Genes from the medicinal leech (Hirudo medicinalis) coding for unusual enzymes that specifically cleave endo-epsilon (gamma-Glu)-Lys isopeptide bonds and help to dissolve blood clots.

PubMed

Zavalova, L; Lukyanov, S; Baskova, I; Snezhkov, E; Akopov, S; Berezhnoy, S; Bogdanova, E; Barsova, E; Sverdlov, E D

1996-11-27

We previously detected in salivary gland secretions of the medicinal leech (Hirudo medicinalis) a novel enzymatic activity, endo-epsilon(gamma-Glu)-Lys isopeptidase, which cleaves isopeptide bonds formed by transglutaminase (Factor XIIIa) between glutamine gamma-carboxamide and the epsilon-amino group of lysine. Such isopeptide bonds, either within or between protein polypeptide chains are formed in many biological processes. However, before we started our work no enzymes were known to be capable of specifically splitting isopeptide bonds in proteins. The isopeptidase activity we detected was specific for isopeptide bonds. The enzyme was termed destabilase. Here we report the first purification of destabilase, part of its amino acid sequence isolation and sequencing of two related cDNAs derived from the gene family that encodes destabilase proteins, and the detection of isopeptidase activity encoded by one of these cDNAs cloned in a baculovirus expression vector. The deduced mature protein products of these cDNAs contain 115 and 116 amino acid residues, including 14 highly conserved Cys residues, and are formed from precursors containing specific leader peptides. No homologous sequences were found in public databases.

Cre-lox Univector acceptor vectors for functional screening in protoplasts: analysis of Arabidopsis donor cDNAs encoding ABSCISIC ACID INSENSITIVE1-Like protein phosphatases

PubMed Central

Jia, Fan; Gampala, Srinivas S.L.; Mittal, Amandeep; Luo, Qingjun; Rock, Christopher D.

2009-01-01

The 14,200 available full length Arabidopsis thaliana cDNAs in the Universal Plasmid System (UPS) donor vector pUNI51 should be applied broadly and efficiently to leverage a “functional map-space” of homologous plant genes. We have engineered Cre-lox UPS host acceptor vectors (pCR701- 705) with N-terminal epitope tags in frame with the loxH site and downstream from the maize Ubiquitin promoter for use in transient protoplast expression assays and particle bombardment transformation of monocots. As an example of the utility of these vectors, we recombined them with several Arabidopsis cDNAs encoding Ser/Thr protein phosphatase type 2C (PP2Cs) known from genetic studies or predicted by hierarchical clustering meta-analysis to be involved in ABA and stress responses. Our functional results in Zea mays mesophyll protoplasts on ABA-inducible expression effects on the Late Embryogenesis Abundant promoter ProEm:GUS reporter were consistent with predictions and resulted in identification of novel activities of some PP2Cs. Deployment of these vectors can facilitate functional genomics and proteomics and identification of novel gene activities. PMID:19499346

cDNAs for the synthesis of cyclic carotenoids in petals of Gentiana lutea and their regulation during flower development.

PubMed

Zhu, Changfu; Yamamura, Saburo; Nishihara, Masashiro; Koiwa, Hiroyuki; Sandmann, Gerhard

2003-02-20

cDNAs encoding lycopene epsilon -cyclase, lycopene beta-cyclase, beta-carotene hydroxylase and zeaxanthin epoxidase were isolated from a Gentiana lutea petal cDNA library. The function of all cDNAs was analyzed by complementation in Escherichia coli. Transcript levels during different stages of flower development of G. lutea were determined and compared to the carotenoid composition. Expression of all genes increased by a factor of up to 2, with the exception of the lycopene epsilon -cyclase gene. The transcript amount of the latter was strongly decreased. These results indicate that during flower development, carotenoid formation is enhanced. Moreover, metabolites are shifted away from the biosynthetic branch to lutein and are channeled into beta-carotene and derivatives.

Sugarcane giant borer transcriptome analysis and identification of genes related to digestion.

PubMed

Fonseca, Fernando Campos de Assis; Firmino, Alexandre Augusto Pereira; de Macedo, Leonardo Lima Pepino; Coelho, Roberta Ramos; de Souza Júnior, José Dijair Antonino; de Sousa Júnior, José Dijair Antonino; Silva-Junior, Orzenil Bonfim; Togawa, Roberto Coiti; Pappas, Georgios Joannis; de Góis, Luiz Avelar Brandão; da Silva, Maria Cristina Mattar; Grossi-de-Sá, Maria Fátima

2015-01-01

Sugarcane is a widely cultivated plant that serves primarily as a source of sugar and ethanol. Its annual yield can be significantly reduced by the action of several insect pests including the sugarcane giant borer (Telchin licus licus), a lepidopteran that presents a long life cycle and which efforts to control it using pesticides have been inefficient. Although its economical relevance, only a few DNA sequences are available for this species in the GenBank. Pyrosequencing technology was used to investigate the transcriptome of several developmental stages of the insect. To maximize transcript diversity, a pool of total RNA was extracted from whole body insects and used to construct a normalized cDNA database. Sequencing produced over 650,000 reads, which were de novo assembled to generate a reference library of 23,824 contigs. After quality score and annotation, 43% of the contigs had at least one BLAST hit against the NCBI non-redundant database, and 40% showed similarities with the lepidopteran Bombyx mori. In a further analysis, we conducted a comparison with Manduca sexta midgut sequences to identify transcripts of genes involved in digestion. Of these transcripts, many presented an expansion or depletion in gene number, compared to B. mori genome. From the sugarcane giant borer (SGB) transcriptome, a number of aminopeptidase N (APN) cDNAs were characterized based on homology to those reported as Cry toxin receptors. This is the first report that provides a large-scale EST database for the species. Transcriptome analysis will certainly be useful to identify novel developmental genes, to better understand the insect's biology and to guide the development of new strategies for insect-pest control.

Sugarcane genes differentially expressed in response to Puccinia melanocephala infection: identification and transcript profiling.

PubMed

Oloriz, María I; Gil, Víctor; Rojas, Luis; Portal, Orelvis; Izquierdo, Yovanny; Jiménez, Elio; Höfte, Monica

2012-05-01

Brown rust caused by the fungus Puccinia melanocephala is a major disease of sugarcane (Saccharum spp.). A sugarcane mutant, obtained by chemical mutagenesis of the susceptible variety B4362, showed a post-haustorial hypersensitive response (HR)-mediated resistance to the pathogen and was used to identify genes differentially expressed in response to P. melanocephala via suppression subtractive hybridization (SSH). Tester cDNA was derived from the brown rust-resistant mutant after inoculation with P. melanocephala, while driver cDNAs were obtained from the non-inoculated resistant mutant and the inoculated susceptible donor variety B4362. Database comparisons of the sequences of the SSH recombinant clones revealed that, of a subset of 89 non-redundant sequences, 88% had similarity to known functional genes, while 12% were of unknown function. Thirteen genes were selected for transcript profiling in the resistant mutant and the susceptible donor variety. Genes involved in glycolysis and C4 carbon fixation were up-regulated in both interactions probably due to disturbance of sugarcane carbon metabolism by the pathogen. Genes related with the nascent polypeptide associated complex, post-translational proteome modulation and autophagy were transcribed at higher levels in the compatible interaction. Up-regulation of a putative L-isoaspartyl O-methyltransferase S-adenosylmethionine gene in the compatible interaction may point to fungal manipulation of the cytoplasmatic methionine cycle. Genes coding for a putative no apical meristem protein, S-adenosylmethionine decarboxylase, non-specific lipid transfer protein, and GDP-L-galactose phosphorylase involved in ascorbic acid biosynthesis were up-regulated in the incompatible interaction at the onset of haustorium formation, and may contribute to the HR-mediated defense response in the rust-resistant mutant.

Sugarcane Giant Borer Transcriptome Analysis and Identification of Genes Related to Digestion

PubMed Central

de Assis Fonseca, Fernando Campos; Firmino, Alexandre Augusto Pereira; de Macedo, Leonardo Lima Pepino; Coelho, Roberta Ramos; de Sousa Júnior, José Dijair Antonino; Silva-Junior, Orzenil Bonfim; Togawa, Roberto Coiti; Pappas, Georgios Joannis; de Góis, Luiz Avelar Brandão; da Silva, Maria Cristina Mattar; Grossi-de-Sá, Maria Fátima

2015-01-01

Sugarcane is a widely cultivated plant that serves primarily as a source of sugar and ethanol. Its annual yield can be significantly reduced by the action of several insect pests including the sugarcane giant borer (Telchin licus licus), a lepidopteran that presents a long life cycle and which efforts to control it using pesticides have been inefficient. Although its economical relevance, only a few DNA sequences are available for this species in the GenBank. Pyrosequencing technology was used to investigate the transcriptome of several developmental stages of the insect. To maximize transcript diversity, a pool of total RNA was extracted from whole body insects and used to construct a normalized cDNA database. Sequencing produced over 650,000 reads, which were de novo assembled to generate a reference library of 23,824 contigs. After quality score and annotation, 43% of the contigs had at least one BLAST hit against the NCBI non-redundant database, and 40% showed similarities with the lepidopteran Bombyx mori. In a further analysis, we conducted a comparison with Manduca sexta midgut sequences to identify transcripts of genes involved in digestion. Of these transcripts, many presented an expansion or depletion in gene number, compared to B. mori genome. From the sugarcane giant borer (SGB) transcriptome, a number of aminopeptidase N (APN) cDNAs were characterized based on homology to those reported as Cry toxin receptors. This is the first report that provides a large-scale EST database for the species. Transcriptome analysis will certainly be useful to identify novel developmental genes, to better understand the insect’s biology and to guide the development of new strategies for insect-pest control. PMID:25706301

Cloning and characterization of cDNAs encoding human gastrin-releasing peptide.

PubMed Central

Spindel, E R; Chin, W W; Price, J; Rees, L H; Besser, G M; Habener, J F

1984-01-01

We have prepared and cloned cDNAs derived from poly(A)+ RNA from a human pulmonary carcinoid tumor rich in immunoreactivity to gastrin-releasing peptide, a peptide closely related in structure to amphibian bombesin. Mixtures of synthetic oligodeoxyribonucleotides corresponding to amphibian bombesin were used as hybridization probes to screen a cDNA library prepared from the tumor RNA. Sequencing of the recombinant plasmids shows that human gastrin-releasing peptide (hGRP) mRNA encodes a precursor of 148 amino acids containing a typical signal sequence, hGRP consisting of 27 or 28 amino acids, and a carboxyl-terminal extension peptide. hGRP is flanked at its carboxyl terminus by two basic amino acids, following a glycine used for amidation of the carboxyl-terminal methionine. RNA blot analyses of tumor RNA show a major mRNA of 900 bases and a minor mRNA of 850 bases. Blot hybridization analyses using human genomic DNA are consistent with a single hGRP-encoding gene. The presence of two mRNAs encoding the hGRP precursor protein in the face of a single hGRP gene raises the possibility of alternative processing of the single RNA transcript. Images PMID:6207529

De novo transcriptome sequencing in Bixa orellana to identify genes involved in methylerythritol phosphate, carotenoid and bixin biosynthesis

DOE PAGES

Cárdenas-Conejo, Yair; Carballo-Uicab, Víctor; Lieberman, Meric; ...

2015-10-28

Bixin or annatto is a commercially important natural orange-red pigment derived from lycopene that is produced and stored in seeds of Bixa orellana L. An enzymatic pathway for bixin biosynthesis was inferred from homology of putative proteins encoded by differentially expressed seed cDNAs. Some activities were later validated in a heterologous system. Nevertheless, much of the pathway remains to be clarified. For example, it is essential to identify the methylerythritol phosphate (MEP) and carotenoid pathways genes. In order to investigate the MEP, carotenoid, and bixin pathways genes, total RNA from young leaves and two different developmental stages of seeds frommore » B. orellana were used for the construction of indexed mRNA libraries, sequenced on the Illumina HiSeq 2500 platform and assembled de novo using Velvet, CLC Genomics Workbench and CAP3 software. A total of 52,549 contigs were obtained with average length of 1,924 bp. Two phylogenetic analyses of inferred proteins, in one case encoded by thirteen general, single-copy cDNAs, in the other from carotenoid and MEP cDNAs, indicated that B. orellana is closely related to sister Malvales species cacao and cotton. Using homology, we identified 7 and 14 core gene products from the MEP and carotenoid pathways, respectively. Surprisingly, previously defined bixin pathway cDNAs were not present in our transcriptome. Here we propose a new set of gene products involved in bixin pathway. In conclusion, the identification and qRT-PCR quantification of cDNAs involved in annatto production suggest a hypothetical model for bixin biosynthesis that involve coordinated activation of some MEP, carotenoid and bixin pathway genes. These findings provide a better understanding of the mechanisms regulating these pathways and will facilitate the genetic improvement of B. orellana.« less

De novo transcriptome sequencing in Bixa orellana to identify genes involved in methylerythritol phosphate, carotenoid and bixin biosynthesis

DOE Office of Scientific and Technical Information (OSTI.GOV)

Cárdenas-Conejo, Yair; Carballo-Uicab, Víctor; Lieberman, Meric

Bixin or annatto is a commercially important natural orange-red pigment derived from lycopene that is produced and stored in seeds of Bixa orellana L. An enzymatic pathway for bixin biosynthesis was inferred from homology of putative proteins encoded by differentially expressed seed cDNAs. Some activities were later validated in a heterologous system. Nevertheless, much of the pathway remains to be clarified. For example, it is essential to identify the methylerythritol phosphate (MEP) and carotenoid pathways genes. In order to investigate the MEP, carotenoid, and bixin pathways genes, total RNA from young leaves and two different developmental stages of seeds frommore » B. orellana were used for the construction of indexed mRNA libraries, sequenced on the Illumina HiSeq 2500 platform and assembled de novo using Velvet, CLC Genomics Workbench and CAP3 software. A total of 52,549 contigs were obtained with average length of 1,924 bp. Two phylogenetic analyses of inferred proteins, in one case encoded by thirteen general, single-copy cDNAs, in the other from carotenoid and MEP cDNAs, indicated that B. orellana is closely related to sister Malvales species cacao and cotton. Using homology, we identified 7 and 14 core gene products from the MEP and carotenoid pathways, respectively. Surprisingly, previously defined bixin pathway cDNAs were not present in our transcriptome. Here we propose a new set of gene products involved in bixin pathway. In conclusion, the identification and qRT-PCR quantification of cDNAs involved in annatto production suggest a hypothetical model for bixin biosynthesis that involve coordinated activation of some MEP, carotenoid and bixin pathway genes. These findings provide a better understanding of the mechanisms regulating these pathways and will facilitate the genetic improvement of B. orellana.« less

Identification of drought-response genes and a study of their expression during sucrose accumulation and water deficit in sugarcane culms.

PubMed

Iskandar, Hayati M; Casu, Rosanne E; Fletcher, Andrew T; Schmidt, Susanne; Xu, Jingsheng; Maclean, Donald J; Manners, John M; Bonnett, Graham D

2011-01-13

The ability of sugarcane to accumulate high concentrations of sucrose in its culm requires adaptation to maintain cellular function under the high solute load. We have investigated the expression of 51 genes implicated in abiotic stress to determine their expression in the context of sucrose accumulation by studying mature and immature culm internodes of a high sucrose accumulating sugarcane cultivar. Using a sub-set of eight genes, expression was examined in mature internode tissues of sugarcane cultivars as well as ancestral and more widely related species with a range of sucrose contents. Expression of these genes was also analysed in internode tissue from a high sucrose cultivar undergoing water deficit stress to compare effects of sucrose accumulation and water deficit. A sub-set of stress-related genes that are potentially associated with sucrose accumulation in sugarcane culms was identified through correlation analysis, and these included genes encoding enzymes involved in amino acid metabolism, a sugar transporter and a transcription factor. Subsequent analysis of the expression of these stress-response genes in sugarcane plants that were under water deficit stress revealed a different transcriptional profile to that which correlated with sucrose accumulation. For example, genes with homology to late embryogenesis abundant-related proteins and dehydrin were strongly induced under water deficit but this did not correlate with sucrose content. The expression of genes encoding proline biosynthesis was associated with both sucrose accumulation and water deficit, but amino acid analysis indicated that proline was negatively correlated with sucrose concentration, and whilst total amino acid concentrations increased about seven-fold under water deficit, the relatively low concentration of proline suggested that it had no osmoprotectant role in sugarcane culms. The results show that while there was a change in stress-related gene expression associated with sucrose accumulation, different mechanisms are responding to the stress induced by water deficit, because different genes had altered expression under water deficit.

Identification of drought-response genes and a study of their expression during sucrose accumulation and water deficit in sugarcane culms

PubMed Central

2011-01-01

Background The ability of sugarcane to accumulate high concentrations of sucrose in its culm requires adaptation to maintain cellular function under the high solute load. We have investigated the expression of 51 genes implicated in abiotic stress to determine their expression in the context of sucrose accumulation by studying mature and immature culm internodes of a high sucrose accumulating sugarcane cultivar. Using a sub-set of eight genes, expression was examined in mature internode tissues of sugarcane cultivars as well as ancestral and more widely related species with a range of sucrose contents. Expression of these genes was also analysed in internode tissue from a high sucrose cultivar undergoing water deficit stress to compare effects of sucrose accumulation and water deficit. Results A sub-set of stress-related genes that are potentially associated with sucrose accumulation in sugarcane culms was identified through correlation analysis, and these included genes encoding enzymes involved in amino acid metabolism, a sugar transporter and a transcription factor. Subsequent analysis of the expression of these stress-response genes in sugarcane plants that were under water deficit stress revealed a different transcriptional profile to that which correlated with sucrose accumulation. For example, genes with homology to late embryogenesis abundant-related proteins and dehydrin were strongly induced under water deficit but this did not correlate with sucrose content. The expression of genes encoding proline biosynthesis was associated with both sucrose accumulation and water deficit, but amino acid analysis indicated that proline was negatively correlated with sucrose concentration, and whilst total amino acid concentrations increased about seven-fold under water deficit, the relatively low concentration of proline suggested that it had no osmoprotectant role in sugarcane culms. Conclusions The results show that while there was a change in stress-related gene expression associated with sucrose accumulation, different mechanisms are responding to the stress induced by water deficit, because different genes had altered expression under water deficit. PMID:21226964

cDNAs encoding [D-Ala2]deltorphin precursors from skin of Phyllomedusa bicolor also contain genetic information for three dermorphin-related opioid peptides.

PubMed

Richter, K; Egger, R; Negri, L; Corsi, R; Severini, C; Kreil, G

1990-06-01

We present the structure of four precursors for [D-Ala2]deltorphins I and II as deduced from cDNAs cloned from skin of the frog Phyllomedusa bicolor. These contain the genetic information for one copy of [D-Ala2]deltorphin II and zero, one, or three copies of [D-Ala2]deltorphin I. In each case, the D-alanine of the end product is encoded by a normal GCG codon for L-alanine. In addition, the existence of three peptides related to dermorphin was predicted from the amino acid sequence of the precursors. These peptides were synthesized with a D-alanine in position 2 and their pharmacological properties were tested. Two of them, [Lys7]dermorphin-OH and [Trp4,Asn7]dermorphin-OH, were found to have roughly the same affinity and selectivity for mu-type opioid receptors as dermorphin.

cDNAs encoding [D-Ala2]deltorphin precursors from skin of Phyllomedusa bicolor also contain genetic information for three dermorphin-related opioid peptides.

PubMed Central

Richter, K; Egger, R; Negri, L; Corsi, R; Severini, C; Kreil, G

1990-01-01

We present the structure of four precursors for [D-Ala2]deltorphins I and II as deduced from cDNAs cloned from skin of the frog Phyllomedusa bicolor. These contain the genetic information for one copy of [D-Ala2]deltorphin II and zero, one, or three copies of [D-Ala2]deltorphin I. In each case, the D-alanine of the end product is encoded by a normal GCG codon for L-alanine. In addition, the existence of three peptides related to dermorphin was predicted from the amino acid sequence of the precursors. These peptides were synthesized with a D-alanine in position 2 and their pharmacological properties were tested. Two of them, [Lys7]dermorphin-OH and [Trp4,Asn7]dermorphin-OH, were found to have roughly the same affinity and selectivity for mu-type opioid receptors as dermorphin. PMID:2352951

Molecular Characterization of Tomato 3-Dehydroquinate Dehydratase-Shikimate:NADP Oxidoreductase1

PubMed Central

Bischoff, Markus; Schaller, Andreas; Bieri, Fabian; Kessler, Felix; Amrhein, Nikolaus; Schmid, Jürg

2001-01-01

Analysis of cDNAs encoding the bifunctional 3-dehydroquinate dehydratase-shikimate:NADP oxidoreductase (DHQase-SORase) from tomato (Lycopersicon esculentum) revealed two classes of cDNAs that differed by 57 bp within the coding regions, but were otherwise identical. Comparison of these cDNA sequences with the sequence of the corresponding single gene unequivocally proved that the primary transcript is differentially spliced, potentially giving rise to two polypeptides that differ by 19 amino acids. Quantitative real-time polymerase chain reaction revealed that the longer transcript constitutes at most 1% to 2% of DHQase-SORase transcripts. Expression of the respective polypeptides in Escherichia coli mutants lacking the DHQase or the SORase activity gave functional complementation only in case of the shorter polypeptide, indicating that skipping of a potential exon is a prerequisite for the production of an enzymatically active protein. The deduced amino acid sequence revealed that the DHQase-SORase is most likely synthesized as a precursor with a very short (13-amino acid) plastid-specific transit peptide. Like other genes encoding enzymes of the prechorismate pathway in tomato, this gene is elicitor-inducible. Tissue-specific expression resembles the patterns obtained for 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase 2 and dehydroquinate synthase genes. This work completes our studies of the prechorismate pathway in that cDNAs for all seven enzymes (including isozymes) of the prechorismate pathway from tomato have now been characterized. PMID:11299368

Complementary DNA sequencing and identification of mRNAs from the venomous gland of Agkistrodon piscivorus leucostoma.

PubMed

Jia, Ying; Cantu, Bruno A; Sánchez, Elda E; Pérez, John C

2008-06-15

To advance our knowledge on the snake venom composition and transcripts expressed in venom gland at the molecular level, we constructed a cDNA library from the venom gland of Agkistrodon piscivorus leucostoma for the generation of expressed sequence tags (ESTs) database. From the randomly sequenced 2112 independent clones, we have obtained ESTs for 1309 (62%) cDNAs, which showed significant deduced amino acid sequence similarity (scores >80) to previously characterized proteins in National Center for Biotechnology Information (NCBI) database. Ribosomal proteins make up 47 clones (2%) and the remaining 756 (36%) cDNAs represent either unknown identity or show BLASTX sequence identity scores of <80 with known GenBank accessions. The most highly expressed gene encoding phospholipase A(2) (PLA(2)) accounting for 35% of A. p. leucostoma venom gland cDNAs was identified and further confirmed by crude venom applied to sodium dodecyl sulfate/polyacrylamide gel electrophoresis (SDS-PAGE) electrophoresis and protein sequencing. A total of 180 representative genes were obtained from the sequence assemblies and deposited to EST database. Clones showing sequence identity to disintegrins, thrombin-like enzymes, hemorrhagic toxins, fibrinogen clotting inhibitors and plasminogen activators were also identified in our EST database. These data can be used to develop a research program that will help us identify genes encoding proteins that are of medical importance or proteins involved in the mechanisms of the toxin venom.

Gaucher disease: Pseudoreversion of a disease mutation`s effects--implications for structure/function and genotype/phenotype correlations

DOE Office of Scientific and Technical Information (OSTI.GOV)

Ponce, E.; Mear, J; Grabowski, G.A.

1994-09-01

Numerous mutations ({approximately}45) of the acid {beta}-glucosidase gene have been identified in patients with Gaucher disease. Many of these have been characterized by partial sequencing of cDNAs derived by RT-PCR or PCR of genomic DNA. In addition, genotype/phenotype correlations have been based on screening for known mutations. Thus, only a part of the gene is characterized in any population of affected patients. Several Gaucher disease alleles contain multiple, authentic point mutations that raises concern about conclusions based on only partial genetic characterization. Several wild-type cDNAs for acid {beta}-glucosidase have been sequenced. One contained a cloning artifact encoding R495H. We expressedmore » this cDNA and showed that the R495H enzyme had normal kinetic and stability properties. A disease-associated allele encoding R496H has been found by several groups. The close association and similarities of these two substitutions led us to question the disease casuality of the R496H allele. To evaluate this, we created and/or expressed cDNAs encoding R495, R496 (wild-type), (R495H, R496), (R495, R496H) and (R495H, R496H). The (wild-type) and (R495H, R496) enzymes had indistinguishable properties whereas the (R495, R496H) enzyme was essentially inactive. The introduction of both mutations (R495H, R496H) produced an enzyme whose activity was 25 to 50% of the wild-type. These results indicate that a pseudoreversion to a functional enzyme can occur by introducing a functionally neutral mutation together with a severe mutation. These results have major implications to structure/function and genotype/phenotype correlations in this disease.« less

Accumulation of Rutin and Betulinic Acid and Expression of Phenylpropanoid and Triterpenoid Biosynthetic Genes in Mulberry (Morus alba L.).

