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Biomedical subjects

R L Rodriguez

Publications and source records attributed to R L Rodriguez.

At least 19 recordsLinked to original sources

LRRK2 mutations in a clinic-based cohort of Parkinson's disease.

In the last decade, major breakthroughs in the understanding of genetic contributions to Parkinson's disease (PD) have been achieved. Recently, mutations in LRRK2, encoding dardarin, have been found to be responsible for an autosomal dominant parkinsonism (OMIM 607060). We screened 311 subjects (cases: n = 202, controls: n = 109) for the three previously reported LRRK2 mutations. Our investigation revealed a sporadic case of PD with a heterozygous mutation G2019S (c.6055G>A). Here, we present the clinical phenotype of this patient and discuss the implications of genetic testing for the G2019S mutation in patients with sporadic PD.

Adolescent↗

New perspectives on the endo-beta-glucanases of glycosyl hydrolase Family 17.

Isozymes of glycosyl hydrolase Family 17 hydrolyze 1,3-beta-glucan polysaccharides found in the cell wall matrix of plants and fungi, enabling these plant enzymes to serve diverse roles in plant defense and plant development. Fourteen genes from Family 17 have been characterized in the genome of rice. A sequence dendrogram analysis divided these genes into four subfamilies. The recombinant GNS1 enzyme from subfamily B had 1,3;1,4-beta-glucanase activity, suggesting a role for this isozyme in plant development.

Amino Acid Sequence↗

Production of functional human alpha 1-antitrypsin by plant cell culture.

Recombinant human alpha 1-antitrypsin (rAAT) was expressed and secreted from transgenic rice cell suspension cultures in its biologically active form. This was accomplished by transforming rice callus tissues with an expression vector, p3D-AAT, containing the cDNA for mature human AAT protein. Regulated expression and secretion of rAAT from this vector was achieved using the promoter, signal peptide, and terminator from a rice alpha-amylase gene Amy3D. The Amy3D gene of rice is tightly controlled by simple sugars such as sucrose. It was possible, therefore, to induce the expression of the rAAT by removing sucrose from the cultured media or by allowing the rice suspension cells to deplete sucrose catabolically. Although transgenic rice cell produced a heterogeneous population of the rAAT molecules, they had the same N-terminal amino acids as those found in serum-derived (native) AAT from humans. This result indicates that the rice signal peptidase recognizes and cleaves the novel sequence between the Amy3D signal peptide and the first amino acid of the mature human AAT. The highest molecular weight band seen on Western blots (AAT top band) was found to have the correct C-terminal amino acid sequence and normal elastase binding activity. Staining with biotin-concanavalin A and avidin horseradish peroxidase confirmed the glycosylation of the rAAT, albeit to a lesser extent than that observed with native AAT. The rAAT, purified by immunoaffinity chromatography, had the same association rate constant for porcine pancreatic elastase as the native AAT. Thermostability studies revealed that the rAAT and native AAT decayed at the same rate, suggesting that the rAAT is correctly folded. The productivity of rice suspension cells expressing rAAT was 4.6-5.7 mg/g dry cell. Taken together, these results support the use of rice cell culture as a promising new expression system for production of biologically active recombinant proteins.

Amino Acid Sequence↗

Differential expression of rice alpha-amylase genes during seedling development under anoxia.

The unique capability of rice (Oryza sativa L.) seedlings to grow under anoxic conditions may result in part from their ability to express alpha-amylase and maintain the supply of sugar needed for energy metabolism. Previous studies have demonstrated that under aerobic conditions the Amy1 and Amy2 subfamily genes are regulated primarily by phytohormones while the Amy3 subfamily genes are induced during sugar starvation. The expression patterns for these alpha-amylase genes were considerably different in anoxic vs. aerobic rice seedlings. The level of total alpha-amylase mRNA under anoxic conditions was decreased in aleurone layers while it increased in the embryo. Anoxic conditions greatly diminished the expression of the Amy1A gene in aleurone. Conversely, expression of many Amy3 subfamily genes was up-regulated and prolonged in embryo tissues under anoxic conditions.

Anaerobiosis↗

Characterization of rice endo-beta-glucanase genes (Gns2-Gns14) defines a new subgroup within the gene family.

