Nature Methods, ISSN 1548-7091, 12/2015, Volume 12, Issue 12, pp. 1163 - 1170
Protein-RNA networks are ubiquitous and central in biological control. We present an approach termed RNA Tagging that enables the user to identify protein-RNA...
MESSENGER-RNA | WIDE IDENTIFICATION | MITOCHONDRIAL BIOGENESIS | BUDDING YEAST | PUF3 PROTEIN | CELL-LYSIS | BIOCHEMICAL RESEARCH METHODS | GLOBAL ANALYSIS | POLY(A) TAIL LENGTH | BINDING PROTEIN | SACCHAROMYCES-CEREVISIAE | RNA-Binding Proteins - genetics | Saccharomyces cerevisiae - genetics | 3' Untranslated Regions - genetics | Repressor Proteins - genetics | Saccharomyces cerevisiae Proteins - genetics | RNA, Messenger - metabolism | RNA, Fungal - metabolism | Saccharomyces cerevisiae - metabolism | Saccharomyces cerevisiae Proteins - metabolism | Protein Binding | Binding Sites | RNA-Binding Proteins - metabolism | Repressor Proteins - metabolism | Genetic markers | RNA | Analysis | Protein binding | RNA-protein interactions | Molecular biology | Binding sites
MESSENGER-RNA | WIDE IDENTIFICATION | MITOCHONDRIAL BIOGENESIS | BUDDING YEAST | PUF3 PROTEIN | CELL-LYSIS | BIOCHEMICAL RESEARCH METHODS | GLOBAL ANALYSIS | POLY(A) TAIL LENGTH | BINDING PROTEIN | SACCHAROMYCES-CEREVISIAE | RNA-Binding Proteins - genetics | Saccharomyces cerevisiae - genetics | 3' Untranslated Regions - genetics | Repressor Proteins - genetics | Saccharomyces cerevisiae Proteins - genetics | RNA, Messenger - metabolism | RNA, Fungal - metabolism | Saccharomyces cerevisiae - metabolism | Saccharomyces cerevisiae Proteins - metabolism | Protein Binding | Binding Sites | RNA-Binding Proteins - metabolism | Repressor Proteins - metabolism | Genetic markers | RNA | Analysis | Protein binding | RNA-protein interactions | Molecular biology | Binding sites
Journal Article
Nature Communications, ISSN 2041-1723, 09/2015, Volume 6, Issue 1, p. 8213
Proteins bind and control mRNAs, directing their localization, translation and stability. Members of the PUF family of RNA-binding proteins control multiple...
SPECIFICITY | TRANSCRIPTOME | CRYSTAL-STRUCTURE | MULTIDISCIPLINARY SCIENCES | SENSITIVITY | VALIDATION | SITES | TARGETS | 3-HYBRID SYSTEM | BINDING PROTEIN | PUMILIO | Crystallization | Saccharomyces cerevisiae Proteins - metabolism | Crystallography, X-Ray | Electrophoretic Mobility Shift Assay | High-Throughput Nucleotide Sequencing | Gene Regulatory Networks | RNA, Messenger - metabolism | Binding Sites | Saccharomyces cerevisiae | Blotting, Western | RNA-Binding Proteins - metabolism | BASIC BIOLOGICAL SCIENCES
SPECIFICITY | TRANSCRIPTOME | CRYSTAL-STRUCTURE | MULTIDISCIPLINARY SCIENCES | SENSITIVITY | VALIDATION | SITES | TARGETS | 3-HYBRID SYSTEM | BINDING PROTEIN | PUMILIO | Crystallization | Saccharomyces cerevisiae Proteins - metabolism | Crystallography, X-Ray | Electrophoretic Mobility Shift Assay | High-Throughput Nucleotide Sequencing | Gene Regulatory Networks | RNA, Messenger - metabolism | Binding Sites | Saccharomyces cerevisiae | Blotting, Western | RNA-Binding Proteins - metabolism | BASIC BIOLOGICAL SCIENCES
Journal Article
Journal of Biological Chemistry, ISSN 0021-9258, 02/2009, Volume 284, Issue 7, pp. 4635 - 4646
Polyamines are ubiquitous components of all living cells, and their depletion usually causes cytostasis, a strategy employed for treatment of West African...