PubMed

Zhao, Shicheng; Park, Chang Ha; Li, Xiaohua; Kim, Yeon Bok; Yang, Jingli; Sung, Gyoo Byung; Park, Nam Il; Kim, Soonok; Park, Sang Un

2015-09-30

Mulberry (Morus alba L.) is used in traditional Chinese medicine and is the sole food source of the silkworm. Here, 21 cDNAs encoding phenylpropanoid biosynthetic genes and 21 cDNAs encoding triterpene biosynthetic genes were isolated from mulberry. The expression levels of genes involved in these biosynthetic pathways and the accumulation of rutin, betulin, and betulinic acid, important secondary metabolites, were investigated in different plant organs. Most phenylpropanoid and triterpene biosynthetic genes were highly expressed in leaves and/or fruit, and most genes were downregulated during fruit ripening. The accumulation of rutin was more than fivefold higher in leaves than in other organs, and higher levels of betulin and betulinic acid were found in roots and leaves than in fruit. By comparing the contents of these compounds with gene expression levels, we speculate that MaUGT78D1 and MaLUS play important regulatory roles in the rutin and betulin biosynthetic pathways.

Molecular mechanism for cadmium-induced anthocyanin accumulation in Azolla imbricata.

PubMed

Dai, Ling-Peng; Dong, Xin-Jiao; Ma, Hai-Hu

2012-04-01

Anthocyanins inducibly synthesized by Cd treatment showed high antioxidant activity and might be involved in internal detoxification mechanisms of Azolla imbricata against Cd toxicity. In order to understand anthocyanin biosynthesis mechanism during Cd stress, the cDNAs encoding chalcone synthase (CHS) and dihydroflavonol reductase (DFR), two key enzymes in the anthocyanin synthesis pathway, were isolated from A. imbricata. Deduced amino acid sequences of the cDNAs showed high homology to the sequences from other plants. Expression of AiDFR, and to a lesser extent AiCHS, was significantly induced in Cd treatment plant in comparison with the control. CHS and DFR enzymatic activities showed similar pattern changes with these genes expression during Cd stress. These results strongly indicate that Cd induced anthocyanin accumulation is probably mediated by up-regulation of structural genes including CHS and DFR, which might further increase the activities of enzymes encoded by these structural genes that control the anthocyanin biosynthetic steps. Copyright © 2011 Elsevier Ltd. All rights reserved.

Novel transcripts of the estrogen receptor α gene in channel catfish

USGS Publications Warehouse

Patino, Reynaldo; Xia, Zhenfang; Gale, William L.; Wu, Chunfa; Maule, Alec G.; Chang, Xiaotian

2000-01-01

Complementary DNA libraries from liver and ovary of an immature female channel catfish were screened with a homologous ERα cDNA probe. The hepatic library yielded two new channel catfish ER cDNAs that encode N-terminal ERα variants of different sizes. Relative to the catfish ERα (medium size; 581 residues) previously reported, these new cDNAs encode Long-ERα (36 residues longer) and Short-ERα (389 residues shorter). The 5′-end of Long-ERα cDNA is identical to that of Medium-ERα but has an additional 503-bp segment with an upstream, in-frame translation-start codon. Recombinant Long-ERα binds estrogen with high affinity (Kd = 3.4 nM), similar to that previously reported for Medium-ERα but lower than reported for catfish ERβ. Short-ERα cDNA encodes a protein that lacks most of the receptor protein and does not bind estrogen. Northern hybridization confirmed the existence of multiple hepatic ERα RNAs that include the size range of the ERα cDNAs obtained from the libraries as well as additional sizes. Using primers for RT-PCR that target locations internal to the protein-coding sequence, we also established the presence of several ERα cDNA variants with in-frame insertions in the ligand-binding and DNA-binding domains and in-frame or out-of-frame deletions in the ligand-binding domain. These internal variants showed patterns of expression that differed between the ovary and liver. Further, the ovarian library yielded a full-length, ERα antisense cDNA containing a poly(A) signal and tail. A limited survey of histological preparations from juvenile catfish by in situ hybridization using directionally synthesized cRNA probes also suggested the expression of ERα antisense RNA in a tissue-specific manner. In conclusion, channel catfish seemingly have three broad classes of ERα mRNA variants: those encoding N-terminal truncated variants, those encoding internal variants (including C-terminal truncated variants), and antisense mRNA. The sense variants may encode functional ERα or related proteins that modulate ERα or ERβ activity. The existence of ER antisense mRNA is reported in this study for the first time. Its role may be to participate in the regulation of ER gene expression.

Dermatoxin and phylloxin from the waxy monkey frog, Phyllomedusa sauvagei: cloning of precursor cDNAs and structural characterization from lyophilized skin secretion.

PubMed

Chen, Tianbao; Walker, Brian; Zhou, Mei; Shaw, Chris

2005-07-15

Amphibian skin is a morphologically, biochemically and physiologically complex organ that performs the wide range of functions necessary for amphibian survival. Here we describe the primary structures of representatives of two novel classes of amphibian skin antimicrobials, dermatoxin and phylloxin, from the skin secretion of Phyllomedusa sauvagei, deduced from their respective precursor encoding cDNAs cloned from a lyophilized skin secretion library. A degenerate primer, designed to a highly conserved domain in the 5'-untranslated region of analogous peptide precursor cDNAs from Phyllomedusa bicolor, was employed in a 3'-RACE reaction. Peptides with molecular masses coincident with precursor-deduced mature toxin peptides were identified in LC/MS fractions of skin secretion and primary structures were confirmed by MS/MS fragmentation. This integrated experimental approach can thus rapidly expedite the primary structural characterization of amphibian skin peptides in a manner that circumvents specimen sacrifice whilst preserving robustness of scientific data.

Functional domains of the poliovirus receptor

DOE Office of Scientific and Technical Information (OSTI.GOV)

Koike, Satoshi; Ise, Iku; Nomoto, Akio

1991-05-15

A number of mutant cDNAs of the human poliovirus receptor were constructed to identify essential regions of the molecule as the receptor. All mutant cDNAs carrying the sequence coding for the entire N-terminal immunoglobulin-like domain (domain I) confer permissiveness for poliovirus to mouse L cells, but a mutant cDNA lacking the sequence for domain I does not. The transformants permissive for poliovirus were able to bind the virus and were also recognized by monoclonal antibody D171, which competes with poliovirus for the cellular receptor. These results strongly suggest that the poliovirus binding site resides in domain I of the receptor.more » Mutant cDNAs for the sequence encoding the intracellular peptide were also constructed and expressed in mouse L cells. Susceptibility of these cells to poliovirus revealed that the entire putative cytoplasmic domain is not essential for virus infection. Thus, the cytoplasmic domain of the molecule appears not to play a role in the penetration of poliovirus.« less

LIFEdb: a database for functional genomics experiments integrating information from external sources, and serving as a sample tracking system

PubMed Central

Bannasch, Detlev; Mehrle, Alexander; Glatting, Karl-Heinz; Pepperkok, Rainer; Poustka, Annemarie; Wiemann, Stefan

2004-01-01

We have implemented LIFEdb (http://www.dkfz.de/LIFEdb) to link information regarding novel human full-length cDNAs generated and sequenced by the German cDNA Consortium with functional information on the encoded proteins produced in functional genomics and proteomics approaches. The database also serves as a sample-tracking system to manage the process from cDNA to experimental read-out and data interpretation. A web interface enables the scientific community to explore and visualize features of the annotated cDNAs and ORFs combined with experimental results, and thus helps to unravel new features of proteins with as yet unknown functions. PMID:14681468

Cloning of cDNAs encoding new peptides of the dermaseptin-family.

PubMed

Wechselberger, C

1998-10-14

Dermaseptins are a group of basic (lysine-rich) peptides, 27-34 amino acids in length and involved in the defense of frog skin against microbial invasion. By using a degenerated oligonucleotide primer binding to the 5'-untranslated region of previously characterized cDNAs of these peptides, it was possible to identify new members of the dermaseptin family in the South American frogs Agalychnis annae and Pachymedusa dacnicolor. Amino acid alignment and secondary structure prediction reveals, that only five of the deduced peptides can be supposed to be also functional homologs to the known dermaseptins from Phyllomedusa bicolor and Phyllomedusa sauvagei. The remaining six peptides described in this paper have not been isolated and characterized yet.

Production of Fatty Acid Components of Meadowfoam Oil in Somatic Soybean Embryos

PubMed Central

Cahoon, Edgar B.; Marillia, Elizabeth-France; Stecca, Kevin L.; Hall, Sarah E.; Taylor, David C.; Kinney, Anthony J.

2000-01-01

The seed oil of meadowfoam (Limnanthes alba) and other Limnanthes spp. is enriched in the unusual fatty acid Δ5-eicosenoic acid (20:1Δ5). This fatty acid has physical and chemical properties that make the seed oil of these plants useful for a number of industrial applications. An expressed sequence tag approach was used to identify cDNAs for enzymes involved in the biosynthesis of 20:1Δ5). By random sequencing of a library prepared from developing Limnanthes douglasii seeds, a class of cDNAs was identified that encode a homolog of acyl-coenzyme A (CoA) desaturases found in animals, fungi, and cyanobacteria. Expression of a cDNA for the L. douglasii acyl-CoA desaturase homolog in somatic soybean (Glycine max) embryos behind a strong seed-specific promoter resulted in the accumulation of Δ5-hexadecenoic acid to amounts of 2% to 3% (w/w) of the total fatty acids of single embryos. Δ5-Octadecenoic acid and 20:1Δ5 also composed <1% (w/w) each of the total fatty acids of these embryos. In addition, cDNAs were identified from the L. douglasii expressed sequence tags that encode a homolog of fatty acid elongase 1 (FAE1), a β-ketoacyl-CoA synthase that catalyzes the initial step of very long-chain fatty acid synthesis. Expression of the L. douglassi FAE1 homolog in somatic soybean embryos was accompanied by the accumulation of C20 and C22 fatty acids, principally as eicosanoic acid, to amounts of 18% (w/w) of the total fatty acids of single embryos. To partially reconstruct the biosynthetic pathway of 20:1Δ5 in transgenic plant tissues, cDNAs for the L. douglasii acyl-CoA desaturase and FAE1 were co-expressed in somatic soybean embryos. In the resulting transgenic embryos, 20:1Δ5 and Δ5-docosenoic acid composed up to 12% of the total fatty acids. PMID:10982439

Production of fatty acid components of meadowfoam oil in somatic soybean embryos.

PubMed

Cahoon, E B; Marillia, E F; Stecca, K L; Hall, S E; Taylor, D C; Kinney, A J

2000-09-01

The seed oil of meadowfoam (Limnanthes alba) and other Limnanthes spp. is enriched in the unusual fatty acid Delta(5)-eicosenoic acid (20:1Delta(5)). This fatty acid has physical and chemical properties that make the seed oil of these plants useful for a number of industrial applications. An expressed sequence tag approach was used to identify cDNAs for enzymes involved in the biosynthesis of 20:1Delta(5)). By random sequencing of a library prepared from developing Limnanthes douglasii seeds, a class of cDNAs was identified that encode a homolog of acyl-coenzyme A (CoA) desaturases found in animals, fungi, and cyanobacteria. Expression of a cDNA for the L. douglasii acyl-CoA desaturase homolog in somatic soybean (Glycine max) embryos behind a strong seed-specific promoter resulted in the accumulation of Delta(5)-hexadecenoic acid to amounts of 2% to 3% (w/w) of the total fatty acids of single embryos. Delta(5)-Octadecenoic acid and 20:1Delta(5) also composed <1% (w/w) each of the total fatty acids of these embryos. In addition, cDNAs were identified from the L. douglasii expressed sequence tags that encode a homolog of fatty acid elongase 1 (FAE1), a beta-ketoacyl-CoA synthase that catalyzes the initial step of very long-chain fatty acid synthesis. Expression of the L. douglassi FAE1 homolog in somatic soybean embryos was accompanied by the accumulation of C(20) and C(22) fatty acids, principally as eicosanoic acid, to amounts of 18% (w/w) of the total fatty acids of single embryos. To partially reconstruct the biosynthetic pathway of 20:1Delta(5) in transgenic plant tissues, cDNAs for the L. douglasii acyl-CoA desaturase and FAE1 were co-expressed in somatic soybean embryos. In the resulting transgenic embryos, 20:1Delta(5) and Delta(5)-docosenoic acid composed up to 12% of the total fatty acids.

Molecular characterization of genes encoding inward rectifier potassium (Kir) channels in the bed bug (Cimex lectularius).

PubMed

Mamidala, Praveen; Mittapelly, Priyanka; Jones, Susan C; Piermarini, Peter M; Mittapalli, Omprakash

2013-04-01

The molecular genetics of inward-rectifier potassium (Kir) channels in insects is poorly understood. To date, Kir channel genes have been characterized only from a few representative dipterans (i.e., fruit flies and mosquitoes). The goal of the present study was to characterize Kir channel cDNAs in a hemipteran, the bed bug (Cimex lectularius). Using our previously reported bed bug transcriptome (RNA-seq), we identified two cDNAs that encode putative Kir channels. One was a full-length cDNA that encodes a protein belonging to the insect 'Kir3' clade, which we designate as 'ClKir3'. The other was a partial cDNA that encodes a protein with similarity to both the insect 'Kir1' and 'Kir2' clades, which we designate as 'ClKir1/2'. Quantitative real-time PCR analysis revealed that ClKir1/2 and ClKir3 exhibited peak expression levels in late-instar nymphs and early-instar nymphs, respectively. Furthermore, ClKir3, but not ClKir1/2, showed tissue-specific expression in Malpighian tubules of adult bed bugs. Lastly, using an improved procedure for delivering double-stranded RNA (dsRNA) to male and female bed bugs (via the cervical membrane) we demonstrate rapid and systemic knockdown of ClKir3 transcripts. In conclusion, we demonstrate that the bed bug possesses at least two genes encoding Kir channels, and that RNAi is possible for at least Kir3, thereby offering a potential approach for elucidating the roles of Kir channel genes in bed bug physiology. Copyright © 2013 Elsevier Inc. All rights reserved.

Identification and characterization of TCRgamma and TCRdelta chains in channel catfish, Ictalurus punctatus

USDA-ARS?s Scientific Manuscript database

Channel catfish, Ictalurus punctatus, T cell receptors (TCR) gamma and delta were identified by mining of expressed sequence tag databases and full length sequences were obtained by 5'-RACE and RT-PCR protocols. cDNAs for each of these TCR chains encode typical variable (V), (diversity; D), joining ...

Functional relevance of three proopiomelanocortin (POMC) genes in darkening camouflage, blind-side hypermelanosis, and appetite of Paralichthys olivaceus.

PubMed

Kang, Duk-Young; Kim, Hyo-Chan

2015-01-01

To determine whether proopiomelanocortin (POMC) genes are involved in darkening color camouflage, blind-side hypermelanosis, and appetite in flatfish, we isolated and cloned three POMC genes from the pituitary of the olive flounder (Paralichthys olivaceus) and compared their amino acid (aa) structures to those of POMC genes from other animals. Next, we examined the relationship of these pituitary POMC genes to camouflage color change, blind-side hypermelanosis, and appetite by quantifying mRNA expression. Olive flounder (of)-POMC1, 2, and 3 cDNAs consisted of 648-bp, 582-bp, and 693-bp open reading frames (ORF) encoding 216 aa, 194 aa, and 231 aa residues, respectively. Structurally, the three of-POMC cDNAs consisted of seven peptides (signal peptide, N-POMC, α-MSH, CLIP, N-β-LPH, β-MSH and β-END [or END-like peptide]) that are similar to those of other fish POMC cDNAs. α-MSH encoded a protein composed of 13 aa and β-MSH encoded a protein composed of 17 aa. The three POMC genes were predominantly expressed in the pituitary gland, but they were also expressed in a variety of tissues, including brain, eye, kidney, heart, testis, and skin. of-POMC2 exhibited the highest expression, while of-POMC3 displayed the lowest expression. The relative levels of of-POMC1 and 3 mRNAs were not influenced by background color and feeding (or fasting), but the relative level of of-POMC2 mRNA significantly increased in response to a dark background and fasting. The relative levels of of-POMC1 and 2 mRNAs were significantly higher in hypermelanic fish; however, we did not determine a direct anorexigenic or orexigenic relationship for the three POMC genes. These results indicate that pituitary POMC genes are related to darkening color change and the differentiation of pigment cells, but they are not directly related to appetite. Copyright © 2014 Elsevier Inc. All rights reserved.

Construction and analysis of cDNA libraries from the antennae of Batocera horsfieldi and expression pattern of putative odorant binding proteins

USDA-ARS?s Scientific Manuscript database

In the natural environment, the longhorned beetle, Batocera horsfieldi (Hope) (Coleoptera: Cerambycidae), finds it’s maturation-feeding and host plants by using chemical cues. In this study, we described the identification and characterization of four new cDNAs that encode Minus-C odorant binding pr...

Molecular cloning of skin peptide precursor-encoding cDNAs from tibial gland secretion of the Giant Monkey Frog, Phyllomedusa bicolor (Hylidae, Anura).

PubMed

König, Enrico; Clark, Valerie C; Shaw, Chris; Bininda-Emonds, Olaf R P

2012-12-01

The skins of phyllomedusine frogs have long been considered as being tremendously rich sources of bioactive peptides. Previous studies of both peptides and cloning of their precursor encoding cDNAs have relied upon methanolic skin extracts or the dissected skins of recently deceased specimens and have not considered the different glands in isolation. We therefore focused our attention on the tibial gland of the Giant Monkey Frog, Phyllomedusa bicolor and constructed a cDNA library from the skin secretion that was obtained via mechanical stimulation of this macrogland. Using shotgun cloning, four precursors encoding host-defense peptides were identified: two archetypal dermaseptins, a phyllokinin and a phylloseptin that is new for this species but has been recently described from the Waxy Monkey Leaf Frog, Phyllomedusa sauvagii. Our study is the first to report defensive peptides specifically isolated from anuran tibial glands, confirming the hypothesis that these glands also contribute to chemical defense. Moreover, the discovery of novel compounds for this otherwise very well characterized species suggests that this largely neglected gland might possess a different cocktail of secretions from glands elsewhere in the same animal. We will also discuss some evolutionary implications of our findings with respect to the adaptive plasticity of secretory glands. Copyright © 2012 Elsevier Inc. All rights reserved.

Identification of cDNAs encoding HSP70 and HSP90 in the abalone Haliotis tuberculata: Transcriptional induction in response to thermal stress in hemocyte primary culture.

PubMed

Farcy, Emilie; Serpentini, Antoine; Fiévet, Bruno; Lebel, Jean-Marc

2007-04-01

Heat-shock proteins are a multigene family of proteins whose expression is induced by a variety of stress factors. This work reports the cloning and sequencing of HSP70 and HSP90 cDNAs in the gastropod Haliotis tuberculata. The deduced amino acid sequences of both HSP70 and HSP90 from H. tuberculata shared a high degree of homology with their homologues in other species, including typical eukaryotic HSP70 and HSP90 signature sequences. We examined their transcription expression pattern in abalone hemocytes exposed to thermal stress. Real-time PCR analysis indicated that both HSP70 and HSP90 mRNA were expressed in control animals but rapidly increased after heat-shock.

Molecular cloning and expression in Saccharomyces cerevisiae of two Aspergillus nidulans xylanase genes.

PubMed Central

Pérez-Gonzalez, J A; De Graaff, L H; Visser, J; Ramón, D

1996-01-01

Two Aspergillus nidulans genes, xlnA and xlnB, encoding the X22 and X24 xylanases from this fungus, respectively, have been cloned and sequenced. Their cDNAs have been expressed in a laboratory Saccharomyces cerevisiae strain under the control of a constitutive yeast promoter, resulting in the construction of recombinant xylanolytic yeast strains. PMID:8787417

Characterization and comparison of fatty acyl Delta6 desaturase cDNAs from freshwater and marine teleost fish species.

PubMed

Zheng, X; Seiliez, I; Hastings, N; Tocher, D R; Panserat, S; Dickson, C A; Bergot, P; Teale, A J

2004-10-01

Fish are the most important dietary source of the n-3 highly unsaturated fatty acids (HUFA), eicosapentaenoic (EPA) and docosahexaenoic acid (DHA), that have particularly important roles in human nutrition reflecting their roles in critical physiological processes. The objective of the study described here was to clone, functionally characterize and compare expressed fatty acid desaturase genes involved in the production of EPA and DHA in freshwater and marine teleost fish species. Putative fatty acid desaturase cDNAs were isolated and cloned from common carp (Cyprinus carpio) and turbot (Psetta maximus). The enzymic activities of the products of these cDNAs, together with those of cDNAs previously cloned from rainbow trout (Oncorhynchus mykiss) and gilthead sea bream (Sparus aurata), were determined by heterologous expression in the yeast Saccharomyces cerevisiae. The carp and turbot desaturase cDNAs included open reading frames (ORFs) of 1335 and 1338 base pairs, respectively, specifying proteins of 444 and 445 amino acids. The protein sequences possessed all the characteristic features of microsomal fatty acid desaturases, including three histidine boxes, two transmembrane regions, and N-terminal cytochrome b(5) domains containing the haem-binding motif, HPGG. Functional expression showed all four fish cDNAs encode basically unifunctional Delta6 fatty acid desaturase enzymes responsible for the first and rate-limiting step in the biosynthesis of HUFA from 18:3n-3 and 18:2n-6. All the fish desaturases were more active towards the n-3 substrate with 59.5%, 31.5%, 23.1% and 7.0% of 18:3n-3 being converted to 18:4n-3 in the case of turbot, trout, sea bream and carp, respectively. The enzymes also showed very low, probably physiologically insignificant, levels of Delta5 desaturase activity, but none of the products showed Delta4 desaturase activity. The cloning and characterization of desaturases from these fish is an important advance, as they are species in which there is a relative wealth of data on the nutritional regulation of fatty acid desaturation and HUFA synthesis, and between which substantive differences occur.

The genome organisation and taxonomy of Sugarcane striate mosaic associated virus.

PubMed

Thompson, N; Randles, J W

2001-08-01

Sugarcane striate mosaic associated virus (SCSMaV) has slightly flexuous 950 nm x 15 nm filamentous particles and is associated with sugarcane striate mosaic disease in central Queensland, Australia. We report the full sequence of its RNA genome, which comprises 5 open reading frames representing the polymerase, movement function proteins encoded in a triple gene block and coat protein. Phylogenetic analyses based on either the full nucleotide sequence, the polymerase protein, or the coat protein all placed SCSMaV in an intermediate position between the genera Foveavirus and Carlavirus, but outside both genera. In addition, the absence of a sixth open reading frame excludes it from the genus Carlavirus, and the coat protein is approximately half the size of the type member for the genus Foveavirus. Although SCSMaV was most closely allied to Cherry green ring mottle virus by genome analysis, the two viruses are morphologically and biologically dissimilar. SCSMaV may therefore represent a new plant virus taxon.

Putative sugarcane FT/TFL1 genes delay flowering time and alter reproductive architecture in Arabidopsis.

PubMed

Coelho, Carla P; Minow, Mark A A; Chalfun-Júnior, Antonio; Colasanti, Joseph

2014-01-01

Agriculturally important grasses such as rice, maize, and sugarcane are evolutionarily distant from Arabidopsis, yet some components of the floral induction process are highly conserved. Flowering in sugarcane is an important factor that negatively affects cane yield and reduces sugar/ethanol production from this important perennial bioenergy crop. Comparative studies have facilitated the identification and characterization of putative orthologs of key flowering time genes in sugarcane, a complex polyploid plant whose genome has yet to be sequenced completely. Using this approach we identified phosphatidylethanolamine-binding protein (PEBP) gene family members in sugarcane that are similar to the archetypical FT and TFL1 genes of Arabidopsis that play an essential role in controlling the transition from vegetative to reproductive growth. Expression analysis of ScTFL1, which falls into the TFL1-clade of floral repressors, showed transcripts in developing leaves surrounding the shoot apex but not at the apex itself. ScFT1 was detected in immature leaves and apical regions of vegetatively growing plants and, after the floral transition, expression also occurred in mature leaves. Ectopic over-expression of ScTFL1 in Arabidopsis caused delayed flowering in Arabidopsis, as might be expected for a gene related to TFL1. In addition, lines with the latest flowering phenotype exhibited aerial rosette formation. Unexpectedly, over-expression of ScFT1, which has greatest similarity to the florigen-encoding FT, also caused a delay in flowering. This preliminary analysis of divergent sugarcane FT and TFL1 gene family members from Saccharum spp. suggests that their expression patterns and roles in the floral transition has diverged from the predicted role of similar PEBP family members.

Roles of Non-Coding RNA in Sugarcane-Microbe Interaction.

PubMed

Thiebaut, Flávia; Rojas, Cristian A; Grativol, Clícia; Calixto, Edmundo P da R; Motta, Mariana R; Ballesteros, Helkin G F; Peixoto, Barbara; de Lima, Berenice N S; Vieira, Lucas M; Walter, Maria Emilia; de Armas, Elvismary M; Entenza, Júlio O P; Lifschitz, Sergio; Farinelli, Laurent; Hemerly, Adriana S; Ferreira, Paulo C G

2017-12-20

Studies have highlighted the importance of non-coding RNA regulation in plant-microbe interaction. However, the roles of sugarcane microRNAs (miRNAs) in the regulation of disease responses have not been investigated. Firstly, we screened the sRNA transcriptome of sugarcane infected with Acidovorax avenae . Conserved and novel miRNAs were identified. Additionally, small interfering RNAs (siRNAs) were aligned to differentially expressed sequences from the sugarcane transcriptome. Interestingly, many siRNAs aligned to a transcript encoding a copper-transporter gene whose expression was induced in the presence of A. avenae , while the siRNAs were repressed in the presence of A. avenae . Moreover, a long intergenic non-coding RNA was identified as a potential target or decoy of miR408. To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR (qRT-PCR). Among these miRNAs, miR408-a copper-microRNA-was downregulated. The cleavage of a putative miR408 target, a laccase, was confirmed by a modified 5'RACE (rapid amplification of cDNA ends) assay. MiR408 was also downregulated in samples infected with other pathogens, but it was upregulated in the presence of a beneficial diazotrophic bacteria. Our results suggest that regulation by miR408 is important in sugarcane sensing whether microorganisms are either pathogenic or beneficial, triggering specific miRNA-mediated regulatory mechanisms accordingly.

