Molecular Development - Revision history

Z8600021 at 01:20, 16 Ocak 2020

2020-01-16T01:20:13Z

← Older revision		Revision as of 11:20, 16 Ocak 2020
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			* '''Multimodal transcriptional control of pattern formation in embryonic development'''{{#pmid:31882445\|PMID31882445}} "Predicting how interactions between transcription factors and regulatory DNA sequence dictate rates of transcription and, ultimately, drive developmental outcomes remains an open challenge in physical biology. Using stripe 2 of the even-skipped gene in Drosophila embryos as a case study, we dissect the regulatory forces underpinning a key step along the developmental decision-making cascade: the generation of cytoplasmic mRNA patterns via the control of transcription in individual cells. Using live imaging and computational approaches, we found that the transcriptional burst frequency is modulated across the stripe to control the mRNA production rate. However, we discovered that bursting alone cannot quantitatively recapitulate the formation of the stripe and that control of the window of time over which each nucleus transcribes even-skipped plays a critical role in stripe formation. Theoretical modeling revealed that these regulatory strategies (bursting and the time window) respond in different ways to input transcription factor concentrations, suggesting that the stripe is shaped by the interplay of 2 distinct underlying {{molecular}} processes." {{Fly}}

	* '''Key role for CTCF in establishing chromatin structure in human embryos'''{{#pmid:31801998\|PMID31801998}} "In the interphase of the cell cycle, chromatin is arranged in a hierarchical structure within the nucleus1,2, which has an important role in regulating gene expression3-6. However, the dynamics of 3D chromatin structure during human embryogenesis remains unknown. Here we report that, unlike mouse sperm, human sperm cells do not express the chromatin regulator CTCF and their chromatin does not contain topologically associating domains (TADs). Following human fertilization, TAD structure is gradually established during embryonic development. In addition, A/B compartmentalization is lost in human embryos at the 2-cell stage and is re-established during embryogenesis. Notably, blocking zygotic genome activation (ZGA) can inhibit TAD establishment in human embryos but not in mouse or Drosophila. Of note, CTCF is expressed at very low levels before ZGA, and is then highly expressed at the ZGA stage when TADs are observed. TAD organization is significantly reduced in CTCF knockdown embryos, suggesting that TAD establishment during ZGA in human embryos requires CTCF expression. Our results indicate that CTCF has a key role in the establishment of 3D chromatin structure during human embryogenesis."		* '''Key role for CTCF in establishing chromatin structure in human embryos'''{{#pmid:31801998\|PMID31801998}} "In the interphase of the cell cycle, chromatin is arranged in a hierarchical structure within the nucleus1,2, which has an important role in regulating gene expression3-6. However, the dynamics of 3D chromatin structure during human embryogenesis remains unknown. Here we report that, unlike mouse sperm, human sperm cells do not express the chromatin regulator CTCF and their chromatin does not contain topologically associating domains (TADs). Following human fertilization, TAD structure is gradually established during embryonic development. In addition, A/B compartmentalization is lost in human embryos at the 2-cell stage and is re-established during embryogenesis. Notably, blocking zygotic genome activation (ZGA) can inhibit TAD establishment in human embryos but not in mouse or Drosophila. Of note, CTCF is expressed at very low levels before ZGA, and is then highly expressed at the ZGA stage when TADs are observed. TAD organization is significantly reduced in CTCF knockdown embryos, suggesting that TAD establishment during ZGA in human embryos requires CTCF expression. Our results indicate that CTCF has a key role in the establishment of 3D chromatin structure during human embryogenesis."

