cycle-coordinated nuclear compartment for Polymerase II transcription encompasses the earliest gene expression before global genome activation. https://t.co/FQ5PMlIyD9 #Morpholino
GiraldezLab: Very interesting study @ferencmueller A cell cycle-coordinated nuclear compartment for Polymerase II ... https://t.co/pwQ65pepIA #bioRxiv complementary to our recent study @GiraldezLab P300 BRd4 regulate genome activation https://t.co/edWRjHoJtY
SubjectInfinite: Biorxiv upload of research we're trying to publish, check it out! Subnuclear structures and all that. "A cell cycle-coordinated nuclear compartment for Polymerase II transcription encompasses the earliest gene expression before global genome activation" https://t.co/qiWcGPouDy
LabMueller: Exciting research from our lab! 'A cell cycle-coordinated nuclear compartment for Polymerase II transcription encompasses the earliest gene expression before global genome activation' https://t.co/vKlSNiU68k
PromPreprint: A cell cycle-coordinated nuclear compartment for Polymerase II transcription encompasses the earliest gene expression before global genome activation https://t.co/WHtC7FStIJ
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Authors: 16
Total Words: 11233
Unqiue Words: 3246

0.0 Mikeys
#7. FGF1 Promotes Xenopus laevis Lens Regeneration
Lisa Moore, Kimberly J Perry, Cindy Sun, Jonathan J Henry
Background: The frog Xenopus laevis has notable regenerative capabilities, including that of the lens. The neural retina provides the factors that trigger lens regeneration from the cornea, but the identity of these factors is largely unknown. In contrast to the cornea, fibroblast growth factors FGF1, 8, and 9 are highly expressed within the retina, and are potential candidates for those factors. The purpose of this study is to determine whether specific FGF proteins can induce lens formation, and if perturbation of FGFR signaling inhibits lens regeneration. Methods: A novel cornea epithelial culture method was developed to investigate the sufficiency of FGFs in lens regeneration. Additionally, transgenic larvae expressing dominant negative FGFR1 were used to investigate the necessity of FGFR signaling in lens regeneration. Results: Treatment of cultured corneas with FGF1 induced lens regeneration in a dose-dependent manner, whereas treatment with FGF2, FGF8, or FGF9 did not result in significant lens regeneration. Inhibition of...
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Authors: 4
Total Words: 9682
Unqiue Words: 2619

0.0 Mikeys
#8. Single-Cell Analysis Identifies Thymic Maturation Delay in Growth-Restricted Neonatal Mice
Wendi A Bacon, Russell S Hamilton, Ziyi Yu, Jens Kieckbuscha, Delia Hawkesa, Ada Krzaka, Christopher Abell, Francesco Colucci, D. Stephen Charnock-Jones
Fetal growth restriction (FGR) causes a wide variety of defects in the neonate which can lead to increased risk of heart disease, diabetes, anxiety and other disorders later in life. However, the effect of FGR on the immune system, is poorly understood. We used a well-characterized mouse model of FGR in which placental Igf-2 production is lost due to deletion of the placental specific Igf-2 P0 promotor. The thymi in such animals were reduced in mass with a ~70% reduction in cellularity. We used single cell RNA sequencing (Drop-Seq) to analyze 7264 thymus cells collected at postnatal day 6. We identified considerable heterogeneity among the Cd8/Cd4 double positive cells with one subcluster showing marked upregulation of transcripts encoding a sub-set of proteins that contribute to the surface of the ribosome. The cells from the FGR animals were underrepresented in this cluster. Furthermore, the distribution of cells from the FGR animals was skewed with a higher proportion of immature double negative cells and fewer mature T- cells....
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drrshamilton: Very excited to have a fourth bioRxiv preprint up so far this year. Single-Cell Analysis Identifies Thymic Maturation Delay in Growth-Restricted Neonatal Mice https://t.co/rz6OzwH48H
JimJohnsonSci: RT @biorxivpreprint: Single-Cell Analysis Identifies Thymic Maturation Delay in Growth-Restricted Neonatal Mice https://t.co/iyvX8hsogY #b…
drrshamilton: RT @biorxivpreprint: Single-Cell Analysis Identifies Thymic Maturation Delay in Growth-Restricted Neonatal Mice https://t.co/iyvX8hsogY #b…
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scRNA-Seq Analysis Scripts to accompany: Bacon, W.A., Hamilton, R.S., Yu, Z., Kieckbusch, J., Hawkes, D., Krzak, A., Abell, C., Colucci, F. & Charnock-Jones, D.S. (2018) Single-Cell Analysis Identifies Thymic Maturation Delay in Growth-Restricted Neonatal Mice

Repository: 2018_Bacon_Charnock-Jones
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Authors: 9
Total Words: 8930
Unqiue Words: 2930

0.0 Mikeys
#9. Different Effects of Three Types of Water on Developmental Behaviors, Lipid Metabolism and Antioxidant Capacity of Juvenile Zebrafish
JiaJin Zhu, Cheng Chang
Adolescence is an important period when people need adequate nutrition for healthy growth and development, whether from food or water. Tap water, bottled water (bottled purified water, and bottled natural water) are now the three most popular drinking waters consumed by adolescents in China. However, the constituents of them differ, which may cause different long-term health effects. In order to determine which type of water is the most beneficial regarding developmental behaviors, lipid metabolism and antioxidant capacity of juvenile zebrafish, 21 dpf (days post-fertilization) zebrafish were given these three waters separately with the same feed until 90 dpf. Results showed that zebrafish in purified water had the lowest survival rate, body weight and body length, while zebrafish in natural water and tap water had similar developmental behaviors; the highest HDL-C level and the lowest TG level were found in natural water, tap water second; and zebrafish in natural water showed the best antioxidant capacity. Thus, the best...
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Authors: 2
Total Words: 7792
Unqiue Words: 2381

0.0 Mikeys
#10. Zebrafish duox mutations provide a model for human congenital hypothyroidism
Enrique Amaya, Shoko Ishibashi, Kunal Chopra
Thyroid dyshormonogenesis is a leading cause of congenital hypothyroidism, a highly prevalent but treatable condition. Thyroid hormone synthesis is dependent on the formation of reactive oxygen species (ROS). In humans, the primary sources for ROS production during thyroid hormone synthesis are the NADPH oxidase, DUOX1 and DUOX2. Indeed mutations in DUOX1 and DUOX2 have been linked with congenital hypothyroidism. Unlike humans, zebrafish has a single orthologue for DUOX1 and DUOX2. In this study, we investigated the phenotypes associated with two nonsense mutant alleles of the single duox gene in zebrafish, sa9892 and sa13017. Both alleles gave rise to readily observable phenotypes reminiscent of congenital hypothyroidism, from the larval stages through to adulthood. By using various methods to examine the external and internal phenotypes, we discovered a strong correlation between TH synthesis and duox function, beginning from the early larval stage, when T4 levels are already noticeably absent in the mutants. Loss of T4...
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Enrique1Amaya: New preprint from the lab. First paper from the lab, which has exclusively involved work on zebrafish. Zebrafish duox mutations provide a model for human congenital hypothyroidism https://t.co/EmqLw7rDGC
Xenopus007: Zebrafish duox mutations provide a model for human congenital hypothyroidism | bioRxiv https://t.co/o3btbqP2AT
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Authors: 3
Total Words: 11815
Unqiue Words: 3724

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