HUMAN MALARIA PARASITES | ADENOSYL-L-METHIONINE | HUMAN-ERYTHROCYTES | BIOCHEMISTRY & MOLECULAR BIOLOGY | GENE-EXPRESSION | ORNITHINE-DECARBOXYLASE | BIOSYNTHETIC-ENZYMES | TANDEM MASS-SPECTROMETRY | POLYAMINE METABOLISM | BRUCEI-RHODESIENSE INFECTIONS | LYSINE DECARBOXYLASE | Transcription, Genetic - physiology | Animals | Humans | Ornithine Decarboxylase - biosynthesis | Plasmodium falciparum - metabolism | Enzyme Repression - physiology | Adenosylmethionine Decarboxylase - biosynthesis | Proteome - metabolism | Protozoan Proteins - biosynthesis | Biogenic Polyamines - metabolism | Genomics, Proteomics, and Bioinformatics
HUMAN MALARIA PARASITES | ADENOSYL-L-METHIONINE | HUMAN-ERYTHROCYTES | BIOCHEMISTRY & MOLECULAR BIOLOGY | GENE-EXPRESSION | ORNITHINE-DECARBOXYLASE | BIOSYNTHETIC-ENZYMES | TANDEM MASS-SPECTROMETRY | POLYAMINE METABOLISM | BRUCEI-RHODESIENSE INFECTIONS | LYSINE DECARBOXYLASE | Transcription, Genetic - physiology | Animals | Humans | Ornithine Decarboxylase - biosynthesis | Plasmodium falciparum - metabolism | Enzyme Repression - physiology | Adenosylmethionine Decarboxylase - biosynthesis | Proteome - metabolism | Protozoan Proteins - biosynthesis | Biogenic Polyamines - metabolism | Genomics, Proteomics, and Bioinformatics
Journal Article
NATURE COMMUNICATIONS, ISSN 2041-1723, 09/2019, Volume 10, Issue 1, pp. 4052 - 14
Metabolites are active controllers of cellular physiology, but their role in complex behaviors is less clear. Here we report metabolic changes that occur...
BRAIN ENERGY-METABOLISM | VISUALIZATION | INTEGRATION | N-ACETYLASPARTATE | MULTIDISCIPLINARY SCIENCES | FEEDING-BEHAVIOR | NEURONS | CYTOSCAPE | TASTE | NUTRIENT SENSOR | SUGAR | Tricarboxylic acid cycle | Hunger | Diet | Metabolites | Insects | Drosophila | Metabolic networks | Fruit flies | Satiety | Nutrients | Metabolism | Sugar
BRAIN ENERGY-METABOLISM | VISUALIZATION | INTEGRATION | N-ACETYLASPARTATE | MULTIDISCIPLINARY SCIENCES | FEEDING-BEHAVIOR | NEURONS | CYTOSCAPE | TASTE | NUTRIENT SENSOR | SUGAR | Tricarboxylic acid cycle | Hunger | Diet | Metabolites | Insects | Drosophila | Metabolic networks | Fruit flies | Satiety | Nutrients | Metabolism | Sugar
Journal Article
Polimery/Polymers, ISSN 0032-2725, 2016, Volume 61, Issue 7-8, pp. 474 - 481
Chemical admixtures are one of the basic components of the contemporary concrete. The most important admixtures are superplasticizers, i.e. the modifiers which...
