131 results on '"Becker, Jörg D"'
Search Results
102. The Sinorhizobium meliloti ExpE1 protein secreted by a type I secretion system involving ExpD1 and ExpD2 is required for biosynthesis or secretion of the exopolysaccharide galactoglucan
- Author
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Moreira, Leonilde M., primary, Becker, Jörg D., additional, Pühler, Alfred, additional, and Becker, Anke, additional
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- 2000
- Full Text
- View/download PDF
103. Cell- and Tissue-Specific Transcriptome Analyses of Medicago truncatula Root Nodules
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Limpens, Erik, Moling, Sjef, Hooiveld, Guido, Pereira, Patrícia A., Bisseling, Ton, Becker, Jörg D., and Küster, Helge
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MEDICAGO truncatula ,ROOT-tubercles ,LEGUMES ,TISSUES ,ENDOSYMBIOSIS ,PLANT development ,GENE expression in plants ,PLANT biotechnology - Abstract
Legumes have the unique ability to host nitrogen-fixing Rhizobium bacteria as symbiosomes inside root nodule cells. To get insight into this key process, which forms the heart of the endosymbiosis, we isolated specific cells/tissues at different stages of symbiosome formation from nodules of the model legume Medicago truncatula using laser-capture microdissection. Next, we determined their associated expression profiles using Affymetrix Medicago GeneChips. Cells were collected from the nodule infection zone divided into a distal (where symbiosome formation and division occur) and proximal region (where symbiosomes are mainly differentiating), as well as infected cells from the fixation zone containing mature nitrogen fixing symbiosomes. As non-infected cells/tissue we included nodule meristem cells and uninfected cells from the fixation zone. Here, we present a comprehensive gene expression map of an indeterminate Medicago nodule and selected genes that show specific enriched expression in the different cells or tissues. Validation of the obtained expression profiles, by comparison to published gene expression profiles and experimental verification, indicates that the data can be used as digital “in situ”. This digital “in situ” offers a genome-wide insight into genes specifically associated with subsequent stages of symbiosome and nodule cell development, and can serve to guide future functional studies. [ABSTRACT FROM AUTHOR]
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- 2013
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104. Nanometer-Schichten in Silizium
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Becker, JöRg D., primary, Zeindl, Hans P., additional, and Eisele, Ignaz, additional
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- 1990
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105. Adaptive associative systems for VLSI
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Rückert, Ulrich, Goser, Karl, Becker, Jörg D., and Eisele, Ignaz
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Adaptive memory ,Hardware_MEMORYSTRUCTURES ,Flat memory model ,Computer architecture ,Computer science ,Cache-only memory architecture ,Semiconductor memory ,Memory refresh ,Content-addressable memory ,Memory map ,Computer memory - Abstract
A physical network of an adaptive associative memory is presented. The concept of the network is derived from the Analog Associative Memory due to T. Kohonen and from the Associative Matrix due to G. Palm. The system concept of such a memory is adapted to the VLSI-technique by being partioned into uniform memory slices and by introducing a nonvolatile memory cell. Especially the task of transferring the system concept into technology in order to realize a microelectronic component with new interesting features will be pointed out. The performance of an adaptive associative memory is discussed by means of computer simulations.
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- 1987
106. Planning a Dynamic Trajectory via Path Finding in Discretized Phase Space
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Ritter, Helge, Schulten, Klaus, and Becker, Jörg D.
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- 1987
107. Genome-wide analysis of PAPS1-dependent polyadenylation identifies novel roles for functionally specialized poly(A) polymerases in Arabidopsis thaliana
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Kappel, Christian, Trost, Gerda, Cseznick, Hjordis, Ramming, Anna, Kolbe, Benjamin, Vi, Son Lang, Becker, Jörg D., de Moor, Cornelia H., Lenhard, Michael, Kappel, Christian, Trost, Gerda, Cseznick, Hjordis, Ramming, Anna, Kolbe, Benjamin, Vi, Son Lang, Becker, Jörg D., de Moor, Cornelia H., and Lenhard, Michael
- Abstract
The poly(A) tail at 3’ ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases,PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression.