Roles of Non-Coding RNA in Sugarcane-Microbe Interaction

PubMed Central

Grativol, Clícia; Motta, Mariana R.; Ballesteros, Helkin G. F.; Peixoto, Barbara; Vieira, Lucas M.; Walter, Maria Emilia; de Armas, Elvismary M.; Entenza, Júlio O. P.; Lifschitz, Sergio; Farinelli, Laurent; Hemerly, Adriana S.

2017-01-01

Studies have highlighted the importance of non-coding RNA regulation in plant-microbe interaction. However, the roles of sugarcane microRNAs (miRNAs) in the regulation of disease responses have not been investigated. Firstly, we screened the sRNA transcriptome of sugarcane infected with Acidovorax avenae. Conserved and novel miRNAs were identified. Additionally, small interfering RNAs (siRNAs) were aligned to differentially expressed sequences from the sugarcane transcriptome. Interestingly, many siRNAs aligned to a transcript encoding a copper-transporter gene whose expression was induced in the presence of A. avenae, while the siRNAs were repressed in the presence of A. avenae. Moreover, a long intergenic non-coding RNA was identified as a potential target or decoy of miR408. To extend the bioinformatics analysis, we carried out independent inoculations and the expression patterns of six miRNAs were validated by quantitative reverse transcription-PCR (qRT-PCR). Among these miRNAs, miR408—a copper-microRNA—was downregulated. The cleavage of a putative miR408 target, a laccase, was confirmed by a modified 5′RACE (rapid amplification of cDNA ends) assay. MiR408 was also downregulated in samples infected with other pathogens, but it was upregulated in the presence of a beneficial diazotrophic bacteria. Our results suggest that regulation by miR408 is important in sugarcane sensing whether microorganisms are either pathogenic or beneficial, triggering specific miRNA-mediated regulatory mechanisms accordingly. PMID:29657296

Transcriptional regulation of genes encoding ABA metabolism enzymes during the fruit development and dehydration stress of pear 'Gold Nijisseiki'.

PubMed

Dai, Shengjie; Li, Ping; Chen, Pei; Li, Qian; Pei, Yuelin; He, Suihuan; Sun, Yufei; Wang, Ya; Kai, Wenbin; Zhao, Bo; Liao, Yalan; Leng, Ping

2014-09-01

To investigate the contribution of abscisic acid (ABA) in pear 'Gold Nijisseiki' during fruit ripening and under dehydration stress, two cDNAs (PpNCED1 and PpNCED2) which encode 9-cis-epoxycarotenoid dioxygenase (NCED) (a key enzyme in ABA biosynthesis), two cDNAs (PpCYP707A1 and PpCYP707A2) which encode 8'-hydroxylase (a key enzyme in the oxidative catabolism of ABA), one cDNA (PpACS3) which encodes 1-aminocyclopropane-1-carboxylic acid (ACC), and one cDNA (PpACO1) which encodes ACC oxidase involved in ethylene biosynthesis were cloned from 'Gold Nijisseiki' fruit. In the pulp, peel and seed, expressions of PpNCED1 and PpNCED2 rose in two stages which corresponded with the increase of ABA levels. The expression of PpCYP707A1 dramatically declined after 60-90 days after full bloom (DAFB) in contrast to the changes of ABA levels during this period, while PpCYP707A2 stayed low during the whole development of fruit. Application of exogenous ABA at 100 DAFB increased the soluble sugar content and the ethylene release but significantly decreased the titratable acid and chlorophyll contents in fruits. When fruits harvested at 100 DAFB were stored in the laboratory (25 °C, 50% relative humidity), the ABA content and the expressions of PpNCED1/2 and PpCYP707A1 in the pulp, peel and seed increased significantly, while ethylene reached its highest value after the maximum peak of ABA accompanied with the expressions of PpACS3 and PpACO1. In sum the endogenous ABA may play an important role in the fruit ripening and dehydration of pear 'Gold Nijisseiki' and the ABA level was regulated mainly by the dynamics of PpNCED1, PpNCED2 and PpCYP707A1 at the transcriptional level. Copyright © 2014 Elsevier Masson SAS. All rights reserved.

Identification of three genotypes of sugarcane yellow leaf virus causing yellow leaf disease from India and their molecular characterization.

PubMed

Viswanathan, R; Balamuralikrishnan, M; Karuppaiah, R

2008-12-01

Sugarcane yellow leaf virus (SCYLV) that causes yellow leaf disease (YLD) in sugarcane (recently reported in India) belongs to Polerovirus. Detailed studies were conducted to characterize the virus based on partial open reading frames (ORFs) 1 and 2 and complete ORFs 3 and 4 sequences in their genome. Reverse-transcriptase polymerase chain reaction (RT-PCR) was performed on 48 sugarcane leaf samples to detect the virus using a specific set of primers. Of the 48 samples, 36 samples (field samples with and without foliar symptoms) including 10 meristem culture derived plants were found to be positive to SCYLV infection. Additionally, an aphid colony collected from symptomatic sugarcane in the field was also found to be SCYLV positive. The amplicons from 22 samples were cloned, sequenced and acronymed as SCYLV-CB isolates. The nucleotide (nt) and amino acid (aa) sequence comparison showed a significant variation between SCYLV-CB and the database sequences at nt (3.7-5.1%) and aa (3.2-5.3%) sequence level in the CP coding region. However, the database sequences comprising isolates of three reported genotypes, viz., BRA, PER and REU, were observed with least nt and aa sequence dissimilarities (0.0-1.6%). The phylogenetic analyses of the overlapping ORFs (ORF 3 and ORF 4) of SCYLV encoding CP and MP determined in this study and additional sequences of 26 other isolates including an Indian isolate (SCYLV-IND) available from GenBank were distributed in four phylogenetic clusters. The SCYLV-CB isolates from this study lineated in two clusters (C1 and C2) and all the other isolates from the worldwide locations into another two clusters (C3 and C4). The sequence variation of the isolates in this study with the database isolates, even in the least variable region of the SCYLV genome, showed that the population existing in India is significantly different from rest of the world. Further, comparison of partial sequences encoding for ORFs 1 and 2 revealed that YLD in sugarcane in India is caused by at least three genotypes, viz., CUB, IND and BRA-PER, of which a majority of the samples were found infected with Cuban genotype (CUB) and lesser by IND and BRA-PER genotypes. The genotype IND was identified as a new genotype from this study, and this was found to have significant variation with the reported genotypes.

Riboflavin accumulation and characterization of cDNAs encoding lumazine synthase and riboflavin synthase in bitter melon (Momordica charantia).

PubMed

Tuan, Pham Anh; Kim, Jae Kwang; Lee, Sanghyun; Chae, Soo Cheon; Park, Sang Un

2012-12-05

Riboflavin (vitamin B2) is the universal precursor of the coenzymes flavin mononucleotide and flavin adenine dinucleotide--cofactors that are essential for the activity of a wide variety of metabolic enzymes in animals, plants, and microbes. Using the RACE PCR approach, cDNAs encoding lumazine synthase (McLS) and riboflavin synthase (McRS), which catalyze the last two steps in the riboflavin biosynthetic pathway, were cloned from bitter melon (Momordica charantia), a popular vegetable crop in Asia. Amino acid sequence alignments indicated that McLS and McRS share high sequence identity with other orthologous genes and carry an N-terminal extension, which is reported to be a plastid-targeting sequence. Organ expression analysis using quantitative real-time RT PCR showed that McLS and McRS were constitutively expressed in M. charantia, with the strongest expression levels observed during the last stage of fruit ripening (stage 6). This correlated with the highest level of riboflavin content, which was detected during ripening stage 6 by HPLC analysis. McLS and McRS were highly expressed in the young leaves and flowers, whereas roots exhibited the highest accumulation of riboflavin. The cloning and characterization of McLS and McRS from M. charantia may aid the metabolic engineering of vitamin B2 in crops.

Molecular characterization and histochemical demonstration of salmon olfactory marker protein in the olfactory epithelium of lacustrine sockeye salmon (Oncorhynchus nerka).

PubMed

Kudo, H; Doi, Y; Ueda, H; Kaeriyama, M

2009-09-01

Despite the importance of olfactory receptor neurons (ORNs) for homing migration, the expression of olfactory marker protein (OMP) is not well understood in ORNs of Pacific salmon (genus Oncorhynchus). In this study, salmon OMP was characterized in the olfactory epithelia of lacustrine sockeye salmon (O. nerka) by molecular biological and histochemical techniques. Two cDNAs encoding salmon OMP were isolated and sequenced. These cDNAs both contained a coding region encoding 173 amino acid residues, and the molecular mass of the two proteins was calculated to be 19,581.17 and 19,387.11Da, respectively. Both amino acid sequences showed marked homology (90%). The protein and nucleotide sequencing demonstrates the existence of high-level homology between salmon OMPs and those of other teleosts. By in situ hybridization using a digoxigenin-labeled salmon OMP cRNA probe, signals for salmon OMP mRNA were observed preferentially in the perinuclear regions of the ORNs. By immunohistochemistry using a specific antibody to salmon OMP, OMP-immunoreactivities were noted in the cytosol of those neurons. The present study is the first to describe cDNA cloning of OMP in salmon olfactory epithelium, and indicate that OMP is a useful molecular marker for the detection of the ORNs in Pacific salmon.

PCR amplification and sequences of cDNA clones for the small and large subunits of ADP-glucose pyrophosphorylase from barley tissues.

PubMed

Villand, P; Aalen, R; Olsen, O A; Lüthi, E; Lönneborg, A; Kleczkowski, L A

1992-06-01

Several cDNAs encoding the small and large subunit of ADP-glucose pyrophosphorylase (AGP) were isolated from total RNA of the starchy endosperm, roots and leaves of barley by polymerase chain reaction (PCR). Sets of degenerate oligonucleotide primers, based on previously published conserved amino acid sequences of plant AGP, were used for synthesis and amplification of the cDNAs. For either the endosperm, roots and leaves, the restriction analysis of PCR products (ca. 550 nucleotides each) has revealed heterogeneity, suggesting presence of three transcripts for AGP in the endosperm and roots, and up to two AGP transcripts in the leaf tissue. Based on the derived amino acid sequences, two clones from the endosperm, beps and bepl, were identified as coding for the small and large subunit of AGP, respectively, while a leaf transcript (blpl) encoded the putative large subunit of AGP. There was about 50% identity between the endosperm clones, and both of them were about 60% identical to the leaf cDNA. Northern blot analysis has indicated that beps and bepl are expressed in both the endosperm and roots, while blpl is detectable only in leaves. Application of the PCR technique in studies on gene structure and gene expression of plant AGP is discussed.

Cloning of two individual cDNAS encoding 9-cis-epoxycarotenoid dioxygenase from Gentiana lutea, their tissue-specific expression and physiological effect in transgenic tobacco.

PubMed

Zhu, Changfu; Kauder, Friedrich; Römer, Susanne; Sandmann, Gerhard

2007-02-01

Two 9-cis-epoxycarotenoid dioxygenase (NCED) cDNAs have been cloned from a petal library of Gentiana lutea. Both cDNAs carry a putative transit sequence for chloroplast import and differ mainly in their length and the 5'-flanking regions. GlNCED1 was evolutionary closely related to Arabidopsis thaliana NCED6 whereas GlNCED2 showed highest homology to tomato NCED1 and A. thaliana NCED3. The amounts of GlNCED2 transcript were below Northern detection in G. lutea. In contrast, GlNCED1 was specifically expressed at higher levels in developing flowers when petals start appearing. By genetic engineering of tobacco with coding regions of either gene under a constitutive promoter, their function was further analyzed. Although mRNA of both genes was detectable in the corresponding transgenic plants, a physiological effect was only found for GlNCED1 but not for GlNCED2. In germination experiments of GlNCED1 transgenic lines, delayed radicle formation and cotyledon appearance were observed. However, the transformants exhibited no improved tolerance against desiccation stress. In contrast to other plants with over-expressed NCEDs, prolonged delay of seed germination is the only abscisic-acid-related phenotypic effect in the GlNCED1 transgenic lines.

Solution Hybrid Selection Capture for the Recovery of Functional Full-Length Eukaryotic cDNAs From Complex Environmental Samples

PubMed Central

Bragalini, Claudia; Ribière, Céline; Parisot, Nicolas; Vallon, Laurent; Prudent, Elsa; Peyretaillade, Eric; Girlanda, Mariangela; Peyret, Pierre; Marmeisse, Roland; Luis, Patricia

2014-01-01

Eukaryotic microbial communities play key functional roles in soil biology and potentially represent a rich source of natural products including biocatalysts. Culture-independent molecular methods are powerful tools to isolate functional genes from uncultured microorganisms. However, none of the methods used in environmental genomics allow for a rapid isolation of numerous functional genes from eukaryotic microbial communities. We developed an original adaptation of the solution hybrid selection (SHS) for an efficient recovery of functional complementary DNAs (cDNAs) synthesized from soil-extracted polyadenylated mRNAs. This protocol was tested on the Glycoside Hydrolase 11 gene family encoding endo-xylanases for which we designed 35 explorative 31-mers capture probes. SHS was implemented on four soil eukaryotic cDNA pools. After two successive rounds of capture, >90% of the resulting cDNAs were GH11 sequences, of which 70% (38 among 53 sequenced genes) were full length. Between 1.5 and 25% of the cloned captured sequences were expressed in Saccharomyces cerevisiae. Sequencing of polymerase chain reaction-amplified GH11 gene fragments from the captured sequences highlighted hundreds of phylogenetically diverse sequences that were not yet described, in public databases. This protocol offers the possibility of performing exhaustive exploration of eukaryotic gene families within microbial communities thriving in any type of environment. PMID:25281543

Stomach Chitinase from Japanese Sardine Sardinops melanostictus: Purification, Characterization, and Molecular Cloning of Chitinase Isozymes with a Long Linker.

PubMed

Kawashima, Satoshi; Ikehata, Hiroki; Tada, Chihiro; Ogino, Tomohiro; Kakizaki, Hiromi; Ikeda, Mana; Fukushima, Hideto; Matsumiya, Masahiro

2016-01-20

Fish express two different chitinases, acidic fish chitinase-1 (AFCase-1) and acidic fish chitinase-2 (AFCase-2), in the stomach. AFCase-1 and AFCase-2 have different degradation patterns, as fish efficiently degrade chitin ingested as food. For a comparison with the enzymatic properties and the primary structures of chitinase isozymes obtained previously from the stomach of demersal fish, in this study, we purified chitinase isozymes from the stomach of Japanese sardine Sardinops melanostictus, a surface fish that feeds on plankton, characterized the properties of these isozymes, and cloned the cDNAs encoding chitinases. We also predicted 3D structure models using the primary structures of S. melanostictus stomach chitinases. Two chitinase isozymes, SmeChiA (45 kDa) and SmeChiB (56 kDa), were purified from the stomach of S. melanostictus. Moreover, two cDNAs, SmeChi-1 encoding SmeChiA, and SmeChi-2 encoding SmeChiB were cloned. The linker regions of the deduced amino acid sequences of SmeChi-1 and SmeChi-2 (SmeChi-1 and SmeChi-2) are the longest among the fish stomach chitinases. In the cleavage pattern groups toward short substrates and the phylogenetic tree analysis, SmeChi-1 and SmeChi-2 were classified into AFCase-1 and AFCase-2, respectively. SmeChi-1 and SmeChi-2 had catalytic domains that consisted of a TIM-barrel (β/α)₈-fold structure and a deep substrate-binding cleft. This is the first study showing the 3D structure models of fish stomach chitinases.

Limnonectins: a new class of antimicrobial peptides from the skin secretion of the Fujian large-headed frog (Limnonectes fujianensis).

PubMed

Wu, Youjia; Wang, Lei; Zhou, Mei; Ma, Chengbang; Chen, Xiaole; Bai, Bing; Chen, Tianbao; Shaw, Chris

2011-06-01

Amphibian skin secretions are rich sources of biologically-active peptides with antimicrobial peptides predominating in many species. Several studies involving molecular cloning of biosynthetic precursor-encoding cDNAs from skin or skin secretions have revealed that these exhibit highly-conserved domain architectures with an unusually high degree of conserved nucleotide and resultant amino acid sequences within the signal peptides. This high degree of nucleotide sequence conservation has permitted the design of primers complementary to such sites facilitating "shotgun" cloning of skin or skin secretion-derived cDNA libraries from hitherto unstudied species. Here we have used such an approach using a skin secretion-derived cDNA library from an unstudied species of Chinese frog - the Fujian large-headed frog, Limnonectes fujianensis - and have discovered two 16-mer peptides of novel primary structures, named limnonectin-1Fa (SFPFFPPGICKRLKRC) and limnonectin-1Fb (SFHVFPPWMCKSLKKC), that represent the prototypes of a new class of amphibian skin antimicrobial peptide. Unusually these limnonectins display activity only against a Gram-negative bacterium (MICs of 35 and 70 μM) and are devoid of haemolytic activity at concentrations up to 160 μM. Thus the "shotgun" cloning approach described can exploit the unusually high degree of nucleotide conservation in signal peptide-encoding domains of amphibian defensive skin secretion peptide precursor-encoding cDNAs to rapidly expedite the discovery of novel and functional defensive peptides in a manner that circumvents specimen sacrifice without compromising robustness of data. Copyright © 2011 Elsevier Masson SAS. All rights reserved.

BIGEL analysis of gene expression in HL60 cells exposed to X rays or 60 Hz magnetic fields

NASA Technical Reports Server (NTRS)

Balcer-Kubiczek, E. K.; Zhang, X. F.; Han, L. H.; Harrison, G. H.; Davis, C. C.; Zhou, X. J.; Ioffe, V.; McCready, W. A.; Abraham, J. M.; Meltzer, S. J.

1998-01-01

We screened a panel of 1,920 randomly selected cDNAs to discover genes that are differentially expressed in HL60 cells exposed to 60 Hz magnetic fields (2 mT) or X rays (5 Gy) compared to unexposed cells. Identification of these clones was accomplished using our two-gel cDNA library screening method (BIGEL). Eighteen cDNAs differentially expressed in X-irradiated compared to control HL60 cells were recovered from a panel of 1,920 clones. Differential expression in experimental compared to control cells was confirmed independently by Northern blotting of paired total RNA samples hybridized to each of the 18 clone-specific cDNA probes. DNA sequencing revealed that 15 of the 18 cDNA clones produced matches with the database for genes related to cell growth, protein synthesis, energy metabolism, oxidative stress or apoptosis (including MYC, neuroleukin, copper zinc-dependent superoxide dismutase, TC4 RAS-like protein, peptide elongation factor 1alpha, BNIP3, GATA3, NF45, cytochrome c oxidase II and triosephosphate isomerase mRNAs). In contrast, BIGEL analysis of the same 1,920 cDNAs revealed no differences greater than 1.5-fold in expression levels in magnetic-field compared to sham-exposed cells. Magnetic-field-exposed and control samples were analyzed further for the presence of mRNA encoding X-ray-responsive genes by hybridization of the 18 specific cDNA probes to RNA from exposed and control HL60 cells. Our results suggest that differential gene expression is induced in approximately 1% of a random pool of cDNAs by ionizing radiation but not by 60 Hz magnetic fields under the present experimental conditions.

Structurally divergent lysophosphatidic acid acyltransferases with high selectivity for saturated medium chain fatty acids from Cuphea seeds.

PubMed

Kim, Hae Jin; Silva, Jillian E; Iskandarov, Umidjon; Andersson, Mariette; Cahoon, Rebecca E; Mockaitis, Keithanne; Cahoon, Edgar B

2015-12-01

Lysophosphatidic acid acyltransferase (LPAT) catalyzes acylation of the sn-2 position on lysophosphatidic acid by an acyl CoA substrate to produce the phosphatidic acid precursor of polar glycerolipids and triacylglycerols (TAGs). In the case of TAGs, this reaction is typically catalyzed by an LPAT2 from microsomal LPAT class A that has high specificity for C18 fatty acids containing Δ9 unsaturation. Because of this specificity, the occurrence of saturated fatty acids in the TAG sn-2 position is infrequent in seed oils. To identify LPATs with variant substrate specificities, deep transcriptomic mining was performed on seeds of two Cuphea species producing TAGs that are highly enriched in saturated C8 and C10 fatty acids. From these analyses, cDNAs for seven previously unreported LPATs were identified, including cDNAs from Cuphea viscosissima (CvLPAT2) and Cuphea avigera var. pulcherrima (CpuLPAT2a) encoding microsomal, seed-specific class A LPAT2s and a cDNA from C. avigera var. pulcherrima (CpuLPATB) encoding a microsomal, seed-specific LPAT from the bacterial-type class B. The activities of these enzymes were characterized in Camelina sativa by seed-specific co-expression with cDNAs for various Cuphea FatB acyl-acyl carrier protein thioesterases (FatB) that produce a variety of saturated medium-chain fatty acids. CvLPAT2 and CpuLPAT2a expression resulted in accumulation of 10:0 fatty acids in the Camelina sativa TAG sn-2 position, indicating a 10:0 CoA specificity that has not been previously described for plant LPATs. CpuLPATB expression generated TAGs with 14:0 at the sn-2 position, but not 10:0. Identification of these LPATs provides tools for understanding the structural basis of LPAT substrate specificity and for generating altered oil functionalities. © 2015 The Authors The Plant Journal © 2015 John Wiley & Sons Ltd.

Localization and physical mapping of genes encoding the A+U-rich element RNA-binding protein AUF1 to human chromosomes 4 and X

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wagner, B.J.; Long, L.; Pettenati, M.J.

Messenger RNAs encoding many oncoproteins and cytokines are relatively unstable. Their instability, which ensures appropriate levels and timing of expression, is controlled in part by proteins that bind to A + U-rich instability elements (AREs) present in the 3{prime}-untranslated regions of the mRNAs. cDNAs encoding the AUF1 family of ARE-binding proteins were cloned from human and murine cDNA libraries. In the present study monochromosomal somatic cell hybrids were used to localize two AUF1 loci to human chromosomes 4 and X. In situ hybridization analyses using P1 clones as probes identified the 4q21.1-q21.2 and Xq12 regions as the locations of themore » AUF1 genes. 10 refs., 2 figs.« less

Expression analysis of β-glucosidase genes that regulate abscisic acid homeostasis during watermelon (Citrullus lanatus) development and under stress conditions.

PubMed

Li, Qian; Li, Ping; Sun, Liang; Wang, Yanping; Ji, Kai; Sun, Yufei; Dai, Shengjie; Chen, Pei; Duan, Chaorui; Leng, Ping

2012-01-01

The aim of this study was to obtain new insights into the mechanisms that regulate endogenous abscisic acid (ABA) levels by β-glucosidase genes during the development of watermelons (Citrullus lanatus) and under drought stress conditions. In total, five cDNAs from watermelons were cloned by using reverse transcription-PCR (RT-PCR). They included three cDNAs (ClBG1, ClBG2 and ClBG3) homologous to those that encode β-glucosidase l that hydrolyzes the ABA glucose ester (ABA-GE) to release active ABA, ClNCED4, which encodes 9-cis-epoxycarotenoid dioxygenase (NCED), a key enzyme in ABA biosynthesis, and ClCYP707A1, encoding ABA 8'-hydroxylase. A BLAST homology search revealed that the sequences of cDNAs and the deduced amino acids of these genes showed a high degree of homology to comparable molecules of other plant species. During fruit development and ripening, the expressions of ClBG1, ClNCED4 and ClCYP707A1 were relatively low at an early stage, increased rapidly along with fruit ripening, and reached the highest levels at 27 days after full bloom (DAFB) at the harvest stage. This trend was consistent with the accumulation of ABA. The ClBG2 gene on the other hand was highly expressed at 5 DAFB, and then decreased gradually with fruit development. Unlike ClBG1 and ClBG2, the expression of ClBG3 was low at an early stage; its expression peak occurred at 15 DAFB and then declined to the lowest point. When watermelon seedlings were subjected to drought stress, expressions of ClBG1 and ClCYP707A1 were significantly down-regulated, while expressions of ClBG2 and ClNCED4 were up-regulated in the roots, stems and leaves. The expression of ClBG3 was down-regulated in root tissue, but was up-regulated in stems and leaves. In conclusion, endogenous ABA content was modulated by a dynamic balance between biosynthesis and catabolism regulated by ClNCED4, ClCYP707A1 and ClBGs during development and under drought stress condition. It seems likely that β-glucosidase genes are important for this regulation process. Copyright © 2011 Elsevier GmbH. All rights reserved.

Lack of hormone binding in COS-7 cells expressing a mutated growth hormone receptor found in Laron dwarfism.