Z8600021 at 21:47, 12 December 2019

2019-12-12T21:47:15Z

← Older revision		Revision as of 07:47, 13 December 2019
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	{\|		{\|
	\|-bgcolor="F5FAFF"		\|-bgcolor="F5FAFF"
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			* '''Key role for CTCF in establishing chromatin structure in human embryos'''{{#pmid:31801998\|PMID31801998}} "In the interphase of the cell cycle, chromatin is arranged in a hierarchical structure within the nucleus1,2, which has an important role in regulating gene expression3-6. However, the dynamics of 3D chromatin structure during human embryogenesis remains unknown. Here we report that, unlike mouse sperm, human sperm cells do not express the chromatin regulator CTCF and their chromatin does not contain topologically associating domains (TADs). Following human fertilization, TAD structure is gradually established during embryonic development. In addition, A/B compartmentalization is lost in human embryos at the 2-cell stage and is re-established during embryogenesis. Notably, blocking zygotic genome activation (ZGA) can inhibit TAD establishment in human embryos but not in mouse or Drosophila. Of note, CTCF is expressed at very low levels before ZGA, and is then highly expressed at the ZGA stage when TADs are observed. TAD organization is significantly reduced in CTCF knockdown embryos, suggesting that TAD establishment during ZGA in human embryos requires CTCF expression. Our results indicate that CTCF has a key role in the establishment of 3D chromatin structure during human embryogenesis."

	* '''Transcriptional control of lung alveolar type 1 cell development and maintenance by NK homeobox 2-1'''{{#pmid:31548395\|PMID31548395}} "The extraordinarily thin alveolar type 1 (AT1) cell constitutes nearly the entire gas exchange surface and allows passive diffusion of oxygen into the blood stream. Despite such an essential role, the transcriptional network controlling AT1 cells remains unclear. Using cell-specific knockout mouse models, genomic profiling, and 3D imaging, we found that NK homeobox 2-1 (Nkx2-1) is expressed in AT1 cells and is required for the development and maintenance of AT1 cells. Without Nkx2-1, developing AT1 cells lose 3 defining features-molecular markers, expansive morphology, and cellular quiescence-leading to alveolar simplification and lethality. NKX2-1 is also cell-autonomously required for the same 3 defining features in mature AT1 cells. Intriguingly, Nkx2-1 mutant AT1 cells activate gastrointestinal (GI) genes and form dense microvilli-like structures apically. Single-cell RNA-seq supports a linear transformation of Nkx2-1 mutant AT1 cells toward a GI fate. Whole lung ChIP-seq shows NKX2-1 binding to 68% of genes that are down-regulated upon Nkx2-1 deletion, including 93% of known AT1 genes, but near-background binding to up-regulated genes. Our results place NKX2-1 at the top of the AT1 cell transcriptional hierarchy and demonstrate remarkable plasticity of an otherwise terminally differentiated cell type. {{respiratory}}		* '''Transcriptional control of lung alveolar type 1 cell development and maintenance by NK homeobox 2-1'''{{#pmid:31548395\|PMID31548395}} "The extraordinarily thin alveolar type 1 (AT1) cell constitutes nearly the entire gas exchange surface and allows passive diffusion of oxygen into the blood stream. Despite such an essential role, the transcriptional network controlling AT1 cells remains unclear. Using cell-specific knockout mouse models, genomic profiling, and 3D imaging, we found that NK homeobox 2-1 (Nkx2-1) is expressed in AT1 cells and is required for the development and maintenance of AT1 cells. Without Nkx2-1, developing AT1 cells lose 3 defining features-molecular markers, expansive morphology, and cellular quiescence-leading to alveolar simplification and lethality. NKX2-1 is also cell-autonomously required for the same 3 defining features in mature AT1 cells. Intriguingly, Nkx2-1 mutant AT1 cells activate gastrointestinal (GI) genes and form dense microvilli-like structures apically. Single-cell RNA-seq supports a linear transformation of Nkx2-1 mutant AT1 cells toward a GI fate. Whole lung ChIP-seq shows NKX2-1 binding to 68% of genes that are down-regulated upon Nkx2-1 deletion, including 93% of known AT1 genes, but near-background binding to up-regulated genes. Our results place NKX2-1 at the top of the AT1 cell transcriptional hierarchy and demonstrate remarkable plasticity of an otherwise terminally differentiated cell type. {{respiratory}}

Z8600021 at 01:04, 3 December 2019

2019-12-03T01:04:14Z

← Older revision		Revision as of 11:04, 3 December 2019
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	{{Amino Acid Table}}		{{Amino Acid Table}}

	~~'''~~Hydropathy Index~~'''{{#pmid:7108955\|PMID7108955}}~~		===Hydropathy Index===
	* a number representing the hydrophobic or hydrophilic properties of the amino acid sidechain.		* a number representing the hydrophobic or hydrophilic properties of the amino acid sidechain.
	* larger the number the more hydrophobic the amino acid.		* larger the number the more hydrophobic the amino acid.