Superplasticizers | Concrete | Polycarboxylate | Cement | Chemical Admixtures | concrete | chemical admixtures | POLYMER SCIENCE | COMB-TYPE SUPERPLASTICIZERS | MOLECULAR-STRUCTURE | CLAY TOLERANCE | PERFORMANCE CONCRETE | ANIONIC FUNCTION | SULFOALUMINATE CEMENT | superplasticizers | NEW-GENERATION SUPERPLASTICIZERS | SIDE-CHAINS | polycarboxylate | cement | SELF-COMPACTING CONCRETE | HYDRATION BEHAVIOR
Superplasticizers | Concrete | Polycarboxylate | Cement | Chemical Admixtures | concrete | chemical admixtures | POLYMER SCIENCE | COMB-TYPE SUPERPLASTICIZERS | MOLECULAR-STRUCTURE | CLAY TOLERANCE | PERFORMANCE CONCRETE | ANIONIC FUNCTION | SULFOALUMINATE CEMENT | superplasticizers | NEW-GENERATION SUPERPLASTICIZERS | SIDE-CHAINS | polycarboxylate | cement | SELF-COMPACTING CONCRETE | HYDRATION BEHAVIOR
Journal Article
Molecular Microbiology, ISSN 0950-382X, 04/2010, Volume 76, Issue 1, pp. 12 - 24
Summary Recent advances in high‐throughput sequencing present a new opportunity to deeply probe an organism's transcriptome. In this study, we used...
SEQUENCES | COMPARATIVE GENOMICS | LANDSCAPE | GENE-EXPRESSION MICROARRAYS | BIOCHEMISTRY & MOLECULAR BIOLOGY | LENGTH | DATABASES | MICROBIOLOGY | MALARIA PARASITES | IDENTIFICATION | CULTURE | DISCOVERY | RNA Splicing | Pseudogenes | Oligonucleotide Array Sequence Analysis | Time Factors | Humans | Plasmodium falciparum - genetics | Gene Expression Profiling | Plasmodium falciparum - growth & development | Erythrocytes - parasitology | Sequence Analysis, DNA - methods | Blood - parasitology | Plasmodium falciparum | DNA microarrays | Malaria | Multiprocessing | Analysis | Genomics | Universities and colleges
SEQUENCES | COMPARATIVE GENOMICS | LANDSCAPE | GENE-EXPRESSION MICROARRAYS | BIOCHEMISTRY & MOLECULAR BIOLOGY | LENGTH | DATABASES | MICROBIOLOGY | MALARIA PARASITES | IDENTIFICATION | CULTURE | DISCOVERY | RNA Splicing | Pseudogenes | Oligonucleotide Array Sequence Analysis | Time Factors | Humans | Plasmodium falciparum - genetics | Gene Expression Profiling | Plasmodium falciparum - growth & development | Erythrocytes - parasitology | Sequence Analysis, DNA - methods | Blood - parasitology | Plasmodium falciparum | DNA microarrays | Malaria | Multiprocessing | Analysis | Genomics | Universities and colleges
Journal Article
Cell Host & Microbe, ISSN 1931-3128, 2009, Volume 5, Issue 2, pp. 191 - 199
Intracellular pathogens have devised mechanisms to exploit their host cells to ensure their survival and replication. The malaria parasite relies on an...
SYSBIO | CHEMBIO | MICROBIO | PATHWAYS | METABOLISM | ARGINASE | NITRIC-OXIDE BIOAVAILABILITY | MALARIA PARASITE | APICOPLAST | MICROBIOLOGY | INFECTION | MASS-SPECTROMETRY | CEREBRAL MALARIA | BLOOD-CELLS | Ornithine - metabolism | Humans | Arginase - metabolism | Metabolome | Arginase - genetics | Gene Knockout Techniques | Protozoan Proteins - genetics | Plasmodium berghei - metabolism | Animals | Protozoan Proteins - metabolism | Arginine - blood | Malaria - parasitology | Plasmodium falciparum - metabolism | Mice | Host-Parasite Interactions | Erythrocytes - parasitology | Mass Spectrometry - methods | Arginine - metabolism | Plasmodium falciparum - chemistry | Plasmodium falciparum | Metabolites | Malaria | Mass spectrometry | Analysis
SYSBIO | CHEMBIO | MICROBIO | PATHWAYS | METABOLISM | ARGINASE | NITRIC-OXIDE BIOAVAILABILITY | MALARIA PARASITE | APICOPLAST | MICROBIOLOGY | INFECTION | MASS-SPECTROMETRY | CEREBRAL MALARIA | BLOOD-CELLS | Ornithine - metabolism | Humans | Arginase - metabolism | Metabolome | Arginase - genetics | Gene Knockout Techniques | Protozoan Proteins - genetics | Plasmodium berghei - metabolism | Animals | Protozoan Proteins - metabolism | Arginine - blood | Malaria - parasitology | Plasmodium falciparum - metabolism | Mice | Host-Parasite Interactions | Erythrocytes - parasitology | Mass Spectrometry - methods | Arginine - metabolism | Plasmodium falciparum - chemistry | Plasmodium falciparum | Metabolites | Malaria | Mass spectrometry | Analysis
Journal Article
RNA, ISSN 1355-8382, 11/2017, Volume 23, Issue 11, pp. 1636 - 1647
A single protein can bind and regulate many mRNAs. Multiple proteins with similar specificities often bind and control overlapping sets of mRNAs. Yet little is...