PubMed Central

Edery, M; Rozakis-Adcock, M; Goujon, L; Finidori, J; Lévi-Meyrueis, C; Paly, J; Djiane, J; Postel-Vinay, M C; Kelly, P A

1993-01-01

A single point mutation in the growth hormone (GH) receptor gene generating a Phe-->Ser substitution in the extracellular binding domain of the receptor has been identified in one family with Laron type dwarfism. The mutation was introduced by site-directed mutagenesis into cDNAs encoding the full-length rabbit GH receptor and the extracellular domain or binding protein (BP) of the human and rabbit GH receptor, and also in cDNAs encoding the full length and the extracellular domain of the related rabbit prolactin (PRL) receptor. All constructs were transiently expressed in COS-7 cells. Both wild type and mutant full-length rabbit GH and PRL receptors, as well as GH and prolactin BPs (wild type and mutant), were detected by Western blot in cell membranes and concentrated culture media, respectively. Immunofluorescence studies showed that wild type and mutant full-length GH receptors had the same cell surface and intracellular distribution and were expressed with comparable intensities. In contrast, all mutant forms (full-length receptors or BPs), completely lost their modify the synthesis ligand. These results clearly demonstrate that this point mutation (patients with Laron syndrome) does not modify the synthesis or the intracellular pathway of receptor proteins, but rather abolishes ability of the receptor or BP to bind GH and is thus responsible for the extreme GH resistance in these patients. Images PMID:8450064

New insights into plant glycoside hydrolase family 32 in Agave species

PubMed Central

Avila de Dios, Emmanuel; Gomez Vargas, Alan D.; Damián Santos, Maura L.; Simpson, June

2015-01-01

In order to optimize the use of agaves for commercial applications, an understanding of fructan metabolism in these species at the molecular and genetic level is essential. Based on transcriptome data, this report describes the identification and molecular characterization of cDNAs and deduced amino acid sequences for genes encoding fructosyltransferases, invertases and fructan exohydrolases (FEH) (enzymes belonging to plant glycoside hydrolase family 32) from four different agave species (A. tequilana, A. deserti, A. victoriae-reginae, and A. striata). Conserved amino acid sequences and a hypervariable domain allowed classification of distinct isoforms for each enzyme type. Notably however neither 1-FFT nor 6-SFT encoding cDNAs were identified. In silico analysis revealed that distinct isoforms for certain enzymes found in a single species, showed different levels and tissue specific patterns of expression whereas in other cases expression patterns were conserved both within the species and between different species. Relatively high levels of in silico expression for specific isoforms of both invertases and fructosyltransferases were observed in floral tissues in comparison to vegetative tissues such as leaves and stems and this pattern was confirmed by Quantitative Real Time PCR using RNA obtained from floral and leaf tissue of A. tequilana. Thin layer chromatography confirmed the presence of fructans with degree of polymerization (DP) greater than DP three in both immature buds and fully opened flowers also obtained from A. tequilana. PMID:26300895

New insights into plant glycoside hydrolase family 32 in Agave species.

PubMed

Avila de Dios, Emmanuel; Gomez Vargas, Alan D; Damián Santos, Maura L; Simpson, June

2015-01-01

In order to optimize the use of agaves for commercial applications, an understanding of fructan metabolism in these species at the molecular and genetic level is essential. Based on transcriptome data, this report describes the identification and molecular characterization of cDNAs and deduced amino acid sequences for genes encoding fructosyltransferases, invertases and fructan exohydrolases (FEH) (enzymes belonging to plant glycoside hydrolase family 32) from four different agave species (A. tequilana, A. deserti, A. victoriae-reginae, and A. striata). Conserved amino acid sequences and a hypervariable domain allowed classification of distinct isoforms for each enzyme type. Notably however neither 1-FFT nor 6-SFT encoding cDNAs were identified. In silico analysis revealed that distinct isoforms for certain enzymes found in a single species, showed different levels and tissue specific patterns of expression whereas in other cases expression patterns were conserved both within the species and between different species. Relatively high levels of in silico expression for specific isoforms of both invertases and fructosyltransferases were observed in floral tissues in comparison to vegetative tissues such as leaves and stems and this pattern was confirmed by Quantitative Real Time PCR using RNA obtained from floral and leaf tissue of A. tequilana. Thin layer chromatography confirmed the presence of fructans with degree of polymerization (DP) greater than DP three in both immature buds and fully opened flowers also obtained from A. tequilana.

Mammalian Wax Biosynthesis

PubMed Central

Cheng, Jeffrey B.; Russell, David W.

2009-01-01

Wax monoesters are synthesized by the esterification of fatty alcohols and fatty acids. A mammalian enzyme that catalyzes this reaction has not been isolated. We used expression cloning to identify cDNAs encoding a wax synthase in the mouse preputial gland. The wax synthase gene is located on the X chromosome and encodes a member of the acyltransferase family of enzymes that synthesize neutral lipids. Expression of wax synthase in cultured cells led to the formation of wax monoesters from straight chain saturated, unsaturated, and polyunsaturated fatty alcohols and acids. Polyisoprenols also were incorporated into wax monoesters by the enzyme. The wax synthase had little or no ability to synthesize cholesteryl esters, diacylglycerols, or triacylglycerols, whereas other acyltransferases, including the acyl-CoA:monoacylglycerol acyltransferase 1 and 2 enzymes and the acyl-CoA:diacylglycerol acyltransferase 1 and 2 enzymes, exhibited modest wax monoester synthesis activities. Confocal light microscopy indicated that the wax synthase was localized in membranes of the endoplasmic reticulum. Wax synthase mRNA was abundant in tissues rich in sebaceous glands such as the preputial gland and eyelid and was present at lower levels in other tissues. Coexpression of cDNAs specifying fatty acyl-CoA reductase 1 and wax synthase led to the synthesis of wax monoesters. The data suggest that wax monoester synthesis in mammals involves a two step biosynthetic pathway catalyzed by fatty acyl-CoA reductase and wax synthase enzymes. PMID:15220349

Expression profiles of defence related cDNAs in oil palm (Elaeis guineensis Jacq.) inoculated with mycorrhizae and Trichoderma harzianum Rifai T32.

PubMed

Tan, Yung-Chie; Wong, Mui-Yun; Ho, Chai-Ling

2015-11-01

Basal stem rot is one of the major diseases of oil palm (Elaies guineensis Jacq.) caused by pathogenic Ganoderma species. Trichoderma and mycorrhizae were proposed to be able to reduce the disease severity. However, their roles in improving oil palm defence system by possibly inducing defence-related genes in the host are not well characterized. To better understand that, transcript profiles of eleven putative defence-related cDNAs in the roots of oil palm inoculated with Trichoderma harzianum T32 and mycorrhizae at different time points were studied. Transcripts encoding putative Bowman-Birk protease inhibitor (EgBBI2) and defensin (EgDFS) increased more than 2 fold in mycorrhizae-treated roots at 6 weeks post inoculation (wpi) compared to those in controls. Transcripts encoding putative dehydrin (EgDHN), glycine-rich RNA binding protein (EgGRRBP), isoflavone reductase (EgIFR), type 2 ribosome inactivating protein (EgT2RIP), and EgDFS increased in the oil palm roots treated with T. harzianum at 6 and/or 12 wpi compared to those in the controls. Some of these genes were also expressed in oil palm roots treated with Ganoderma boninense. This study provides an insight of some defence-related genes induced by Trichoderma and mycorrhizae, and their roles as potential agents to boost the plant defence system. Copyright © 2015 Elsevier Masson SAS. All rights reserved.

Virtual Northern analysis of the human genome.

PubMed

Hurowitz, Evan H; Drori, Iddo; Stodden, Victoria C; Donoho, David L; Brown, Patrick O

2007-05-23

We applied the Virtual Northern technique to human brain mRNA to systematically measure human mRNA transcript lengths on a genome-wide scale. We used separation by gel electrophoresis followed by hybridization to cDNA microarrays to measure 8,774 mRNA transcript lengths representing at least 6,238 genes at high (>90%) confidence. By comparing these transcript lengths to the Refseq and H-Invitational full-length cDNA databases, we found that nearly half of our measurements appeared to represent novel transcript variants. Comparison of length measurements determined by hybridization to different cDNAs derived from the same gene identified clones that potentially correspond to alternative transcript variants. We observed a close linear relationship between ORF and mRNA lengths in human mRNAs, identical in form to the relationship we had previously identified in yeast. Some functional classes of protein are encoded by mRNAs whose untranslated regions (UTRs) tend to be longer or shorter than average; these functional classes were similar in both human and yeast. Human transcript diversity is extensive and largely unannotated. Our length dataset can be used as a new criterion for judging the completeness of cDNAs and annotating mRNA sequences. Similar relationships between the lengths of the UTRs in human and yeast mRNAs and the functions of the proteins they encode suggest that UTR sequences serve an important regulatory role among eukaryotes.

cDNA, deduced polypeptide structure and chromosomal assignment of human pulmonary surfactant proteolipid, SPL(pVal)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Glasser, S.W.; Korfhagen, T.R.; Weaver, T.E.

1988-01-05

In hyaline membrane disease of premature infants, lack of surfactant leads to pulmonary atelectasis and respiratory distress. Hydrophobic surfactant proteins of M/sub r/ = 5000-14,000 have been isolated from mammalian surfactants which enhance the rate of spreading and the surface tension lowering properties of phospholipids during dynamic compression. The authors have characterized the amino-terminal amino acid sequence of pulmonary proteolipids from ether/ethanol extracts of bovine, canine, and human surfactant. Two distinct peptides were identified and termed SPL(pVal) and SPL(Phe). An oligonucleotide probe based on the valine-rich amino-terminal amino acid sequence of SPL(pVal) was utilized to isolate cDNA and genomic DNAmore » encoding the human protein, termed surfactant proteolipid SPL(pVal) on the basis of its unique polyvaline domain. The primary structure of a precursor protein of 20,870 daltons, containing the SPL(pVal) peptide, was deduced from the nucleotide sequence of the cDNAs. Hybrid-arrested translation and immunoprecipitation of labeled translation products of human mRNA demonstrated a precursor protein, the active hydrophobic peptide being produced by proteolytic processing. Two classes of cDNAs encoding SPL(pVal) were identified. Human SPL(pVal) mRNA was more abundant in the adult than in fetal lung. The SPL(pVal) gene locus was assigned to chromosome 8.« less

Molecular cloning and sequence analysis of full-length growth hormone cDNAs from six important economic fishes.

PubMed

Zhang, Jing-Nan; Song, Ping; Hu, Jia-Rui; Mo, Sai-Jun; Peng, Mao-Yu; Zhou, Wei; Zou, Ji-Xing; Hu, Yin-Chang

2005-01-01

In this study,the full-length cDNAs of GH (Growth Hormone) gene was isolated from six important economic fishes, Siniperca kneri, Epinephelus coioides, Monopterus albus, Silurus asotus, Misgurnus anguillicaudatus and Carassius auratus gibelio Bloch. It is the first time to clone these GH sequences except E. coioides GH. The lengths of the above cDNAs are as follows: 953 bp, 1 023 bp, 825 bp, 1 082 bp, 1 154 bp and 1 180 bp. Each sequence includes an ORF of about 600 bp which encodes a protein of about 200 amino acid: S. kneri, E. coioides and M. albus GHs of 204 amino acid, S. asotus GH of 200 amino acid, M. anguillicaudatus and C. auratus gibelio GHs of 210 amino acid. Then detailed sequence analysis of the six GHs with many other fish sequences was performed. The six sequences all showed high homology to other sequences, especially to sequences within the same order, and many conserved residues were identified, most localized in five domains. The phylogenetic trees (MP and NJ) of many fish GH ORF sequences (including the new six) with Amia calva as outgroup were generally resolved and largely congruent with the morphology-based tree though some incongruities were observed, suggesting GH ORF should be paid more attention to in teleostean phylogeny.

Gene discovery in the hamster: a comparative genomics approach for gene annotation by sequencing of hamster testis cDNAs

PubMed Central

Oduru, Sreedhar; Campbell, Janee L; Karri, SriTulasi; Hendry, William J; Khan, Shafiq A; Williams, Simon C

2003-01-01

Background Complete genome annotation will likely be achieved through a combination of computer-based analysis of available genome sequences combined with direct experimental characterization of expressed regions of individual genomes. We have utilized a comparative genomics approach involving the sequencing of randomly selected hamster testis cDNAs to begin to identify genes not previously annotated on the human, mouse, rat and Fugu (pufferfish) genomes. Results 735 distinct sequences were analyzed for their relatedness to known sequences in public databases. Eight of these sequences were derived from previously unidentified genes and expression of these genes in testis was confirmed by Northern blotting. The genomic locations of each sequence were mapped in human, mouse, rat and pufferfish, where applicable, and the structure of their cognate genes was derived using computer-based predictions, genomic comparisons and analysis of uncharacterized cDNA sequences from human and macaque. Conclusion The use of a comparative genomics approach resulted in the identification of eight cDNAs that correspond to previously uncharacterized genes in the human genome. The proteins encoded by these genes included a new member of the kinesin superfamily, a SET/MYND-domain protein, and six proteins for which no specific function could be predicted. Each gene was expressed primarily in testis, suggesting that they may play roles in the development and/or function of testicular cells. PMID:12783626

Isolation of a Novel Peroxisomal Catalase Gene from Sugarcane, Which Is Responsive to Biotic and Abiotic Stresses

PubMed Central

Ling, Hui; Chen, Shanshan; Wang, Shanshan; Xu, Liping; Allan, Andrew C.; Que, Youxiong

2014-01-01

Catalase is an iron porphyrin enzyme, which serves as an efficient scavenger of reactive oxygen species (ROS) to avoid oxidative damage. In sugarcane, the enzymatic activity of catalase in a variety (Yacheng05–179) resistant to the smut pathogen Sporisorium scitamineum was always higher than that of the susceptible variety (Liucheng03–182), suggesting that catalase activity may have a positive correlation with smut resistance in sugarcane. To understand the function of catalase at the molecular level, a cDNA sequence of ScCAT1 (GenBank Accession No. KF664183), was isolated from sugarcane infected by S. scitamineum. ScCAT1 was predicted to encode 492 amino acid residues, and its deduced amino acid sequence shared a high degree of homology with other plant catalases. Enhanced growth of ScCAT1 in recombinant Escherichia coli Rosetta cells under the stresses of CuCl2, CdCl2 and NaCl indicated its high tolerance. Q-PCR results showed that ScCAT1 was expressed at relatively high levels in the bud, whereas expression was moderate in stem epidermis and stem pith. Different kinds of stresses, including S. scitamineum challenge, plant hormones (SA, MeJA and ABA) treatments, oxidative (H2O2) stress, heavy metal (CuCl2) and hyper-osmotic (PEG and NaCl) stresses, triggered a significant induction of ScCAT1. The ScCAT1 protein appeared to localize in plasma membrane and cytoplasm. Furthermore, histochemical assays using DAB and trypan blue staining, as well as conductivity measurement, indicated that ScCAT1 may confer the sugarcane immunity. In conclusion, the positive response of ScCAT1 to biotic and abiotic stresses suggests that ScCAT1 is involved in protection of sugarcane against reactive oxidant-related environmental stimuli. PMID:24392135

Cloning of human cDNAs for Apg-1 and Apg-2, members of the Hsp110 family, and chromosomal assignment of their genes.

PubMed

Nonoguchi, K; Itoh, K; Xue, J H; Tokuchi, H; Nishiyama, H; Kaneko, Y; Tatsumi, K; Okuno, H; Tomiwa, K; Fujita, J

1999-09-03

In mice, the Hsp110/SSE family is composed of the heat shock protein (Hsp)110/105, Apg-1 and Apg-2. In humans, however, only the Hsp110/105 homolog has been identified as a member, and two cDNAs, Hsp70RY and HS24/p52, potentially encoding proteins structurally similar to, but smaller than, mouse Apg-2 have been reported. To clarify the membership of Hsp110 family in humans, we isolated Apg-1 and Apg-2 cDNAs from a human testis cDNA library. The human Apg-1 was 100% and 91.8% identical in length and amino acid (aa) sequence, respectively, to mouse Apg-1. Human Apg-2 was one aa shorter than and 95.5% identical in sequence to mouse Apg-2. In ECV304, human endothelial cells Apg-1 but not Apg-2 transcripts were induced in 2 h by a temperature shift from 32 degrees C to 39 degrees C. As found in mice, the response was stronger than that to a 37-42 degrees C shift. The human Apg-1 and Apg-2 genes were mapped to the chromosomal loci 4q28 and 5q23.3-q31.1, respectively, by fluorescence in-situ hybridization. We isolated cDNA and genomic clones encompassing the region critical for the difference between Apg-2 and HS24/p52. Although the primer sets used were derived from the sequences common to both cDNAs, all cDNA and genomic clones corresponded to Apg-2. Using a similar approach, the relationship between Apg-2 and Hsp70RY was assessed, and no clone corresponding to Hsp70RY was obtained. These results demonstrated that the Hsp110 family consists of at least three members, Apg-1, Apg-2 and Hsp110 in humans as well as in mice. The significance of HS24/p52 and Hsp70RY cDNAs previously reported remains to be determined.

Two Closely Related Genes of Arabidopsis Encode Plastidial Cytidinediphosphate Diacylglycerol Synthases Essential for Photoautotrophic Growth1[C

PubMed Central

Haselier, André; Akbari, Hana; Weth, Agnes; Baumgartner, Werner; Frentzen, Margrit

2010-01-01

Cytidinediphosphate diacylglycerol synthase (CDS) catalyzes the formation of cytidinediphosphate diacylglycerol, an essential precursor of anionic phosphoglycerolipids like phosphatidylglycerol or -inositol. In plant cells, CDS isozymes are located in plastids, mitochondria, and microsomes. Here, we show that these isozymes are encoded by five genes in Arabidopsis (Arabidopsis thaliana). Alternative translation initiation or alternative splicing of CDS2 and CDS4 transcripts can result in up to 10 isoforms. Most of the cDNAs encoding the various plant isoforms were functionally expressed in yeast and rescued the nonviable phenotype of the mutant strain lacking CDS activity. The closely related genes CDS4 and CDS5 were found to encode plastidial isozymes with similar catalytic properties. Inactivation of both genes was required to obtain Arabidopsis mutant lines with a visible phenotype, suggesting that the genes have redundant functions. Analysis of these Arabidopsis mutants provided further independent evidence for the importance of plastidial phosphatidylglycerol for structure and function of thylakoid membranes and, hence, for photoautotrophic growth. PMID:20442275

Stomach Chitinase from Japanese Sardine Sardinops melanostictus: Purification, Characterization, and Molecular Cloning of Chitinase Isozymes with a Long Linker

PubMed Central

Kawashima, Satoshi; Ikehata, Hiroki; Tada, Chihiro; Ogino, Tomohiro; Kakizaki, Hiromi; Ikeda, Mana; Fukushima, Hideto; Matsumiya, Masahiro

2016-01-01

Fish express two different chitinases, acidic fish chitinase-1 (AFCase-1) and acidic fish chitinase-2 (AFCase-2), in the stomach. AFCase-1 and AFCase-2 have different degradation patterns, as fish efficiently degrade chitin ingested as food. For a comparison with the enzymatic properties and the primary structures of chitinase isozymes obtained previously from the stomach of demersal fish, in this study, we purified chitinase isozymes from the stomach of Japanese sardine Sardinops melanostictus, a surface fish that feeds on plankton, characterized the properties of these isozymes, and cloned the cDNAs encoding chitinases. We also predicted 3D structure models using the primary structures of S. melanostictus stomach chitinases. Two chitinase isozymes, SmeChiA (45 kDa) and SmeChiB (56 kDa), were purified from the stomach of S. melanostictus. Moreover, two cDNAs, SmeChi-1 encoding SmeChiA, and SmeChi-2 encoding SmeChiB were cloned. The linker regions of the deduced amino acid sequences of SmeChi-1 and SmeChi-2 (SmeChi-1 and SmeChi-2) are the longest among the fish stomach chitinases. In the cleavage pattern groups toward short substrates and the phylogenetic tree analysis, SmeChi-1 and SmeChi-2 were classified into AFCase-1 and AFCase-2, respectively. SmeChi-1 and SmeChi-2 had catalytic domains that consisted of a TIM-barrel (β/α)8–fold structure and a deep substrate-binding cleft. This is the first study showing the 3D structure models of fish stomach chitinases. PMID:26805857

Molecular Cloning and Expression of Three Polygalacturonase cDNAs from the Tarnished Plant Bug, Lygus lineolaris

PubMed Central

Allen, Margaret L.; Mertens, Jeffrey A.

2008-01-01

Three unique cDNAs encoding putative polygalacturonase enzymes were isolated from the tarnished plant bug, Lygus lineolaris (Palisot de Beauvois) (Hemiptera: Miridae). The three nucleotide sequences were dissimilar to one another, but the deduced amino acid sequences were similar to each other and to other polygalacturonases from insects, fungi, plants, and bacteria. Four conserved segments characteristic of polygalacturonases were present, but with some notable semiconservative substitutions. Two of four expected disulfide bridge—forming cysteine pairs were present. All three inferred protein translations included predicted signal sequences of 17 to 20 amino acids. Amplification of genomic DNA identified an intron in one of the genes, Llpg1, in the 5′ untranslated region. Semiquantitative RT-PCR revealed expression in all stages of the insect except the eggs. Expression in adults, male and female, was highly variable, indicating a family of highly inducible and diverse enzymes adapted to the generalist polyphagous nature of this important pest. PMID:20233096

Antisense and sense poly(A)-RNAs from the Xenopus laevis pyruvate dehydrogenase gene loci are regulated with message production during embryogenesis.

PubMed

Islam, N; Poitras, L; Gagnon, F; Moss, T

1996-10-17

The structure and temporal expression of two Xenopus cDNAs encoding the beta subunit of pyruvate dehydrogenase (XPdhE1 beta) have been determined. XPdhE1 beta was 88% homologous to mature human PdhE1 beta, but the putative N-terminal mitochondrial signal peptide was poorly conserved. Zygotic expression of XPdhE1 beta mRNA was detected at neural tube closure and increased until stage 40. RT-PCR cloning identified a short homology to a protein kinase open reading frame within the 3' non-coding sequence of the XPdhE1 beta cDNAs. This homology, which occurred on the antisense cDNA strand, was shown by strand specific RT-PCR to be transcribed in vivo as part of an antisense RNA. Northern analysis showed that this RNA formed part of an abundant and heterogeneous population of antisense and sense poly(A)-RNAs transcribed from the XPdhE1 beta loci and coordinately regulated with message production.

Alleviation of carbon catabolite repression in Enterobacter aerogenes for efficient utilization of sugarcane molasses for 2,3-butanediol production.

PubMed

Jung, Moo-Young; Jung, Hwi-Min; Lee, Jinwon; Oh, Min-Kyu

2015-01-01

Due to its cost-effectiveness and rich sugar composition, sugarcane molasses is considered to be a promising carbon source for biorefinery. However, the sugar mixture in sugarcane molasses is not consumed as efficiently as glucose in microbial fermentation due to complex interactions among their utilizing pathways, such as carbon catabolite repression (CCR). In this study, 2,3-butanediol-producing Enterobacter aerogenes was engineered to alleviate CCR and improve sugar utilization by modulating its carbon preference. The gene encoding catabolite repressor/activator (Cra) was deleted in the genome of E. aerogenes to increase the fructose consumption rate. However, the deletion mutation repressed sucrose utilization, resulting in the accumulation of sucrose in the fermentation medium. Cra regulation on expression of the scrAB operon involved in sucrose catabolism was verified by reverse transcription and real-time PCR, and the efficiency of sucrose utilization was restored by disrupting the scrR gene and overexpressing the scrAB operon. In addition, overexpression of the ptsG gene involved in glucose utilization enhanced the glucose preference among mixed sugars, which relieved glucose accumulation in fed-batch fermentation. In fed-batch fermentation using sugarcane molasses, the maximum titer of 2,3-butanediol production by the mutant reached 140.0 g/L at 54 h, which was by far the highest titer of 2,3-butanediol with E. aerogenes achieved through genetic engineering. We have developed genetically engineered E. aerogenes as a 2,3-butanediol producer that efficiently utilizes sugarcane molasses. The fermentation efficiency was dramatically improved by the alleviation of CCR and modulation of carbon preference. These results offer a metabolic engineering approach for achieving highly efficient utilization of mixed sugars for the biorefinery industry.

Regulation and Functional Expression of Cinnamate 4-Hydroxylase from Parsley

PubMed Central

Koopmann, Edda; Logemann, Elke; Hahlbrock, Klaus

1999-01-01

A previously isolated parsley (Petroselinum crispum) cDNA with high sequence similarity to cinnamate 4-hydroxylase (C4H) cDNAs from several plant sources was expressed in yeast (Saccharomyces cerevisiae) containing a plant NADPH:cytochrome P450 oxidoreductase and verified as encoding a functional C4H (CYP73A10). Low genomic complexity and the occurrence of a single type of cDNA suggest the existence of only one C4H gene in parsley. The encoded mRNA and protein, in contrast to those of a functionally related NADPH:cytochrome P450 oxidoreductase, were strictly coregulated with phenylalanine ammonia-lyase mRNA and protein, respectively, as demonstrated by coinduction under various conditions and colocalization in situ in cross-sections from several different parsley tissues. These results support the hypothesis that the genes encoding the core reactions of phenylpropanoid metabolism form a tight regulatory unit. PMID:9880345

Vanilloid receptor-related osmotically activated channel (VR-OAC), a candidate vertebrate osmoreceptor

PubMed Central

Liedtke, Wolfgang; Choe, Yong; Martí-Renom, Marc A.; Bell, Andrea M.; Denis, Charlotte S.; Šali, Andrej; Hudspeth, A. J.; Friedman, Jeffrey M.; Heller, Stefan

2008-01-01

SUMMARY The detection of osmotic stimuli is essential for all organisms, yet few osmoreceptive proteins are known, none of them in vertebrates. By employing a candidate-gene approach based on genes encoding members of the TRP superfamily of ion channels, we cloned cDNAs encoding the vanilloid receptor-related osmotically activated channel (VR-OAC) from the rat, mouse, human, and chicken. This novel cation-selective channel is gated by exposure to hypotonicity within the physiological range. In the central nevous system, the channel is expressed neurons of the circumventricular organs, neurosensory cells responsive to systemic osmotic pressure. The channel also occurs in other neurosensory cells, including inner-ear hair cells, sensory neurons, and Merkel cells. PMID:11081638

[Spectral diversity among the members of the family of Green Fluorescent Protein in hydroid jellyfish (Cnidaria, Hydrozoa)].