Z8600021 at 22:46, 19 November 2019

2019-11-19T22:46:30Z

← Older revision		Revision as of 08:46, 20 November 2019
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			* '''Transcriptional control of lung alveolar type 1 cell development and maintenance by NK homeobox 2-1'''{{#pmid:31548395\|PMID31548395}} "The extraordinarily thin alveolar type 1 (AT1) cell constitutes nearly the entire gas exchange surface and allows passive diffusion of oxygen into the blood stream. Despite such an essential role, the transcriptional network controlling AT1 cells remains unclear. Using cell-specific knockout mouse models, genomic profiling, and 3D imaging, we found that NK homeobox 2-1 (Nkx2-1) is expressed in AT1 cells and is required for the development and maintenance of AT1 cells. Without Nkx2-1, developing AT1 cells lose 3 defining features-molecular markers, expansive morphology, and cellular quiescence-leading to alveolar simplification and lethality. NKX2-1 is also cell-autonomously required for the same 3 defining features in mature AT1 cells. Intriguingly, Nkx2-1 mutant AT1 cells activate gastrointestinal (GI) genes and form dense microvilli-like structures apically. Single-cell RNA-seq supports a linear transformation of Nkx2-1 mutant AT1 cells toward a GI fate. Whole lung ChIP-seq shows NKX2-1 binding to 68% of genes that are down-regulated upon Nkx2-1 deletion, including 93% of known AT1 genes, but near-background binding to up-regulated genes. Our results place NKX2-1 at the top of the AT1 cell transcriptional hierarchy and demonstrate remarkable plasticity of an otherwise terminally differentiated cell type. {{respiratory}}

	* '''Cell-matrix signals (integrin β1) specify bone endothelial cells during developmental osteogenesis'''{{#pmid:28218908\|PMID28218908}} “Blood vessels in the mammalian skeletal system control bone formation and support haematopoiesis by generating local niche environments. Here, we report that embryonic and early postnatal long bone contains a specialized endothelial cell subtype, termed type E, which strongly supports osteoblast lineage cells and later gives rise to other endothelial cell subpopulations. The differentiation and functional properties of bone endothelial cells require cell-matrix signalling interactions." [[Musculoskeletal_System_-_Bone_Development\|Bone Development]] \| [https://omim.org/entry/135630 INTEGRIN BETA-1]		* '''Cell-matrix signals (integrin β1) specify bone endothelial cells during developmental osteogenesis'''{{#pmid:28218908\|PMID28218908}} “Blood vessels in the mammalian skeletal system control bone formation and support haematopoiesis by generating local niche environments. Here, we report that embryonic and early postnatal long bone contains a specialized endothelial cell subtype, termed type E, which strongly supports osteoblast lineage cells and later gives rise to other endothelial cell subpopulations. The differentiation and functional properties of bone endothelial cells require cell-matrix signalling interactions." [[Musculoskeletal_System_-_Bone_Development\|Bone Development]] \| [https://omim.org/entry/135630 INTEGRIN BETA-1]

	* '''foxl3 is a germ cell-intrinsic factor involved in sperm-egg fate decision in medaka'''{{#pmid:26067255\|PMID26067255}} "Sex determination is an essential step in the commitment of a germ cell to a sperm or egg. However, the intrinsic factors that determine the sexual fate of vertebrate germ cells are unknown. Here we show that foxl3, which is expressed in germ cells but not somatic cells in the gonad, is involved in sperm-egg fate decision in medaka fish. Adult XX medaka with disrupted foxl3 developed functional sperm in the expanded germinal epithelium of a histologically functional ovary. In chimeric medaka, mutant germ cells initiated spermatogenesis in female wild-type gonad. These results indicate that a germ cell-intrinsic cue for the sperm-egg fate decision is present in medaka and that spermatogenesis can proceed in a female gonadal environment." ( Forkhead Transcription Factor foxl3 is an ancient duplicated copy of [http://omim.org/entry/605597?search=foxl2&highlight=foxl2 foxl2] \| [[Medaka Development]] \| [[Oocyte Development]] \| [[Spermatozoa Development]])		* '''foxl3 is a germ cell-intrinsic factor involved in sperm-egg fate decision in medaka'''{{#pmid:26067255\|PMID26067255}} "Sex determination is an essential step in the commitment of a germ cell to a sperm or egg. However, the intrinsic factors that determine the sexual fate of vertebrate germ cells are unknown. Here we show that foxl3, which is expressed in germ cells but not somatic cells in the gonad, is involved in sperm-egg fate decision in medaka fish. Adult XX medaka with disrupted foxl3 developed functional sperm in the expanded germinal epithelium of a histologically functional ovary. In chimeric medaka, mutant germ cells initiated spermatogenesis in female wild-type gonad. These results indicate that a germ cell-intrinsic cue for the sperm-egg fate decision is present in medaka and that spermatogenesis can proceed in a female gonadal environment." ( Forkhead Transcription Factor foxl3 is an ancient duplicated copy of [http://omim.org/entry/605597?search=foxl2&highlight=foxl2 foxl2] \| [[Medaka Development]] \| [[Oocyte Development]] \| [[Spermatozoa Development]])