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108. Genome-wide analysis of PAPS1-dependent polyadenylation identifies novel roles for functionally specialized poly(A) polymerases in Arabidopsis thaliana
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Kappel, Christian, Trost, Gerda, Cseznick, Hjordis, Ramming, Anna, Kolbe, Benjamin, Vi, Son Lang, Becker, Jörg D., de Moor, Cornelia H., Lenhard, Michael, Kappel, Christian, Trost, Gerda, Cseznick, Hjordis, Ramming, Anna, Kolbe, Benjamin, Vi, Son Lang, Becker, Jörg D., de Moor, Cornelia H., and Lenhard, Michael
- Abstract
The poly(A) tail at 3’ ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases,PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression.
- Full Text
- View/download PDF
109. Genome-wide analysis of PAPS1-dependent polyadenylation identifies novel roles for functionally specialized poly(A) polymerases in Arabidopsis thaliana
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Kappel, Christian, Trost, Gerda, Cseznick, Hjordis, Ramming, Anna, Kolbe, Benjamin, Vi, Son Lang, Becker, Jörg D., de Moor, Cornelia H., Lenhard, Michael, Kappel, Christian, Trost, Gerda, Cseznick, Hjordis, Ramming, Anna, Kolbe, Benjamin, Vi, Son Lang, Becker, Jörg D., de Moor, Cornelia H., and Lenhard, Michael
- Abstract
The poly(A) tail at 3’ ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases,PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression.
- Full Text
- View/download PDF
110. Genome-wide analysis of PAPS1-dependent polyadenylation identifies novel roles for functionally specialized poly(A) polymerases in Arabidopsis thaliana
- Author
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Kappel, Christian, Trost, Gerda, Cseznick, Hjordis, Ramming, Anna, Kolbe, Benjamin, Vi, Son Lang, Becker, Jörg D., de Moor, Cornelia H., Lenhard, Michael, Kappel, Christian, Trost, Gerda, Cseznick, Hjordis, Ramming, Anna, Kolbe, Benjamin, Vi, Son Lang, Becker, Jörg D., de Moor, Cornelia H., and Lenhard, Michael
- Abstract
The poly(A) tail at 3’ ends of eukaryotic mRNAs promotes their nuclear export, stability and translational efficiency, and changes in its length can strongly impact gene expression. The Arabidopsis thaliana genome encodes three canonical nuclear poly(A) polymerases,PAPS1, PAPS2 and PAPS4. As shown by their different mutant phenotypes, these three isoforms are functionally specialized, with PAPS1 modifying organ growth and suppressing a constitutive immune response. However, the molecular basis of this specialization is largely unknown. Here, we have estimated poly(A)-tail lengths on a transcriptome-wide scale in wild-type and paps1 mutants. This identified categories of genes as particularly strongly affected in paps1 mutants, including genes encoding ribosomal proteins, cell-division factors and major carbohydrate-metabolic proteins. We experimentally verified two novel functions of PAPS1 in ribosome biogenesis and redox homoeostasis that were predicted based on the analysis of poly(A)-tail length changes in paps1 mutants. When overlaying the PAPS1-dependent effects observed here with coexpression analysis based on independent microarray data, the two clusters of transcripts that are most closely coexpressed with PAPS1 show the strongest change in poly(A)-tail length and transcript abundance in paps1 mutants in our analysis. This suggests that their coexpression reflects at least partly the preferential polyadenylation of these transcripts by PAPS1 versus the other two poly(A)-polymerase isoforms. Thus, transcriptome-wide analysis of poly(A)-tail lengths identifies novel biological functions and likely target transcripts for polyadenylation by PAPS1. Data integration with large-scale co-expression data suggests that changes in the relative activities of the isoforms are used as an endogenous mechanism to co-ordinately modulate plant gene expression.
