Talk:Worm Development - Revision history

Z8600021 at 18:46, 27 August 2020

2020-08-27T18:46:37Z

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	{{10 Most Recent}}		{{10 Most Recent}}

	===~~Worm Development~~===		==2020==
	~~<pubmed limit~~=~~5>Worm Development</pubmed>~~
			{{#pmid:32814896}}

			'''Unique homeobox codes delineate all the neuron classes of C. elegans'''

			It is not known at present whether neuronal cell-type diversity-defined by cell-type-specific anatomical, biophysical, functional and molecular signatures-can be reduced to relatively simple molecular descriptors of neuronal identity1. Here we show, through examination of the expression of all of the conserved homeodomain proteins encoded by the Caenorhabditis elegans genome2, that the complete set of 118 neuron classes of C. elegans can be described individually by unique combinations of the expression of homeodomain proteins, thereby providing-to our knowledge-the simplest currently known descriptor of neuronal diversity. Computational and genetic loss-of-function analyses corroborate the notion that homeodomain proteins not only provide unique descriptors of neuron type, but also have a critical role in specifying neuronal identity. We speculate that the pervasive use of homeobox genes in defining unique neuronal identities reflects the evolutionary history of neuronal cell-type specification

			https://www.nature.com/articles/s41586-020-2618-9?WT.ec_id=NATURE-20200827&utm_source=nature_etoc&utm_medium=email&utm_campaign=20200827&sap-outbound-id=1BD32BB033E552764B0ACA50976A082D813BBF93

	~~===Worm Embryology===~~
	~~<pubmed limit=5>Worm Embryology</pubmed>~~

	==2013==		==2013==

Z8600021 at 21:36, 24 December 2012

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			==10 Most Recent Papers==
			{{10 Most Recent}}

			===Worm Development===
			<pubmed limit=5>Worm Development</pubmed>

			===Worm Embryology===
			<pubmed limit=5>Worm Embryology</pubmed>

			==2013==

	==2012==		==2012==

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2012

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	==2012==		==2012==

			===Nucleologenesis in the Caenorhabditis elegans Embryo===
			Korčeková D, Gombitová A, Raška I, Cmarko D, Lanctôt C (2012) Nucleologenesis in the Caenorhabditis elegans Embryo. PLoS ONE 7(7): e40290. doi:10.1371/journal.pone.0040290

			In the Caenorhabditis elegans nematode, the oocyte nucleolus disappears prior to fertilization. We have now investigated the re-formation of the nucleolus in the early embryo of this model organism by immunostaining for fibrillarin and DAO-5, a putative NOLC1/Nopp140 homolog involved in ribosome assembly. We find that labeled nucleoli first appear in somatic cells at around the 8-cell stage, at a time when transcription of the embryonic genome begins. Quantitative analysis of radial positioning showed the nucleolus to be localized at the nuclear periphery in a majority of early embryonic nuclei. At the ultrastructural level, the embryonic nucleolus appears to be composed of a relatively homogenous core surrounded by a crescent-shaped granular structure. Prior to embryonic genome activation, fibrillarin and DAO-5 staining is seen in numerous small nucleoplasmic foci. This staining pattern persists in the germline up to the ~100-cell stage, until the P4 germ cell divides to give rise to the Z2/Z3 primordial germ cells and embryonic transcription is activated in this lineage. In the ncl-1 mutant, which is characterized by increased transcription of rDNA, DAO-5-labeled nucleoli are already present at the 2-cell stage. Our results suggest a link between the activation of transcription and the initial formation of nucleoli in the C. elegans embryo.

			http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0040290

	===A regulatory network modeled from wild-type gene expression data guides functional predictions in Caenorhabditis elegant development===		===A regulatory network modeled from wild-type gene expression data guides functional predictions in Caenorhabditis elegant development===

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2012-06-30T00:30:09Z

2012

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	http://www.biomedcentral.com/1752-0509/6/77/abstract		http://www.biomedcentral.com/1752-0509/6/77/abstract


			===Basic Caenorhabditis elegans Methods: Synchronization and Observation===
			J Vis Exp. 2012 Jun 10;(64). pii: 4019. doi: 10.3791/4019.

			Porta-de-la-Riva M, Fontrodona L, Villanueva A, Cerón J.
			Source
			Department of Cancer and Human Molecular Genetics, Bellvitge Institute for Biomedical Research.

			Abstract

			Research into the molecular and developmental biology of the nematode Caenorhabditis elegans was begun in the early seventies by Sydney Brenner and it has since been used extensively as a model organism (1). C. elegans possesses key attributes such as simplicity, transparency and short life cycle that have made it a suitable experimental system for fundamental biological studies for many years (2). Discoveries in this nematode have broad implications because many cellular and molecular processes that control animal development are evolutionary conserved (3). C. elegans life cycle goes through an embryonic stage and four larval stages before animals reach adulthood. Development can take 2 to 4 days depending on the temperature. In each of the stages several characteristic traits can be observed. The knowledge of its complete cell lineage (4,5) together with the deep annotation of its genome turn this nematode into a great model in fields as diverse as the neurobiology (6), aging (7,8), stem cell biology (9) and germ line biology (10). An additional feature that makes C. elegans an attractive model to work with is the possibility of obtaining populations of worms synchronized at a specific stage through a relatively easy protocol. The ease of maintaining and propagating this nematode added to the possibility of synchronization provide a powerful tool to obtain large amounts of worms, which can be used for a wide variety of small or high-throughput experiments such as RNAi screens, microarrays, massive sequencing, immunoblot or in situ hybridization, among others. Because of its transparency, C. elegans structures can be distinguished under the microscope using Differential Interference Contrast microscopy, also known as Nomarski microscopy. The use of a fluorescent DNA binder, DAPI (4',6-diamidino-2-phenylindole), for instance, can lead to the specific identification and localization of individual cells, as well as subcellular structures/defects associated to them.