PubMed

Ianushevich, Iu G; Shagin, D A; Fradkov, A F; Shakhbazov, K S; Barsova, E V; Gurskaia, N G; Labas, Iu A; Matts, M V; Luk'ianov, k A; Lul'ianov, S A

2005-01-01

The cDNAs encoding the genes of new proteins homologous to the well-known Green Fluorescent Protein (GFP) from the hydroid jellyfish Aequorea victoria were cloned. Two green fluorescent proteins from one un-identified anthojellyfish, a yellow fluorescent protein from Phialidium sp., and a nonfluorescent chromoprotein from another unidentified anthojellyfish were characterized. Thus, a broad diversity of GFP-like proteins among the organisms of the class Hydrozoa in both spectral properties and primary structure was shown.

Inkjet Gene Printing: A Novel Approach to Achieve Gene Modified Cells for Tissue Engineering

DTIC Science & Technology

2008-12-01

and pIRES-VEGF-GFP (BD Biosciences, Bedford, MA) encoding the cDNAs of jellyfish Aequorea victoria green fluorescent protein, driven by the...prepared from rat-tail Type I collagen gels using a previously reported protocol(Xu et al. 2005). Briefly, rat- tail Type I collagen (BD Biosciences...aliquots of the mixture were dispersed onto coverslips and cured in an incubator for 3–5 h. Once the gel set, the collagen bio-paper was ready for

cDNA cloning and expression of carotenogenic genes during flower development in Gentiana lutea.

PubMed

Zhu, Changfu; Yamamura, Saburo; Koiwa, Hiroyuki; Nishihara, Masashiro; Sandmann, Gerhard

2002-02-01

All cDNAs involved in carotenoid biosynthesis leading to lycopene in yellow petals of Gentiana lutea have been cloned from a cDNA library. They encode a geranylgeranyl pyrophosphate synthase, a phytoene synthase, a phytoene desaturase and a zeta-carotene desaturase. The indicated function of all cDNAs was established by heterologous complementation in Escherichia coli. The amino acid sequences deduced from the cDNAs were between 47.5% and 78.9% identical to those reported for the corresponding enzymes from other higher plants. Southern analysis suggested that the genes for each enzyme probably represent a small multi-gene family. Tissue-specific expression of the genes and expression during flower development was investigated. The expression of the phytoene synthase gene, psy, was enhanced in flowers but transcripts were not detected in stems and leaves by northern blotting. Transcripts of the genes for geranylgeranyl pyrophosphate (ggpps), phytoene desaturase (pds) and zeta-carotene desaturase (zds) were detected in flowers and leaves but not in stems. Analysis of the expression of psy and zds in petals revealed that levels of the transcripts were lowest in young buds and highest in fully open flowers, in parallel with the formation of carotenoids. Obviously, the transcription of these genes control the accumulation of carotenoids during flower development in G. lutea. For pds only a very slight increase of mRNA was found whereas the transcripts of ggpps decreased during flower development.

Synthesis, antimicrobial activity and gene structure of a novel member of the dermaseptin B family.

PubMed

Fleury, Y; Vouille, V; Beven, L; Amiche, M; Wróblewski, H; Delfour, A; Nicolas, P

1998-03-09

Dermaseptins are a family of cationic (Lys-rich) antimicrobial peptides that are abundant in the skin secretions of the arboreal frogs Phyllomedusa bicolor and P. sauvagii. In vitro, these peptides are microbicidal against a wide variety of microorganisms including Gram-positive and Gram-negative bacteria, yeasts, protozoa and fungi. To date, 6 dermaseptin B mature peptides, 24-34 residues long, 2 dermaseptin B cDNAs and 2 gene sequences have been identified in P. bicolor. To assess dermaseptin related genes further, we screened a P. bicolor genomic library with 32P-labeled cDNAs coding either for prepro-dermaseptins B1 or B2 (adenoregulin). A gene sequence was identified that coded a novel dermaseptin B, termed Drg3, which exhibits 23-42% amino acids identities with other members of the family. Analysis of the cDNAs coding precursors for several opioid and antimicrobial peptides originating from the skin of various amphibian species revealed that the 25-residue preproregion of these preproforms are all encoded by conserved nucleotides encompassed by the first coding exon of the Drg3 gene. Synthetic dermaseptin Drg3 exhibited a bactericidal activity towards several species of mollicutes (wall-less eubacteria), firmicutes (Gram-positive eubacteria), and gracilicutes (Gram-negative eubacteria), with minimal inhibitory concentrations (MICs) ranging from 6.25 to 100 microM. Experiments performed on Acholeplasma laidlawii cells revealed that this peptide is membranotropic and that if efficiently depolarizes the plasma membrane.

Characterization of CENH3 proteins and centromere-associated DNA sequences in diploid and allotetraploid Brassica species.

PubMed

Wang, Guixiang; He, Qunyan; Liu, Fan; Cheng, Zhukuan; Talbert, Paul B; Jin, Weiwei

2011-08-01

CENH3 is a centromere-specific histone H3 variant and has been used as a marker to identify active centromeres and DNA sequences associated with functional centromere/kinetochore complexes. In this study, up to four distinct CENH3 (BrCENH3) cDNAs were identified in individuals of each of three diploid species of Brassica. Comparison of the BrCENH3 cDNAs implied three related gene families: BrCENH3-A in Brassica rapa (AA), BrCENH3-B in B. nigra (BB), and BrCENH3-C in B. oleracea (CC). Each family encoded a histone fold domain and N-terminal histone tails that vary in length in all three families. The BrCENH3-B cDNAs have a deletion of two exons relative to BrCENH3-A and BrCENH3-C, consistent with the more ancient divergence of the BB genome. Chromatin immunoprecipitation and immunolabeling tests with anti-BrCENH3 antibodies indicated that both centromeric tandem repeats and the centromere-specific retrotransposons of Brassica are directly associated with BrCENH3 proteins. In three allotetraploid species, we find either co-transcription of the BrCENH3 genes of the ancestral diploid species or gene suppression of the BrCENH3 from one ancestor. Although B genome centromeres are occupied by BrCENH3-B in the ancestral species B. nigra, in allotetraploids both BrCENH3-A and BrCENH3-C proteins appear to assemble at these centromeres.

The delta-subunit of murine guanine nucleotide exchange factor eIF-2B. Characterization of cDNAs predicts isoforms differing at the amino-terminal end.

PubMed

Henderson, R A; Krissansen, G W; Yong, R Y; Leung, E; Watson, J D; Dholakia, J N

1994-12-02

Protein synthesis in mammalian cells is regulated at the level of the guanine nucleotide exchange factor, eIF-2B, which catalyzes the exchange of eukaryotic initiation factor 2-bound GDP for GTP. We have isolated and sequenced cDNA clones encoding the delta-subunit of murine eIF-2B. The cDNA sequence encodes a polypeptide of 544 amino acids with molecular mass of 60 kDa. Antibodies against a synthetic polypeptide of 30 amino acids deduced from the cDNA sequence specifically react with the delta-subunit of mammalian eIF-2B. The cDNA-derived amino acid sequence shows significant homology with the yeast translational regulator Gcd2, supporting the hypothesis that Gcd2 may be the yeast homolog of the delta-subunit of mammalian eIF-2B. Primer extension studies and anchor polymerase chain reaction analysis were performed to determine the 5'-end of the transcript for the delta-subunit of eIF-2B. Results of these experiments demonstrate two different mRNAs for the delta-subunit of eIF-2B in murine cells. The isolation and characterization of two different full-length cDNAs also predicts the presence of two alternate forms of the delta-subunit of eIF-2B in murine cells. These differ at their amino-terminal end but have identical nucleotide sequences coding for amino acids 31-544.

Expression of mRNAs encoding ARPP-16/19, ARPP-21, and DARPP-32 in human brain tissue.

PubMed

Brené, S; Lindefors, N; Ehrlich, M; Taubes, T; Horiuchi, A; Kopp, J; Hall, H; Sedvall, G; Greengard, P; Persson, H

1994-03-01

In this study we have isolated and sequenced human cDNAs for the phosphoproteins DARPP-32, ARPP-21, and ARPP-16/19, and have compared these sequences to previously characterized bovine and rat cDNAs. In situ hybridization and Northern blot analysis with the human cDNA probes were used to study the expression of mRNAs encoding ARPP-16/19, ARPP-21, and DARPP-32 in human postmortem brain tissue. In situ hybridization was performed using horizontal whole hemisphere sections. Five representative levels of the brain ranging from 71 mm to 104 mm ventral to vertex were examined. All three probes showed distinct hybridization patterns in the caudate nucleus, putamen, nucleus accumbens, and the amygdaloid complex. For ARPP-16/19 mRNA, a hybridization signal comparable to the signal in caudate nucleus, putamen, and nucleus accumbens was also detected in the neocortex. ARPP-21 and DARPP-32 mRNA, on the other hand, were present in lower levels in neocortical regions. DARPP-32 mRNA was abundant in the cerebellar cortex at the level of the Purkinje cell layer. High levels of ARPP-16/19 and ARPP-21 mRNA were also found in the cerebellar cortex, where they were confined to deeper layers. The present result demonstrate that mRNAs for the three phosphoproteins are expressed in overlapping, but also distinct, areas of the human brain that in many cases coincide with previously described distribution of the dopamine D1 receptor.

Cloning, characterization, and expression of xyloglucan endotransglucosylase/hydrolase and expansin genes associated with petal growth and development during carnation flower opening

PubMed Central

Harada, Taro; Torii, Yuka; Morita, Shigeto; Onodera, Reiko; Hara, Yoshinao; Yokoyama, Ryusuke; Nishitani, Kazuhiko; Satoh, Shigeru

2011-01-01

Growth of petal cells is a basis for expansion and morphogenesis (outward bending) of petals during opening of carnation flowers (Dianthus caryophyllus L.). Petal growth progressed through elongation in the early stage, expansion with outward bending in the middle stage, and expansion of the whole area in the late stage of flower opening. In the present study, four cDNAs encoding xyloglucan endotransglucosylase/hydrolase (XTH) (DcXTH1–DcXTH4) and three cDNAs encoding expansin (DcEXPA1–DcEXPA3) were cloned from petals of opening carnation flowers and characterized. Real-time reverse transcription-PCR analyses showed that transcript levels of XTH and expansin genes accumulated differently in floral and vegetative tissues of carnation plants with opening flowers, indicating regulated expression of these genes. DcXTH2 and DcXTH3 transcripts were detected in large quantities in petals as compared with other tissues. DcEXPA1 and DcEXPA2 transcripts were markedly accumulated in petals of opening flowers. The action of XTH in growing petal tissues was confirmed by in situ staining of xyloglucan endotransglucosylase (XET) activity using a rhodamine-labelled xyloglucan nonasaccharide as a substrate. Based on the present findings, it is suggested that two XTH genes (DcXTH2 and DcXTH3) and two expansin genes (DcEXPA1 and DcEXPA2) are associated with petal growth and development during carnation flower opening. PMID:20959626

A diverse family of serine proteinase genes expressed in cotton boll weevil (Anthonomus grandis): implications for the design of pest-resistant transgenic cotton plants.

PubMed

Oliveira-Neto, Osmundo B; Batista, João A N; Rigden, Daniel J; Fragoso, Rodrigo R; Silva, Rodrigo O; Gomes, Eliane A; Franco, Octávio L; Dias, Simoni C; Cordeiro, Célia M T; Monnerat, Rose G; Grossi-De-Sá, Maria F

2004-09-01

Fourteen different cDNA fragments encoding serine proteinases were isolated by reverse transcription-PCR from cotton boll weevil (Anthonomus grandis) larvae. A large diversity between the sequences was observed, with a mean pairwise identity of 22% in the amino acid sequence. The cDNAs encompassed 11 trypsin-like sequences classifiable into three families and three chymotrypsin-like sequences belonging to a single family. Using a combination of 5' and 3' RACE, the full-length sequence was obtained for five of the cDNAs, named Agser2, Agser5, Agser6, Agser10 and Agser21. The encoded proteins included amino acid sequence motifs of serine proteinase active sites, conserved cysteine residues, and both zymogen activation and signal peptides. Southern blotting analysis suggested that one or two copies of these serine proteinase genes exist in the A. grandis genome. Northern blotting analysis of Agser2 and Agser5 showed that for both genes, expression is induced upon feeding and is concentrated in the gut of larvae and adult insects. Reverse northern analysis of the 14 cDNA fragments showed that only two trypsin-like and two chymotrypsin-like were expressed at detectable levels. Under the effect of the serine proteinase inhibitors soybean Kunitz trypsin inhibitor and black-eyed pea trypsin/chymotrypsin inhibitor, expression of one of the trypsin-like sequences was upregulated while expression of the two chymotrypsin-like sequences was downregulated. Copyright 2004 Elsevier Ltd.

Virtual Northern Analysis of the Human Genome

PubMed Central

Hurowitz, Evan H.; Drori, Iddo; Stodden, Victoria C.; Donoho, David L.; Brown, Patrick O.

2007-01-01

Background We applied the Virtual Northern technique to human brain mRNA to systematically measure human mRNA transcript lengths on a genome-wide scale. Methodology/Principal Findings We used separation by gel electrophoresis followed by hybridization to cDNA microarrays to measure 8,774 mRNA transcript lengths representing at least 6,238 genes at high (>90%) confidence. By comparing these transcript lengths to the Refseq and H-Invitational full-length cDNA databases, we found that nearly half of our measurements appeared to represent novel transcript variants. Comparison of length measurements determined by hybridization to different cDNAs derived from the same gene identified clones that potentially correspond to alternative transcript variants. We observed a close linear relationship between ORF and mRNA lengths in human mRNAs, identical in form to the relationship we had previously identified in yeast. Some functional classes of protein are encoded by mRNAs whose untranslated regions (UTRs) tend to be longer or shorter than average; these functional classes were similar in both human and yeast. Conclusions/Significance Human transcript diversity is extensive and largely unannotated. Our length dataset can be used as a new criterion for judging the completeness of cDNAs and annotating mRNA sequences. Similar relationships between the lengths of the UTRs in human and yeast mRNAs and the functions of the proteins they encode suggest that UTR sequences serve an important regulatory role among eukaryotes. PMID:17520019

Olfactory Proteins Mediating Chemical Communication in the Navel Orangeworm Moth, Amyelois transitella

PubMed Central

Leal, Walter S.; Ishida, Yuko; Pelletier, Julien; Xu, Wei; Rayo, Josep; Xu, Xianzhong; Ames, James B.

2009-01-01

Background The navel orangeworm, Amyelois transitella Walker (Lepidoptera: Pyralidae), is the most serious insect pest of almonds and pistachios in California for which environmentally friendly alternative methods of control — like pheromone-based approaches — are highly desirable. Some constituents of the sex pheromone are unstable and could be replaced with parapheromones, which may be designed on the basis of molecular interaction of pheromones and pheromone-detecting olfactory proteins. Methodology By analyzing extracts from olfactory and non-olfactory tissues, we identified putative olfactory proteins, obtained their N-terminal amino acid sequences by Edman degradation, and used degenerate primers to clone the corresponding cDNAs by SMART RACE. Additionally, we used degenerate primers based on conserved sequences of known proteins to fish out other candidate olfactory genes. We expressed the gene encoding a newly identified pheromone-binding protein, which was analyzed by circular dichroism, fluorescence, and nuclear magnetic resonance, and used in a binding assay to assess affinity to pheromone components. Conclusion We have cloned nine cDNAs encoding olfactory proteins from the navel orangeworm, including two pheromone-binding proteins, two general odorant-binding proteins, one chemosensory protein, one glutathione S-transferase, one antennal binding protein X, one sensory neuron membrane protein, and one odorant receptor. Of these, AtraPBP1 is highly enriched in male antennae. Fluorescence, CD and NMR studies suggest a dramatic pH-dependent conformational change, with high affinity to pheromone constituents at neutral pH and no binding at low pH. PMID:19789654

Cloning of cDNAs for H1F0, TOP1, CLTA and CDK1 and the effects of cryopreservation on the expression of their mRNA transcripts in yak (Bos grunniens) oocytes.

PubMed

Niu, Hui-Ran; Zi, Xiang-Dong; Xiao, Xiao; Xiong, Xian-Rong; Zhong, Jin-Cheng; Li, Jian; Wang, Li; Wang, Yong

2014-08-01

We cloned and sequenced four pivotal cDNAs involved in DNA structural maintenance (H1F0 and TOP1) and the cell cycle (CLTA and CDK1) from yak oocytes. In addition, we studied the consequences of freezing-thawing (F/T) processes on the expression of their mRNA transcripts in yak immature and in vitro matured (MII) oocytes. H1F0, TOP1, CLTA and CDK1 cDNAs were cloned from yak oocytes by reverse transcriptase-polymerase chain reaction (RT-PCR) strategy. The expression of their mRNA transcript analyses were performed upon fresh and frozen-thawed immature germinal vesicle (GV) and MII yak oocytes following normalization of transcripts with GAPDH by real-time PCR. The yak H1F0, TOP1, CLTA and CDK1 cDNA sequences were found to consist of CDK1 585, 2539, 740, and 894 bp, respectively. Their coding regions encoded 195, 768, 244, and 298 amino acids, respectively. The homology with that of cattle was very high (95.2%, 98.8%, 93.6%, and 89.5%, respectively nucleotide sequence level, and 94.3%, 98.2%, 87.7%, and 90.9%, respectively at the deduced amino acid level). The overall mRNA expression levels of these four transcripts were reduced by F/T process, albeit at different levels. TOP1 in GV-oocytes, and H1F0 and CDK1 in MII-oocytes of the yak were significantly down-regulated (P<0.05). This is the first isolation and characterization of H1F0, TOP1, CLTA, and CDK1 cDNAs from yak oocytes. The lower fertility and developmental ability of yak oocytes following fertilization after cryopreservation may be explained by the alterations to their gene expression profiles. Copyright © 2014 Elsevier Inc. All rights reserved.

Characterization of a cDNA encoding a protein involved in formation of the skeleton during development of the sea urchin Lytechinus pictus.

PubMed

Livingston, B T; Shaw, R; Bailey, A; Wilt, F

1991-12-01

In order to investigate the role of proteins in the formation of mineralized tissues during development, we have isolated a cDNA that encodes a protein that is a component of the organic matrix of the skeletal spicule of the sea urchin, Lytechinus pictus. The expression of the RNA encoding this protein is regulated over development and is localized to the descendents of the micromere lineage. Comparison of the sequence of this cDNA to homologous cDNAs from other species of urchin reveal that the protein is basic and contains three conserved structural motifs: a signal peptide, a proline-rich region, and an unusual region composed of a series of direct repeats. Studies on the protein encoded by this cDNA confirm the predicted reading frame deduced from the nucleotide sequence and show that the protein is secreted and not glycosylated. Comparison of the amino acid sequence to databases reveal that the repeat domain is similar to proteins that form a unique beta-spiral supersecondary structure.

Description and phylogenetic placement of Beauveria hoplocheli sp. nov. used in the biological control of the sugarcane white grub, Hoplochelus marginalis, on Reunion Island.

PubMed

Robène-Soustrade, Isabelle; Jouen, Emmanuel; Pastou, Didier; Payet-Hoarau, Magali; Goble, Tarryn; Linderme, Daphné; Lefeuvre, Pierre; Calmès, Cédric; Reynaud, Bernard; Nibouche, Samuel; Costet, Laurent

2015-01-01

On Reunion Island successful biological control of the sugarcane white grub Hoplochelus marginalis Fairmaire (Coleoptera: Melolonthidae) has been conducted for decades with strains from the entomopathogenic fungal genus Beauveria (Ascomycota: Hypocreales). A study based on morphological characters combined with a multisequence phylogenetic analysis of genes that encode the translation elongation factor 1-alpha (TEF1), RNA polymerase II largest subunit (RPB1), RNA polymerase II second largest subunit (RPB2) and the Bloc nuc intergenic region was carried out on Beauveria strains isolated on Reunion and Madagascar from H. marginalis. This study revealed that these strains, previously identified as Beauveria brongniartii, did not match that species and are closely related to but still distinct from B. malawiensis strains. Therefore we describe the Reunion Island fungus as the new species B. hoplocheli. © 2015 by The Mycological Society of America.

Molecular cloning and biochemical characterization of three phosphoglycerate kinase isoforms from developing sunflower (Helianthus annuus L.) seeds.

PubMed

Troncoso-Ponce, M A; Rivoal, J; Venegas-Calerón, M; Dorion, S; Sánchez, R; Cejudo, F J; Garcés, R; Martínez-Force, E

2012-07-01

Three cDNAs encoding different phosphoglycerate kinase (PGK, EC 2.7.2.3) isoforms, two cytosolic (HacPGK1 and HacPGK2) and one plastidic (HapPGK), were cloned and characterized from developing sunflower (Helianthus annuus L.) seeds. The expression profiles of these genes showed differences in heterotrophic tissues, such as developing seeds and roots, where HacPGK1 was predominant, while HapPGK was highly expressed in photosynthetic tissues. The cDNAs were expressed in Escherichia coli, and the corresponding proteins purified to electrophoretic homogeneity, using immobilized metal ion affinity chromatography, and biochemically characterized. Despite the high level of identity between sequences, the HacPGK1 isoform showed strong differences in terms of specific activity, temperature stability and pH sensitivity in comparison to HacPGK2 and HapPGK. A polyclonal immune serum was raised against the purified HacPGK1 isoform, which showed cross-immunoreactivity with the other PGK isoforms. This serum allowed the localization of high expression levels of PGK isozymes in embryo tissues. Copyright © 2012 Elsevier Ltd. All rights reserved.

Cloning and purification of alpha-neurotoxins from king cobra (Ophiophagus hannah).

PubMed

He, Ying-Ying; Lee, Wei-Hui; Zhang, Yun

2004-09-01

Thirteen complete and three partial cDNA sequences were cloned from the constructed king cobra (Ophiophagus hannah) venom gland cDNA library. Phylogenetic analysis of nucleotide sequences of king cobra with those from other snake venoms revealed that obtained cDNAs are highly homologous to snake venom alpha-neurotoxins. Alignment of deduced mature peptide sequences of the obtained clones with those of other reported alpha-neurotoxins from the king cobra venom indicates that our obtained 16 clones belong to long-chain neurotoxins (seven), short-chain neurotoxins (seven), weak toxin (one) and variant (one), respectively. Up to now, two out of 16 newly cloned king cobra alpha-neurotoxins have identical amino acid sequences with CM-11 and Oh-6A/6B, which have been characterized from the same venom. Furthermore, five long-chain alpha-neurotoxins and two short-chain alpha-neurotoxins were purified from crude venom and their N-terminal amino acid sequences were determined. The cDNAs encoding the putative precursors of the purified native peptide were also determined based on the N-terminal amino acid sequencing. The purified alpha-neurotoxins showed different lethal activities on mice.

Identification and Analysis of a Gene from Calendula officinalis Encoding a Fatty Acid Conjugase

PubMed Central

Qiu, Xiao; Reed, Darwin W.; Hong, Haiping; MacKenzie, Samuel L.; Covello, Patrick S.

2001-01-01

Two homologous cDNAs, CoFad2 and CoFac2, were isolated from a Calendula officinalis developing seed by a polymerase chain reaction-based cloning strategy. Both sequences share similarity to FAD2 desaturases and FAD2-related enzymes. In C. officinalis plants CoFad2 was expressed in all tissues tested, whereas CoFac2 expression was specific to developing seeds. Expression of CoFad2 cDNA in yeast (Saccharomyces cerevisiae) indicated it encodes a Δ12 desaturase that introduces a double bond at the 12 position of 16:1(9Z) and 18:1(9Z). Expression of CoFac2 in yeast revealed that the encoded enzyme acts as a fatty acid conjugase converting 18:2(9Z, 12Z) to calendic acid 18:3(8E, 10E, 12Z). The enzyme also has weak activity on the mono-unsaturates 16:1(9Z) and 18:1(9Z) producing compounds with the properties of 8,10 conjugated dienes. PMID:11161042

Gene 2 of the sigma rhabdovirus genome encodes the P protein, and gene 3 encodes a protein related to the reverse transcriptase of retroelements.

PubMed

Landès-Devauchelle, C; Bras, F; Dezélée, S; Teninges, D

1995-11-10

The nucleotide sequence of the genes 2 and 3 of the Drosophila rhabdovirus sigma was determined from cDNAs to viral genome and poly(A)+ mRNAs. Gene 2 comprises 1032 nucleotides and contains a long ORF encoding a molecular weight 35,208 polypeptide present in infected cells and in virions which migrates in SDS-PAGE as a doublet of M(r) about 60 kDa. The distribution of acidic charges as well as the electrophoretic properties of the protein are characteristic of the rhabdovirus P proteins. Gene 3 comprises 923 nucleotides and contains a long ORF capable of coding a polypeptide of 298 amino acids of MW 33,790. The putative protein (PP3) is similar in size to a minor component of the virions. Computer analysis shows that the sequence of PP3 contains three motifs related to the conserved motifs of reverse transcriptases.