			\|}
			{\| class="wikitable mw-collapsible mw-collapsed"
			! Older papers
			\|-
			\| {{Older papers}}
	* '''The Encyclopedia of DNA Elements (ENCODE) project''' Wed, Sep 5, 2012 "The Human Genome Project produced an almost complete order of the 3 billion pairs of chemical letters in the DNA that embodies the human genetic code — but little about the way this blueprint works. Now, after a multi-year concerted effort by more than 440 researchers in 32 labs around the world, a more dynamic picture gives the first holistic view of how the human genome actually does its job." [http://www.genome.gov/27549810 NIH] [http://www.nature.com/encode/ Nature]		* '''The Encyclopedia of DNA Elements (ENCODE) project''' Wed, Sep 5, 2012 "The Human Genome Project produced an almost complete order of the 3 billion pairs of chemical letters in the DNA that embodies the human genetic code — but little about the way this blueprint works. Now, after a multi-year concerted effort by more than 440 researchers in 32 labs around the world, a more dynamic picture gives the first holistic view of how the human genome actually does its job." [http://www.genome.gov/27549810 NIH] [http://www.nature.com/encode/ Nature]

	* '''Properties of developmental gene regulatory networks'''{{#pmid:19104053\|PMID19104053}} Introductory paper from the "Gene Networks in Development and Evolution Special Feature Sackler Colloquium" (2008) "The modular components, or subcircuits, of developmental gene regulatory networks (GRNs) execute specific developmental functions, such as the specification of cell identity. We survey examples of such subcircuits and relate their structures to corresponding developmental functions. These relations transcend organisms and genes, as illustrated by the similar structures of the subcircuits controlling the specification of the mesectoderm in the Drosophila embryo and the endomesoderm in the sea urchin, even though the respective subcircuits are composed of nonorthologous regulatory genes."		* '''Properties of developmental gene regulatory networks'''{{#pmid:19104053\|PMID19104053}} Introductory paper from the "Gene Networks in Development and Evolution Special Feature Sackler Colloquium" (2008) "The modular components, or subcircuits, of developmental gene regulatory networks (GRNs) execute specific developmental functions, such as the specification of cell identity. We survey examples of such subcircuits and relate their structures to corresponding developmental functions. These relations transcend organisms and genes, as illustrated by the similar structures of the subcircuits controlling the specification of the mesectoderm in the Drosophila embryo and the endomesoderm in the sea urchin, even though the respective subcircuits are composed of nonorthologous regulatory genes."
	\|}		\|}

	==Movies==		==Movies==
	{{Translation movie}}		{{Translation movie}}

Z8600021 at 00:31, 14 November 2019

2019-11-14T00:31:07Z

← Older revision		Revision as of 10:31, 14 November 2019
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	==Starting Out==		==Starting Out==
	[[File:SHH signaling model.png\|thumb\|Model of Sonic hedgehog signaling in the drosophila wing]]		[[File:SHH signaling model.png\|thumb\|Model of Sonic hedgehog signaling in the drosophila wing{{#pmid:19787036\|PMID19787036}}]]

	There are several different ways to begin to look at molecular development.		There are several different ways to begin to look at molecular development.

