January 2013 - Seminars - maillist.psb.ugent.be

PSB event reminder
by contact＠psb.vib-ugent.be 30 Jan '13

30 Jan '13

Calendar Name: seminars Scheduled for: Wednesday, January 30 2013, 11:00 - 12:30 Event text: Dr Jens Boch Martin Luther University Halle-Wittenberg Institute of Biology Department of Genetics Halle (Saale) GERMANY Details: Postdoc Innovation seminar �TALEs and TALENs for targeted genome engineering and expression control� ABSTRACT The DNA-binding domain of TALEs (transcription activator-like effectors) from plant-pathogenic Xanthomonas bacteria has become an important tool for the programmable and specific targeting of DNA. Natural TALEs function as transcription factors in plant cells to support pathogen colonization of host plants. TALE proteins bind to DNA via near-identical tandem repeats of 34 amino acids. Each repeat recognizes one base in the target DNA sequence via repeat-variable diresidues (RVDs). The simple and modular repeat architecture allows rearrangement of TALE repeats to generate artificial TALEs with virtually any tailored DNA-binding specificity1. Highly specific genome-editing TALE nucleases (TALENs) can be engineered for targeted mutagenesis in plants and a wide variety of other eukaryotic organisms. We analyzed specificities and activities of TALEs experimentally in a transient reporter system using Agrobacterium-mediated expression in planta. Different RVDs exist in nature, but the DNA-specificity of only a few of them is known, so far. We will present novel results on RVD specificity and efficiency2, as well as the design of programmable gene switches and programmable precision mutagenesis tools. TALEs and TALENs are versatile virulence factors for the pathogen and exceptional tools for biotechnology. 1. Boch, J. et al. Science 326, 1509-1512 (2009). 2. Streubel et al. Nat. Biotechnol. 30, 593-595 (2012).

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Postdoc Innovation Seminar Dr Jens Boch on Wednesday, January 30 at 11am
by Delphine Verspeel 29 Jan '13

29 Jan '13

You are receiving this e-mail because you subscribed to our seminars announcements and reminders service at https://maillist.psb.ugent.be/mailman/listinfo/seminars . If you do not wish to receive this information anymore, please unsubscribe from future mailings at https://maillist.psb.ugent.be/mailman/options/seminars . cid:946540515@15122008-0D1CPSBcid:946540515@15122008-0D23 VIB - Department of Plant Systems Biology Technologiepark 927 B - 9052 Gent/Zwijnaarde Phone: +32 9 33 13 800 Fax: +32 9 33 13 809 Http://www.psb.vib-ugent.be

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Seminar Dr John Ryals on Monday, February 4 at 3 pm in the Jozef Schell Seminar Room
by Delphine Verspeel 29 Jan '13

29 Jan '13

You are receiving this e-mail because you subscribed to our seminars announcements and reminders service at https://maillist.psb.ugent.be/mailman/listinfo/seminars . If you do not wish to receive this information anymore, please unsubscribe from future mailings at https://maillist.psb.ugent.be/mailman/options/seminars . cid:946540515@15122008-0D1CPSBcid:946540515@15122008-0D23 VIB - Department of Plant Systems Biology Technologiepark 927 B - 9052 Gent/Zwijnaarde Phone: +32 9 33 13 800 Fax: +32 9 33 13 809 Http://www.psb.vib-ugent.be

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Seminar Prof Achim Walter on Monday, February 4 at 11 am
by Delphine Verspeel 28 Jan '13

28 Jan '13

You are receiving this e-mail because you subscribed to our seminars announcements and reminders service at https://maillist.psb.ugent.be/mailman/listinfo/seminars . If you do not wish to receive this information anymore, please unsubscribe from future mailings at https://maillist.psb.ugent.be/mailman/options/seminars . cid:946540515@15122008-0D1CPSBcid:946540515@15122008-0D23 VIB - Department of Plant Systems Biology Technologiepark 927 B - 9052 Gent/Zwijnaarde Phone: +32 9 33 13 800 Fax: +32 9 33 13 809 Http://www.psb.vib-ugent.be

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Upcoming seminars February
by Delphine Verspeel 28 Jan '13