Characterization and analysis of ribosomal proteins in two marine calanoid copepods

NASA Astrophysics Data System (ADS)

Yang, Feifei; Xu, Donghui; Zhuang, Yunyun; Huang, Yousong; Yi, Xiaoyan; Chen, Hongju; Liu, Guangxing; Zhang, Huan

2016-11-01

Copepods are among the most abundant and successful metazoans in the marine ecosystem. However, genomic resources related to fundamental cellular processes are still limited in this particular group of crustaceans. Ribosomal proteins are the building blocks of ribosomes, the primary site for protein synthesis. In this study, we characterized and analyzed the cDNAs of cytoplasmic ribosomal proteins (cRPs) of two calanoid copepods, Pseudodiaptomus poplesia and Acartia pacifica. We obtained 79 cRP cDNAs from P. poplesia and 67 from A. pacifica by cDNA library construction/sequencing and rapid amplification of cDNA ends. Analysis of the nucleic acid composition showed that the copepod cRP-encoding genes had higher GC content in the protein-coding regions (CDSs) than in the untranslated regions (UTRs), and single nucleotide repeats (>3 repeats) were common, with "A" repeats being the most frequent, especially in the CDSs. The 3'-UTRs of the cRP genes were significantly longer than the 5'-UTRs. Codon usage analysis showed that the third positions of the codons were dominated by C or G. The deduced amino acid sequences of the cRPs contained high proportions of positively charged residues and had high pI values. This is the first report of a complete set of cRP-encoding genes from copepods. Our results shed light on the characteristics of cRPs in copepods, and provide fundamental data for further studies of protein synthesis in copepods. The copepod cRP information revealed in this study indicates that additional comparisons and analysis should be performed on different taxonomic categories such as orders and families.

Identification of a mouse B-type cyclin which exhibits developmentally regulated expression in the germ line

NASA Technical Reports Server (NTRS)

Chapman, D. L.; Wolgemuth, D. J.

1992-01-01

To begin to examine the function of cyclins in mammalian germ cells, we have screened an adult mouse testis cDNA library for the presence of B-type cyclins. We have isolated cDNAs that encode a murine B-type cyclin, which has been designated cycB1. cycB1 was shown to be expressed in several adult tissues and in the midgestation mouse embryo. In the adult tissues, the highest levels of cycB1 transcripts were seen in the testis and ovary, which contain germ cells at various stages of differentiation. The major transcripts corresponding to cycB1 are 1.7 and 2.5 kb, with the 1.7 kb species being the predominant testicular transcript and the 2.5 kb species more abundant in the ovary. Examination of cDNAs corresponding to the 2.5 kb and 1.7 kb mRNAs revealed that these transcripts encode identical proteins, differing only in the polyadenylation signal used and therefore in the length of their 3' untranslated regions. Northern blot and in situ hybridization analyses revealed that the predominant sites of cycB1 expression in the testis and ovary were in the germinal compartment, particularly in early round spermatids in the testis and growing oocytes in the ovary. Thus cycB1 is expressed in both meiotic and postmeiotic cells. This pattern of cycB1 expression further suggests that cycB1 may have different functions in the two cell types, only one of which correlates with progression of the cell cycle.

Recombinant pinoresinol/lariciresinol reductase, recombinant dirigent protein, and methods of use

DOEpatents

Lewis, Norman G.; Davin, Laurence B.; Dinkova-Kostova, Albena T.; Fujita, Masayuki; Gang, David R.; Sarkanen, Simo; Ford, Joshua D.

2001-04-03

Dirigent proteins and pinoresinol/lariciresinol reductases have been isolated, together with cDNAs encoding dirigent proteins and pinoresinol/lariciresinol reductases. Accordingly, isolated DNA sequences are provided which code for the expression of dirigent proteins and pinoresinol/lariciresinol reductases. In other aspects, replicable recombinant cloning vehicles are provided which code for dirigent proteins or pinoresinol/lariciresinol reductases or for a base sequence sufficiently complementary to at least a portion of dirigent protein or pinoresinol/lariciresinol reductase DNA or RNA to enable hybridization therewith. In yet other aspects, modified host cells are provided that have been transformed, transfected, infected and/or injected with a recombinant cloning vehicle and/or DNA sequence encoding dirigent protein or pinoresinol/lariciresinol reductase. Thus, systems and methods are provided for the recombinant expression of dirigent proteins and/or pinoresinol/lariciresinol reductases.

Cloning and sequence analysis of a cDNA encoding the alpha-subunit of mouse beta-N-acetylhexosaminidase and comparison with the human enzyme.

PubMed Central

Beccari, T; Hoade, J; Orlacchio, A; Stirling, J L

1992-01-01

cDNAs encoding the mouse beta-N-acetylhexosaminidase alpha-subunit were isolated from a mouse testis library. The longest of these (1.7 kb) was sequenced and showed 83% similarity with the human alpha-subunit cDNA sequence. The 5' end of the coding sequence was obtained from a genomic DNA clone. Alignment of the human and mouse sequences showed that all three putative N-glycosylation sites are conserved, but that the mouse alpha-subunit has an additional site towards the C-terminus. All eight cysteines in the human sequence are conserved in the mouse. There are an additional two cysteines in the mouse alpha-subunit signal peptide. All amino acids affected in Tay-Sachs-disease mutations are conserved in the mouse. Images Fig. 1. PMID:1379046

Molecular cloning of pepsinogens A and C from adult newt (Cynops pyrrhogaster) stomach.

PubMed

Inokuchi, Tomofumi; Ikuzawa, Masayuki; Yamazaki, Shin; Watanabe, Yukari; Shiota, Koushiro; Katoh, Takuma; Kobayashi, Ken-Ichiro

2013-08-01

The full-length cDNAs of three pepsinogens (Pgs) were cloned from the stomach of newt, Cynops pyrrhogaster, and nucleotide sequences of the full-length cDNAs were determined. Molecular phylogenetic analysis showed that two Pgs, named PgC1 and PgC2, belong to the pepsinogen C group, and one Pg, named PgA, belongs to the pepsinogen A group. The sequences contain an open reading frame (ORF) encoding 385 amino acid residues for PgC1, 383 amino acid residues for PgC2 and 377 amino acid residues for PgA. In addition, all of the three amino acid sequences conserve some unique characteristics such as six cysteine residues and putative active site two aspartic acid residues. All of the pepsinogen mRNAs were detected in the stomach by RT-PCR but not in other organs. Although a slight difference at the time of the start of expression was seen among the three pepsinogen genes, all of them were expressed in the larval stage after hatching. This is the first report on cloning of pepsinogens from urodele stomach. Copyright © 2013 Elsevier Inc. All rights reserved.

Twelve actin-encoding cDNAs from the American lobster, Homarus americanus: cloning and tissue expression of eight skeletal muscle, one heart, and three cytoplasmic isoforms.

PubMed

Kim, Bo Kwang; Kim, Kyoung Sun; Oh, Chul-Woong; Mykles, Donald L; Lee, Sung Gu; Kim, Hak Jun; Kim, Hyun-Woo

2009-06-01

Lobster muscles express a diverse array of myofibrillar protein isoforms. Three fiber types (fast, slow-twitch or S1, and slow-tonic or S2) differ qualitatively and quantitatively in myosin heavy and light chains, troponin-T, -I, and -C, paramyosin, and tropomyosin variants. However, little is known about the diversity of actin isoforms present in crustacean tissues. In this report we characterized cDNAs that encode twelve actin isoforms in the American lobster, Homarus americanus: eight from skeletal muscle (Ha-ActinSK1-8), one from heart (Ha-ActinHT1), and three cytoplasmic type actins from hepatopancreas (Ha-ActinCT1-3). All twelve cDNAs were products of distinct genes, as indicated by differences in the 3'-untranslated regions (UTRs). The open reading frames specified polypeptides 376 or 377 amino acids in length. Although key amino residues are conserved in the lobster actins, variations in nearby sequences may affect actin polymerization and/or interactions with other myofibrillar proteins. Quantitative reverse transcription-polymerase chain reaction showed muscle fiber type- and tissue-specific expression patterns. Ha-Actin-HT1 was expressed exclusively in heart (87% of the total; 12% of the total was Ha-ActinCT1). Ha-ActinCT1 was expressed in all tissues, while CT2 and CT3 were expressed only in hepatopancreas, with Ha-ActinCT2 as the major isoform (93% of the total). Ha-ActinSK1 and SK2 were the major isoforms (88% and 12% of the total, respectively) in the S1 fibers of crusher claw closer muscle. Fast fibers in the cutter claw closer and deep abdominal muscles differed in SK isoforms. Ha-ActinSK3, SK4, and SK5 were the major isoforms in cutter claw closer muscle (12%, 48%, and 37% of the total, respectively). Ha-ActinSK5 and SK8 were the major isoforms in deep abdominal flexor (31% and 65% of the total, respectively) and extensor (46% and 53% of the total, respectively) muscles, with SK6 and SK7 expressed at low levels. These data indicate that fast fibers in cutter claw and abdominal muscles show a phenotypic plasticity with respect to the expression of actin isoforms and may constitute discrete subtypes that differ in contractile properties.

Recominant Pinoresino-Lariciresinol Reductase, Recombinant Dirigent Protein And Methods Of Use

DOEpatents

Lewis, Norman G.; Davin, Laurence B.; Dinkova-Kostova, Albena T.; Fujita, Masayuki , Gang; David R. , Sarkanen; Simo , Ford; Joshua D.

2003-10-21

Dirigent proteins and pinoresinol/lariciresinol reductases have been isolated, together with cDNAs encoding dirigent proteins and pinoresinol/lariciresinol reductases. Accordingly, isolated DNA sequences are provided from source species Forsythia intermedia, Thuja plicata, Tsuga heterophylla, Eucommia ulmoides, Linum usitatissimum, and Schisandra chinensis, which code for the expression of dirigent proteins and pinoresinol/lariciresinol reductases. In other aspects, replicable recombinant cloning vehicles are provided which code for dirigent proteins or pinoresinol/lariciresinol reductases or for a base sequence sufficiently complementary to at least a portion of dirigent protein or pinoresinol/lariciresinol reductase DNA or RNA to enable hybridization therewith. In yet other aspects, modified host cells are provided that have been transformed, transfected, infected and/or injected with a recombinant cloning vehicle and/or DNA sequence encoding dirigent protein or pinoresinol/lariciresinol reductase. Thus, systems and methods are provided for the recombinant expression of dirigent proteins and/or pinoresinol/lariciresinol reductases.

Opsin cDNA sequences of a UV and green rhodopsin of the satyrine butterfly Bicyclus anynana.

PubMed

Vanhoutte, K J A; Eggen, B J L; Janssen, J J M; Stavenga, D G

2002-11-01

The cDNAs of an ultraviolet (UV) and long-wavelength (LW) (green) absorbing rhodopsin of the bush brown Bicyclus anynana were partially identified. The UV sequence, encoding 377 amino acids, is 76-79% identical to the UV sequences of the papilionids Papilio glaucus and Papilio xuthus and the moth Manduca sexta. A dendrogram derived from aligning the amino acid sequences reveals an equidistant position of Bicyclus between Papilio and Manduca. The sequence of the green opsin cDNA fragment, which encodes 242 amino acids, represents six of the seven transmembrane regions. At the amino acid level, this fragment is more than 80% identical to the corresponding LW opsin sequences of Dryas, Heliconius, Papilio (rhodopsin 2) and Manduca. Whereas three LW absorbing rhodopsins were identified in the papilionid butterflies, only one green opsin was found in B. anynana.

Isolation of candidate genes for apomictic development in buffelgrass (Pennisetum ciliare).

PubMed

Singh, Manjit; Burson, Byron L; Finlayson, Scott A

2007-08-01

Asexual reproduction through seeds, or apomixis, is a process that holds much promise for agricultural advances. However, the molecular mechanisms underlying apomixis are currently poorly understood. To identify genes related to female gametophyte development in apomictic ovaries of buffelgrass (Pennisetum ciliare (L.) Link), Suppression Subtractive Hybridization of ovary cDNA with leaf cDNA was performed. Through macroarray screening of subtracted cDNAs two genes were identified, Pca21 and Pca24, that showed differential expression between apomictic and sexual ovaries. Sequence analysis showed that both Pca21 and Pca24 are novel genes not previously characterized in plants. Pca21 shows homology to two wheat genes that are also expressed during reproductive development. Pca24 has similarity to coiled-coil-helix-coiled-coil-helix (CHCH) domain containing proteins from maize and sugarcane. Northern blot analysis revealed that both of these genes are expressed throughout female gametophyte development in apomictic ovaries. In situ hybridizations localized the transcript of these two genes to the developing embryo sacs in the apomictic ovaries. Based on the expression patterns it was concluded that Pca21 and Pca24 likely play a role during apomictic development in buffelgrass.

The CYP88A cytochrome P450, ent-kaurenoic acid oxidase, catalyzes three steps of the gibberellin biosynthesis pathway

PubMed Central

Helliwell, Chris A.; Chandler, Peter M.; Poole, Andrew; Dennis, Elizabeth S.; Peacock, W. James

2001-01-01

We have shown that ent-kaurenoic acid oxidase, a member of the CYP88A subfamily of cytochrome P450 enzymes, catalyzes the three steps of the gibberellin biosynthetic pathway from ent-kaurenoic acid to GA12. A gibberellin-responsive barley mutant, grd5, accumulates ent-kaurenoic acid in developing grains. Three independent grd5 mutants contain mutations in a gene encoding a member of the CYP88A subfamily of cytochrome P450 enzymes, defined by the maize Dwarf3 protein. Mutation of the Dwarf3 gene gives rise to a gibberellin-responsive dwarf phenotype, but the lesion in the gibberellin biosynthesis pathway has not been identified. Arabidopsis thaliana has two CYP88A genes, both of which are expressed. Yeast strains expressing cDNAs encoding each of the two Arabidopsis and the barley CYP88A enzymes catalyze the three steps of the GA biosynthesis pathway from ent-kaurenoic acid to GA12. Sequence comparison suggests that the maize Dwarf3 locus also encodes ent-kaurenoic acid oxidase. PMID:11172076

Functional characterization of nine Norway Spruce TPS genes and evolution of gymnosperm terpene synthases of the TPS-d subfamily.

PubMed

Martin, Diane M; Fäldt, Jenny; Bohlmann, Jörg

2004-08-01

Constitutive and induced terpenoids are important defense compounds for many plants against potential herbivores and pathogens. In Norway spruce (Picea abies L. Karst), treatment with methyl jasmonate induces complex chemical and biochemical terpenoid defense responses associated with traumatic resin duct development in stems and volatile terpenoid emissions in needles. The cloning of (+)-3-carene synthase was the first step in characterizing this system at the molecular genetic level. Here we report the isolation and functional characterization of nine additional terpene synthase (TPS) cDNAs from Norway spruce. These cDNAs encode four monoterpene synthases, myrcene synthase, (-)-limonene synthase, (-)-alpha/beta-pinene synthase, and (-)-linalool synthase; three sesquiterpene synthases, longifolene synthase, E,E-alpha-farnesene synthase, and E-alpha-bisabolene synthase; and two diterpene synthases, isopimara-7,15-diene synthase and levopimaradiene/abietadiene synthase, each with a unique product profile. To our knowledge, genes encoding isopimara-7,15-diene synthase and longifolene synthase have not been previously described, and this linalool synthase is the first described from a gymnosperm. These functionally diverse TPS account for much of the structural diversity of constitutive and methyl jasmonate-induced terpenoids in foliage, xylem, bark, and volatile emissions from needles of Norway spruce. Phylogenetic analyses based on the inclusion of these TPS into the TPS-d subfamily revealed that functional specialization of conifer TPS occurred before speciation of Pinaceae. Furthermore, based on TPS enclaves created by distinct branching patterns, the TPS-d subfamily is divided into three groups according to sequence similarities and functional assessment. Similarities of TPS evolution in angiosperms and modeling of TPS protein structures are discussed.

Mo-CBP3, an Antifungal Chitin-Binding Protein from Moringa oleifera Seeds, Is a Member of the 2S Albumin Family

PubMed Central

Freire, José E. C.; Vasconcelos, Ilka M.; Moreno, Frederico B. M. B.; Batista, Adelina B.; Lobo, Marina D. P.; Pereira, Mirella L.; Lima, João P. M. S.; Almeida, Ricardo V. M.; Sousa, Antônio J. S.; Monteiro-Moreira, Ana C. O.; Oliveira, José T. A.; Grangeiro, Thalles B.

2015-01-01

Mo-CBP3 is a chitin-binding protein from M. oleifera seeds that inhibits the germination and mycelial growth of phytopathogenic fungi. This protein is highly thermostable and resistant to pH changes, and therefore may be useful in the development of new antifungal drugs. However, the relationship of MoCBP3 with the known families of carbohydrate-binding domains has not been established. In the present study, full-length cDNAs encoding 4 isoforms of Mo-CBP3 (Mo-CBP3-1, Mo-CBP3-2, Mo-CBP3-3 and Mo-CBP3-4) were cloned from developing seeds. The polypeptides encoded by the Mo-CBP3 cDNAs were predicted to contain 160 (Mo-CBP3-3) and 163 amino acid residues (Mo-CBP3-1, Mo-CBP3-2 and Mo-CBP3-4) with a signal peptide of 20-residues at the N-terminal region. A comparative analysis of the deduced amino acid sequences revealed that Mo-CBP3 is a typical member of the 2S albumin family, as shown by the presence of an eight-cysteine motif, which is a characteristic feature of the prolamin superfamily. Furthermore, mass spectrometry analysis demonstrated that Mo-CBP3 is a mixture of isoforms that correspond to different mRNA products. The identification of Mo-CBP3 as a genuine member of the 2S albumin family reinforces the hypothesis that these seed storage proteins are involved in plant defense. Moreover, the chitin-binding ability of Mo-CBP3 reveals a novel functionality for a typical 2S albumin. PMID:25789746

Characterization of a gene family abundantly expressed in Oenothera organensis pollen that shows sequence similarity to polygalacturonase.

PubMed Central

Brown, S M; Crouch, M L

1990-01-01

We have isolated and characterized cDNA clones of a gene family (P2) expressed in Oenothera organensis pollen. This family contains approximately six to eight family members and is expressed at high levels only in pollen. The predicted protein sequence from a near full-length cDNA clone shows that the protein products of these genes are at least 38,000 daltons. We identified the protein encoded by one of the cDNAs in this family by using antibodies to beta-galactosidase/pollen cDNA fusion proteins. Immunoblot analysis using these antibodies identifies a family of proteins of approximately 40 kilodaltons that is present in mature pollen, indicating that these mRNAs are not stored solely for translation after pollen germination. These proteins accumulate late in pollen development and are not detectable in other parts of the plant. Although not present in unpollinated or self-pollinated styles, the 40-kilodalton to 45-kilodalton antigens are detectable in extracts from cross-pollinated styles, suggesting that the proteins are present in pollen tubes growing through the style during pollination. The proteins are also present in pollen tubes growing in vitro. Both nucleotide and amino acid sequences are similar to the published sequences for cDNAs encoding the enzyme polygalacturonase, which suggests that the P2 gene family may function in depolymerizing pectin during pollen development, germination, and tube growth. Cross-hybridizing RNAs and immunoreactive proteins were detected in pollen from a wide variety of plant species, which indicates that the P2 family of polygalacturonase-like genes are conserved and may be expressed in the pollen from many angiosperms. PMID:2152116

Categorizing sugarcane cultivar resistance to the sugarcane aphid and yellow sugarcane aphid (Hemiptera: Aphididae)

USDA-ARS?s Scientific Manuscript database

Sugarcane in the U.S. is chiefly colonized by two aphid species, the sugarcane aphid, Melanaphis sacchari, and the yellow sugarcane aphid, Sipha flava, which vector economically important viruses of the crop. Greenhouse experiments were conducted to categorize commercial sugarcane cultivars for the...

Categorizing Sugarcane Cultivar Resistance to the Sugarcane Aphid and Yellow Sugarcane Aphid (Hemiptera: Aphidae)

USDA-ARS?s Scientific Manuscript database

Sugarcane in Louisiana is colonized by two aphid species, the sugarcane aphid, Melanaphis sacchari (Zehntner), and the yellow sugarcane aphid, Sipha flava (Forbes). The main problem associated with M. sacchari is transmission of sugarcane yellow leaf virus, a disease that has been added to certifica...

Determining seed transmission of sugarcane mosaic virus and sugarcane yellow leaf virus in sugarcane

USDA-ARS?s Scientific Manuscript database

The importation of sugarcane germplasm is essential to diversify sugarcane germplasm used in United States breeding programs. Foreign germplasm is received primarily as vegetative cuttings. Current permit requirements for importing sugarcane seed into the United States are impractical and limit the ...

Molecular and Functional Characterization of cDNAs Putatively Encoding Carboxylesterases from the Migratory Locust, Locusta migratoria

PubMed Central

Zhang, Jianqin; Li, Daqi; Ge, Pingting; Guo, Yaping; Zhu, Kun Yan; Ma, Enbo; Zhang, Jianzhen

2014-01-01

Carboxylesterases (CarEs) belong to a superfamily of metabolic enzymes encoded by a number of genes and are widely distributed in microbes, plants and animals including insects. These enzymes play important roles in detoxification of insecticides and other xenobiotics, degradation of pheromones, regulation of neurodevelopment, and control of animal development. In this study, we characterized a total of 39 full-length cDNAs putatively encoding different CarEs from the migratory locust, Locusta migratoria, one of the most severe insect pests in many regions of the world, and evaluated the role of four CarE genes in insecticide detoxification. Our phylogenetic analysis grouped the 39 CarEs into five different clades including 20 CarEs in clade A, 3 in D, 13 in E, 1 in F and 2 in I. Four CarE genes (LmCesA3, LmCesA20, LmCesD1, LmCesE1), representing three different clades (A, D and E), were selected for further analyses. The transcripts of the four genes were detectable in all the developmental stages and tissues examined. LmCesA3 and LmCesE1 were mainly expressed in the fat bodies and Malpighian tubules, whereas LmCesA20 and LmCesD1 were predominately expressed in the muscles and hemolymph, respectively. The injection of double-stranded RNA (dsRNA) synthesized from each of the four CarE genes followed by the bioassay with each of four insecticides (chlorpyrifos, malathion, carbaryl and deltamethrin) increased the nymphal mortalities by 37.2 and 28.4% in response to malathion after LmCesA20 and LmCesE1 were silenced, respectively. Thus, we proposed that both LmCesA20 and LmCesE1 played an important role in detoxification of malathion in the locust. These results are expected to help researchers reveal the characteristics of diverse CarEs and assess the risk of insecticide resistance conferred by CarEs in the locust and other insect species. PMID:24722667

Elimination of five sugarcane viruses from sugarcane using in vitro culture of axillary bud and apical meristem

USDA-ARS?s Scientific Manuscript database

Procedures were developed for the in vitro elimination of Sugarcane mosaic virus (SCMV), Sorghum mosaic virus (SrMV), Sugarcane streak mosaic virus (SCSMV), Sugarcane yellow leaf virus (SCYLV) and Fiji disease virus (FDV) from infected sugarcane. In vitro shoot regeneration, elongation and virus el...

Determination of flavonoids in cultivated sugarcane leaves, bagasse, juice and in transgenic sugarcane by liquid chromatography-UV detection.

PubMed

Colombo, Renata; Lanças, Fernando M; Yariwake, Janete H

2006-01-20

A high-performance liquid chromatography (HPLC) method with photo-diode array (DAD) detection was developed to separate and quantify flavonoids in sugarcane leaves and bagasse (= the crushed sugarcane refuse from juice extraction), and in sugarcane juice. Sugarcane flavonoids consist of a complex mixture of aglycones and glycosides (including flavonolignan glycosides), and the HPLC-UV method herein proposed is suitable for their quantification as total flavonoids. This method was applied to analyze samples of cultivated sugarcane, commercial juice and transgenic sugarcane leaves. Sugarcane leaves proved a promising source of flavonoids: an average of 1.10 mg of total flavonoids/g plant material was found in fresh leaves. Moreover, the flavonoid content of sugarcane juice (0.6 mg/mL) is comparable to other food sources of flavonoids previously reported. Transgenic sugarcane leaves ("Bowman-Birk" and "Kunitz") were compared with non-modified ("control") plant samples using the proposed HPLC-UV method, which indicated that the content of total flavonoids in transgenic plants is different from that in non-modified sugarcane.

Characterization of cDNAs encoding the chick retinoic acid receptor gamma 2 and preferential distribution of retinoic acid receptor gamma transcripts during chick skin development.

PubMed

Michaille, J J; Blanchet, S; Kanzler, B; Garnier, J M; Dhouailly, D

1994-12-01

Retinoic acid receptors alpha, beta and gamma (RAR alpha, beta and gamma) are ligand-inductible transcriptional activators which belong to the steroid/thyroid hormone receptor superfamily. At least two major isoforms (1 and 2) of each RAR arise by differential use of two promoters and alternative splicing. In mouse, the three RAR genes are expressed in stage- and tissue-specific patterns during embryonic development. In order to understand the role of the different RARs in chick, RAR gamma 2 cDNAs were isolated from an 8.5-day (stage 35 of Hamburger and Hamilton) chick embryo skin library. The deduced chick RAR gamma 2 amino acid sequence displays uncommon features such as 21 specific amino acid replacements, 12 of them being clustered in the amino-terminal region (domains A2 and B), and a truncated acidic carboxy-terminal region (F domain). However, the pattern of RAR gamma expression in chick embryo resembles that reported in mouse, particularly in skin where RAR gamma expression occurs in both the dermal and epidermal layers at the beginning of feather formation, and is subsequently restricted to the differentiating epidermal cells. Northern blot analysis suggests that different RAR gamma isoforms could be successively required during chick development.

Self-assembly of proglycinin and hybrid proglycinin synthesized in vitro from cDNA

PubMed Central

Dickinson, Craig D.; Floener, Liliane A.; Lilley, Glenn G.; Nielsen, Niels C.