Z8600021 at 00:15, 14 November 2019

2019-11-14T00:15:02Z

← Older revision		Revision as of 10:15, 14 November 2019
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	{{External Links}}		{{External Links}}

	* NHGR- [http://www.genome.gov/10005107#al-1 The ENCODE Project] ENCyclopedia Of DNA Elements		===Gene Ontology Consortium===

			* [http://geneontology.org Gene Ontology Consortium] - "The mission of the [http://geneontology.org GO Consortium] is to develop a comprehensive, computational model of biological systems, ranging from the molecular to the organism level, across the multiplicity of species in the tree of life."
			* NHGR - [http://www.genome.gov/10005107#al-1 The ENCODE Project] ENCyclopedia Of DNA Elements
	* Foldit - [http://foldit.wikia.com/wiki/Amino_Acids Amino Acids]		* Foldit - [http://foldit.wikia.com/wiki/Amino_Acids Amino Acids]
	* [http://www.cytoscape.org Cytoscape] - open source software platform for visualizing complex networks and integrating these with any type of attribute data.		* [http://www.cytoscape.org Cytoscape] - open source software platform for visualizing complex networks and integrating these with any type of attribute data.

Z8600021 at 23:28, 24 Ocak 2019

2019-01-24T23:28:10Z

← Older revision		Revision as of 09:28, 25 Ocak 2019
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	In recent years this RNA family, shown in the table below, has been expanded to include newly identified members: small nuclear RNA (snRNA) , small nucleolar RNA (snoRNA), and short regulatory RNA (piwi-associated RNA (piRNA), endogenous short-interfering RNA (endo-siRNA) and microRNA (miRNA) and now long non-coding RNA (lncRNA). Each of these new family members has a range of potential roles in development and differentiation.		In recent years this RNA family, shown in the table below, has been expanded to include newly identified members: small nuclear RNA (snRNA) , small nucleolar RNA (snoRNA), and short regulatory RNA (piwi-associated RNA (piRNA), endogenous short-interfering RNA (endo-siRNA) and microRNA (miRNA) and now long non-coding RNA (lncRNA). Each of these new family members has a range of potential roles in development and differentiation.

	{~~\| class="wikitable sortable"~~		{{RNA Class table}}
	\|-
	! RNA Class ~~!! Acronym !! Roles !! Examples !! Reviews~~
	\|-
	~~\| transfer RNA \|\| tRNA \|\| carry amino acid in cell cytoplasm to ribosome \|\| \|\| PMID 24966867~~
	\|-
	~~\| messenger RNA \|\| mRNA \|\| transcribed from DNA in cell nucleus and relocate to cytoplasm for translation on the ribosome\|\| Example~~
	\|-
	~~\| ribosomal RNA \|\| rRNA \|\| structural RNA that allow the assembly of ribosomal proteins in the cytoplasm into ribosomal subunits required for protein translation\|\| Example~~
	\|-
	~~\| small nuclear RNA \|\| snRNA \|\| involved in cell nucleus RNA splicing\|\| \|\| PMID 23980890~~
	\|-
	~~\| small nucleolar RNA \|\| snoRNA \|\| modify other small RNAs (rRNAs and tRNAs) \|\| box C/D snoRNAs and the box H/ACA \|\| PMID 21664409 PMID 19446021~~
	\|-
	~~\| microRNA \|\| miRNA \|\| post-transcriptional regulator of gene expression\|\| \|\| PMID 25128264~~
	\|-
	~~\| endogenous short-interfering RNA \|\| endo-siRNA \|\| short regulatory RNA \|\| mainly characterised in plants \|\| PMID 22578318~~
	\|-
	~~\| piwi-associated RNA \|\| piRNA \|\| short regulatory RNA \|\| \|\| PMID 18032451 PMID 22103557~~
	\|-
	~~\| long non-coding RNA \|\| ncRNA \|\| non-coding RNA greater than 200bp in length may have different roles in signalling, protein processing and differentiation \|\| \|\| PMID 24829860~~
	\|}

