- Seminars - maillist.psb.ugent.be

seminar Prof Richard C. Leegood 18/05
by Nathalie Vanden Hautte 26 Apr '10

26 Apr '10

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 <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 <https://maillist.psb.ugent.be/mailman/options/seminars> . 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 20 Apr '10

20 Apr '10

Calendar Name: seminars Scheduled for: Tuesday, April 20 2010, 11:00 - 12:30 Event text: Catherine Perrot-Rechenmann Institut des Sciences du V�g�tal (ISV), CNRS Gif sur Yvette FRANCE Details: �Cross-talk between ABP1 and TIR1/AFB auxin receptors� ABSTRACT The phytohormone auxin is a major regulator of plant growth and development. Many aspects of these processes depend on the multiple controls exerted by auxin on cellular responses as cell expansion and cell division, and mediated at the molecular level by the regulation of auxin-responsive genes. Two classes of auxin receptors have been identified to date: first, the TIR1/AFB F-box proteins which are part of ubiquitin E3 ligase complexes and, according to the current auxin signalling model (reviewed by 1), recruit the AUX/IAA transcriptional repressors in the presence of auxin to induce their ubiquitination and degradation by the 26S proteasome; second, the long-standing and unique auxin binding protein 1, ABP1, initially identified on its capacity to bind auxin and demonstrated to induce activation of ion fluxes at the plasma after auxin binding. Recently, the detailed characterization of conditional ABP1 knock-down plants 2,3 revealed that ABP1 is required for almost all auxin-mediated responses including modulation of gene expression. In consequence, TIR1/AFB and ABP1 appear to share the regulation of auxin responsive genes. We have investigated the relationship between the TIR1/AFBs- and ABP1-mediated pathways. We have further analyzed the requirement of ABP1 for auxin mediated gene expression in roots and developed biochemical and genetic approaches to analyze its functional interaction with the SCFTIR1/AFB pathway. Original data leads to a novel model integrating ABP1 and SCFTIR1/AFBs into a sophisticated multicomponent auxin signaling pathway, essential for regulation of auxin responses. 1. Chapman EJ, Estelle M: Annu Rev Genet 2009, 43:265-285. 2. Braun N, Wyrzykowska J, Muller P, David K, Couch D, Perrot-Rechenmann C, Fleming AJ Plant Cell 2008, 10:2746-2762. 3. Tromas A, Braun N, Muller P, Khodus T, Paponov IA, et al. PLoS One 2009, 4:e6648.

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PSB event reminder
by contact＠psb.vib-ugent.be 18 Apr '10

18 Apr '10

Calendar Name: seminars Scheduled for: Tuesday, April 20 2010, 11:00 - 12:30 Event text: Catherine Perrot-Rechenmann Institut des Sciences du V�g�tal (ISV), CNRS Gif sur Yvette FRANCE Details: �Cross-talk between ABP1 and TIR1/AFB auxin receptors� ABSTRACT The phytohormone auxin is a major regulator of plant growth and development. Many aspects of these processes depend on the multiple controls exerted by auxin on cellular responses as cell expansion and cell division, and mediated at the molecular level by the regulation of auxin-responsive genes. Two classes of auxin receptors have been identified to date: first, the TIR1/AFB F-box proteins which are part of ubiquitin E3 ligase complexes and, according to the current auxin signalling model (reviewed by 1), recruit the AUX/IAA transcriptional repressors in the presence of auxin to induce their ubiquitination and degradation by the 26S proteasome; second, the long-standing and unique auxin binding protein 1, ABP1, initially identified on its capacity to bind auxin and demonstrated to induce activation of ion fluxes at the plasma after auxin binding. Recently, the detailed characterization of conditional ABP1 knock-down plants 2,3 revealed that ABP1 is required for almost all auxin-mediated responses including modulation of gene expression. In consequence, TIR1/AFB and ABP1 appear to share the regulation of auxin responsive genes. We have investigated the relationship between the TIR1/AFBs- and ABP1-mediated pathways. We have further analyzed the requirement of ABP1 for auxin mediated gene expression in roots and developed biochemical and genetic approaches to analyze its functional interaction with the SCFTIR1/AFB pathway. Original data leads to a novel model integrating ABP1 and SCFTIR1/AFBs into a sophisticated multicomponent auxin signaling pathway, essential for regulation of auxin responses. 1. Chapman EJ, Estelle M: Annu Rev Genet 2009, 43:265-285. 2. Braun N, Wyrzykowska J, Muller P, David K, Couch D, Perrot-Rechenmann C, Fleming AJ Plant Cell 2008, 10:2746-2762. 3. Tromas A, Braun N, Muller P, Khodus T, Paponov IA, et al. PLoS One 2009, 4:e6648.