Thirteen new beta-glucanase-encoding genes have been identified in the rice genome. These genes, together with other monocot beta-glucanases, have now been classified into four subfamilies based on the structure and function of the genes. Two tandem gene clusters, Gns2-Gns3-Gns4 and Gns5-Gns6, were classified in the defense-related Subfamily A. Growth-related 1,3;1,4-beta-glucanase Gns1 was classified in Subfamily B. Gns7 and Gns8, together with the barley genes GVI and Hv34, represent Subfamily C. Gns9 and a beta-glucanase gene from wheat were grouped in Subfamily D. Genes in Subfamilies C and D have structures that are distinct from those of the other subfamilies, but there are very little data available on the biochemical or physiological roles of these genes. Gene expression in growing tissues and lack of gene induction in response to disease-related treatments suggest that Subfamilies C and D may function in control of plant growth.

Amino Acid Sequence↗

Three cis-elements required for rice alpha-amylase Amy3D expression during sugar starvation.

Expression of alpha-amylase genes during seedling development plays a key role in production of sugar from the starch stored in the cereal seed. Rice alpha-amylase Amy3D promoter/GUS constructs in transgenic rice cell lines were studied to identify cis elements in the promoter of this metabolite-regulated gene. Three sequences having the greatest effects on Amy3D gene expression included the amylase element (TATCCAT), the CGACG element, and a G box-related element (CTACGTGGCCA). These promoter cis elements are needed for high-level expression of Amy3D under conditions of sugar starvation. The involvement of G box cis-elements in environmental stress responses suggest a link between the nutrient stress and the environmental stress responses of the plant.

Base Sequence↗

Characterization of rice alpha-amylase isozymes expressed by Saccharomyces cerevisiae.

Two rice alpha-amylase isozymes, AmylA and Amy3D, were produced by secretion from genetically engineered strains of Saccharomyces cerevisiae. They have distinct differences in enzymatic characteristics that can be related to the physiology of the germinating rice seed. The rice isozymes were purified with immunoaffinity chromatography. The pH optima for Amy3D (pH optimum 5.5) and Amy1A (pH optimum 4.2) correlate with the pH of the endosperm tissue at the times in rice seedling development when these isozymes are produced. Amy3D showed 10-14 times higher reactivity to oligosaccharides than Amy1A. Amy1A, on the other hand, showed higher reactivity to soluble starch and starch granules than Amy3D. These results suggest that the isozyme Amy3D, which is expressed at an early stage of germination, produces sugars from soluble starch during the early stage of seed germination and that the isozyme Amy1A works to initiate hydrolysis of the starch granules.

Carbohydrate Metabolism↗

Sequence-specific interactions of a nuclear protein factor with the promoter region of a rice gene for alpha-amylase, RAmy3D.

The expression of a rice gene for alpha-amylase, RAmy3D, in suspension-cultured cells is induced at the transcriptional level by the deprivation of sugars. Binding of a nuclear protein from suspension-cultured rice cells to the promoter region of the RAmy3D gene was studied by gel-retardation and DNase I footprinting assays. Gel-retardation assays indicated that a 358-bp fragment of the promoter region interacted specifically with a protein factor from suspension-cultured cells. DNase I footprinting analysis allowed us to define three protein-binding regions. Each of these protein-binding sequences contained the GCCG G/C CG motif, which is specifically present in the promoter region of the sugar-regulated gene, RAmy3D, for rice alpha-amylase and not in that of the gibberellin-regulated RAmy1A gene. Subsequent cross-competition experiments using gel-retardation assay and synthetic oligonucleotides showed that the GCCG G/C CG motifs directly mediated the binding of a nuclear protein. These observations are discussed in relation to expression of the gene for alpha-amylase in suspension-cultured cells.

Base Sequence↗

Metabolic regulation of alpha-amylase gene expression in transgenic cell cultures of rice (Oryza sativa L.).

