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The nature and action of genes (Lecture 2) by Fernando Casares
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Program
ICTP - ICTS Winter School on Quantitative Systems Biology
ORGANIZERS: Buzz Baum, Guillaume Salbreux, Stefano Di Talia and Vijaykumar Krishnamurthy
DATE: 03 December 2019 to 20 December 2019
VENUE: Ramanujan Lecture Hall, ICTS Bangalore
The development of an organism from a single-celled zygote to an embryo involves a tight integration between gene expression, signalling and mechanochemical processes. In recent years, there has been an explosion in studies that attempt to unravel the physical principles behind how organisms self-organize to generate their three-dimensional shape and functional form. Novel microscopy techniques are giving unprecedented views into the processes of development at very high spatiotemporal resolution. This deluge of data necessitates a larger scale systems-level understanding how organisms build themselves.
The eighth edition of the ICTP - ICTS winter school on quantitative systems biology is focussed on Morphogenesis and will enable students from different backgrounds to become familiar with exciting developments at the interface of Physics and Developmental Biology. The participants of the school will be exposed to contemporary research areas, covering a large variety of topics, including mechanochemical pattern formation, regeneration and growth regulation, evolutionary-developmental biology. The school will emphasize how major questions in developmental biology such as stem cell differentiation, morphogenesis, tissue patterning and tissue mechanics, can be asked with the help of quantification and physical theory.
The main school will be held between December 9-20, 2019 and will be preceded by a pedagogic and intensive ‘Pre-School’ between December 3-6, 2019. The Pre-School will cover the basic concepts in cell and developmental biology and will have short modules on mathematical modelling and physical approaches to biology.
Scientists and students from all over the world can apply for the School. Researchers from developing countries are particularly encouraged to apply. As the program will be conducted in English, participants should have an adequate working knowledge of this language. The subsistence expenses of all selected outstation participants will be borne by the School. As a rule, travel expenses of the participants should be borne by the home institution. Every effort should be made by the candidates to secure support for their fare. However, limited travel grants are available to support the attendance of participants from developing countries from Pratiksha Trust scholarships, ICTS, Bengaluru. Selected participants are expected to attend the entire main school. Selection for the main school automatically guarantees selection for the pre-school, but attending the pre-school is not compulsory. There is no registration fee.
ORGANISING COMMITTEE
Buzz Baum (University College London)
Stefano Di Talia (Duke University)
Vijay Krishnamurthy (ICTS, Bengaluru, Local organizer)
Guillaume Salbreux (Francis Crick Institute)
SCIENTIFIC ADVISORY COMMITTEE
Vijay Balasubramanian (University of Pennsylvania)
Antonio Celani (ICTP Trieste)
Sanjay Jain (University of Delhi)
Matteo Marsili (ICTP Trieste)
Mukund Thattai (NCBS Bengaluru)
Previous editions of this school
2018
2017
2016
2015
2014
2013
2012
0:00:00 The nature and action of genes (Lecture 2)
0:00:10 Actual mechanism: Modularity of Gene Expression Regulation
0:06:16 Finding CREs: Mutations
0:10:32 Finding CREs: Conservation
0:14:50 Finding CREs: Epigenetic marks & chromatin accessibility
0:23:25 Chip-sequencing
0:30:33 Chromatin accessibility: ATAC-seq
0:33:02 Finding CREs: Epigenetic marks & chromatin accessibility
0:34:12 A realistic scheme of a gene
0:35:57 Gene Expression Regulation and very long distances
0:40:18 Higher order organization of the chromatin
0:41:55 Concentration & Space
0:47:22 "Epigenetic Landscape" makes explicit the control of changes in cell state by genes
0:48:56 Makes explicit the genes, but the control mechanisms are implicit
0:50:38 Coupled Gene Regulatory Networks
0:54:24 Regulatory state are read by specific DNA sequences
0:55:13 Regulatory state are read by specific DNA sequences: CREs
1:00:25 Gene regulatory networks: Represent very complex reactions
1:01:38 Stable Gene Expression
1:04:36 Maintenance of Gene Expression in Growing Domains
1:10:03 Feedback (Auto repression)
1:11:37 Progressive decision-making during organogenesis
1:13:17 And yet, the power of the Gene
ICTP - ICTS Winter School on Quantitative Systems Biology
ORGANIZERS: Buzz Baum, Guillaume Salbreux, Stefano Di Talia and Vijaykumar Krishnamurthy
DATE: 03 December 2019 to 20 December 2019
VENUE: Ramanujan Lecture Hall, ICTS Bangalore
The development of an organism from a single-celled zygote to an embryo involves a tight integration between gene expression, signalling and mechanochemical processes. In recent years, there has been an explosion in studies that attempt to unravel the physical principles behind how organisms self-organize to generate their three-dimensional shape and functional form. Novel microscopy techniques are giving unprecedented views into the processes of development at very high spatiotemporal resolution. This deluge of data necessitates a larger scale systems-level understanding how organisms build themselves.