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- View/download PDF
111. Self-organizing hierarchical modular systems
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Scarpetta, G., Simoncelli, G., Goos, G., editor, Hartmanis, J., editor, Barstow, D., editor, Brauer, W., editor, Brinch Hansen, P., editor, Gries, D., editor, Luckham, D., editor, Moler, C., editor, Pnueli, A., editor, Seegmüller, G., editor, Stoer, J., editor, Wirth, N., editor, Becker, Jörg D., editor, and Eisele, Ignaz, editor
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- 1987
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112. Analyzing mental representation by means of NLP (Neuro Linguistic Programming)
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Molzberger, Peter, Goos, G., editor, Hartmanis, J., editor, Barstow, D., editor, Brauer, W., editor, Brinch Hansen, P., editor, Gries, D., editor, Luckham, D., editor, Moler, C., editor, Pnueli, A., editor, Seegmüller, G., editor, Stoer, J., editor, Wirth, N., editor, Becker, Jörg D., editor, and Eisele, Ignaz, editor
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- 1987
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113. Nonmonotonic reasoning formalizations and implementations
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Brewka, Gerhard, Goos, G., editor, Hartmanis, J., editor, Barstow, D., editor, Brauer, W., editor, Brinch Hansen, P., editor, Gries, D., editor, Luckham, D., editor, Moler, C., editor, Pnueli, A., editor, Seegmüller, G., editor, Stoer, J., editor, Wirth, N., editor, Becker, Jörg D., editor, and Eisele, Ignaz, editor
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- 1987
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- View/download PDF
114. Pyramidal architectures for image processing
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Cantoni, V., Ferretti, M., Goos, G., editor, Hartmanis, J., editor, Barstow, D., editor, Brauer, W., editor, Brinch Hansen, P., editor, Gries, D., editor, Luckham, D., editor, Moler, C., editor, Pnueli, A., editor, Seegmüller, G., editor, Stoer, J., editor, Wirth, N., editor, Becker, Jörg D., editor, and Eisele, Ignaz, editor
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- 1987
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115. MIMD algorithms and their implementation
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Weidner, P., Goos, G., editor, Hartmanis, J., editor, Barstow, D., editor, Brauer, W., editor, Brinch Hansen, P., editor, Gries, D., editor, Luckham, D., editor, Moler, C., editor, Pnueli, A., editor, Seegmüller, G., editor, Stoer, J., editor, Wirth, N., editor, Becker, Jörg D., editor, and Eisele, Ignaz, editor
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- 1987
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116. Planning a dynamic trajectory via path finding in discretized phase space
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Ritter, H., Schulten, K., Goos, G., editor, Hartmanis, J., editor, Barstow, D., editor, Brauer, W., editor, Brinch Hansen, P., editor, Gries, D., editor, Luckham, D., editor, Moler, C., editor, Pnueli, A., editor, Seegmüller, G., editor, Stoer, J., editor, Wirth, N., editor, Becker, Jörg D., editor, and Eisele, Ignaz, editor
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- 1987
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117. Numerical simulation of physical phenomena by parallel computing
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Fritsch, Gerhard, Goos, G., editor, Hartmanis, J., editor, Barstow, D., editor, Brauer, W., editor, Brinch Hansen, P., editor, Gries, D., editor, Luckham, D., editor, Moler, C., editor, Pnueli, A., editor, Seegmüller, G., editor, Stoer, J., editor, Wirth, N., editor, Becker, Jörg D., editor, and Eisele, Ignaz, editor
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- 1987
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118. Molecular electronics: Storage and transport
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Mehring, M., Sixl, H., Goos, G., editor, Hartmanis, J., editor, Barstow, D., editor, Brauer, W., editor, Brinch Hansen, P., editor, Gries, D., editor, Luckham, D., editor, Moler, C., editor, Pnueli, A., editor, Seegmüller, G., editor, Stoer, J., editor, Wirth, N., editor, Becker, Jörg D., editor, and Eisele, Ignaz, editor
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- 1987
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119. Technological developments for three-dimensional circuitry
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Eisele, I., Goos, G., editor, Hartmanis, J., editor, Barstow, D., editor, Brauer, W., editor, Brinch Hansen, P., editor, Gries, D., editor, Luckham, D., editor, Moler, C., editor, Pnueli, A., editor, Seegmüller, G., editor, Stoer, J., editor, Wirth, N., editor, Becker, Jörg D., editor, and Eisele, Ignaz, editor
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- 1987
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120. Parallel algorithms and the classification of problems