Z8600021 at 23:36, 12 March 2018

2018-03-12T23:36:35Z

← Older revision		Revision as of 09:36, 13 March 2018
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	==Introduction==		==Introduction==
	[[File:Amphibian_oocyte_transcription.jpg\|thumb\|Amphibian oocyte transcription]]		[[File:Amphibian_oocyte_transcription.jpg\|thumb\|Amphibian oocyte transcription]]
	[[File:Epigenetics cartoon.jpg\|thumb\|Epigenetics mechanisms~~<ref><pubmed>~~16688142~~</pubmed></ref>~~]]		[[File:Epigenetics cartoon.jpg\|thumb\|Epigenetics mechanisms{{#pmid:16688142\|PMID16688142}}]]
	This page is a link to many different resources related to molecular development. I am 2.85 billion nucleotides of DNA, but so is a chimpanzee, and all this DNA encodes only about 20,000-25,000 protein-coding genes. In development, I am not that different from a mouse or a fly and many of the signals that regulate development are used time and time again.		This page is a link to many different resources related to molecular development. I am 2.85 billion nucleotides of DNA, but so is a chimpanzee, and all this DNA encodes only about 20,000-25,000 protein-coding genes. In development, I am not that different from a mouse or a fly and many of the signals that regulate development are used time and time again.

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	\| [[File:Fly_antennapedia_head.jpg\|250px]]		\| [[File:Fly_antennapedia_head.jpg\|250px]]
	\|-		\|-
	\| Fly wild-type head~~<ref name="~~PMID108157~~"><pubmed>108157</pubmed></ref>~~		\| Fly wild-type head{{#pmid:108157\|PMID108157}}
	\| Fly antennapedia mutant head~~<ref name="~~PMID108157~~" />~~		\| Fly antennapedia mutant head{{#pmid:108157\|PMID108157}}
	\|}		\|}

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	* '''Cell-matrix signals (integrin β1) specify bone endothelial cells during developmental osteogenesis'''~~<ref name=~~PMID28218908~~><pubmed>28218908</pubmed></ref>~~ “Blood vessels in the mammalian skeletal system control bone formation and support haematopoiesis by generating local niche environments. Here, we report that embryonic and early postnatal long bone contains a specialized endothelial cell subtype, termed type E, which strongly supports osteoblast lineage cells and later gives rise to other endothelial cell subpopulations. The differentiation and functional properties of bone endothelial cells require cell-matrix signalling interactions." [[Musculoskeletal_System_-_Bone_Development\|Bone Development]] \| [https://omim.org/entry/135630 INTEGRIN BETA-1]		* '''Cell-matrix signals (integrin β1) specify bone endothelial cells during developmental osteogenesis'''{{#pmid:28218908\|PMID28218908}} “Blood vessels in the mammalian skeletal system control bone formation and support haematopoiesis by generating local niche environments. Here, we report that embryonic and early postnatal long bone contains a specialized endothelial cell subtype, termed type E, which strongly supports osteoblast lineage cells and later gives rise to other endothelial cell subpopulations. The differentiation and functional properties of bone endothelial cells require cell-matrix signalling interactions." [[Musculoskeletal_System_-_Bone_Development\|Bone Development]] \| [https://omim.org/entry/135630 INTEGRIN BETA-1]
	* '''foxl3 is a germ cell-intrinsic factor involved in sperm-egg fate decision in medaka'''~~<ref name="PMID26067255"><pubmed>~~26067255~~</pubmed>~~\| ~~[http://www.sciencemag.org/content/early/2015/06/10/science.aaa2657.abstract Science.]</ref>~~ "Sex determination is an essential step in the commitment of a germ cell to a sperm or egg. However, the intrinsic factors that determine the sexual fate of vertebrate germ cells are unknown. Here we show that foxl3, which is expressed in germ cells but not somatic cells in the gonad, is involved in sperm-egg fate decision in medaka fish. Adult XX medaka with disrupted foxl3 developed functional sperm in the expanded germinal epithelium of a histologically functional ovary. In chimeric medaka, mutant germ cells initiated spermatogenesis in female wild-type gonad. These results indicate that a germ cell-intrinsic cue for the sperm-egg fate decision is present in medaka and that spermatogenesis can proceed in a female gonadal environment." ( Forkhead Transcription Factor foxl3 is an ancient duplicated copy of [http://omim.org/entry/605597?search=foxl2&highlight=foxl2 foxl2] \| [[Medaka Development]] \| [[Oocyte Development]] \| [[Spermatozoa Development]])
			* '''foxl3 is a germ cell-intrinsic factor involved in sperm-egg fate decision in medaka'''{{#pmid:26067255\|PMID26067255}} "Sex determination is an essential step in the commitment of a germ cell to a sperm or egg. However, the intrinsic factors that determine the sexual fate of vertebrate germ cells are unknown. Here we show that foxl3, which is expressed in germ cells but not somatic cells in the gonad, is involved in sperm-egg fate decision in medaka fish. Adult XX medaka with disrupted foxl3 developed functional sperm in the expanded germinal epithelium of a histologically functional ovary. In chimeric medaka, mutant germ cells initiated spermatogenesis in female wild-type gonad. These results indicate that a germ cell-intrinsic cue for the sperm-egg fate decision is present in medaka and that spermatogenesis can proceed in a female gonadal environment." ( Forkhead Transcription Factor foxl3 is an ancient duplicated copy of [http://omim.org/entry/605597?search=foxl2&highlight=foxl2 foxl2] \| [[Medaka Development]] \| [[Oocyte Development]] \| [[Spermatozoa Development]])