28 Jan '13

Dear All, Enclosed you can find our upcoming seminars for February. Kind regards, Delphine ___________________________________________ Delphine Verspeel Administrative Assistant VIB, Department of Plant Systems Biology Ghent University Technologiepark 927 9052 Gent Belgium Phone: +32/9/33.13.800 Fax: +32/9/33.13.809 Http://www.psb.ugent.be despe(a)psb.vib-ugent.be

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PSB event reminder
by contact＠psb.vib-ugent.be 28 Jan '13

28 Jan '13

Calendar Name: seminars Scheduled for: Wednesday, January 30 2013, 11:00 - 12:30 Event text: Dr Jens Boch Martin Luther University Halle-Wittenberg Institute of Biology Department of Genetics Halle (Saale) GERMANY Details: Postdoc Innovation seminar �TALEs and TALENs for targeted genome engineering and expression control� ABSTRACT The DNA-binding domain of TALEs (transcription activator-like effectors) from plant-pathogenic Xanthomonas bacteria has become an important tool for the programmable and specific targeting of DNA. Natural TALEs function as transcription factors in plant cells to support pathogen colonization of host plants. TALE proteins bind to DNA via near-identical tandem repeats of 34 amino acids. Each repeat recognizes one base in the target DNA sequence via repeat-variable diresidues (RVDs). The simple and modular repeat architecture allows rearrangement of TALE repeats to generate artificial TALEs with virtually any tailored DNA-binding specificity1. Highly specific genome-editing TALE nucleases (TALENs) can be engineered for targeted mutagenesis in plants and a wide variety of other eukaryotic organisms. We analyzed specificities and activities of TALEs experimentally in a transient reporter system using Agrobacterium-mediated expression in planta. Different RVDs exist in nature, but the DNA-specificity of only a few of them is known, so far. We will present novel results on RVD specificity and efficiency2, as well as the design of programmable gene switches and programmable precision mutagenesis tools. TALEs and TALENs are versatile virulence factors for the pathogen and exceptional tools for biotechnology. 1. Boch, J. et al. Science 326, 1509-1512 (2009). 2. Streubel et al. Nat. Biotechnol. 30, 593-595 (2012).

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PSB event reminder
by contact＠psb.vib-ugent.be 24 Jan '13

24 Jan '13

Calendar Name: seminars Scheduled for: Thursday, January 24 2013, 11:00 - 12:30 Event text: Dr Steven Maere VIB, Dept. of Plant Systems Biology Ghent University Gent BELGIUM Details: �Innovation through gen(om)e duplication� ABSTRACT Gene and genome duplications are believed to facilitate evolutionary innovation. However, the mechanisms shaping the fate of duplicated genes remain heavily debated because the molecular processes and evolutionary forces involved are difficult to reconstruct. The first part of the talk will focus on the MALS gene family, a large family of fungal glucosidase genes with members generally having activity on only one of two broad substrate classes. We reconstructed several key ancestral enzymes and show that the very first preduplication enzyme was primarily active on maltose-like substrates, but had trace activity for isomaltose-like sugars. Structural analysis and activity measurements on resurrected and present-day enzymes suggest that both activities cannot be fully optimized in a single enzyme. However, gene duplications repeatedly spawned daughter genes in which mutations optimized either isomaltase or maltase activity. Interestingly, similar shifts in enzyme activity were reached multiple times via different evolutionary routes. Together, our results provide a detailed picture of the molecular mechanisms that drove divergence and innovation in the MALS gene family. In the second part of the talk, I will discuss a framework we developed for simulating the evolution of small biological systems in silico. The genotype-phenotype map (GPM) of any molecular system results from a highly multilayered information processing cascade, in which gene regulatory networks (GRNs) play a crucial role. Several simplifying mathematical representations of GPMs have been developed in the past. However, these representations generally lack biological realism in the genotypic encoding of the structure and parameters of GRNs. To study GPMs in mechanistic detail, we have developed a sequence-based dynamical modeling framework built upon biochemical first principles. As a proof of concept, we focus on genomes coding for small GRNs displaying oscillatory expression phenotypes. We show that genome duplication drastically impacts the navigability of the fitness landscape and the accessibility of novel phenotypes.