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Bertoni, A., Goldwurm, M., Mauri, G., Sabadini, N., Goos, G., editor, Hartmanis, J., editor, Barstow, D., editor, Brauer, W., editor, Brinch Hansen, P., editor, Gries, D., editor, Luckham, D., editor, Moler, C., editor, Pnueli, A., editor, Seegmüller, G., editor, Stoer, J., editor, Wirth, N., editor, Becker, Jörg D., editor, and Eisele, Ignaz, editor
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- 1987
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121. Neural nets and cellular automata
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Caianiello, E. R., Marinaro, M., Goos, G., editor, Hartmanis, J., editor, Barstow, D., editor, Brauer, W., editor, Brinch Hansen, P., editor, Gries, D., editor, Luckham, D., editor, Moler, C., editor, Pnueli, A., editor, Seegmüller, G., editor, Stoer, J., editor, Wirth, N., editor, Becker, Jörg D., editor, and Eisele, Ignaz, editor
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- 1987
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122. Pattern storage and associative memory in quasi-neural networks
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Forshaw, M. R. B., Goos, G., editor, Hartmanis, J., editor, Barstow, D., editor, Brauer, W., editor, Brinch Hansen, P., editor, Gries, D., editor, Luckham, D., editor, Moler, C., editor, Pnueli, A., editor, Seegmüller, G., editor, Stoer, J., editor, Wirth, N., editor, Becker, Jörg D., editor, and Eisele, Ignaz, editor
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- 1987
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123. Towards a complex notion of time
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von Müller, Albrecht A. C., Goos, G., editor, Hartmanis, J., editor, Barstow, D., editor, Brauer, W., editor, Brinch Hansen, P., editor, Gries, D., editor, Luckham, D., editor, Moler, C., editor, Pnueli, A., editor, Seegmüller, G., editor, Stoer, J., editor, Wirth, N., editor, Becker, Jörg D., editor, and Eisele, Ignaz, editor
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- 1987
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124. Structure and parallel processing
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Becker, J. D., Goos, G., editor, Hartmanis, J., editor, Barstow, D., editor, Brauer, W., editor, Brinch Hansen, P., editor, Gries, D., editor, Luckham, D., editor, Moler, C., editor, Pnueli, A., editor, Seegmüller, G., editor, Stoer, J., editor, Wirth, N., editor, Becker, Jörg D., editor, and Eisele, Ignaz, editor
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- 1987
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125. FACS-based purification of Arabidopsis microspores, sperm cells and vegetative nuclei
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Telma Lopes, Leonor C. Boavida, Filipe Borges, R. Keith Slotkin, Rui Gardner, Robert A. Martienssen, Jörg Becker, Joseph P. Calarco, Instituto Gulbenkian de Ciência, Cold Spring Harbor Laboratory (CSHL), Department of Molecular Genetics, and Becker, Jörg D.
- Subjects
0106 biological sciences ,Somatic cell ,Microgametogenesis ,[SDV]Life Sciences [q-bio] ,Arabidopsis ,Plant Science ,Biology ,lcsh:Plant culture ,Pollen ,Fluorescence-activated cell sorting ,Microspore ,Plant germline ,Sperm cell ,Vegetative nucleus ,01 natural sciences ,03 medical and health sciences ,Genetics ,medicine ,lcsh:SB1-1110 ,Mitosis ,lcsh:QH301-705.5 ,030304 developmental biology ,0303 health sciences ,Methodology ,Cell sorting ,biology.organism_classification ,Sperm ,Cell biology ,medicine.anatomical_structure ,lcsh:Biology (General) ,Germ cell ,010606 plant biology & botany ,Biotechnology - Abstract
Background The male germline in flowering plants differentiates by asymmetric division of haploid uninucleated microspores, giving rise to a vegetative cell enclosing a smaller generative cell, which eventually undergoes a second mitosis to originate two sperm cells. The vegetative cell and the sperm cells activate distinct genetic and epigenetic mechanisms to control pollen tube growth and germ cell specification, respectively. Therefore, a comprehensive characterization of these processes relies on efficient methods to isolate each of the different cell types throughout male gametogenesis. Results We developed stable transgenic Arabidopsis lines and reliable purification tools based on Fluorescence-Activated Cell Sorting (FACS) in order to isolate highly pure and viable fractions of each cell/nuclei type before and after pollen mitosis. In the case of mature pollen, this was accomplished by expressing GFP and RFP in the sperm and vegetative nuclei, respectively, resulting in 99% pure sorted populations. Microspores were also purified by FACS taking advantage of their characteristic small size and autofluorescent properties, and were confirmed to be 98% pure. Conclusions We provide simple and efficient FACS-based purification protocols for Arabidopsis microspores, vegetative nuclei and sperm cells. This paves the way for subsequent molecular analysis such as transcriptomics, DNA methylation analysis and chromatin immunoprecipitation, in the developmental context of microgametogenesis in Arabidopsis.