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seminar Catherine Perrot-Rechenmann 20/04
by Nathalie Vanden Hautte 02 Apr '10

02 Apr '10

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 <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 <https://maillist.psb.ugent.be/mailman/options/seminars> . 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 April
by Nathalie Vanden Hautte 02 Apr '10

02 Apr '10

Dear All Enclosed you can find an overview of our upcoming seminars in April. Kind regards Nathalie ____________________________________________ Nathalie Vanden Hautte Administrative Assistant VIB, Department of Plant Systems Biology Ghent University Technologiepark 927 9052 Gent Belgium Phone: +32/9/33.13.800 Fax: +32/33.13.809 Http://www.psb.ugent.be nahau(a)psb.vib-ugent.be

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PSB event reminder
by contact＠psb.vib-ugent.be 25 Mar '10

25 Mar '10

Calendar Name: seminars Scheduled for: Thursday, March 25 2010, 10:00 - 12:00 Event text: Mini-Symposium on "BGI and Genomics in China - 'Life Sciences for all' in the 21st Century" Details: 10:00 - 10:40 "BGI and Genomics in China - Life Sciences in the 21st Century" Huanming Yang, Ph.D. Professor & President BGI (Beijing Genomics Institute)-Shenzhen, China The recent progresses in biotechnology, such as iPS and stem cell research, animal cloning and bio-plants, synthetic biology and many others, have made it even more obvious that life sciences would have significant impact on every respect of our life and society in the 21st Century. It is also widely accepted that reading and decoding genome sequences of an organism is the basis and beginning for any biological studies on it. Based on its persistent belief that �life is of sequence� and �life is digital�, BGI, a flagship in genomics in China for the decade, has built its powerful capacity in sequencing and bio-computing with its young and innovative teams, and greatly contributed to the global genomics and to the future development of biotechnology as one of the biggest and most influential genomics centers in the world. As a later comer in the modern life sciences, the growth of BGI is deeply rooted in the Chinese tradition and Culture, for example: 1) Foresight: �Success could not be made without foresight, failure from no prediction�. 2) Persistence: �Winners are only those with persistence�. 3) Learning: �Among those three passing by, at least one is qualified to be your teacher�. 4) Confidence: �The later comers always do a better job because of the pioneers ahead�. 5) Collaboration: �Nobody could be a hero without three partners�. 6) Appreciation: �When you drink sweet water, never forget those helped dig the well�. As an institute in the developing part of the world, BGI has been raising the banner of both science and humanity, and actively participating in the discussion on HELSOC issues (Humanitarian, Ethical, Legal, SOcial, and Cultural issues) that are essential to �life science for all� in the 21st century. 10:40 - 11:20 "Harvest the fruits of genomics - to upgrade agriculture with new breeding tools" Sanwen Huang, Ph.D. Key Laboratory of Genomics, Ministry of Agriculture Chinese Academy of Agricultural Sciences (CAAS) and Beijing Genomics Institute (BGI) The global food security is in menace because of the rapidly growing human population, the depletion of agricultural resources as arable land, water, and petroleum-based pesticide and fertilizer, and the climatic changes. The genetic improvement of crops is the most viable approach by which food production can try to keep pace with the anticipated growth of the human population. The efficiency of crop breeding relies on our knowledge on the biology of the ~60 species that uses about 95% of the arable land and a dozen of livestocks. The most fundamental biological knowledge of a crop is stored in its genome. Next generation sequencing (NGS) technologies, such as Illumina GA, SOLiD, and 454, made it feasible and economical acceptable to sequence genomes of all crops. However, as NGS often produces millions of shorter reads in a single run, it also meet computational and algorithmic challenges. BGI constructed a powerful platform mainly based on sequencing-by-synthesis technology, including >30 Illumina GA II, a 10,000-CPU cluster, and a software package, Short Oligonucleotide Analysis Program (SOAP). The genomes of cucumber (350 Mb), Brassica rapa (500Mb), potato (830Mb), duck (2 Gb), and even giant panda (2.3 Gb)have been assembled and analyzed, giving the first set of examples that NGS can be used in de novo sequencing of large plant and animal genomes. Large scale germplasm resequencing was conducted on rice, silkworm, and cucumber, which produced millions of SNPs and structural variations and identified hundreds of genes that likely underwent selection during domestications and breeding. With the newly established Key Laboratory of Genomics (MOA), BGI, CAAS, and other agricultural research institutions will sequence 100 crops, 100 species of livestocks and insects, core collection of every important species, and also perform genome-scan of over 400,000 accessions of various crops are stored in the National Seed Bank. Combined with genetic analysis and robust phenotyping, this huge resource will lead to high-throughput isolation of trait genes. The knowledge of trait genes will give rise to new breeding tools that can be used to deliberately design crops and animals that suit to various environment, agricultural practices, and applications. 11:20 - 12:00 "More than just sequencing - Bioinformatics tools developed at BGI" Ruibang LUO, B.S. Bioinformatics project manager BGI (Beijing Genomics Institute)-Shenzhen, China �The day is not far off when more biology will be done at the computer than at the bench!� Roos et al. said in 2002. Nowadays, with the rapid development of information technology, not only the computational resources but also talents of this field could be acquired much more easily. It has also demonstrated its powerful ability in assistance of solving complex biological, especially genomic problems. BGI, a flagship in genomics in China for the decade, has created our own series of tools and pipelines for the analysis including the genome, SNP, structural variation, methylation, RNA, assembly and etc. Next-generation massively parallel DNA sequencing technologies provide ultra-high throughput at a substantially lower unit data cost; however, the data is very short read length sequences, making de novo assembly extremely challenging. We�ve just described a novel method for de novo assembly of large genomes from short-read sequences. We successfully assembled both the Asian and African human genome sequences, achieving an N50 contig size of 7.4 and 5.9 Kb and scaffold of 446.3 and 61.9 Kb, respectively. Comparison of these assemblies to the NCBI reference genome demonstrated the capability of accurate identification of structural variations, especially small deletions and insertions that are difficult to identify using a resequencing method. The development of this de novo short-read assembly method creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.