1987-01-01

An in vitro system was developed that results in the self-assembly of subunit precursors into complexes that resemble those found naturally in the endoplasmic reticulum. Subunits of glycinin, the predominant seed protein of soybeans, were synthesized from modified cDNAs using a combination of the SP6 transcription and the rabbit reticulocyte translation systems. Subunits produced from plasmid constructions that encoded either Gy4 or Gy5 gene products, but modified such that their signal sequences were absent, self-assembled into trimers equivalent in size to those precursors found in the endoplasmic reticulum. In contrast, proteins synthesized in vitro from Gy4 constructs failed to self-assemble when the signal sequence was left intact (e.g., preproglycinin) or when the coding sequence was modified to remove 27 amino acids from an internal hydrophobic region, which is highly conserved among the glycinin subunits. Various hybrid subunits were also produced by trading portions of Gy4 and Gy5 cDNAs and all self-assembled in our system. The in vitro assembly system provides an opportunity to study the self-assembly of precursors and to probe for regions important for assembly. It will also be helpful in attempts to engineer beneficial nutritional changes into this important food protein. Images PMID:16593868

Molecular Cloning of Drebrin: Progress and Perspectives.

PubMed

Kojima, Nobuhiko

2017-01-01

Chicken drebrin isoforms were first identified in the optic tectum of developing brain. Although the time course of protein expression was different in each drebrin isoform, the similarity between their protein structures was suggested by biochemical analysis of purified protein. To determine their protein structures, the cloning of drebrin cDNAs was conducted. Comparison between the cDNA sequences shows that all drebrin cDNAs are identical except that the internal insertion sequences are present or absent in their sequences. Chicken drebrin are now classified into three isoforms, namely, drebrins E1, E2, and A. Genomic cloning demonstrated that the three isoforms are generated by an alternative splicing of individual exons encoding the insertion sequences from single drebrin gene. The mechanism should be precisely regulated in cell-type-specific and developmental stage-specific fashion. Drebrin protein, which is well conserved in various vertebrate species, although mammalian drebrin has only two isoforms, namely, drebrin E and drebrin A, is different from chicken drebrin that has three isoforms. Drebrin belongs to an actin-depolymerizing factor homology (ADF-H) domain protein family. Besides the ADF-H domain, drebrin has other domains, including the actin-binding domain and Homer-binding motifs. Diversity of protein isoform and multiple domains of drebrin could interact differentially with the actin cytoskeleton and other intracellular proteins and regulate diverse cellular processes.

Molecular cloning, molecular evolution and gene expression of cDNAs encoding thyrotropin-releasing hormone receptor subtypes in a teleost, the sockeye salmon (Oncorhynchus nerka).

PubMed

Saito, Yuichi; Mekuchi, Miyuki; Kobayashi, Noriaki; Kimura, Makoto; Aoki, Yasuhiro; Masuda, Tomohiro; Azuma, Teruo; Fukami, Motohiro; Iigo, Masayuki; Yanagisawa, Tadashi

2011-11-01

Molecular cloning of thyrotropin-releasing hormone receptors (TRHR) was performed in a teleost, the sockeye salmon (Oncorhynchus nerka). Four different TRHR cDNAs were cloned and named TRHR1, TRHR2a, TRHR2b and TRHR3 based on their similarity to known TRHR subtypes in vertebrates. Important residues for TRH binding were conserved in deduced amino acid sequences of the three TRHR subtypes except for the TRHR2b. Seven transmembrane domains were predicted for TRHR1, TRHR2a and TRHR3 proteins but only five for TRHR2b which appears to be truncated. In silico database analysis identified putative TRHR sequences including invertebrate TRHR and reptilian, avian and mammalian TRHR3. Phylogenetic analyses predicted the molecular evolution of TRHR in vertebrates: from the common ancestral TRHR (i.e. invertebrate TRHR), the TRHR2 subtype diverged first and then TRHR1 and TRHR3 diverged. Reverse transcription-polymerase chain reaction analyses revealed TRHR1 transcripts in the brain (hypothalamus), retina, pituitary gland and large intestine; TRHR2a in the brain (telencephalon and hypothalamus); and TRHR3 in the brain (olfactory bulbs) and retina. Copyright © 2011 Elsevier Inc. All rights reserved.

Actin genes and their expression in pacific white shrimp, Litopenaeus vannamei.

PubMed

Zhang, Xiaoxi; Zhang, Xiaojun; Yuan, Jianbo; Du, Jiangli; Li, Fuhua; Xiang, Jianhai

2018-04-01

Actin is a multi-functional gene family that can be divided into muscle-type actins and non-muscle-type actins. In this study, 37 unigenes encoding actins were identified from RNA-Seq data of Pacific white shrimp, Litopenaeus vannamei. According to phylogenetic analysis, four and three cDNAs belong to cytoplasmic- and heart-type actins and were named LvActinCT and LvActinHT, respectively. 10 cDNAs belong to the slow-type skeletal muscle actins, and 18 belong to the fast-type skeletal muscle actins; they were designated LvActinSSK and LvActinFSK, respectively. Some muscle actin genes formed gene clusters in the genome. Multiple alternative transcription starts sites (ATSSs) were found for LvActinCT1. Based on the early developmental expression profile, almost all LvActins were highly expressed between the early limb bud and post-larval stages. Using LvActinSSK5 as probes, slow-type muscle was localized in pleopod muscle and superficial ventral muscle. We also found three actin genes that were down-regulated in the hemocytes of white spot syndrome virus (WSSV)- and Vibrio parahaemolyticus-infected L. vannamei. This study provides valuable information on the actin gene structure of shrimp, furthers our understanding of the shrimp muscle system and helps us develop strategies for disease control and sustainable shrimp farming.

Rapid and efficient cDNA library screening by self-ligation of inverse PCR products (SLIP).

PubMed

Hoskins, Roger A; Stapleton, Mark; George, Reed A; Yu, Charles; Wan, Kenneth H; Carlson, Joseph W; Celniker, Susan E

2005-12-02

cDNA cloning is a central technology in molecular biology. cDNA sequences are used to determine mRNA transcript structures, including splice junctions, open reading frames (ORFs) and 5'- and 3'-untranslated regions (UTRs). cDNA clones are valuable reagents for functional studies of genes and proteins. Expressed Sequence Tag (EST) sequencing is the method of choice for recovering cDNAs representing many of the transcripts encoded in a eukaryotic genome. However, EST sequencing samples a cDNA library at random, and it recovers transcripts with low expression levels inefficiently. We describe a PCR-based method for directed screening of plasmid cDNA libraries. We demonstrate its utility in a screen of libraries used in our Drosophila EST projects for 153 transcription factor genes that were not represented by full-length cDNA clones in our Drosophila Gene Collection. We recovered high-quality, full-length cDNAs for 72 genes and variously compromised clones for an additional 32 genes. The method can be used at any scale, from the isolation of cDNA clones for a particular gene of interest, to the improvement of large gene collections in model organisms and the human. Finally, we discuss the relative merits of directed cDNA library screening and RT-PCR approaches.

Nutritional and productive performance of dairy cows fed corn silage or sugarcane silage with or without additives.

PubMed

de Andrade, Felipe Leite; Rodrigues, João Paulo Pacheco; Detmann, Edenio; Valadares Filho, Sebastião de Campos; Castro, Marcelo Messias Duarte; Trece, Aline Souza; Silva, Tadeu Eder; Fischer, Vivian; Weiss, Kirsten; Marcondes, Marcos Inácio

2016-04-01

The objective of this study was to compare the intake, digestibility, and performance of dairy cows fed corn silage, fresh sugarcane, and sugarcane ensiled in three different forms. Twenty-five Holstein cows at 114 ± 12.6 days in milk (DIM) were used. A randomized block design was adopted, using an arrangement of repeated measures over time. The following treatments were tested: corn silage (CS); fresh sugarcane (FS); sugarcane silage without additives (SCS); sugarcane silage enriched with calcium oxide at 5 g/kg of forage (SCSc); and sugarcane silage enriched with Lactobacillus buchneri at 5 × 10(4) cfu/kg of forage (SCSb). The roughage to concentrate ratio was 60:40 for the CS diet and 40:60 for the sugarcane-based diets. The dry matter intake (DMI) as a function of body weight had a downward trend for the cows fed sugarcane silage, compared with those fed FS. The sugarcane silages had higher digestibilities of dry matter (DM), organic matter (OM), and neutral detergent fiber (NDFap), compared with FS. The use of L. buchneri or calcium oxide improved the diet's digestibility. The use of FS, sugarcane silage, or sugarcane silage with additives had no effects on milk and fat-corrected milk yield, compared to corn silage. Cows fed FS presented lower milk total solids content and had a downward trend for milk fat, compared with cows fed sugarcane-silage diets. Cows fed sugarcane silages produced milk with higher casein stability in the alcohol test than cows fed fresh-sugarcane diet. Sugarcane silage, with or without additives, did not reduce the intake of dairy cows, and the use of additives improved the fiber's digestibility.

Viral metagenomic-based screening of sugarcane from Florida reveals occurrence of six sugarcane-infecting viruses and high prevalence of Sugarcane yellow leaf virus

USDA-ARS?s Scientific Manuscript database

A viral metagenomics study of the sugarcane virome in Florida was performed in 2013/2014 to analyze the occurrence of known and potentially new viruses. Two hundred and fourteen sugarcane leaf samples were collected from commercial sugarcane (Saccharum interspecific hybrids) fields in Florida and fr...

Aspergillus parasiticus communities associated with sugarcane in the Rio Grande Valley of Texas: implications of global transport and host association within Aspergillus section Flavi.

PubMed

Garber, N P; Cotty, P J

2014-05-01

In the Rio Grande Valley of Texas (RGV), values of maize and cottonseed crops are significantly reduced by aflatoxin contamination. Aflatoxin contamination of susceptible crops is the product of communities of aflatoxin producers and the average aflatoxin-producing potentials of these communities influence aflatoxin contamination risk. Cropping pattern influences community composition and, thereby, the epidemiology of aflatoxin contamination. In 2004, Aspergillus parasiticus was isolated from two fields previously cropped to sugarcane but not from 23 fields without recent history of sugarcane cultivation. In 2004 and 2005, A. parasiticus composed 18 to 36% of Aspergillus section Flavi resident in agricultural soils within sugarcane-producing counties. A. parasiticus was not detected in counties that do not produce sugarcane. Aspergillus section Flavi soil communities within sugarcane-producing counties differed significantly dependent on sugarcane cropping history. Fields cropped to sugarcane within the previous 5 years had greater quantities of A. parasiticus (mean = 16 CFU/g) than fields not cropped to sugarcane (mean = 0.1 CFU/g). The percentage of Aspergillus section Flavi composed of A. parasiticus increased to 65% under continuous sugarcane cultivation and remained high the first season of rotation out of sugarcane. Section Flavi communities in fields rotated to non-sugarcane crops for 3 to 5 years were composed of <5% A. parasiticus, and fields with no sugarcane history averaged only 0.2% A. parasiticus. The section Flavi community infecting RGV sugarcane stems ranged from 95% A. parasiticus in billets prepared for commercial planting to 52% A. parasiticus in hand-collected sugarcane stems. Vegetative compatibility assays and multilocus phylogenies verified that aflatoxin contamination of raw sugar was previously attributed to similar A. parasiticus in Japan. Association of closely related A. parasiticus genotypes with sugarcane produced in Japan and RGV, frequent infection of billets by these genotypes, and the ephemeral nature of A. parasiticus in RGV soils suggests global transport with sugarcane planting material.

Poor Fertility, Short Longevity, and Low Abundance in the Soil Seed Bank Limit Volunteer Sugarcane from Seed

PubMed Central

Pierre, Johann S.; Perroux, Jai; Whan, Alex; Rae, Anne L.; Bonnett, Graham D.

2015-01-01

The recent development of genetically modified sugarcane, with the aim of commercial production, requires an understanding of the potential risks of increased weediness of sugarcane as a result of spread and persistence of volunteer sugarcane. As sugarcane is propagated vegetatively from pieces of stalk and the seed plays no part in the production cycle, the fate of seed in the environment is yet to be studied. In this study, sugarcane seed samples, collected in fields over a 2-year period, were used to determine the overall level of sugarcane fertility, seed dormancy, and longevity of seed under field conditions. A survey of the soil seed bank in and around sugarcane fields was used to quantify the presence of sugarcane seeds and to identify and quantify the weeds that would compete with sugarcane seedlings. We demonstrated that under field conditions, sugarcane has low fertility and produces non-dormant seed. The viability of the seeds decayed rapidly (half-life between 1.5 and 2.1 months). This means that, in Australia, sugarcane seeds die before they encounter climatic conditions that could allow them to germinate and establish. Finally, the soil seed bank analysis revealed that there were very few sugarcane seeds relative to the large number of weed seeds that exert a large competitive effect. In conclusion, low fertility, short persistence, and poor ability to compete limit the capacity of sugarcane seed spread and persistence in the environment. PMID:26090363

Poor Fertility, Short Longevity, and Low Abundance in the Soil Seed Bank Limit Volunteer Sugarcane from Seed.

PubMed

Pierre, Johann S; Perroux, Jai; Whan, Alex; Rae, Anne L; Bonnett, Graham D

2015-01-01

The recent development of genetically modified sugarcane, with the aim of commercial production, requires an understanding of the potential risks of increased weediness of sugarcane as a result of spread and persistence of volunteer sugarcane. As sugarcane is propagated vegetatively from pieces of stalk and the seed plays no part in the production cycle, the fate of seed in the environment is yet to be studied. In this study, sugarcane seed samples, collected in fields over a 2-year period, were used to determine the overall level of sugarcane fertility, seed dormancy, and longevity of seed under field conditions. A survey of the soil seed bank in and around sugarcane fields was used to quantify the presence of sugarcane seeds and to identify and quantify the weeds that would compete with sugarcane seedlings. We demonstrated that under field conditions, sugarcane has low fertility and produces non-dormant seed. The viability of the seeds decayed rapidly (half-life between 1.5 and 2.1 months). This means that, in Australia, sugarcane seeds die before they encounter climatic conditions that could allow them to germinate and establish. Finally, the soil seed bank analysis revealed that there were very few sugarcane seeds relative to the large number of weed seeds that exert a large competitive effect. In conclusion, low fertility, short persistence, and poor ability to compete limit the capacity of sugarcane seed spread and persistence in the environment.

Multiple genes for functional 6 fatty acyl desaturases (Fad) in Atlantic salmon (Salmo salar L.): gene and cDNA characterization, functional expression, tissue distribution and nutritional regulation.

PubMed

Monroig, Oscar; Zheng, Xiaozhong; Morais, Sofia; Leaver, Michael J; Taggart, John B; Tocher, Douglas R

2010-09-01

Fish are the primary source in the human food basket of the n-3 long-chain polyunsaturated fatty acids, eicosapentaenoate (EPA; 20:5n-3) and docosahexaenoate (DHA; 22:6n-3), that are crucial to the health of higher vertebrates. Atlantic salmon are able to synthesize EPA and DHA from 18:3n-3 through reactions catalyzed by fatty acyl desaturases (Fad) and elongases of very long chain fatty acids. Previously, two cDNAs encoding functionally distinct Delta5 and Delta6 Fads were isolated, but screening of a genomic DNA library revealed the existence of more putative fad genes in the Atlantic salmon genome. In the present study, we show that there are at least four genes encoding putative Fad proteins in Atlantic salmon. Two genes, Delta6fad_a and Delta5fad, corresponded to the previously cloned Delta6 and Delta5 Fad cDNAs. Functional characterization by heterologous expression in yeast showed that the cDNAs for both the two further putative fad genes, Delta6fad_b and Delta6fad_c, had only Delta6 activity, converting 47 % and 12 % of 18:3n-3 to 18:4n-3, and 25 and 7 % of 18:2n-6 to 18:3n-6, for 6Fad_b and Delta6fad_c, respectively. Both 6fad_a and 6fad_b genes were highly expressed in intestine (pyloric caeca), liver and brain, with 6fad_b also highly expressed in gill, whereas 6fad_c transcript was found predominantly in brain, with lower expression levels in all other tissues. The expression levels of the 6fad_a gene in liver and the 6fad_b gene in intestine were significantly higher in fish fed diets containing vegetable oil compared to fish fed fish oil suggesting up-regulation in response to reduced dietary EPA and DHA. In contrast, no significant differences were found between transcript levels for 6fad_a in intestine, 6fad_b in liver, or 6fad_c in liver or intestine of fish fed vegetable oil compared to fish fed fish oil. The observed differences in tissue expression and nutritional regulation of the fad genes are discussed in relation to gene structures and fish physiology. 2010 Elsevier B.V. All rights reserved.

AmeriFlux US-SuM Maui Sugarcane Middle

DOE Data Explorer

Anderson, Ray [USDA-Agricultural Research Service, United States Salinity Laboratory, Contaminant Fate and Transport Unit; Wang, Dong [USDA - Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Water Management Research Unit

2016-01-01

This is the AmeriFlux version of the carbon flux data for the site US-SuM Maui Sugarcane Middle. Site Description - Continuous, irrigated, sugarcane cultivation for >100 years. Practice is to grow plant sugarcane for 2 years, drydown, burn leaves, harvest cane, and then till and replant very shortly after harvest. Site differs from Sugarcane Windy and Sugarcane Lee/sheltered in soil and meteorology.

AmeriFlux US-SuW Maui Sugarcane Windy

DOE Data Explorer

Anderson, Ray [USDA-Agricultural Research Service, United States Salinity Laboratory, Contaminant Fate and Transport Unit; Wang, Dong [USDA - Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Water Management Research Unit

2016-01-01

This is the AmeriFlux version of the carbon flux data for the site US-SuW Maui Sugarcane Windy. Site Description - Continuous, irrigated, sugarcane cultivation for >100 years. Practice is to grow plant sugarcane for 2 years, drydown, burn leaves, harvest cane, and then till and replant very shortly after harvest. Site differs from Sugarcane Lee/Sheltered and Sugarcane Middle in soil type and site meteorology.

Glutathione peroxidases of the potato cyst nematode Globodera Rostochiensis.

PubMed

Jones, J T; Reavy, B; Smant, G; Prior, A E

2004-01-07

We report the cloning and characterisation of full-length DNAs complementary to RNA (cDNAs) encoding two glutathione peroxidases (GpXs) from a plant parasitic nematode, the potato cyst nematode (PCN) Globodera rostochiensis. One protein has a functional signal peptide that targets the protein for secretion from animal cells while the other is predicted to be intracellular. Both genes are expressed in all parasite stages tested. The mRNA encoding the intracellular GpX is present throughout the nematode second stage juvenile and is particularly abundant in metabolically active tissues including the genital primordia. The mRNA encoding the secreted GpX is restricted to the hypodermis, the outermost cellular layer of the nematode, a location from which it is likely to be secreted to the parasite surface. Biochemical studies confirmed the secreted protein as a functional GpX and showed that, like secreted GpXs of other parasitic nematodes, it does not metabolise hydrogen peroxide but has a preference for larger hydroperoxide substrates. The intracellular protein is likely to have a role in metabolism of active oxygen species derived from internal body metabolism while the secreted protein may protect the parasite from host defences. Other functional roles for this protein are discussed.

Sugarcane Improvement Through Breeding and Biotechnology

USDA-ARS?s Scientific Manuscript database

The advancements in sugarcane breeding and the improvement of sugarcane through biotechnology have been reviewed by a team of leading sugarcane specialists from around the world. Topics covered in the breeding section include the evolution and origin of sugarcane, early history of conventional sugar...

Evaluation of aphid resistance among sugarcane cultivars in Louisiana

USDA-ARS?s Scientific Manuscript database

Sugarcane, interspecific hybrids of Saccharum spp., in Louisiana is colonized by two aphid species, the sugarcane aphid, Melanaphis sacchari (Zehntner), and the yellow sugarcane aphid, Sipha flava (Forbes). Five sugarcane cultivars, LCP 85-384, HoCP 91-555, Ho 95-988, HoCP 96-540, and L 97-128, rep...

A report on the transmissibility of Sugarcane mosaic virus and Sugarcane yellow leaf virus through seed in sugarcane

USDA-ARS?s Scientific Manuscript database

In the United States, exotic germplasm of sugarcane (Saccharum spp.) is mainly received as vegetative cuttings because the extensive actions required to meet existing APHIS (Animal and Plant Health Inspection Service) permit conditions make the importation of sugarcane seed impractical. While taking...

Effect of Sugarcane Mosaic caused by Sorghum mosaic virus on sugarcane in Louisiana

USDA-ARS?s Scientific Manuscript database

Sugarcane mosaic is caused by two viruses, Sugarcane mosaic virus (SCVM) or Sorghum mosaic virus (SrMV). In Louisiana, SrMV is the predominant mosaic pathogen affecting sugarcane. In a field experiment established in 2012, plots were planted with seed cane with or without mosaic symptoms. The mosaic...

Screening for sugarcane brown rust in first clonal stage of the Canal Point sugarcane breeding program

USDA-ARS?s Scientific Manuscript database

Sugarcane (Saccharum spp.) brown rust (caused by Puccinia melanocephala H. & P. Sydow) was first reported in the United States in 1978 and is still one of great challenges for sugarcane production. A better understanding of sugarcane genotypic variation in response to brown rust will help optimize b...

Registration of ‘Ho 02-113’ Sugarcane

USDA-ARS?s Scientific Manuscript database

‘Ho 02-113’ sugarcane was released by the USDA-ARS Sugarcane Research Unit working cooperatively with the Louisiana State University Agricultural Center, and the American Sugarcane League of the U.S.A. This high-fiber sugarcane variety was released for use as a biofuel feedstock to fill the rising i...

Expressed sequence tag analysis of adult human lens for the NEIBank Project: over 2000 non-redundant transcripts, novel genes and splice variants.

PubMed

Wistow, Graeme; Bernstein, Steven L; Wyatt, M Keith; Behal, Amita; Touchman, Jeffrey W; Bouffard, Gerald; Smith, Don; Peterson, Katherine

2002-06-15

To explore the expression profile of the human lens and to provide a resource for microarray studies, expressed sequence tag (EST) analysis has been performed on cDNA libraries from adult lenses. A cDNA library was constructed from two adult (40 year old) human lenses. Over two thousand clones were sequenced from the unamplified, un-normalized library. The library was then normalized and a further 2200 sequences were obtained. All the data were analyzed using GRIST (GRouping and Identification of Sequence Tags), a procedure for gene identification and clustering. The lens library (by) contains a low percentage of non-mRNA contaminants and a high fraction (over 75%) of apparently full length cDNA clones. Approximately 2000 reads from the unamplified library yields 810 clusters, potentially representing individual genes expressed in the lens. After normalization, the content of crystallins and other abundant cDNAs is markedly reduced and a similar number of reads from this library (fs) yields 1455 unique groups of which only two thirds correspond to named genes in GenBank. Among the most abundant cDNAs is one for a novel gene related to glutamine synthetase, which was designated "lengsin" (LGS). Analyses of ESTs also reveal examples of alternative transcripts, including a major alternative splice form for the lens specific membrane protein MP19. Variant forms for other transcripts, including those encoding the apoptosis inhibitor Livin and the armadillo repeat protein ARVCF, are also described. The lens cDNA libraries are a resource for gene discovery, full length cDNAs for functional studies and microarrays. The discovery of an abundant, novel transcript, lengsin, and a major novel splice form of MP19 reflect the utility of unamplified libraries constructed from dissected tissue. Many novel transcripts and splice forms are represented, some of which may be candidates for genetic diseases.

Characterization and mapping of cDNA encoding aspartate aminotransferase in rice, Oryza sativa L.

PubMed

Song, J; Yamamoto, K; Shomura, A; Yano, M; Minobe, Y; Sasaki, T

1996-10-31

Fifteen cDNA clones, putatively identified as encoding aspartate aminotransferase (AST, EC 2.6.1.1.), were isolated and partially sequenced. Together with six previously isolated clones putatively identified to encode ASTs (Sasaki, et al. 1994, Plant Journal 6, 615-624), their sequences were characterized and classified into 4 cDNA species. Two of the isolated clones, C60213 and C2079, were full-length cDNAs, and their complete nucleotide sequences were determined. C60213 was 1612 bp long and its deduced amino acid sequence showed 88% homology with that of Panicum miliaceum L. mitochondrial AST. The C60213-encoded protein had an N-terminal amino acid sequence that was characteristic of a mitochondrial transit peptide. On the other hand, C2079 was 1546 bp long and had 91% amino acid sequence homology with P. miliaceum L. cytosolic AST but lacked in the transit peptide sequence. The homologies of nucleotide sequences and deduced amino acid sequences of C2079 and C60213 were 54% and 52%, respectively. C2079 and C60213 were mapped on chromosomes 1 and 6, respectively, by restriction fragment length polymorphism linkage analysis. Northern blot analysis using C2079 as a probe revealed much higher transcript levels in callus and root than in green and etiolated shoots, suggesting tissue-specific variations of AST gene expression.

AmeriFlux US-SuS Maui Sugarcane Lee/Sheltered

DOE Data Explorer

Anderson, Ray [USDA-Agricultural Research Service, United States Salinity Laboratory, Contaminant Fate and Transport Unit; Wang, Dong [USDA - Agricultural Research Service, San Joaquin Valley Agricultural Sciences Center, Water Management Research Unit

2016-01-01

This is the AmeriFlux version of the carbon flux data for the site US-SuS Maui Sugarcane Lee/Sheltered. Site Description - Continuous, irrigated, sugarcane cultivation for >100 years. Practice is to grow plant sugarcane for 2 years, drydown, burn leaves, harvest cane, and then till and replant very shortly after harvest. First cycle of observations were from July 2011 to November 2012. Second cycle was from April 2013 to December 2013. Site differs from Sugarcane Windy and Sugarcane Middle in soil type and meteorology.