- Published
- 2012
126. Genetic and epigenetic control of germline specification in Arabidopsis pollen
- Author
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Borges, Filipe de Sousa, Becker, Jörg D., and Feijó, José A., 1962
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Polén ,Teses de doutoramento - 2012 ,Arabidopsis ,MicroRNA ,Metilação de ADN - Abstract
Tese de doutoramento, Biologia (Biologia Celular), Universidade de Lisboa, Faculdade de Ciências, 2012 Submitted by amelia Janeiro (ajaneiro@reitoria.ul.pt) on 2012-04-04T11:31:40Z No. of bitstreams: 9 ulsd062282_td_Filipe_Borges.pdf: 27536803 bytes, checksum: 3e0a88b074663b6ebf36f3af1f8a51f9 (MD5) ulsd062282_td_apendice_S3_1.xls: 8517632 bytes, checksum: 07eb78f6fc95d82fe2ea05c0cd9b6fc1 (MD5) ulsd062282_td_apendice_S3_2.xls: 513536 bytes, checksum: f49d0fb973084f9356c236743aa1d4af (MD5) ulsd062282_td_apendice_S4_2.xlsx: 412148 bytes, checksum: 09394a037ca4d749e5461f1e75aefc52 (MD5) ulsd062282_td_apendice_video_S5_1.mov: 7744485 bytes, checksum: ad4bbead0d05ea57859b897f0f66f1fd (MD5) ulsd062282_td_apendice_S5_2.mov: 1235821 bytes, checksum: c8c1e22cc8456039d017c6687223774d (MD5) ulsd062282_td_apendice_S5_1.xls: 57856 bytes, checksum: 649fbb30df0480642d07792c900f0a96 (MD5) ulsd062282_td_apendice_S5_3.xls: 265728 bytes, checksum: d35550bf754210fc1d4dc737f279eae8 (MD5) ulsd062282_td_apendice_S5_4.xlsx: 355866 bytes, checksum: 659b92deec025529f249a44351a055ad (MD5) Made available in DSpace on 2012-04-04T11:35:42Z (GMT). No. of bitstreams: 9 ulsd062282_td_Filipe_Borges.pdf: 27536803 bytes, checksum: 3e0a88b074663b6ebf36f3af1f8a51f9 (MD5) ulsd062282_td_apendice_S3_1.xls: 8517632 bytes, checksum: 07eb78f6fc95d82fe2ea05c0cd9b6fc1 (MD5) ulsd062282_td_apendice_S3_2.xls: 513536 bytes, checksum: f49d0fb973084f9356c236743aa1d4af (MD5) ulsd062282_td_apendice_S4_2.xlsx: 412148 bytes, checksum: 09394a037ca4d749e5461f1e75aefc52 (MD5) ulsd062282_td_apendice_video_S5_1.mov: 7744485 bytes, checksum: ad4bbead0d05ea57859b897f0f66f1fd (MD5) ulsd062282_td_apendice_S5_2.mov: 1235821 bytes, checksum: c8c1e22cc8456039d017c6687223774d (MD5) ulsd062282_td_apendice_S5_1.xls: 57856 bytes, checksum: 649fbb30df0480642d07792c900f0a96 (MD5) ulsd062282_td_apendice_S5_3.xls: 265728 bytes, checksum: d35550bf754210fc1d4dc737f279eae8 (MD5) ulsd062282_td_apendice_S5_4.xlsx: 355866 bytes, checksum: 659b92deec025529f249a44351a055ad (MD5) Previous issue date: 2012 Fundação para a Ciência e a Tecnologia (FCT, SFRH/BD/48761/2008) e Fundação Calouste Gulbenkian