			PMID 22710399

	==2010==		==2010==

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2012

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	This work provides a strong example for a mathematical modeling approach that solely uses wild-type data to predict an underlying gene regulatory network. The modeling approach complements traditional methods of data analysis, suggesting non-intuitive network relationships and guiding future experiments.		This work provides a strong example for a mathematical modeling approach that solely uses wild-type data to predict an underlying gene regulatory network. The modeling approach complements traditional methods of data analysis, suggesting non-intuitive network relationships and guiding future experiments.

	PMID 22734688		PMID 22734688

			http://www.biomedcentral.com/1752-0509/6/77/abstract

	==2010==		==2010==

Z8600021 at 00:25, 30 Haziran 2012

2012-06-30T00:25:24Z

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			==2012==

			===A regulatory network modeled from wild-type gene expression data guides functional predictions in Caenorhabditis elegant development===
			BMC Syst Biol. 2012 Jun 26;6(1):77. [Epub ahead of print]

			Stigler B, Chamberlin HM.
			Abstract

			ABSTRACT:
			BACKGROUND:
			Complex gene regulatory networks underlie many cellular and developmental processes. While a variety of experimental approaches can be used to discover how genes interact, few biological systems have been systematically evaluated to the extent required for an experimental definition of the underlying network. Therefore, the development of computational methods that can use limited experimental data to define and model a gene regulatory network would provide a useful tool to evaluate many important but incompletely understood biological processes. Such methods can assist in extracting all relevant information from data that are available, identify unexpected regulatory relationships and prioritize future experiments.
			RESULTS:
			To facilitate the analysis of gene regulatory networks, we have developed a computational modeling pipeline method that complements traditional evaluation of experimental data. For a proof-of-concept example, we have focused on the gene regulatory network in the nematode C. elegans that mediates the developmental choice between mesodermal (muscle) and ectodermal (skin) cell fates in the embryonic C lineage. We have used gene expression data to build two models: a knowledge-driven model based on gene expression changes following gene perturbation experiments, and a data-driven mathematical model derived from time-course gene expression data recovered from wild-type animals. We show that both models can identify a rich set of network gene interactions. Importantly, the mathematical model built only from wild-type data can predict interactions demonstrated by the perturbation experiments better than chance, and better than an existing knowledge-driven model built from the same data set. The mathematical model also provides new biological insight, including a dissection of zygotic from maternal functions of a key transcriptional regulator, PAL-1, and identification of non-redundant activities of the T-box genes tbx-8 and tbx-9.
			CONCLUSIONS:
			This work provides a strong example for a mathematical modeling approach that solely uses wild-type data to predict an underlying gene regulatory network. The modeling approach complements traditional methods of data analysis, suggesting non-intuitive network relationships and guiding future experiments.

			PMID 22734688

	==2010==		==2010==

Z8600021 at 00:22, 30 Haziran 2012

2012-06-30T00:22:50Z

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			==2010==

	===Neurogenesis in the nematode Caenorhabditis elegans===		===Neurogenesis in the nematode Caenorhabditis elegans===
	Hobert O.		Hobert O.
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	The nervous system represents the most complex tissue of C. elegans both in terms of numbers (302 neurons and 56 glial cells = 37% of the somatic cells in a hermaphrodite) and diversity (118 morphologically distinct neuron classes). The lineage and morphology of each neuron type has been described in detail and neuronal fate markers exists for virtually all neurons in the form of fluorescent reporter genes. The ability to "phenotype" neurons at high resolution combined with the amenability of C. elegans to genetic mutant analysis make the C. elegans nervous system a prime model system to elucidate the nature of the gene regulatory programs that build a nervous system-a central question of developmental neurobiology. Discussing a number of regulatory genes involved in neuronal lineage determination and neuronal differentiation, I will try to carve out in this review a few general principles of neuronal development in C. elegans. These principles may be conserved across phylogeny.		The nervous system represents the most complex tissue of C. elegans both in terms of numbers (302 neurons and 56 glial cells = 37% of the somatic cells in a hermaphrodite) and diversity (118 morphologically distinct neuron classes). The lineage and morphology of each neuron type has been described in detail and neuronal fate markers exists for virtually all neurons in the form of fluorescent reporter genes. The ability to "phenotype" neurons at high resolution combined with the amenability of C. elegans to genetic mutant analysis make the C. elegans nervous system a prime model system to elucidate the nature of the gene regulatory programs that build a nervous system-a central question of developmental neurobiology. Discussing a number of regulatory genes involved in neuronal lineage determination and neuronal differentiation, I will try to carve out in this review a few general principles of neuronal development in C. elegans. These principles may be conserved across phylogeny.

	PMID: 20891032		PMID 20891032

	http://www.ncbi.nlm.nih.gov/pubmed/20891032		http://www.ncbi.nlm.nih.gov/pubmed/20891032
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	Joyce EF, McKim KS.		Joyce EF, McKim KS.
	PLoS Genet. 2010 Aug 12;6(8). pii: e1001059.		PLoS Genet. 2010 Aug 12;6(8). pii: e1001059.
	PMID: 20711363
			PMID 20711363

	http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001059		http://www.plosgenetics.org/article/info%3Adoi%2F10.1371%2Fjournal.pgen.1001059

			==2009==

	===xol-1, the master sex-switch gene in C. elegans, is a transcriptional target of the terminal sex-determining factor TRA-1===		===xol-1, the master sex-switch gene in C. elegans, is a transcriptional target of the terminal sex-determining factor TRA-1===

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2010-11-06T20:40:32Z

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