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PSB event reminder
by contact＠psb.vib-ugent.be 22 Jan '13

22 Jan '13

Calendar Name: seminars Scheduled for: Thursday, January 24 2013, 11:00 - 12:30 Event text: Dr Steven Maere VIB, Dept. of Plant Systems Biology Ghent University Gent BELGIUM Details: �Innovation through gen(om)e duplication� ABSTRACT Gene and genome duplications are believed to facilitate evolutionary innovation. However, the mechanisms shaping the fate of duplicated genes remain heavily debated because the molecular processes and evolutionary forces involved are difficult to reconstruct. The first part of the talk will focus on the MALS gene family, a large family of fungal glucosidase genes with members generally having activity on only one of two broad substrate classes. We reconstructed several key ancestral enzymes and show that the very first preduplication enzyme was primarily active on maltose-like substrates, but had trace activity for isomaltose-like sugars. Structural analysis and activity measurements on resurrected and present-day enzymes suggest that both activities cannot be fully optimized in a single enzyme. However, gene duplications repeatedly spawned daughter genes in which mutations optimized either isomaltase or maltase activity. Interestingly, similar shifts in enzyme activity were reached multiple times via different evolutionary routes. Together, our results provide a detailed picture of the molecular mechanisms that drove divergence and innovation in the MALS gene family. In the second part of the talk, I will discuss a framework we developed for simulating the evolution of small biological systems in silico. The genotype-phenotype map (GPM) of any molecular system results from a highly multilayered information processing cascade, in which gene regulatory networks (GRNs) play a crucial role. Several simplifying mathematical representations of GPMs have been developed in the past. However, these representations generally lack biological realism in the genotypic encoding of the structure and parameters of GRNs. To study GPMs in mechanistic detail, we have developed a sequence-based dynamical modeling framework built upon biochemical first principles. As a proof of concept, we focus on genomes coding for small GRNs displaying oscillatory expression phenotypes. We show that genome duplication drastically impacts the navigability of the fitness landscape and the accessibility of novel phenotypes.

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Seminar Dr Steven Maere on Thursday, January 24 at 11 am
by Delphine Verspeel 16 Jan '13

16 Jan '13

You are receiving this e-mail because you subscribed to our seminars announcements and reminders service at https://maillist.psb.ugent.be/mailman/listinfo/seminars . If you do not wish to receive this information anymore, please unsubscribe from future mailings at https://maillist.psb.ugent.be/mailman/options/seminars . cid:946540515@15122008-0D1CPSBcid:946540515@15122008-0D23 VIB - Department of Plant Systems Biology Technologiepark 927 B - 9052 Gent/Zwijnaarde Phone: +32 9 33 13 800 Fax: +32 9 33 13 809 Http://www.psb.vib-ugent.be

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PSB event reminder
by contact＠psb.vib-ugent.be 15 Jan '13

15 Jan '13

Calendar Name: seminars Scheduled for: Tuesday, January 15 2013, 11:00 - 12:30 Event text: Prof Lieven De Veylder VIB, Dept. of Plant Systems Biology Ghent University Gent BELGIUM Details: �DNA replication and endocycle control in arabidopsis thaliana� ABSTRACT Due to their sedentary life style, plants are unavoidably in close contact with agents that target their genome integrity. DNA stress is a recurrent problem in agriculture; not only because of an increase in UV-B irradiation due to depletion of the ozone layer, but also because of metalloid soil elements such as aluminum and boron. To sense and react to these treats, plants have evolved DNA stress checkpoint mechanisms to arrest the cell cycle when DNA replication errors or DNA breaks occur. In this way, cells can repair the damaged DNA before entering mitosis and prevent the propagation of mutations. The identification of such checkpoint mechanisms can help in obtaining corps with increased growth performance under genotoxic growth conditions. Previously we identified the cyclin-depenent kinase (CDK) inhibitory kinase WEE1 as an essential checkpoint regulator upon DNA replication stress. However, WEE1 knockout plants do not suffer from double-strand breaks, suggesting redundant checkpoint mechanisms. On basis of a compendium of microarray experiments we identified a novel group of genes that are rapidly and strongly induced upon diverse forms of DNA stress in an ATM/ATR dependent manner. The encoded proteins bind directly to CDKs, to inhibit their activity and to arrest cells in the G2 phase of the cell cycle. Through knockout analysis we illustrated that these novel proteins, in combination with WEE1, control the adaptation of plants towards DNA stress.

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