Protein–RNA networks | RNA-binding proteins | Protein–RNA interactions | PUF proteins | RNA control | CELLS | TRANSCRIPTOME | BIOCHEMISTRY & MOLECULAR BIOLOGY | GLOBAL ANALYSIS | protein-RNA interactions | IDENTIFICATION | YEAST | protein-RNA networks | MESSENGER-RNA | BINDING PROTEINS | GENOME-WIDE ANALYSIS | GENE-EXPRESSION | TARGETS | protein–RNA networks | protein–RNA interactions
Protein–RNA networks | RNA-binding proteins | Protein–RNA interactions | PUF proteins | RNA control | CELLS | TRANSCRIPTOME | BIOCHEMISTRY & MOLECULAR BIOLOGY | GLOBAL ANALYSIS | protein-RNA interactions | IDENTIFICATION | YEAST | protein-RNA networks | MESSENGER-RNA | BINDING PROTEINS | GENOME-WIDE ANALYSIS | GENE-EXPRESSION | TARGETS | protein–RNA networks | protein–RNA interactions
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 12/2017, Volume 114, Issue 51, pp. E10854 - E10855
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 04/2017, Volume 114, Issue 14, pp. E2816 - E2825
Alterations in regulatory networks contribute to evolutionary change. Transcriptional networks are reconfigured by changes in the binding specificity of...
3'UTR elements | Evolution | RNA regulation | PUF proteins | TRANSCRIPTION FACTOR-BINDING | NUCLEOTIDE RESOLUTION | HIGH-THROUGHPUT | GENE DUPLICATION | MULTIDISCIPLINARY SCIENCES | 3 ' UTR elements | evolution | 3-HYBRID SYSTEM | MESSENGER-RNAS | PROTEIN INTERACTIONS | PUF FAMILY | IN-VIVO | Gene Expression Regulation, Fungal | RNA-Binding Proteins - genetics | Aspergillus nidulans - genetics | RNA, Messenger - genetics | Fungal Proteins - genetics | Phylogeny | Saccharomyces cerevisiae Proteins - genetics | Gene Regulatory Networks | Neurospora crassa - genetics | Saccharomyces cerevisiae Proteins - metabolism | 3' Untranslated Regions | Binding Sites | RNA-Binding Proteins - metabolism | Evolution, Molecular | Fungal Proteins - metabolism | RNA sequencing | Genetic regulation | Observations | Methods | Biological Sciences | 3′UTR elements | PNAS Plus
3'UTR elements | Evolution | RNA regulation | PUF proteins | TRANSCRIPTION FACTOR-BINDING | NUCLEOTIDE RESOLUTION | HIGH-THROUGHPUT | GENE DUPLICATION | MULTIDISCIPLINARY SCIENCES | 3 ' UTR elements | evolution | 3-HYBRID SYSTEM | MESSENGER-RNAS | PROTEIN INTERACTIONS | PUF FAMILY | IN-VIVO | Gene Expression Regulation, Fungal | RNA-Binding Proteins - genetics | Aspergillus nidulans - genetics | RNA, Messenger - genetics | Fungal Proteins - genetics | Phylogeny | Saccharomyces cerevisiae Proteins - genetics | Gene Regulatory Networks | Neurospora crassa - genetics | Saccharomyces cerevisiae Proteins - metabolism | 3' Untranslated Regions | Binding Sites | RNA-Binding Proteins - metabolism | Evolution, Molecular | Fungal Proteins - metabolism | RNA sequencing | Genetic regulation | Observations | Methods | Biological Sciences | 3′UTR elements | PNAS Plus
Journal Article
ISSN 1355-8382, 11/2017, Volume 23, Issue 11, p. 1636
A single protein can bind and regulate many mRNAs. Multiple proteins with similar specificities often bind and control overlapping sets of mRNAs. Yet little is...