Expression of two genes in the alpha-amylase gene family is controlled by metabolic regulation in rice cultured cells. The levels of RAmy3D and RAmy3E mRNAs in rice cultured cells are inversely related to the concentration of sugar in the culture medium. Other genes in the rice alpha-amylase gene family have little or no expression in cultured cells; these expression levels are not controlled by metabolic regulation. A RAmy3D promoter/GUS gene fusion was metabolically regulated in the transgenic rice cell line 3DG, just as the endogenous RAmy3D gene is regulated. An assay of GUS enzyme activity in 3DG cells demonstrated that RAmy3D/GUS expression is repressed when sugar is present in the culture medium and induced when sugar is removed from the medium. The 942 bp fragment of the RAmy3D promoter that was linked to the coding region of the GUS reporter gene thus contains all of the regulatory sequences necessary for metabolic regulation of the gene.

Base Sequence↗

Classification and evolution of alpha-amylase genes in plants.

The DNA sequences for 17 plant genes for alpha-amylase (EC 3.2.1.1) were analyzed to determine their phylogenetic relationship. A phylogeny for these genes was obtained using two separate approaches, one based on molecular clock assumptions and the other based on a comparison of sequence polymorphisms (i.e., small and localized insertions) in the alpha-amylase genes. These polymorphisms are called "alpha-amylase signatures" because they are diagnostic of the gene subfamily to which a particular alpha-amylase gene belongs. Results indicate that the cereal alpha-amylase genes fall into two major classes: AmyA and AmyB. The AmyA class is subdivided into the Amy1 and Amy2 subfamilies previously used to classify alpha-amylase genes in barley and wheat. The AmyB class includes the Amy3 subfamily to which most of the alpha-amylase genes of rice belong. Using polymerase chain reaction and oligonucleotide primers that flank one of the two signature regions, we show that the AmyA and AmyB gene classes are present in approximately equal amounts in all grass species examined except barley. The AmyB (Amy3 subfamily) genes in the latter case are comparatively underrepresented. Additional evidence suggests that the AmyA genes appeared recently and may be confined to the grass family.

Base Sequence↗

RAmy2A; a novel alpha-amylase-encoding gene in rice.

The structure and expression of the alpha-amylase-encoding gene, RAmy2A, are described. This only representative of the Amy2 subfamily in rice differs from other cereal alpha-amylase-encoding genes in several respects. It contains the largest introns of all the cereal alpha-amylase-encoding genes examined to date. Moreover, the second of three introns in this gene contains a long inverted repeat sequence that can potentially form a large and stable stem-loop structure in the unspliced RNA transcript. Finally, RAmy2A is constitutively expressed at very low levels in germinated seeds, root, etiolated leaves, immature seeds and callus. This is in marked contrast to the Amy2 genes of wheat and barley which are highly expressed in the aleurone layer of the germinated seeds.

Amino Acid Sequence↗

Structure of a rice beta-glucanase gene regulated by ethylene, cytokinin, wounding, salicylic acid and fungal elicitors.

A rice beta-glucanase gene was sequenced and its expression analyzed at the level of mRNA accumulation. This gene (Gns1) is expressed at relatively low levels in germinating seeds, shoots, leaves, panicles and callus, but it is expressed at higher levels in roots. Expression in the roots appears to be constitutive. Shoots express Gns1 at much higher levels when treated with ethylene, cytokinin, salicylic acid, and fungal elicitors derived from the pathogen Sclerotium oryzae or from the non-pathogen Saccharomyces cereviseae. Shoots also express Gns1 at higher levels in response to wounding. Expression in the shoots is not significantly affected by auxin, gibberellic acid or abscisic acid. The beta-glucanase shows 82% amino acid similarity to the barley 1,3;1,4-beta-D-glucanases, and from hybridization studies it is the beta-glucanase gene in the rice genome closest to the barley 1,3;1,4-beta-glucanase EI gene. The mature peptide has a calculated molecular mass of 32 kDa. The gene has a large 3145 bp intron in the codon for the 25th amino acid of the signal peptide. The gene exhibits a very strong codon bias of 99% G + C in the third position of the codon in the mature peptide coding region, but only 61% G + C in the signal peptide region.

Amino Acid Sequence↗

Metabolic regulation of rice alpha-amylase and sucrose synthase genes in planta.