- Published
- 2012
127. The conserved genetic program of male germ cells uncovers ancient regulators of human spermatogenesis.
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Brattig-Correia R, Almeida JM, Wyrwoll MJ, Julca I, Sobral D, Misra CS, Di Persio S, Guilgur LG, Schuppe HC, Silva N, Prudêncio P, Nóvoa A, Leocádio AS, Bom J, Laurentino S, Mallo M, Kliesch S, Mutwil M, Rocha LM, Tüttelmann F, Becker JD, and Navarro-Costa P
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- Male, Humans, Animals, Evolution, Molecular, Transcriptome, Mice, Spermatozoa metabolism, Germ Cells metabolism, Spermatocytes metabolism, Spermatogenesis genetics
- Abstract
Male germ cells share a common origin across animal species, therefore they likely retain a conserved genetic program that defines their cellular identity. However, the unique evolutionary dynamics of male germ cells coupled with their widespread leaky transcription pose significant obstacles to the identification of the core spermatogenic program. Through network analysis of the spermatocyte transcriptome of vertebrate and invertebrate species, we describe the conserved evolutionary origin of metazoan male germ cells at the molecular level. We estimate the average functional requirement of a metazoan male germ cell to correspond to the expression of approximately 10,000 protein-coding genes, a third of which defines a genetic scaffold of deeply conserved genes that has been retained throughout evolution. Such scaffold contains a set of 79 functional associations between 104 gene expression regulators that represent a core component of the conserved genetic program of metazoan spermatogenesis. By genetically interfering with the acquisition and maintenance of male germ cell identity, we uncover 161 previously unknown spermatogenesis genes and three new potential genetic causes of human infertility. These findings emphasize the importance of evolutionary history on human reproductive disease and establish a cross-species analytical pipeline that can be repurposed to other cell types and pathologies., Competing Interests: RB, JA, MW, IJ, DS, CM, SD, LG, HS, NS, PP, AN, AL, JB, SL, MM, SK, MM, LR, FT, JB, PN No competing interests declared, (© 2024, Brattig-Correia, Almeida, Wyrwoll et al.)
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- 2024
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128. Isolation of Arabidopsis Pollen, Sperm Cells, and Vegetative Nuclei by Fluorescence-Activated Cell Sorting (FACS).
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Santos MR, Bispo C, and Becker JD
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- Arabidopsis genetics, Cell Nucleus genetics, Epigenomics methods, Flow Cytometry, Gene Expression Regulation, Plant genetics, Gene Expression Regulation, Plant physiology, Pollen genetics, Transcriptome genetics, Arabidopsis metabolism, Cell Nucleus metabolism, Pollen metabolism
- Abstract
Efficient methods to isolate highly purified Arabidopsis thaliana pollen and the subcellular components of the male gametophyte (the vegetative nucleus and two sperm cells) have enabled genome-scale studies revealing a highly dynamic reprogramming of the transcriptome and epigenome during pollen development. Here, we describe the isolation of uninucleate microspores, mature pollen, as well as sperm cells and vegetative nuclei by Fluorescence-Activated Cell Sorting.
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- 2017
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129. Effects of Delta1 and Jagged1 on early human hematopoiesis: correlation with expression of notch signaling-related genes in CD34+ cells.
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Neves H, Weerkamp F, Gomes AC, Naber BA, Gameiro P, Becker JD, Lúcio P, Clode N, van Dongen JJ, Staal FJ, and Parreira L
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- Antigens, Surface biosynthesis, Cell Proliferation, Cells, Cultured, Culture Media, Fetal Blood cytology, Fetal Blood metabolism, Gene Expression Regulation, Hematopoietic Stem Cells cytology, Humans, Intracellular Signaling Peptides and Proteins, Jagged-1 Protein, Lipopolysaccharide Receptors biosynthesis, Receptors, Notch genetics, Serrate-Jagged Proteins, Signal Transduction physiology, Stromal Cells cytology, Antigens, CD34 biosynthesis, Calcium-Binding Proteins physiology, Hematopoiesis physiology, Hematopoietic Stem Cells metabolism, Intercellular Signaling Peptides and Proteins physiology, Membrane Proteins physiology, Receptors, Notch metabolism, Stromal Cells metabolism
- Abstract
It has been shown that Notch signaling mediated by ligands of both Jagged and Delta families expands the hematopoietic stem cell compartment while blocking or delaying terminal myeloid differentiation. Here we show that Delta1- and Jagged1-expressing stromal cells have distinct effects on the clonogenic and differentiation capacities of human CD34(+) CD38(+) cells. Jagged1 increases the number of bipotent colony-forming unit-granulocyte macrophage (CFU-GM) and unipotent progenitors (CFU-granulocytes and CFU-macrophages), without quantitatively affecting terminal cell differentiation, whereas Delta1 reduces the number of CFU-GM and differentiated monocytic cells. Expression analysis of genes coding for Notch receptors, Notch targets, and Notch signaling modulators in supernatant CD34(+) cells arising upon contact with Jagged1 and Delta1 shows dynamic and differential gene expression profiles over time. At early time points, modest upregulation of Notch1, Notch3, and Hes1 was observed in Jagged1-CD34(+) cells, whereas those in contact with Delta1 strikingly upregulated Notch3 and Hes1. Later, myeloid progenitors with strong clonogenic potential emerging upon contact with Jagged1 upregulated Notch1 and Deltex and downregulated Notch signaling modulators, whereas T/NK progenitors originated by Delta1 strikingly upregulated Notch3 and Deltex and, to a lesser extent, Hes1, Lunatic Fringe, and Numb. Together, the data unravel previously unrecognized expression patterns of Notch signaling-related genes in CD34(+) CD38(+) cells as they develop in Jagged1- or Delta1-stromal cell environments, which appear to reflect sequential maturational stages of CD34(+) cells into distinct cell lineages.