The eighth edition of the ICTP - ICTS winter school on quantitative systems biology is focussed on Morphogenesis and will enable students from different backgrounds to become familiar with exciting developments at the interface of Physics and Developmental Biology. The participants of the school will be exposed to contemporary research areas, covering a large variety of topics, including mechanochemical pattern formation, regeneration and growth regulation, evolutionary-developmental biology. The school will emphasize how major questions in developmental biology such as stem cell differentiation, morphogenesis, tissue patterning and tissue mechanics, can be asked with the help of quantification and physical theory.
The main school will be held between December 9-20, 2019 and will be preceded by a pedagogic and intensive ‘Pre-School’ between December 3-6, 2019. The Pre-School will cover the basic concepts in cell and developmental biology and will have short modules on mathematical modelling and physical approaches to biology.
Scientists and students from all over the world can apply for the School. Researchers from developing countries are particularly encouraged to apply. As the program will be conducted in English, participants should have an adequate working knowledge of this language. The subsistence expenses of all selected outstation participants will be borne by the School. As a rule, travel expenses of the participants should be borne by the home institution. Every effort should be made by the candidates to secure support for their fare. However, limited travel grants are available to support the attendance of participants from developing countries from Pratiksha Trust scholarships, ICTS, Bengaluru. Selected participants are expected to attend the entire main school. Selection for the main school automatically guarantees selection for the pre-school, but attending the pre-school is not compulsory. There is no registration fee.
ORGANISING COMMITTEE
Buzz Baum (University College London)
Stefano Di Talia (Duke University)
Vijay Krishnamurthy (ICTS, Bengaluru, Local organizer)
Guillaume Salbreux (Francis Crick Institute)
SCIENTIFIC ADVISORY COMMITTEE
Vijay Balasubramanian (University of Pennsylvania)
Antonio Celani (ICTP Trieste)
Sanjay Jain (University of Delhi)
Matteo Marsili (ICTP Trieste)
Mukund Thattai (NCBS Bengaluru)
Previous editions of this school
2018
2017
2016
2015
2014
2013
2012
0:00:00 The nature and action of genes (Lecture 2)
0:00:10 Actual mechanism: Modularity of Gene Expression Regulation
0:06:16 Finding CREs: Mutations
0:10:32 Finding CREs: Conservation
0:14:50 Finding CREs: Epigenetic marks & chromatin accessibility
0:23:25 Chip-sequencing
0:30:33 Chromatin accessibility: ATAC-seq
0:33:02 Finding CREs: Epigenetic marks & chromatin accessibility
0:34:12 A realistic scheme of a gene
0:35:57 Gene Expression Regulation and very long distances
0:40:18 Higher order organization of the chromatin
0:41:55 Concentration & Space
0:47:22 "Epigenetic Landscape" makes explicit the control of changes in cell state by genes
0:48:56 Makes explicit the genes, but the control mechanisms are implicit
0:50:38 Coupled Gene Regulatory Networks
0:54:24 Regulatory state are read by specific DNA sequences
0:55:13 Regulatory state are read by specific DNA sequences: CREs
1:00:25 Gene regulatory networks: Represent very complex reactions
1:01:38 Stable Gene Expression
1:04:36 Maintenance of Gene Expression in Growing Domains
1:10:03 Feedback (Auto repression)
1:11:37 Progressive decision-making during organogenesis
1:13:17 And yet, the power of the Gene
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