Mona Damaj - Academia.edu (original) (raw)

Papers by Mona Damaj

International journal of plant genomics, 2009

High-throughput functional genomic procedures depend on the quality of the RNA used. Copurifying ... more High-throughput functional genomic procedures depend on the quality of the RNA used. Copurifying molecules can negatively impact the functionality of some plant RNA preparations employed in these procedures. We present a simplified, rapid, and scalable SDS/phenol-based method that provides the high-quantity and -quality RNA required by the newly emerging biotechnology applications. The method is applied to isolating RNA from tissues of two biotechnologically important crop plants, sugarcane and citrus, which provide a challenge due to the presence of fiber, polysaccharides, or secondary metabolites. The RNA isolated by this method is suitable for several downstream applications including northern blot hybridization, microarray analysis, and quantitative RT-PCR. This method has been used in a diverse range of projects ranging from screening plant lines overexpressing mammalian genes to analyzing plant responses to viral infection and defense signaling molecules.

Sugar Tech, 2011

The physiological response of four commercial sugarcane genotypes to water stress was evaluated b... more The physiological response of four commercial sugarcane genotypes to water stress was evaluated by measuring the photochemical efficiency of the photosystem II (chlorophyll a fluorescence ratio, F v /F m ), estimated chlorophyll content (SPAD unit), leaf temperature (LT) and leaf relative water content (RWC). A field trial was established in the subtropical area with well-watered and water-stressed genotypes, in completely randomized blocks with four replicates in a 4 9 2 9 3 factorial design (genotype 9 irrigation 9 evaluation date). Physiological measurements were done during a 90 day-period of formative stage of plants. The analysis of variance showed that the interaction of genotype 9 irrigation 9 evaluation date had a significant effect for three physiological markers tested, F v /F m , SPAD unit and RWC. Under non-stressed conditions, all genotypes showed similar responses for the four markers. Under water deficiency stress, two droughttolerant genotypes, HOCP01-523 and TCP89-3505 displayed higher values for F v /F m , SPAD unit and RWC, and lower values for LT, and could be classified as tolerant. It is therefore possible to use these physiological water stress associated traits as scorable marker traits for selecting drought-tolerant sugarcane genotypes in future breeding programs.

Heterochromatin protein 1 (HP1) is a conserved component of the highly compact chromatin of highe... more Heterochromatin protein 1 (HP1) is a conserved component of the highly compact chromatin of higher eukaryotic centromeres and telomeres. Cytogenetic experiments in Drosophila have shown that HP1 localization into this chromatin is perturbed in mutants for the origin recognition complex (ORC) 2 subunit. ORC has a multisubunit DNA-binding activity that binds origins of DNA replication where it is required for origin firing. The DNA-binding activity of ORC is also used in the recruitment of the Sir1 protein to silence nucleation sites flanking silent copies of the mating-type genes in Saccharomyces cerevisiae. A fraction of HP1 in the maternally loaded cytoplasm of the early Drosophila embryo is associated with a multiprotein complex containing Drosophila melanogaster ORC subunits. This complex appears to be poised to function in heterochromatin assembly later in embryonic development. Here we report the identification of a novel component of this complex, the HP1/ORC-associated protein. This protein contains similarity to DNA sequence-specific HMG proteins and is shown to bind specific satellite sequences and the telomere-associated sequence in vitro. The protein is shown to have heterochromatic localization in both diploid interphase and mitotic chromosomes and polytene chromosomes. Moreover, the gene encoding HP1/ORC-associated protein was found to display reciprocal dose-dependent variegation modifier phenotypes, similar to those for mutants in HP1 and the ORC 2 subunit.

Planta, 2010

Transcription proWling analysis identiWed Saccharum hybrid DIRIGENT (SHDIR16) and -METHYL-TRANSFE... more Transcription proWling analysis identiWed Saccharum hybrid DIRIGENT (SHDIR16) and -METHYL-TRANSFERASE (SHOMT), putative defense and Wber biosynthesis-related genes that are highly expressed in the stem of sugarcane, a major sucrose accumulator and biomass producer. Promoters (Pro) of these genes were isolated and fused to the -glucuronidase (GUS) reporter gene. Transient and stable transgene expression analyses showed that both Pro DIR16 :GUS and Pro OMT :GUS retain the expression characteristics of their respective endogenous genes in sugarcane and function in orthologous monocot species, including rice, maize and sorghum. Furthermore, both promoters conferred stem-regulated expression, which was further enhanced in the stem and induced in the leaf and root by salicylic acid, jasmonic acid and methyl jasmonate, key regulators of biotic and abiotic stresses. Pro DIR16 and Pro OMT will enable functional gene analysis in monocots, and will facilitate engineering monocots for improved carbon metabolism, enhanced stress tolerance and bioenergy production.

Genome, 2010

The availability of a wider range of promoters for regulated expression in valuable transgenic cr... more The availability of a wider range of promoters for regulated expression in valuable transgenic crops would benefit functional genomics studies and current biotechnology programs aimed at improved productivity. Polymerase chain reaction (PCR)-based genome walking techniques are commonly used to isolate promoters or 5' flanking genomic regions adjacent to known cDNA sequences in genomes that are not yet completely sequenced. However, these techniques are problematic when applied directly to DNA isolated from crops with highly complex and large genomes. An adaptor ligation-mediated PCR-based BAC genome walking method is described here for the efficient isolation of promoters of multigene family members, such as the putative defense and fiber biosynthesis DIRIGENT genes that are abundant in the stem of sugarcane, a species with a highly polyploid genome. The advantage of this method is the efficient and specific amplification of the target promoter using BAC genomic DNA as template for the adaptor ligation-mediated PCR walking.