Isolated rice embryos were used to investigate the regulatory effects of endosperm extracts and pure sugars on the expression of alpha-amylase gene RAmy3D and a sucrose synthase gene homologous to the maize isozyme Ss2. The high-level expression of RAmy3D in the scutella of isolated embryos could be inhibited by a variety of sugars as well as endosperm extracts from germinated rice grains. Glucose, at a concentration of 250 mM, was most effective in repressing RAmy3D mRNA accumulation. Furthermore, this repression was reversible. Interestingly, RAmy3D repression was always accompanied by the induction of sucrose synthase gene expression. These results support a model in which the expression of alpha-amylase and sucrose synthase genes in the rice scutellum are counter-regulated by the influx of sugars from the endosperm.

Animals↗

Differential expression of alpha-amylase genes in germinating rice and barley seeds.

Steady-state levels of mRNA from individual alpha-amylase genes were measured in the embryo and aleurone tissues of rice (Oryza sativa) and two varieties of barley (Hordeum vulgare L. cv. Himalaya and cv. Klages) during germination. Each member of the alpha-amylase multigene families of rice and barley was differentially expressed in each tissue. In rice, alpha-amylase genes displayed tissue-specific expression in which genes RAmy3B, RAmy3C, and RAmy3E were preferentially expressed in the aleurone layer, genes RAmy1A, RAmy1B and RAmy3D were expressed in both the embryo and aleurone, and genes RAmy3A and RAmy2A were not expressed in either tissue. Whenever two or more genes were expressed in any tissue, the rate of mRNA accumulation from each gene was unique. In contrast to rice, barley alpha-amylase gene expression was not tissue-specific. Messenger RNAs encoding low- and high-pI alpha-amylase isozymes were detectable in both the embryo and aleurone and accumulated at different rates in each tissue. In particular, peak levels of mRNA encoding high-pI alpha-amylases always preceded those encoding low-pI alpha-amylases. Two distinct differences in alpha-amylase gene expression were observed between the two barley varieties. Levels of high-pI alpha-amylase mRNA peaked two days earlier in Klages embryos than in Himalaya embryos. Throughout six days of germination, Klages produced three times as much high-pI alpha-amylase mRNA and nearly four times as much low-pI alpha-amylase mRNA than the slower-germinating Himalaya variety.

Blotting, Northern↗

Characterization of an alpha-amylase multigene cluster in rice.

Rice genomic clones containing eight different alpha-amylase genes have been previously classified into five groups based on DNA hybridization studies and restriction site mapping. This report describes the clustering of three Group 3 genes (RAmy3A, RAmy3B and RAmy3C) within 28 kb of genomic DNA. The genes are separated from each other by about 5 kb and transcribed in the same direction. At the protein level, RAmy3B and RAmy3C are 95% homologous while each is 78% homologous to RAmy3A. All three genes have relatively small introns in the first and third positions. RAmy3A; however, has an additional 409 bp intron in the second intron insertion site. Nucleotide sequence comparisons of the coding and 3' flanking regions suggest that clustering of the RAmy3 genes occurred by gene duplication resulting from unequal crossing-over at repetitive sequences. A comparison of the 5' flanking regions revealed several sequences that may be involved in transcription. Expression of RAmy3B/C first appears in the germinating seed after two days and at a higher level after four days. Quantitative primer extension analysis indicates that RAmy3B and RAmy3C contribute 25% and 75%, respectively, of the transcripts from this cluster at four days of germination. No primer extension band specific to RAmy3A transcripts could be detected at this time point. However, RAmy3A PCR products could be amplified from RNA isolated from embryo-derived callus tissue.

Base Sequence↗

Vulvar reconstruction using a pedicle flap based on the superficial external pudendal artery.

We present a new method for vulvar reconstruction based on recently described vasculature of the lower abdominal skin and subcutaneous tissue. The superficial external pudendal artery supplies the region encompassing the suprapubic and infraumbilical skin. Thus, a pedicled skin flap based on the superficial external pudendal artery is designed in the suprapubic area and rotated into place for vulvar reconstruction. Because of the thickness and pliability of the flap as well as the inconspicuous donor scar, we believe this method of reconstruction to be superior to skin grafts or bulkier (ie, musculo- and fasciocutaneous) tissue flaps.

Adult↗