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PSB event reminder
by contact＠psb.vib-ugent.be 23 Mar '10

23 Mar '10

Calendar Name: seminars Scheduled for: Thursday, March 25 2010, 10:00 - 12:00 Event text: Mini-Symposium on "BGI and Genomics in China - 'Life Sciences for all' in the 21st Century" Details: 10:00 - 10:40 "BGI and Genomics in China - Life Sciences in the 21st Century" Huanming Yang, Ph.D. Professor & President BGI (Beijing Genomics Institute)-Shenzhen, China The recent progresses in biotechnology, such as iPS and stem cell research, animal cloning and bio-plants, synthetic biology and many others, have made it even more obvious that life sciences would have significant impact on every respect of our life and society in the 21st Century. It is also widely accepted that reading and decoding genome sequences of an organism is the basis and beginning for any biological studies on it. Based on its persistent belief that �life is of sequence� and �life is digital�, BGI, a flagship in genomics in China for the decade, has built its powerful capacity in sequencing and bio-computing with its young and innovative teams, and greatly contributed to the global genomics and to the future development of biotechnology as one of the biggest and most influential genomics centers in the world. As a later comer in the modern life sciences, the growth of BGI is deeply rooted in the Chinese tradition and Culture, for example: 1) Foresight: �Success could not be made without foresight, failure from no prediction�. 2) Persistence: �Winners are only those with persistence�. 3) Learning: �Among those three passing by, at least one is qualified to be your teacher�. 4) Confidence: �The later comers always do a better job because of the pioneers ahead�. 5) Collaboration: �Nobody could be a hero without three partners�. 6) Appreciation: �When you drink sweet water, never forget those helped dig the well�. As an institute in the developing part of the world, BGI has been raising the banner of both science and humanity, and actively participating in the discussion on HELSOC issues (Humanitarian, Ethical, Legal, SOcial, and Cultural issues) that are essential to �life science for all� in the 21st century. 10:40 - 11:20 "Harvest the fruits of genomics - to upgrade agriculture with new breeding tools" Sanwen Huang, Ph.D. Key Laboratory of Genomics, Ministry of Agriculture Chinese Academy of Agricultural Sciences (CAAS) and Beijing Genomics Institute (BGI) The global food security is in menace because of the rapidly growing human population, the depletion of agricultural resources as arable land, water, and petroleum-based pesticide and fertilizer, and the climatic changes. The genetic improvement of crops is the most viable approach by which food production can try to keep pace with the anticipated growth of the human population. The efficiency of crop breeding relies on our knowledge on the biology of the ~60 species that uses about 95% of the arable land and a dozen of livestocks. The most fundamental biological knowledge of a crop is stored in its genome. Next generation sequencing (NGS) technologies, such as Illumina GA, SOLiD, and 454, made it feasible and economical acceptable to sequence genomes of all crops. However, as NGS often produces millions of shorter reads in a single run, it also meet computational and algorithmic challenges. BGI constructed a powerful platform mainly based on sequencing-by-synthesis technology, including >30 Illumina GA II, a 10,000-CPU cluster, and a software package, Short Oligonucleotide Analysis Program (SOAP). The genomes of cucumber (350 Mb), Brassica rapa (500Mb), potato (830Mb), duck (2 Gb), and even giant panda (2.3 Gb)have been assembled and analyzed, giving the first set of examples that NGS can be used in de novo sequencing of large plant and animal genomes. Large scale germplasm resequencing was conducted on rice, silkworm, and cucumber, which produced millions of SNPs and structural variations and identified hundreds of genes that likely underwent selection during domestications and breeding. With the newly established Key Laboratory of Genomics (MOA), BGI, CAAS, and other agricultural research institutions will sequence 100 crops, 100 species of livestocks and insects, core collection of every important species, and also perform genome-scan of over 400,000 accessions of various crops are stored in the National Seed Bank. Combined with genetic analysis and robust phenotyping, this huge resource will lead to high-throughput isolation of trait genes. The knowledge of trait genes will give rise to new breeding tools that can be used to deliberately design crops and animals that suit to various environment, agricultural practices, and applications. 11:20 - 12:00 "More than just sequencing - Bioinformatics tools developed at BGI" Ruibang LUO, B.S. Bioinformatics project manager BGI (Beijing Genomics Institute)-Shenzhen, China �The day is not far off when more biology will be done at the computer than at the bench!� Roos et al. said in 2002. Nowadays, with the rapid development of information technology, not only the computational resources but also talents of this field could be acquired much more easily. It has also demonstrated its powerful ability in assistance of solving complex biological, especially genomic problems. BGI, a flagship in genomics in China for the decade, has created our own series of tools and pipelines for the analysis including the genome, SNP, structural variation, methylation, RNA, assembly and etc. Next-generation massively parallel DNA sequencing technologies provide ultra-high throughput at a substantially lower unit data cost; however, the data is very short read length sequences, making de novo assembly extremely challenging. We�ve just described a novel method for de novo assembly of large genomes from short-read sequences. We successfully assembled both the Asian and African human genome sequences, achieving an N50 contig size of 7.4 and 5.9 Kb and scaffold of 446.3 and 61.9 Kb, respectively. Comparison of these assemblies to the NCBI reference genome demonstrated the capability of accurate identification of structural variations, especially small deletions and insertions that are difficult to identify using a resequencing method. The development of this de novo short-read assembly method creates new opportunities for building reference sequences and carrying out accurate analyses of unexplored genomes in a cost effective way.