- Published
- 2006
- Full Text
- View/download PDF
130. Gametophyte interaction and sexual reproduction: how plants make a zygote.
- Author
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Boavida LC, Vieira AM, Becker JD, and Feijó JA
- Subjects
- Flowers growth & development, Germ Cells growth & development, Models, Biological, Plant Physiological Phenomena, Pollen growth & development, Reproduction, Zygote growth & development, Plant Development
- Abstract
The evolutionary success of higher plants relies on a very short gametophytic phase, which underlies the sexual reproduction cycle. Sexual plant reproduction takes place in special organs of the flower: pollen, the male gametophyte, is released from the anthers and then adheres, grows and interacts along various tissues of the female organs, collectively known as the pistil. Finally, it fertilizes the female gametophyte, the embryo sac. Pollen is released as bi or tricellular, highly de-hydrated and presumably containing all the biochemical components and transcripts to germinate. Upon hydration on the female tissues, it develops a cytoplasmic extension, the pollen tube, which is one of the fastest growing cells in nature. Pollen is completely "ready-to-go", but despite this seemingly simple reaction, very complex interactions take place with the female tissues. In higher animals, genetic mechanisms for sex determination establish striking developmental differences between males and females. In contrast, most higher plant species develop both male and female structures within the same flower, allowing self-fertilization. Outcrossing is ensured by self-incompatibility mechanisms, which evolved under precise genetic control, controlling self-recognition and cell-to-cell interaction. Equally important is pollen selection along the female tissues, where interactions between different cell types with inherent signalling properties correspond to check-points to ensure fertilization. Last but not least, pollen-pistil interaction occurs in a way that enables the correct targeting of the pollen tubes to the receptive ovules. In this review, we cover the basic mechanisms underlying sexual plant reproduction, from the structural and cellular determinants, to the most recent genetic advances.
- Published
- 2005
- Full Text
- View/download PDF
131. The making of gametes in higher plants.
- Author
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Boavida LC, Becker JD, and Feijó JA
- Subjects
- Flowers growth & development, Gametogenesis, Gene Expression Regulation, Developmental, Gene Expression Regulation, Plant, Germ Cells cytology, Models, Biological, Plant Physiological Phenomena, Plants genetics, Pollen growth & development, Reproduction, Transcription, Genetic, Plant Cells, Plant Development
- Abstract
Higher plants have evolved to be one of the predominant life forms on this planet. A great deal of this evolutionary success relies in a very short gametophytic phase which underlies the sexual reproduction cycle. Sexual plant reproduction takes place in special organs of the flower. In most species the processes of gametogenesis, pollination, syngamy and embryogenesis are sequentially coordinated to give rise to a functional seed in a matter of few weeks. Any of these processes is so intricately complex and precisely regulated that it becomes no wonder that each involves more specific genes and cellular processes than any other function in the plant life cycle. While variability generation - the evolutionary output of the sexual cycle - is the same as in any other Kingdom, plants do it using a completely original set of mechanisms, many of which are not yet comprehended. In this paper, we cover the fundamental features of male and female gametogenesis. While the physiological and cellular bases of these processes have been continuously described since the early nineteen century, recent usage of Arabidopsis and other species as central models has brought about a great deal of specific information regarding their genetic regulation. Transcriptomics has recently enlarged the repertoire and pollen became the first gametophyte to have a fully described transcriptome in plants. We thus place special emphasis on the way this newly accumulated genetic and transcriptional information impacts our current understanding of the mechanisms of gametogenesis.
- Published
- 2005
- Full Text
- View/download PDF
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