Proteins | Ribonucleic acid--RNA
Proteins | Ribonucleic acid--RNA
Journal Article
Proceedings of the National Academy of Sciences of the United States of America, ISSN 0027-8424, 04/2017, Volume 114, Issue 14, p. E2816
Alterations in regulatory networks contribute to evolutionary change. Transcriptional networks are reconfigured by changes in the binding specificity of...
Proteins | Fungi | Evolution | Ribonucleic acid--RNA
Proteins | Fungi | Evolution | Ribonucleic acid--RNA
Journal Article
Proceedings of the National Academy of Sciences, USA, ISSN 0027-8424, 04/2017, Volume 114, Issue 14, pp. E2816 - E2816
Alterations in regulatory networks contribute to evolutionary change. Transcriptional networks are reconfigured by changes in the binding specificity of...
Journal Article
14.
Full Text
Clonally variant gene families in Plasmodium falciparum share a common activation factor
Molecular Microbiology, ISSN 0950-382X, 09/2009, Volume 73, Issue 6, pp. 1171 - 1185
Summary The genome of the malaria parasite Plasmodium falciparum contains several multicopy gene families, including var, rifin, stevor and Pfmc‐2TM. These...
TRANSCRIPTION FACTORS | PARASITES | DNA-BINDING | PFMC-2TM SUPERFAMILIES | ANTIGENIC VARIATION | PROMOTERS | MUTUALLY EXCLUSIVE EXPRESSION | EPIGENETIC MEMORY | BIOCHEMISTRY & MOLECULAR BIOLOGY | MICROBIOLOGY | INFECTED ERYTHROCYTES | MALARIA VIRULENCE GENES | Promoter Regions, Genetic | Animals | Models, Biological | Plasmodium falciparum - genetics | Transcriptional Activation | Gene Expression Regulation | Genes, Protozoan | Plasmodium falciparum - physiology | Protozoan Proteins - biosynthesis | Genetic research | Plasmodium falciparum | Genetic aspects | Molecular genetics | Malaria
TRANSCRIPTION FACTORS | PARASITES | DNA-BINDING | PFMC-2TM SUPERFAMILIES | ANTIGENIC VARIATION | PROMOTERS | MUTUALLY EXCLUSIVE EXPRESSION | EPIGENETIC MEMORY | BIOCHEMISTRY & MOLECULAR BIOLOGY | MICROBIOLOGY | INFECTED ERYTHROCYTES | MALARIA VIRULENCE GENES | Promoter Regions, Genetic | Animals | Models, Biological | Plasmodium falciparum - genetics | Transcriptional Activation | Gene Expression Regulation | Genes, Protozoan | Plasmodium falciparum - physiology | Protozoan Proteins - biosynthesis | Genetic research | Plasmodium falciparum | Genetic aspects | Molecular genetics | Malaria
Journal Article
Nature Communications, ISSN 2041-1723, 04/2016, Volume 6, Issue 8213
Journal Article
Journal of Biological Chemistry, ISSN 0021-9258, 02/2012, Volume 287, Issue 9, pp. 6949 - 6957
mRNA control networks depend on recognition of specific RNA sequences. Pumilio-fem-3 mRNA binding factor (PUF) RNA-binding proteins achieve that specificity...
