scholarly journals The people behind the papers – Ping Kao and Michael Nodine

Development ◽  
2021 ◽  
Vol 148 (13) ◽  
Keyword(s):  
Gene Expression ◽  
Molecular Biology ◽  
Assistant Professor ◽  
Cell Type ◽  
High Quality ◽  
Mrna Sequencing ◽  
Sequencing Technologies ◽  
The People ◽  
Gene Expression Dynamics ◽  
Gregor Mendel

ABSTRACT The application of single-cell mRNA sequencing technologies to plant embryos promises to reveal the gene expression dynamics underlying cell-type differentiation. A new paper in Development reports the generation of high-quality transcriptomes from single embryonic nuclei without contamination from maternal tissues. To find out more about the story, we caught up with first author Ping Kao and his supervisor Michael Nodine, who recently moved from the Gregor Mendel Institute in Vienna to become Assistant Professor in the Laboratory of Molecular Biology at Wageningen University in the Netherlands.

scholarly journals Single-cell RNA-sequencing reveals thoracolumbar vertebra heterogeneity and rib-genesis in pigs

2021 ◽  
Author(s):  
Jianbo Li ◽  
Ligang Wang ◽  
Dawei Yu ◽  
Junfeng Hao ◽  
Longchao Zhang ◽  
...  
Keyword(s):  
Gene Expression ◽  
Single Cell ◽  
Lumbar Vertebra ◽  
Cell Types ◽  
Cell Type ◽  
Specific Expression ◽  
Coupled Process ◽  
Gene Expression Dynamics ◽  
Cell Type Specific ◽  
Thoracolumbar Vertebra

Thoracolumbar vertebra (TLV) and rib primordium (RP) development is a common evolutionary feature across vertebrates although whole-organism analysis of TLV and RP gene expression dynamics has been lacking. Here we investigated the single-cell transcriptomic landscape of thoracic vertebra (TV), lumbar vertebra (LV), and RP cells from a pig embryo at 27 days post-fertilization (dpf) and identified six cell types with distinct gene-expression signatures. In-depth dissection of the gene-expression dynamics and RNA velocity revealed a coupled process of osteogenesis and angiogenesis during TLV and rib development. Further analysis of cell-type-specific and strand-specific expression uncovered the extremely high levels of HOXA10 3'-UTR sequence specific to osteoblast of LV cells, which may function as anti-HOXA10-antisense by counteracting the HOXA10-antisense effect to determine TLV transition. Thus, this work provides a valuable resource for understanding embryonic osteogenesis and angiogenesis underlying vertebrate TLV and RP development at the cell-type-specific resolution, which serves as a comprehensive view on the transcriptional profile of animal embryo development.

scholarly journals Regenerated crustacean limbs are precise replicas

2021 ◽  
Author(s):  
Alba Almazan ◽  
Cagri Cevrim ◽  
Jacob M Musser ◽  
Michalis Averof ◽  
Mathilde Paris
Keyword(s):  
Gene Expression ◽  
Spatial Distribution ◽  
Sensory Function ◽  
Original Structure ◽  
Cellular Composition ◽  
Cell Type ◽  
Cell Type Composition ◽  
Type Composition ◽  
Gene Expression Dynamics ◽  
Molecular Profiles

Animals can regenerate complex organs, yet this frequently results in imprecise replicas of the original structure. In the crustacean Parhyale, embryonic and regenerating legs differ in gene expression dynamics but produce apparently similar mature structures. We examine the fidelity of Parhyale leg regeneration using complementary approaches to investigate microanatomy, sensory function, cellular composition and cell molecular profiles. We find that regeneration precisely replicates the complex microanatomy and spatial distribution of external sensory organs, and restores their sensory function. Single-nuclei sequencing shows that regenerated and uninjured legs are indistinguishable in terms of cell type composition and transcriptional profiles. This remarkable fidelity highlights the ability of organisms to achieve identical outcomes via distinct processes.

Transcription as a force partitioning the eukaryotic genome

2014 ◽  
Vol 395 (11) ◽  
pp. 1301-1305 ◽  
Author(s):  
Anne Zirkel ◽  
Argyris Papantonis
Keyword(s):  
Gene Expression ◽  
Molecular Biology ◽  
Dna Sequencing ◽  
Chromatin Structure ◽  
Three Dimensional ◽  
Eukaryotic Genome ◽  
Linear Dna ◽  
Sequencing Technologies ◽  
New Gene ◽  
Eukaryotic Genomes

Abstract Eukaryotic genomes – until recently dealt with as if they were a cohort of linear DNA molecules – are perplexed three-dimensional structures, the exact conformation of which profoundly affects genome function. Recent advances in molecular biology and DNA sequencing technologies have led to a new understanding of the folding of chromatin in the nucleus. Changes in chromatin structure underlie deployment of new gene expression programs during development, differentiation, or disease. In this review, we revisit data pointing to, arguably, the major force that shapes genomes: transcription of DNA into RNA.

scholarly journals Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing

2018 ◽  
Author(s):  
Kathryn J. Grive ◽  
Yang Hu ◽  
Eileen Shu ◽  
Andrew Grimson ◽  
Olivier Elemento ◽  
...  
Keyword(s):  
Gene Expression ◽  
Germ Cell ◽  
Single Cell ◽  
Cell Population ◽  
Cell Types ◽  
Mrna Sequencing ◽  
Male Gametes ◽  
Developmental Age ◽  
Gene Expression Dynamics ◽  
Resolution Single