	* '''The Encyclopedia of DNA Elements (ENCODE) project''' Wed, Sep 5, 2012 "The Human Genome Project produced an almost complete order of the 3 billion pairs of chemical letters in the DNA that embodies the human genetic code — but little about the way this blueprint works. Now, after a multi-year concerted effort by more than 440 researchers in 32 labs around the world, a more dynamic picture gives the first holistic view of how the human genome actually does its job." [http://www.genome.gov/27549810 NIH] [http://www.nature.com/encode/ Nature]		* '''The Encyclopedia of DNA Elements (ENCODE) project''' Wed, Sep 5, 2012 "The Human Genome Project produced an almost complete order of the 3 billion pairs of chemical letters in the DNA that embodies the human genetic code — but little about the way this blueprint works. Now, after a multi-year concerted effort by more than 440 researchers in 32 labs around the world, a more dynamic picture gives the first holistic view of how the human genome actually does its job." [http://www.genome.gov/27549810 NIH] [http://www.nature.com/encode/ Nature]
	* '''Properties of developmental gene regulatory networks'''~~<ref><pubmed>~~19104053~~</pubmed>~~\| ~~[http://www.pnas.org/content/105/51.toc PNAS]</ref>~~ Introductory paper from the "Gene Networks in Development and Evolution Special Feature Sackler Colloquium" (2008) "The modular components, or subcircuits, of developmental gene regulatory networks (GRNs) execute specific developmental functions, such as the specification of cell identity. We survey examples of such subcircuits and relate their structures to corresponding developmental functions. These relations transcend organisms and genes, as illustrated by the similar structures of the subcircuits controlling the specification of the mesectoderm in the Drosophila embryo and the endomesoderm in the sea urchin, even though the respective subcircuits are composed of nonorthologous regulatory genes."
			* '''Properties of developmental gene regulatory networks'''{{#pmid:19104053\|PMID19104053}} Introductory paper from the "Gene Networks in Development and Evolution Special Feature Sackler Colloquium" (2008) "The modular components, or subcircuits, of developmental gene regulatory networks (GRNs) execute specific developmental functions, such as the specification of cell identity. We survey examples of such subcircuits and relate their structures to corresponding developmental functions. These relations transcend organisms and genes, as illustrated by the similar structures of the subcircuits controlling the specification of the mesectoderm in the Drosophila embryo and the endomesoderm in the sea urchin, even though the respective subcircuits are composed of nonorthologous regulatory genes."
	\|}		\|}

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	{{Amino Acid Table}}		{{Amino Acid Table}}

	'''Hydropathy Index'''~~<ref name="~~PMID7108955~~"><pubmed>7108955</pubmed></ref>~~		'''Hydropathy Index'''{{#pmid:7108955\|PMID7108955}}
	* a number representing the hydrophobic or hydrophilic properties of the amino acid sidechain.		* a number representing the hydrophobic or hydrophilic properties of the amino acid sidechain.
	* larger the number the more hydrophobic the amino acid.		* larger the number the more hydrophobic the amino acid.
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	[[File:Hedgehog signaling pathway.jpg\|600px]]		[[File:Hedgehog signaling pathway.jpg\|600px]]

	Hedgehog signaling pathway~~<ref><pubmed>~~19040769~~</pubmed>\| [http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2614485 PMC2614485]~~ \| ~~[http://genomebiology.com/content/9/11/241 Genome Biology]</ref>~~		Hedgehog signaling pathway{{#pmid:19040769\|PMID19040769}}