SYSTEM | CODE | RECOGNITION | GENE | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | TARGETS | FEM-3 | Protein Structure, Tertiary | Amino Acid Sequence | RNA-Binding Proteins - genetics | Caenorhabditis elegans - metabolism | Caenorhabditis elegans - genetics | Saccharomyces cerevisiae - genetics | Caenorhabditis elegans Proteins - chemistry | RNA-Binding Proteins - chemistry | Caenorhabditis elegans Proteins - metabolism | Molecular Sequence Data | Crystallography, X-Ray | Structure-Activity Relationship | Saccharomyces cerevisiae Proteins - genetics | RNA, Messenger - metabolism | Saccharomyces cerevisiae - metabolism | Animals | Cytosine - metabolism | Saccharomyces cerevisiae Proteins - metabolism | Caenorhabditis elegans Proteins - genetics | RNA-Binding Proteins - metabolism | Evolution, Molecular | Saccharomyces cerevisiae Proteins - chemistry | Gene Regulation | RNA Metabolism | PUF Proteins | RNA | X-ray Crystallography | RNA-binding Proteins
SYSTEM | CODE | RECOGNITION | GENE | CRYSTAL-STRUCTURE | BIOCHEMISTRY & MOLECULAR BIOLOGY | TARGETS | FEM-3 | Protein Structure, Tertiary | Amino Acid Sequence | RNA-Binding Proteins - genetics | Caenorhabditis elegans - metabolism | Caenorhabditis elegans - genetics | Saccharomyces cerevisiae - genetics | Caenorhabditis elegans Proteins - chemistry | RNA-Binding Proteins - chemistry | Caenorhabditis elegans Proteins - metabolism | Molecular Sequence Data | Crystallography, X-Ray | Structure-Activity Relationship | Saccharomyces cerevisiae Proteins - genetics | RNA, Messenger - metabolism | Saccharomyces cerevisiae - metabolism | Animals | Cytosine - metabolism | Saccharomyces cerevisiae Proteins - metabolism | Caenorhabditis elegans Proteins - genetics | RNA-Binding Proteins - metabolism | Evolution, Molecular | Saccharomyces cerevisiae Proteins - chemistry | Gene Regulation | RNA Metabolism | PUF Proteins | RNA | X-ray Crystallography | RNA-binding Proteins
Journal Article
Journal of Biological Chemistry, ISSN 0021-9258, 02/2012, Volume 287, Issue 9, pp. 6949 - 6957
Journal Article
01/2015, ISBN 9781321761450
Proteins bind and control mRNAs, directing their localization, translation, and stability. Members of the PUF family of RNA-binding proteins control multiple...
Molecular biology | Biochemistry
Molecular biology | Biochemistry
Dissertation
RNA (New York, N.Y.), 11/2017, Volume 23, Issue 11, p. 1636
A single protein can bind and regulate many mRNAs. Multiple proteins with similar specificities often bind and control overlapping sets of mRNAs. Yet little is...
RNA-Binding Proteins - genetics | Saccharomyces cerevisiae - genetics | RNA, Fungal - chemistry | RNA, Messenger - genetics | RNA-Binding Proteins - chemistry | Models, Molecular | Binding Sites - genetics | Saccharomyces cerevisiae Proteins - genetics | Gene Regulatory Networks | RNA, Messenger - metabolism | RNA, Fungal - metabolism | Saccharomyces cerevisiae - metabolism | Saccharomyces cerevisiae Proteins - metabolism | Protein Binding | RNA, Messenger - chemistry | RNA, Fungal - genetics | Nucleotidyltransferases - metabolism | RNA-Binding Proteins - metabolism | Saccharomyces cerevisiae Proteins - chemistry
RNA-Binding Proteins - genetics | Saccharomyces cerevisiae - genetics | RNA, Fungal - chemistry | RNA, Messenger - genetics | RNA-Binding Proteins - chemistry | Models, Molecular | Binding Sites - genetics | Saccharomyces cerevisiae Proteins - genetics | Gene Regulatory Networks | RNA, Messenger - metabolism | RNA, Fungal - metabolism | Saccharomyces cerevisiae - metabolism | Saccharomyces cerevisiae Proteins - metabolism | Protein Binding | RNA, Messenger - chemistry | RNA, Fungal - genetics | Nucleotidyltransferases - metabolism | RNA-Binding Proteins - metabolism | Saccharomyces cerevisiae Proteins - chemistry
Journal Article
European Heart Journal, ISSN 0195-668X, 08/2012, Volume 33, Issue suppl 1, pp. 19 - 338
Journal Article
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