AbstractSpermatogenesis is the process by which male gametes are formed from a self-renewing population of spermatogonial stem cells (SSCs) residing in the testis. SSCs represent less than 1% of the total testicular cell population, but must achieve a stable balance between self-renewal and differentiation. Once differentiation has occurred, the newly formed and highly proliferative spermatogonia must then enter the meiotic program in which DNA content is doubled, then halved twice to create haploid gametes. While much is known about the critical cellular processes that take place during the specialized cell division that is meiosis, much less is known about how the spermatocytes in the “first-wave” compare to those that contribute to long-term, “steady-state” spermatogenesis. Given the strictly-defined developmental process of spermatogenesis, this study was aimed at exploring the transcriptional profiles of developmental cell stages over the age of the animal. Using a combination of comprehensive germ cell sampling with high-resolution, single-cell-mRNA-sequencing, we have generated a reference dataset of germ cell gene expression. We show that discrete developmental stages possess significant differences in the transcriptional profiles from neonates compared to juveniles and adults. Importantly, these gene expression dynamics are also reflected at the protein level in their respective cell types. We also show differential utilization of many biological pathways with age in both spermatogonia and spermatocytes, demonstrating significantly different underlying gene regulatory programs in these cell types over the course of testis development and spermatogenic waves. This dataset represents the first unbiased sampling of spermatogonia and spermatocytes in the developing testis over developmental age, at high-resolution, single-cell depth. Not only does this analysis reveal previously unknown transcriptional dynamics of a highly transitional cell population, it has also begun to reveal critical differences in biological pathway utilization in developing spermatogonia and spermatocytes, including response to DNA damage and double-strand breaks.Author SummarySpermatogenesis is the process by which male gametes – mature spermatozoa – are produced in the testis. This process requires exquisite control over many developmental transitions, including the self-renewal of the germline stem cell population, commitment to meiosis, and ultimately, spermiogenesis. While much is known about molecular mechanisms regulating single transitions at single time points in the mouse, much less is understood about how the spermatogenic progenitor cells, spermatogonia, or the meiotic cells, spermatocytes, of the testis change over developmental age.Our single-cell-mRNA-sequencing analysis is the first to profile both spermatogonia and spermatocytes from neonatal mice through adulthood, revealing novel gene expression dynamics and differential utilization of biological pathways. These discoveries help us to understand how the spermatogenic progenitors of this population modulate their activity to adapt to a changing testicular environment. Furthermore, they also begin to explain previously-observed differences - and deficiencies - in spermatocytes that are derived from the first “wave” of spermatogenesis. Overall, this dataset is the first of its kind to comprehensively profile gene expression dynamics in male germ cell populations over time, enriching our understanding of the complex and highly-orchestrated process of spermatogenesis.

scholarly journals A gene expression atlas of embryonic neurogenesis in Drosophila reveals complex spatiotemporal regulation of lncRNAs

2018 ◽  
Author(s):  
Alexandra L. McCorkindale ◽  
Philipp Wahle ◽  
Sascha Werner ◽  
Irwin Jungreis ◽  
Peter Menzel ◽  
...  
Keyword(s):  
Gene Expression ◽  
Nervous System ◽  
System Development ◽  
Cell Types ◽  
Nervous System Development ◽  
Cell Type ◽  
Gene Expression Atlas ◽  
Expression Atlas ◽  
Gene Expression Dynamics ◽  
Cell Type Specific

Summary statementWe present a spatiotemporal transcriptome during early Drosophila embryonic nervous system development, revealing a complex cell type-specific network of mRNAs and lncRNAs.AbstractCell type specification during early nervous system development in Drosophila melanogaster requires precise regulation of gene expression in time and space. Resolving the programs driving neurogenesis has been a major challenge owing to the complexity and rapidity with which distinct cell populations arise. To resolve the cell type-specific gene expression dynamics in early nervous system development, we have sequenced the transcriptomes of purified neurogenic cell types across consecutive time points covering critical events in neurogenesis. The resulting gene expression atlas comprises a detailed resource of global transcriptome dynamics that permits systematic analysis of how cells in the nervous system acquire distinct fates. We resolve known gene expression dynamics and uncover novel expression signatures for hundreds of genes among diverse neurogenic cell types, most of which remain unstudied. We also identified a set of conserved and tissue-specifically regulated long-noncoding RNAs (lncRNAs) that exhibit spatiotemporal expression during neurogenesis with exquisite specificity. LncRNA expression is highly dynamic and demarcates specific subpopulations within neurogenic cell types. Our spatiotemporal transcriptome atlas provides a comprehensive resource to investigate the function of coding genes and noncoding RNAs during critical stages of early neurogenesis.

Editorial - year end note

2020 ◽  
Vol 9 (4) ◽  
pp. 7-12
Author(s):  
Tom G. Ondicho ◽  
Keyword(s):  
Guest Editor ◽  
Value Chain ◽  
First Year ◽  
High Quality ◽  
The People ◽  
African Journal

On behalf of the editorial board and the entire value chain including authors, reviewers, and staff, I am delighted to present the Volume 9 Number 3 edition of the of the African Journal of Gender, Society and Development (AJGSD). This is the last issue for 2020 and marks the end of my first year as guest editor. It is therefore a time of reflection and an opportunity to thank all the people who have contributed in one way or another to the success of the journal over the year. First and foremost, I would like to acknowledge and appreciate the authors who have continued to display their unwavering support to the journal with an ever-increasing rate of high-quality submissions. I say a big thank you to all our esteemed authors and hope they will continue to choose AJGSD as their favored place of publication.

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