	Note spelling difference: USA signaling, UK signalling.		Note spelling difference: USA signaling, UK signalling.
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	[[File:Embryo_left-right_asymmetry_pathway.jpg\|600px]]		[[File:Embryo_left-right_asymmetry_pathway.jpg\|600px]]

	Embryo left-right asymmetry pathway~~<ref><pubmed>~~23256866~~</pubmed>~~\| ~~[http://www.biomedcentral.com/1741-7007/10/102 BMC Biology]</ref>~~		Embryo left-right asymmetry pathway{{#pmid:23256866\|PMID23256866}}

	The mechanisms that specify location within the embryo, therefore establishing axes, appears to be controlled by similar signaling mechanisms in different species.		The mechanisms that specify location within the embryo, therefore establishing axes, appears to be controlled by similar signaling mechanisms in different species.

Z8600021 at 08:22, 12 August 2017

2017-08-12T08:22:24Z

← Older revision		Revision as of 18:22, 12 August 2017
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	<div id="GRN"></div>		<div id="GRN"></div>
	'''Gene Regulatory Network''' ({{GRN}}) a ~~term broadly used~~ to ~~describe~~ the molecular mechanisms/pathways used in the development of specific cell types and tissues ~~within the embryo~~.		'''Gene Regulatory Network''' ({{GRN}}) is a set of genes, or parts of genes, that interact with each other to control a specific cell function. In the embryo, these are the molecular mechanisms/pathways used in the development and differentiation of specific cell types and tissues.

	A continuing theme also seems to be the reuse of signals at different times and places within the embryo, for diiferent jobs. This has given rise to the concept of "switches" which by themselves may contain no "information" but to activate other genes or switches. Finally, you can imagine that of our 20,000-25,000 protein-coding genes, a large number of these may only be expressed during development or if reused, have a completely different role in the mature animal. The new field of epigenetics has also begun to florish with some recent important findings.		A continuing theme also seems to be the reuse of signals at different times and places within the embryo, for diiferent jobs. This has given rise to the concept of "switches" which by themselves may contain no "information" but to activate other genes or switches. Finally, you can imagine that of our 20,000-25,000 protein-coding genes, a large number of these may only be expressed during development or if reused, have a completely different role in the mature animal. The new field of epigenetics has also begun to florish with some recent important findings.

Z8600021 at 07:51, 12 August 2017

2017-08-12T07:51:41Z

← Older revision		Revision as of 17:51, 12 August 2017
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	<div id="GRN"></div>		<div id="GRN"></div>
	'''Gene Regulatory Network''' ({{GRN}}) is broadly used to describe the molecular mechanisms/pathways used in the development of specific cell types and tissues within the embryo.		'''Gene Regulatory Network''' ({{GRN}}) a term broadly used to describe the molecular mechanisms/pathways used in the development of specific cell types and tissues within the embryo.

	A continuing theme also seems to be the reuse of signals at different times and places within the embryo, for diiferent jobs. This has given rise to the concept of "switches" which by themselves may contain no "information" but to activate other genes or switches. Finally, you can imagine that of our 20,000-25,000 protein-coding genes, a large number of these may only be expressed during development or if reused, have a completely different role in the mature animal.		A continuing theme also seems to be the reuse of signals at different times and places within the embryo, for diiferent jobs. This has given rise to the concept of "switches" which by themselves may contain no "information" but to activate other genes or switches. Finally, you can imagine that of our 20,000-25,000 protein-coding genes, a large number of these may only be expressed during development or if reused, have a completely different role in the mature animal. The new field of epigenetics has also begun to florish with some recent important findings.


	~~In terms of molecular mechanisms, the~~ field of epigenetics has begun to florish with some recent important findings.


	Molecular mechanisms of development is an exciting area and requires a variety of different skills. This page introduces only a few examples and should give you a feel for the topic. Note that each section of system notes has a page covering molecular development in that system. I have included information about the basic building blocks of proteins (amino acids).		Molecular mechanisms of development is an exciting area and requires a variety of different skills. This page introduces only a few examples and should give you a feel for the topic. Note that each section of system notes has a page covering molecular development in that system. I have included information about the basic building blocks of proteins (amino acids).


	{{Molecular Links}}		{{Molecular Links}}