Edwards Allen - Academia.edu (original) (raw)

Papers by Edwards Allen

Research paper thumbnail of Procedes pour produire une graine hybride

L'invention concerne des procedes servant a produire une graine hybride non naturelle. L'... more L'invention concerne des procedes servant a produire une graine hybride non naturelle. L'invention concerne egalement des micro-ARN specifiques, des sites de reconnaissance de micro-ARN utiles pour conferer une sterilite induite a une plante cultivee, ainsi qu'un ADN de synthese recombine comprenant de tels sites de reconnaissance de micro-ARN exogene.

Research paper thumbnail of Double-stranded RNA stabilized in planta

Research paper thumbnail of AG01-miR173 complex initiates phased siRNA formation in plants

Proceedings of the National Academy of Sciences of the United States of America, 2008

Research paper thumbnail of Recombinant DNA constructs compressing engineered plant microRNAs and methods for controlling gene expression

Research paper thumbnail of Engineered miRNA precursors for suppressing target gene expression in plants

Research paper thumbnail of Phased small rnas

Research paper thumbnail of Methods and DNA Constructs for Autoregulating Transgene Silencing

Research paper thumbnail of SUPPLEMENTAL RESULTS AND EXPERIMENTAL PROCEDURES Synthetic tasiRNA Construct Design

All TAS3a-based syn-tasiRNA sequences were substituted at positions occupied by tasiR2141 and tas... more All TAS3a-based syn-tasiRNA sequences were substituted at positions occupied by tasiR2141 and tasiR2142. Therefore, developmental defects associated with missexpression of active TAS3 tasiRNAs was avoided (Adenot et al., 2006; Allen et al.,

Research paper thumbnail of Windows from the ASRP database website

<b>Copyright information:</b>Taken from "ASRP: the Small RNA Project Database&qu... more <b>Copyright information:</b>Taken from "ASRP: the Small RNA Project Database"Nucleic Acids Research 2004 ;33(Database Issue):D637-D640.Published online 17 Dec 2004 PMCID:PMC540081.Copyright © 2005 Oxford University Press () A partial list of all miRNAs in the database. () Information specific to a single miRNA. () Display from the genome browser.

Research paper thumbnail of plant microRNA and procedures for their use

A method for decreasing the activity of the miRNA in a plant cell that comprises expressing in a ... more A method for decreasing the activity of the miRNA in a plant cell that comprises expressing in a plant cell a recombinant DNA construct comprising a heterologous promoter operably linked to a DNA encoding at least one decoy sequence of a synthetic miRNA consisting of 19 to 36 contiguous RNA nucleotides, in which the decoy sequence of said synthetic miRNA is recognized and linked, but not cleaved, by a miRNA expressed in said plant cell, resulting in a base pairing between said synthetic miRNA decoy sequence and said mature miRNA, thus forming an excision resistant RNA duplex comprising at least one incorrect match between said synthetic miRNA decoy sequence and said mature miRNA at positions 9, 10, or 11 of said mature plant miRNA, or at minus an insert in a position of said synthetic miRNA decoy sequence corresponding to positions 10-11 of said mature miRNA, whereby the activity of said mature miRNA in said plant cell decreases, with respect to that in which said recombinant DNA co...

Research paper thumbnail of Evaluating maize phenotypic variance, heritability, and yield relationships at multiple biological scales across agronomically relevant environments

Plant, Cell & Environment, 2019

A challenge to improve an integrative phenotype, like yield, is the interaction between the broad... more A challenge to improve an integrative phenotype, like yield, is the interaction between the broad range of possible molecular and physiological traits that contribute to yield and the multitude of potential environmental conditions in which they are expressed. This study collected data on 31 phenotypic traits, 83 annotated metabolites, and nearly 22,000 transcripts from a set of 57 diverse, commercially relevant maize hybrids across three years in central U.S. Corn Belt environments. Although variability in characteristics created a complex picture of how traits interact produce yield, phenotypic traits and gene expression were more consistent across environments, while metabolite levels showed low repeatability. Phenology traits, such as green leaf number and grain moisture and whole plant nitrogen content showed the most consistent correlation with yield. A machine learning predictive analysis of phenotypic traits revealed that ear traits, phenology, and root traits were most important to predicting yield. Analysis suggested little correlation between biomass traits and yield, suggesting there is more of a sink limitation to yield under the conditions studied here. This work suggests that continued improvement of maize yields requires a strong understanding of baseline variation of plant characteristics across commercially-relevant germplasm to drive strategies for consistently improving yield.