International journal of plant genomics, 2009

High-throughput functional genomic procedures depend on the quality of the RNA used. Copurifying ... more High-throughput functional genomic procedures depend on the quality of the RNA used. Copurifying molecules can negatively impact the functionality of some plant RNA preparations employed in these procedures. We present a simplified, rapid, and scalable SDS/phenol-based method that provides the high-quantity and -quality RNA required by the newly emerging biotechnology applications. The method is applied to isolating RNA from tissues of two biotechnologically important crop plants, sugarcane and citrus, which provide a challenge due to the presence of fiber, polysaccharides, or secondary metabolites. The RNA isolated by this method is suitable for several downstream applications including northern blot hybridization, microarray analysis, and quantitative RT-PCR. This method has been used in a diverse range of projects ranging from screening plant lines overexpressing mammalian genes to analyzing plant responses to viral infection and defense signaling molecules.

Sugar Tech, 2011

The physiological response of four commercial sugarcane genotypes to water stress was evaluated b... more The physiological response of four commercial sugarcane genotypes to water stress was evaluated by measuring the photochemical efficiency of the photosystem II (chlorophyll a fluorescence ratio, F v /F m ), estimated chlorophyll content (SPAD unit), leaf temperature (LT) and leaf relative water content (RWC). A field trial was established in the subtropical area with well-watered and water-stressed genotypes, in completely randomized blocks with four replicates in a 4 9 2 9 3 factorial design (genotype 9 irrigation 9 evaluation date). Physiological measurements were done during a 90 day-period of formative stage of plants. The analysis of variance showed that the interaction of genotype 9 irrigation 9 evaluation date had a significant effect for three physiological markers tested, F v /F m , SPAD unit and RWC. Under non-stressed conditions, all genotypes showed similar responses for the four markers. Under water deficiency stress, two droughttolerant genotypes, HOCP01-523 and TCP89-3505 displayed higher values for F v /F m , SPAD unit and RWC, and lower values for LT, and could be classified as tolerant. It is therefore possible to use these physiological water stress associated traits as scorable marker traits for selecting drought-tolerant sugarcane genotypes in future breeding programs.

Heterochromatin protein 1 (HP1) is a conserved component of the highly compact chromatin of highe... more Heterochromatin protein 1 (HP1) is a conserved component of the highly compact chromatin of higher eukaryotic centromeres and telomeres. Cytogenetic experiments in Drosophila have shown that HP1 localization into this chromatin is perturbed in mutants for the origin recognition complex (ORC) 2 subunit. ORC has a multisubunit DNA-binding activity that binds origins of DNA replication where it is required for origin firing. The DNA-binding activity of ORC is also used in the recruitment of the Sir1 protein to silence nucleation sites flanking silent copies of the mating-type genes in Saccharomyces cerevisiae. A fraction of HP1 in the maternally loaded cytoplasm of the early Drosophila embryo is associated with a multiprotein complex containing Drosophila melanogaster ORC subunits. This complex appears to be poised to function in heterochromatin assembly later in embryonic development. Here we report the identification of a novel component of this complex, the HP1/ORC-associated protein. This protein contains similarity to DNA sequence-specific HMG proteins and is shown to bind specific satellite sequences and the telomere-associated sequence in vitro. The protein is shown to have heterochromatic localization in both diploid interphase and mitotic chromosomes and polytene chromosomes. Moreover, the gene encoding HP1/ORC-associated protein was found to display reciprocal dose-dependent variegation modifier phenotypes, similar to those for mutants in HP1 and the ORC 2 subunit.

Planta, 2010

Transcription proWling analysis identiWed Saccharum hybrid DIRIGENT (SHDIR16) and -METHYL-TRANSFE... more Transcription proWling analysis identiWed Saccharum hybrid DIRIGENT (SHDIR16) and -METHYL-TRANSFERASE (SHOMT), putative defense and Wber biosynthesis-related genes that are highly expressed in the stem of sugarcane, a major sucrose accumulator and biomass producer. Promoters (Pro) of these genes were isolated and fused to the -glucuronidase (GUS) reporter gene. Transient and stable transgene expression analyses showed that both Pro DIR16 :GUS and Pro OMT :GUS retain the expression characteristics of their respective endogenous genes in sugarcane and function in orthologous monocot species, including rice, maize and sorghum. Furthermore, both promoters conferred stem-regulated expression, which was further enhanced in the stem and induced in the leaf and root by salicylic acid, jasmonic acid and methyl jasmonate, key regulators of biotic and abiotic stresses. Pro DIR16 and Pro OMT will enable functional gene analysis in monocots, and will facilitate engineering monocots for improved carbon metabolism, enhanced stress tolerance and bioenergy production.

Genome, 2010

The availability of a wider range of promoters for regulated expression in valuable transgenic cr... more The availability of a wider range of promoters for regulated expression in valuable transgenic crops would benefit functional genomics studies and current biotechnology programs aimed at improved productivity. Polymerase chain reaction (PCR)-based genome walking techniques are commonly used to isolate promoters or 5' flanking genomic regions adjacent to known cDNA sequences in genomes that are not yet completely sequenced. However, these techniques are problematic when applied directly to DNA isolated from crops with highly complex and large genomes. An adaptor ligation-mediated PCR-based BAC genome walking method is described here for the efficient isolation of promoters of multigene family members, such as the putative defense and fiber biosynthesis DIRIGENT genes that are abundant in the stem of sugarcane, a species with a highly polyploid genome. The advantage of this method is the efficient and specific amplification of the target promoter using BAC genomic DNA as template for the adaptor ligation-mediated PCR walking.