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BGI mini-symposium 25/03
by Nathalie Vanden Hautte 09 Mar '10

09 Mar '10

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 <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 <https://maillist.psb.ugent.be/mailman/options/seminars> . 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 08 Mar '10

08 Mar '10

Calendar Name: seminars Scheduled for: Monday, March 8 2010, 11:00 - 12:30 Event text: Dr Stig Uggerh�j Andersen Department of Molecular Biology University of Aarhus Aarhus C DENMARK Details: "SHOREmap: simultaneous mapping and mutation identification by deep sequencing" ABSTRACT Identification of causative point mutations after forward genetic mutant screens typically begins with genetic mapping, followed by transformation rescue or candidate gene sequencing. We present a one step alternative: performing hundreds of thousands of genotyping assays while sequencing all candidate genes. This is accomplished by deep sequencing of a pool of F2 progeny obtained by crossing to a polymorphic strain and does not require prior knowledge of mapping markers. The application of high-throughput sequencing shortens the overall time required for genetic mapping from months to weeks and, importantly, greatly reduces investigator hands-on time. The steps requiring investigator input are: DNA isolation (1 day), library preparation and validation (4 days), Illumina cluster generation and sequencing (2 days), and data analysis (1 day). Once the mapping population has been established, the present method therefore allows a single investigator to identify a causative mutation within only eight working days � approximately an order of magnitude faster than with conventional methods.

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PSB event reminder
by contact＠psb.vib-ugent.be 05 Mar '10

05 Mar '10

Calendar Name: seminars Scheduled for: Monday, March 8 2010, 11:00 - 12:30 Event text: Dr Stig Uggerh�j Andersen Department of Molecular Biology University of Aarhus Aarhus C DENMARK Details: "SHOREmap: simultaneous mapping and mutation identification by deep sequencing" ABSTRACT Identification of causative point mutations after forward genetic mutant screens typically begins with genetic mapping, followed by transformation rescue or candidate gene sequencing. We present a one step alternative: performing hundreds of thousands of genotyping assays while sequencing all candidate genes. This is accomplished by deep sequencing of a pool of F2 progeny obtained by crossing to a polymorphic strain and does not require prior knowledge of mapping markers. The application of high-throughput sequencing shortens the overall time required for genetic mapping from months to weeks and, importantly, greatly reduces investigator hands-on time. The steps requiring investigator input are: DNA isolation (1 day), library preparation and validation (4 days), Illumina cluster generation and sequencing (2 days), and data analysis (1 day). Once the mapping population has been established, the present method therefore allows a single investigator to identify a causative mutation within only eight working days � approximately an order of magnitude faster than with conventional methods.

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