Research paper thumbnail of comprising a promoter with maize endosperm-specific expression operably linked to heterologous DNA; transgenic maize plant cell; improved stress tolerance, yield, process and storage quality

Research paper thumbnail of Methods for Producing Hybrid Seed

Research paper thumbnail of Recombinant DNA constructs and methods for controlling gene expression

Research paper thumbnail of Double-stranded RNA stabilized in planta

Research paper thumbnail of Plant microRNAs and methods of use thereof

Research paper thumbnail of Temporal Regulation of Gene Expression by MicroRNAs

Research paper thumbnail of Base-Pairing between Untranslated Regions Facilitates Translation of Uncapped, Nonpolyadenylated Viral RNA

Research paper thumbnail of Method to trigger RNA interference

Research paper thumbnail of Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana

Nature Genetics, 2004

MicroRNAs (miRNAs) in plants and animals function as post-transcriptional regulators of target ge... more MicroRNAs (miRNAs) in plants and animals function as post-transcriptional regulators of target genes, many of which are involved in multicellular development. miRNAs guide effector complexes to target mRNAs through base-pair complementarity, facilitating site-specific cleavage or translational repression. Biogenesis of miRNAs involves nucleolytic processing of a precursor transcript with extensive foldback structure. Here, we provide evidence that genes encoding miRNAs in plants originated by inverted duplication of target gene sequences. Several recently evolved genes encoding miRNAs in Arabidopsis thaliana and other small RNA-generating loci possess the hallmarks of inverted duplication events that formed the arms on each side of their respective foldback precursors. We propose a model for miRNA evolution that suggests a mechanism for de novo generation of new miRNA genes with unique target specificities.

Research paper thumbnail of Procedes pour produire une graine hybride

L'invention concerne des procedes servant a produire une graine hybride non naturelle. L'... more L'invention concerne des procedes servant a produire une graine hybride non naturelle. L'invention concerne egalement des micro-ARN specifiques, des sites de reconnaissance de micro-ARN utiles pour conferer une sterilite induite a une plante cultivee, ainsi qu'un ADN de synthese recombine comprenant de tels sites de reconnaissance de micro-ARN exogene.

Research paper thumbnail of Double-stranded RNA stabilized in planta

Research paper thumbnail of AG01-miR173 complex initiates phased siRNA formation in plants

Proceedings of the National Academy of Sciences of the United States of America, 2008

Research paper thumbnail of Recombinant DNA constructs compressing engineered plant microRNAs and methods for controlling gene expression

Research paper thumbnail of Engineered miRNA precursors for suppressing target gene expression in plants

Research paper thumbnail of Phased small rnas

Research paper thumbnail of Methods and DNA Constructs for Autoregulating Transgene Silencing

Research paper thumbnail of SUPPLEMENTAL RESULTS AND EXPERIMENTAL PROCEDURES Synthetic tasiRNA Construct Design

All TAS3a-based syn-tasiRNA sequences were substituted at positions occupied by tasiR2141 and tas... more All TAS3a-based syn-tasiRNA sequences were substituted at positions occupied by tasiR2141 and tasiR2142. Therefore, developmental defects associated with missexpression of active TAS3 tasiRNAs was avoided (Adenot et al., 2006; Allen et al.,

Research paper thumbnail of Windows from the ASRP database website

<b>Copyright information:</b>Taken from "ASRP: the Small RNA Project Database&qu... more <b>Copyright information:</b>Taken from "ASRP: the Small RNA Project Database"Nucleic Acids Research 2004 ;33(Database Issue):D637-D640.Published online 17 Dec 2004 PMCID:PMC540081.Copyright © 2005 Oxford University Press () A partial list of all miRNAs in the database. () Information specific to a single miRNA. () Display from the genome browser.

Research paper thumbnail of plant microRNA and procedures for their use

A method for decreasing the activity of the miRNA in a plant cell that comprises expressing in a ... more A method for decreasing the activity of the miRNA in a plant cell that comprises expressing in a plant cell a recombinant DNA construct comprising a heterologous promoter operably linked to a DNA encoding at least one decoy sequence of a synthetic miRNA consisting of 19 to 36 contiguous RNA nucleotides, in which the decoy sequence of said synthetic miRNA is recognized and linked, but not cleaved, by a miRNA expressed in said plant cell, resulting in a base pairing between said synthetic miRNA decoy sequence and said mature miRNA, thus forming an excision resistant RNA duplex comprising at least one incorrect match between said synthetic miRNA decoy sequence and said mature miRNA at positions 9, 10, or 11 of said mature plant miRNA, or at minus an insert in a position of said synthetic miRNA decoy sequence corresponding to positions 10-11 of said mature miRNA, whereby the activity of said mature miRNA in said plant cell decreases, with respect to that in which said recombinant DNA co...

Research paper thumbnail of Evaluating maize phenotypic variance, heritability, and yield relationships at multiple biological scales across agronomically relevant environments

Plant, Cell & Environment, 2019

A challenge to improve an integrative phenotype, like yield, is the interaction between the broad... more A challenge to improve an integrative phenotype, like yield, is the interaction between the broad range of possible molecular and physiological traits that contribute to yield and the multitude of potential environmental conditions in which they are expressed. This study collected data on 31 phenotypic traits, 83 annotated metabolites, and nearly 22,000 transcripts from a set of 57 diverse, commercially relevant maize hybrids across three years in central U.S. Corn Belt environments. Although variability in characteristics created a complex picture of how traits interact produce yield, phenotypic traits and gene expression were more consistent across environments, while metabolite levels showed low repeatability. Phenology traits, such as green leaf number and grain moisture and whole plant nitrogen content showed the most consistent correlation with yield. A machine learning predictive analysis of phenotypic traits revealed that ear traits, phenology, and root traits were most important to predicting yield. Analysis suggested little correlation between biomass traits and yield, suggesting there is more of a sink limitation to yield under the conditions studied here. This work suggests that continued improvement of maize yields requires a strong understanding of baseline variation of plant characteristics across commercially-relevant germplasm to drive strategies for consistently improving yield.

Research paper thumbnail of comprising a promoter with maize endosperm-specific expression operably linked to heterologous DNA; transgenic maize plant cell; improved stress tolerance, yield, process and storage quality

Research paper thumbnail of Methods for Producing Hybrid Seed

Research paper thumbnail of Recombinant DNA constructs and methods for controlling gene expression

Research paper thumbnail of Double-stranded RNA stabilized in planta

Research paper thumbnail of Plant microRNAs and methods of use thereof

Research paper thumbnail of Temporal Regulation of Gene Expression by MicroRNAs

Research paper thumbnail of Base-Pairing between Untranslated Regions Facilitates Translation of Uncapped, Nonpolyadenylated Viral RNA

Research paper thumbnail of Method to trigger RNA interference

Research paper thumbnail of Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana

Nature Genetics, 2004

MicroRNAs (miRNAs) in plants and animals function as post-transcriptional regulators of target ge... more MicroRNAs (miRNAs) in plants and animals function as post-transcriptional regulators of target genes, many of which are involved in multicellular development. miRNAs guide effector complexes to target mRNAs through base-pair complementarity, facilitating site-specific cleavage or translational repression. Biogenesis of miRNAs involves nucleolytic processing of a precursor transcript with extensive foldback structure. Here, we provide evidence that genes encoding miRNAs in plants originated by inverted duplication of target gene sequences. Several recently evolved genes encoding miRNAs in Arabidopsis thaliana and other small RNA-generating loci possess the hallmarks of inverted duplication events that formed the arms on each side of their respective foldback precursors. We propose a model for miRNA evolution that suggests a mechanism for de novo generation of new miRNA genes with unique target specificities.