Potential for Genetic Improvement of Sugarcane as a Source of Biomass for Biofuels

PubMed Central

Hoang, Nam V.; Furtado, Agnelo; Botha, Frederik C.; Simmons, Blake A.; Henry, Robert J.

2015-01-01

Sugarcane (Saccharum spp. hybrids) has great potential as a major feedstock for biofuel production worldwide. It is considered among the best options for producing biofuels today due to an exceptional biomass production capacity, high carbohydrate (sugar + fiber) content, and a favorable energy input/output ratio. To maximize the conversion of sugarcane biomass into biofuels, it is imperative to generate improved sugarcane varieties with better biomass degradability. However, unlike many diploid plants, where genetic tools are well developed, biotechnological improvement is hindered in sugarcane by our current limited understanding of the large and complex genome. Therefore, understanding the genetics of the key biofuel traits in sugarcane and optimization of sugarcane biomass composition will advance efficient conversion of sugarcane biomass into fermentable sugars for biofuel production. The large existing phenotypic variation in Saccharum germplasm and the availability of the current genomics technologies will allow biofuel traits to be characterized, the genetic basis of critical differences in biomass composition to be determined, and targets for improvement of sugarcane for biofuels to be established. Emerging options for genetic improvement of sugarcane for the use as a bioenergy crop are reviewed. This will better define the targets for potential genetic manipulation of sugarcane biomass composition for biofuels. PMID:26636072

Dehydration-induced tps gene transcripts from an anhydrobiotic nematode contain novel spliced leaders and encode atypical GT-20 family proteins.

PubMed

Goyal, K; Browne, J A; Burnell, A M; Tunnacliffe, A

2005-06-01

Accumulation of the non-reducing disaccharide trehalose is associated with desiccation tolerance during anhydrobiosis in a number of invertebrates, but there is little information on trehalose biosynthetic genes in these organisms. We have identified two trehalose-6-phosphate synthase (tps) genes in the anhydrobiotic nematode Aphelenchus avenae and determined full length cDNA sequences for both; for comparison, full length tps cDNAs from the model nematode, Caenorhabditis elegans, have also been obtained. The A. avenae genes encode very similar proteins containing the catalytic domain characteristic of the GT-20 family of glycosyltransferases and are most similar to tps-2 of C. elegans; no evidence was found for a gene in A. avenae corresponding to Ce-tps-1. Analysis of A. avenae tps cDNAs revealed several features of interest, including alternative trans-splicing of spliced leader sequences in Aav-tps-1, and four different, novel SL1-related trans-spliced leaders, which were different to the canonical SL1 sequence found in all other nematodes studied. The latter observation suggests that A. avenae does not comply with the strict evolutionary conservation of SL1 sequences observed in other species. Unusual features were also noted in predicted nematode TPS proteins, which distinguish them from homologues in other higher eukaryotes (plants and insects) and in micro-organisms. Phylogenetic analysis confirmed their membership of the GT-20 glycosyltransferase family, but indicated an accelerated rate of molecular evolution. Furthermore, nematode TPS proteins possess N- and C-terminal domains, which are unrelated to those of other eukaryotes: nematode C-terminal domains, for example, do not contain trehalose-6-phosphate phosphatase-like sequences, as seen in plant and insect homologues. During onset of anhydrobiosis, both tps genes in A. avenae are upregulated, but exposure to cold or increased osmolarity also results in gene induction, although to a lesser extent. Trehalose seems likely therefore to play a role in a number of stress responses in nematodes.

Molecular characterization of cDNAs for two anionic peroxidases from suspension cultures of sweet potato.

PubMed

Kim, K Y; Huh, G H; Lee, H S; Kwon, S Y; Hur, Y; Kwak, S S

1999-07-01

Two cDNAs for anionic peroxidase (PODs), swpa2 and swpa3, were isolated from suspension cultures of sweet potato (Ipomoea batatas), and their expression was investigated with a view to understanding the physiological function of PODs in relation to environmental stresses. Swpa2 (whose putative mature protein product would have a pI value of 4.1) and swpa3 (4.3) encode polypeptides of 358 and 349 amino acids, respectively. The genes from which they were derived are predominantly expressed in cultured cells of sweet potato; transcripts of swpa2 were not detected in any tissues of the intact plant, and transcripts of swpa3 were detected at a low level only in the stem tissue. During cell culture, the expression patterns of the two genes differed; the level of swpa2 RNA progressively increased during cell growth, whereas that of swpa3 reached a maximum at the stationary phase and decreased on further culture. The two genes responded differently to stresses such as wounding or chilling of leaves. Swpa2 was strongly induced 48 h after wounding, but swpa3 was not affected by this treatment. The two genes were also highly expressed upon chilling (4 degrees C), but expression was reduced by prior acclimation at 15 degrees C. In addition, both genes were strongly induced immediately after treatment with ozone, and expression had decreased to the basal level 12 h after treatment. The response of these two genes to stresses such as aging, wounding, and chilling are different from those of the POD genes (swpa1 encoding an anionic product and swpn1 a neutral peroxidase) that we described previously. The responses of the two genes were also different from each other. These results suggest that the two new POD genes are involved in overcoming oxidative environmental stress, and each POD gene may be regulated by cell growth and environmental stress in different ways.

Expression of the leukemia-associated CBF{beta}/SMMHC chimeric gene causes transformation of 3T3 cells

DOE Office of Scientific and Technical Information (OSTI.GOV)

Hajra, A.; Liu, P.; Collins, E.S.

1994-09-01

A pericentric inversion of chromosome 16 (inv(16)(p13;q22)) is consistently seen in acute myeloid leukemia of the M4Eo subtype. This inversion fuses almost the entire coding region of the gene encoding of the {beta} subunit of the heterodimeric transcription factor CBF/PEBP2 to the region of the MYH11 gene encoding the rod domain for the smooth muscle myosin heavy chain (SMMHC). To investigate the biological properties of the CBF{beta}/SMMHC fusion protein, we have generated 3T3 cell lines that stably express the CBF{beta}/SMMHC chimeric cDNA or the normal, nonchimeric CBF{beta} and SMMHC cDNAs. 3T3 cells expressing CBF{beta}/SMMHC acquire a transformed phenotype, as indicatedmore » by altered cell morphology, formation of foci, and growth in soft agar. Cells constitutively overexpressing the normal CBF{beta} cDNA or the rod region of SMMHC remain nontransformed. Western blot analysis using antibodies to CBF{beta} and the SMMHC rod demonstrates that stably transfected cells express the appropriate chimeric or normal protein. Electrophoretic mobility shift assays reveal that cells transformed by the chimeric cDNA do not have a CBF-DNA complex of the expected mobility, but instead contain a large complex with CBF DNA-binding activity that fails to migrate out of the gel wells. In order to define the regions of CBF{beta}/SMMHC necessary for 3T3 transformation, we have stably transfected cells with mutant CBF{beta}/SMMHC cDNAs containing various deletions of the coding region. Analysis of these cell lines indicates that the transformation property of CBF{beta}/SMMHC requires regions of CBF{beta} known to be necessary for association with the DNA-binding CBF{alpha} subunit, and also requires an intact SMMHC carboxyl terminus, which is necessary for formation of the coiled coil domain of the myosin rod.« less

Identification of white campion (Silene latifolia) guaiacol O-methyltransferase involved in the biosynthesis of veratrole, a key volatile for pollinator attraction

PubMed Central

2012-01-01

Background Silene latifolia and its pollinator, the noctuid moth Hadena bicruris, represent an open nursery pollination system wherein floral volatiles, especially veratrole (1, 2-dimethoxybenzene), lilac aldehydes, and phenylacetaldehyde are of key importance for floral signaling. Despite the important role of floral scent in ensuring reproductive success in S. latifolia, the molecular basis of scent biosynthesis in this species has not yet been investigated. Results We isolated two full-length cDNAs from S. latifolia that show similarity to rose orcinol O-methyltransferase. Biochemical analysis showed that both S. latifolia guaiacol O-methyltransferase1 (SlGOMT1) &S. latifolia guaiacol O-methyltransferase2 (SlGOMT2) encode proteins that catalyze the methylation of guaiacol to form veratrole. A large Km value difference between SlGOMT1 (~10 μM) and SlGOMT2 (~501 μM) resulted that SlGOMT1 is 31-fold more catalytically efficient than SlGOMT2. qRT-PCR expression analysis showed that the SlGOMT genes are specifically expressed in flowers and male S. latifolia flowers had 3- to 4-folds higher level of GOMT gene transcripts than female flower tissues. Two related cDNAs, S. dioica O-methyltransferase1 (SdOMT1) and S. dioica O-methyltransferase2 (SdOMT2), were also obtained from the sister species Silene dioica, but the proteins they encode did not methylate guaiacol, consistent with the lack of veratrole emission in the flowers of this species. Our evolutionary analysis uncovered that SlGOMT1 and SlGOMT2 genes evolved under positive selection, whereas SdOMT1 and SdOMT2 genes show no evidence for selection. Conclusions Altogether, we report the identification and functional characterization of the gene, SlGOMT1 that efficiently catalyzes veratrole formation, whereas another copy of this gene with only one amino acid difference, SlGOMT2 was found to be less efficient for veratrole synthesis in S. latifolia. PMID:22937972

Novel antimicrobial peptides isolated from the skin secretions of Hainan odorous frog, Odorrana hainanensis.

PubMed

Wang, Hui; Yu, Zhijun; Hu, Yuhong; Li, Fengjiao; Liu, Limeng; Zheng, Hongyuan; Meng, Hao; Yang, Shujie; Yang, Xiaolong; Liu, Jingze

2012-06-01

Long time geographical isolation of Hainan Island from the China continent has resulted in appearance of many novel frog species. As one of them, Hainan odorous frog, Odorrana hainanensis possesses some special antimicrobial peptides distinct from those found in other Odorrana. In this study, three antimicrobial peptides have been purified and characterized from the skin secretion of O. hainanensis. With the similarity to the temporin family, two peptides are characterized by amidated C-terminals, so they are named as temporin-HN1 (AILTTLANWARKFL-NH(2)) and temporin-HN2 (NILNTIINLAKKIL-NH(2)). The third antimicrobial peptide belongs to the brevinin-1 family which is widely distributed in Eurasian ranids, and thus, it is named as brevinin-1HN1 (FLPLIASLAANFVPKIFCKITKKC). Furthermore, after sequencing 68 clones, eight cDNAs encoding antimicrobial peptide precursors were cloned from the skin-derived cDNA library of O. hainanensis. These eight cDNAs can encode seven mature antimicrobial peptides including the above three, as well as brevinin-1V, brevinin-2HS2, odorranain-A6, and odorranain-B1. Twelve different species of microorganisms were chosen, including Gram-positive, Gram-negative and fungi, to test the antimicrobial activities of temporin-HN1, temporin-HN2, brevinin-1HN1, brevinin-1V, and brevinin-2HS2. The result shows that, in addition to their activities against Gram-positive bacteria, temporin-HN1 and temporin-HN2 also possess activities against some Gram-negative bacteria and fungi. However, the two antimicrobial peptides, brevinin-1HN1 and brevinin-1V of the brevinin-1 family have stronger antimicrobial activities than temporin-HN1 and temporin-HN2 of the temporin family. Brevinin-1HN1 possesses activity against Staphylococcus aureus (ATCC25923), Rhodococcus rhodochrous X15, and Slime mould 090223 at the concentration of 1.2 μM. Copyright © 2012 Elsevier Inc. All rights reserved.

Characterization of two genes encoding leucine-rich repeat-containing proteins in grass carp Ctenopharyngodon idellus.

PubMed

Chang, M X; Nie, P; Xie, H X; Sun, B J; Gao, Q

2005-01-01

The cDNAs and genes of two different types of leucine-rich repeat-containing proteins from grass carp (Ctenopharyngodon idellus) were cloned. Homology search revealed that the two genes, designated as GC-GARP and GC-LRG, have 37% and 32% deduced amino-acid sequence similarities with human glycoprotein A repetitions predominant precursor (GARP) and leucine-rich alpha2-glycoprotein (LRG), respectively. The cDNAs of GC-GARP and GC-LRG encoded 664 and 339 amino acid residues, respectively. GC-GARP and GC-LRG contain many distinct structural and/or functional motifs of the leucine-rich repeat (LRR) subfamily, such as multiple conserved 11-residue segments with the consensus sequence LxxLxLxxN/CxL (x can be any amino acid). The genes GC-GARP and GC-LRG consist of two exons, with 4,782 bp and 2,119 bp in total length, respectively. The first exon of each gene contains a small 5'-untranslated region and partial open reading frame. The putative promoter region of GC-GARP was found to contain transcription factor binding sites for GATA-1, IRF4, Oct-1, IRF-7, IRF-1, AP1, GATA-box and NFAT, and the promoter region of GC-LRG for MYC-MAX, MEIS1, ISRE, IK3, HOXA9 and C/EBP alpha. Phylogenetic analysis showed that GC-GARP and mammalian GARPs were clustered into one branch, while GC-LRG and mammalian LRGs were in another branch. The GC-GARP gene was only detected in head kidney, and GC-LRG in the liver, spleen and heart in the copepod (Sinergasilus major)-infected grass carp, indicating the induction of gene expression by the parasite infection. The results obtained in the present study provide insight into the structure of fish LRR genes, and further study should be carried out to understand the importance of LRR proteins in host-pathogen interactions.

Impact of sugarcane bagasse ash as an amendment on the physical properties, nutrient content and seedling growth of a certified organic greenhouse growing media

USDA-ARS?s Scientific Manuscript database

Sugarcane bagasse is the fibrous material remaining after removing the sucrose, water, and other impurities (filter mud) from the milable sugarcane. Louisiana sugarcane mills use a portion of the sugarcane bagasse to produce steam power to run equipment within the mill and/or as a boiler fuel for th...

Two divergent endo-beta-1,4-glucanase genes exhibit overlapping expression in ripening fruit and abscising flowers.

PubMed Central

Lashbrook, C C; Gonzalez-Bosch, C; Bennett, A B

1994-01-01

Two structurally divergent endo-beta-1,4-glucanase (EGase) cDNAs were cloned from tomato. Although both cDNAs (Cel1 and Cel2) encode potentially glycosylated, basic proteins of 51 to 53 kD and possess multiple amino acid domains conserved in both plant and microbial EGases, Cel1 and Cel2 exhibit only 50% amino acid identity at the overall sequence level. Amino acid sequence comparisons to other plant EGases indicate that tomato Cel1 is most similar to bean abscission zone EGase (68%), whereas Cel2 exhibits greatest sequence identity to avocado fruit EGase (57%). Sequence comparisons suggest the presence of at least two structurally divergent EGase families in plants. Unlike ripening avocado fruit and bean abscission zones in which a single EGase mRNA predominates, EGase expression in tomato reflects the overlapping accumulation of both Cel1 and Cel2 transcripts in ripening fruit and in plant organs undergoing cell separation. Cel1 mRNA contributes significantly to total EGase mRNA accumulation within plant organs undergoing cell separation (abscission zones and mature anthers), whereas Cel2 mRNA is most abundant in ripening fruit. The overlapping expression of divergent EGase genes within a single species may suggest that multiple activities are required for the cooperative disassembly of cell wall components during fruit ripening, floral abscission, and anther dehiscence. PMID:7994180

Construction of cDNA expression library of watermelon for isolation of ClWRKY1 transcription factors gene involved in resistance to Fusarium wilt.

PubMed

Yang, Bing-Yan; Huo, Xiu-Ai; Li, Peng-Fei; Wang, Cui-Xia; Duan, Hui-Jun

2014-08-01

Full-length cDNAs are very important for genome annotation and functional analysis of genes. The number of full-length cDNAs from watermelon remains limited. Here we report first the construction of a full-length enriched cDNA library from Fusarium wilt stressed watermelon (Citrullus lanatus Thunb.) cultivar PI296341 root tissues using the SMART method. The titer of primary cDNA library and amplified library was 2.21 x 10(6) and 2.0 x 10(10) pfu/ml, respectively and the rate of recombinant was above 85%. The size of insert fragment ranged from 0.3 to 2.0 kb. In this study, we first cloned a gene named ClWRKY1, which was 1981 bp long and encoded a protein consisting of 394 amino acids. It contained two characteristic WRKY domains and two zinc finger motifs. Quantitative real-time PCR showed that ClWRKY1 expression levels reached maximum level at 12 h after inoculation with Fusarium oxysporum f. sp. niveum. The full-length cDNA library of watermelon root tissues is not only essential for the cloning of genes which are known, but also an initial key for the screening and cloning of new genes that might be involved in resistance to Fusarium wilt.

Molecular cloning of two human liver 3 alpha-hydroxysteroid/dihydrodiol dehydrogenase isoenzymes that are identical with chlordecone reductase and bile-acid binder.

PubMed Central

Deyashiki, Y; Ogasawara, A; Nakayama, T; Nakanishi, M; Miyabe, Y; Sato, K; Hara, A

1994-01-01

Human liver contains two dihydrodiol dehydrogenases, DD2 and DD4, associated with 3 alpha-hydroxysteroid dehydrogenase activity. We have raised polyclonal antibodies that cross-reacted with the two enzymes and isolated two 1.2 kb cDNA clones (C9 and C11) for the two enzymes from a human liver cDNA library using the antibodies. The clones of C9 and C11 contained coding sequences corresponding to 306 and 321 amino acid residues respectively, but lacked 5'-coding regions around the initiation codon. Sequence analyses of several peptides obtained by enzymic and chemical cleavages of the two purified enzymes verified that the C9 and C11 clones encoded DD2 and DD4 respectively, and further indicated that the sequence of DD2 had at least additional 16 residues upward from the N-terminal sequence deduced from the cDNA. There was 82% amino acid sequence identity between the two enzymes, indicating that the enzymes are genetic isoenzymes. A computer-based comparison of the cDNAs of the isoenzymes with the DNA sequence database revealed that the nucleotide and amino acid sequences of DD2 and DD4 are virtually identical with those of human bile-acid binder and human chlordecone reductase cDNAs respectively. Images Figure 1 PMID:8172617

Single Cell Transcriptomics of Hypothalamic Warm Sensitive Neurons that Control Core Body Temperature and Fever Response

PubMed Central

Eberwine, James; Bartfai, Tamas

2011-01-01

We report on an ‘unbiased’ molecular characterization of individual, adult neurons, active in a central, anterior hypothalamic neuronal circuit, by establishing cDNA libraries from each individual, electrophysiologically identified warm sensitive neuron (WSN). The cDNA libraries were analyzed by Affymetrix microarray. The presence and frequency of cDNAs was confirmed and enhanced with Illumina sequencing of each single cell cDNA library. cDNAs encoding the GABA biosynthetic enzyme. GAD1 and of adrenomedullin, galanin, prodynorphin, somatostatin, and tachykinin were found in the WSNs. The functional cellular and in vivo studies on dozens of the more than 500 neurotransmitter -, hormone- receptors and ion channels, whose cDNA was identified and sequence confirmed, suggest little or no discrepancy between the transcriptional and functional data in WSNs; whenever agonists were available for a receptor whose cDNA was identified, a functional response was found.. Sequencing single neuron libraries permitted identification of rarely expressed receptors like the insulin receptor, adiponectin receptor2 and of receptor heterodimers; information that is lost when pooling cells leads to dilution of signals and mixing signals. Despite the common electrophysiological phenotype and uniform GAD1 expression, WSN- transcriptomes show heterogenity, suggesting strong epigenetic influence on the transcriptome. Our study suggests that it is well-worth interrogating the cDNA libraries of single neurons by sequencing and chipping. PMID:20970451

Two Novel Dermaseptin-Like Antimicrobial Peptides with Anticancer Activities from the Skin Secretion of Pachymedusa dacnicolor.

PubMed

Shi, Daning; Hou, Xiaojuan; Wang, Lei; Gao, Yitian; Wu, Di; Xi, Xinping; Zhou, Mei; Kwok, Hang Fai; Duan, Jinao; Chen, Tianbao; Shaw, Chris

2016-05-12

The dermaseptin antimicrobial peptide family contains members of 27-34 amino acids in length that have been predominantly isolated from the skins/skin secretions of phyllomedusine leaf frogs. By use of a degenerate primer in Rapid amplification of cDNA ends (RACE) PCR designed to a common conserved domain within the 5'-untranslated regions of previously-characterized dermaseptin encoding cDNAs, two novel members of this peptide family, named dermaseptin-PD-1 and dermaseptin-PD-2, were identified in the skin secretion of the phyllomedusine frog, Pachymedusa dacnicolor. The primary structures of both peptides were predicted from cloned cDNAs, as well as being confirmed by mass spectral analysis of crude skin secretion fractions resulted from reversed-phase high-performance liquid chromatography. Chemically-synthesized replicates of dermaseptin-PD-1 and dermaseptin-PD-2 were investigated for antimicrobial activity using standard model microorganisms (Gram-positive bacteria, Gram-negative bacteria and a yeast) and for cytotoxicity using mammalian red blood cells. The possibility of synergistic effects between the two peptides and their anti-cancer cell proliferation activities were assessed. The peptides exhibited moderate to high inhibition against the growth of the tested microorganisms and cancer cell lines with low haemolytic activity. Synergistic interaction between the two peptides in inhibiting the proliferation of Escherichia coli and human neuronal glioblastoma cell line, U251MG was also manifested.

[Effects of reduced nitrogen application and soybean intercropping on nitrogen balance of sugarcane field].

PubMed

Liu, Yu; Zhang, Ying; Yang, Wen-ting; Li, Zhi-xian; Guan, Ao-mei

2015-03-01

A four-year (2010-2013) field experiment was carried out to explore the effects of three planting patterns (sugarcane, soybean monoculture and sugarcane-soybean 1:2 intercropping) with two nitrogen input levels (300 and 525 kg . hm-2) on soybean nitrogen fixation, sugarcane and soybean nitrogen accumulation, and ammonia volatilization and nitrogen leaching in sugarcane field. The results showed that the soybean nitrogen fixation efficiency (NFE) of sugarcane-soybean inter-cropping was lower than that of soybean monoculture. There was no significant difference in NFE among the treatments with the two nitrogen application rates. The nitrogen application rate and inter-cropping did not remarkably affect nitrogen accumulation of sugarcane and soybean. The ammonia volatilization of the reduced nitrogen input treatment was significantly lower than that of the conventional nitrogen input treatment. Furthermore, there was no significant difference in nitrogen leaching at different nitrogen input levels and among different planting patterns. The sugarcane field nitrogen balance analysis indicated that the nitrogen application rate dominated the nitrogen budget of sugarcane field. During the four-year experiment, all treatments leaved a nitrogen surplus (from 73.10 to 400.03 kg . hm-2) , except a nitrogen deficit of 66.22 kg . hm-2 in 2011 in the treatment of sugarcane monoculture with the reduced nitrogen application. The excessive nitrogen surplus might increase the risk of nitrogen pollution in the field. In conclusion, sugarcane-soybean intercropping with reduced nitrogen application is feasible to practice in consideration of enriching the soil fertility, reducing nitrogen pollution and saving production cost in sugarcane field.

Comparing costs and returns for sugarcane production on sand and muck soils of southern Florida, 2008-2009

DOE PAGES

Roka, Fritz M.; Baucum, Leslie E.; Rice, Ronald W.; ...

2010-01-01

Sugarcane production in Florida is concentrated south and west of Lake Okeechobee and is grown on both muck and sand soils. During the 2008-2009 season, more than 12 million metric tons of sugarcane was harvested and supported important sugarcane milling and sugar refining operations located in southern Florida. Farms on muck soils account for 80% of Florida’s annual sugarcane crop, while farms on sand soils account for the remaining 20%. This paper compares revenues, production costs and net annual returns from two equally sized sugarcane farms (2,000 hectare) representing typical growing conditions on sand and muck soils. Sugarcane growers onmore » muck soils enjoy two distinct advantages over their counterparts farming sugarcane on sand soils. First, total farm revenues are higher because of greater yields and a higher percentage of land that can be grown for commercial harvest. Second, unit costs of production are lower due to the inherent organic matter in muck soils, allowing growers to apply substantially less quantities of fertilizers. Annual net returns to land, management and risk from growing sugarcane on muck soils are estimated to be 400 dollars/ha, more than five times higher than estimated net returns from growing sugarcane on sand soils (70 dollars/ha). Furthermore, while sugarcane production on sand soils is less profitable relative to muck soils, economic returns from sugarcane on sand soils are higher than from cattle operations, offer less risk than presently associated with citrus production, and occupy land area far beyond the capacity of the vegetable industry to absorb.« less

Early changes in arbuscular mycorrhiza development in sugarcane under two harvest management systems.

PubMed

de Azevedo, Lucas Carvalho Basilio; Stürmer, Sidney Luiz; Lambais, Marcio Rodrigues

2014-01-01

Sugarcane (Saccharum spp.) is grown on over 8 million ha in Brazil and is used to produce ethanol and sugar. Some sugarcane fields are burned to facilitate harvesting, which can affect the soil microbial community. However, whether sugarcane pre-harvest burning affects the community of arbuscular mycorrhizal fungi (AMF) and symbioses development is not known. In this study, we investigated the early impacts of harvest management on AMF spore communities and root colonization in three sugarcane varieties, under two harvest management systems (no-burning and pre-harvest burning). Soil and root samples were collected in the field after the first harvest of sugarcane varieties SP813250, SP801842, and RB72454, and AMF species were identified based on spore morphology. Diversity indices were determined based on spore populations and root colonization determined as an indicator of symbioses development. Based on the diversity indices, spore number and species occurrence in soil, no significant differences were observed among the AMF communities, regardless of harvest management type, sugarcane variety or interactions between harvest management type and sugarcane variety. However, mycorrhiza development was stimulated in sugarcane under the no-burning management system. Our data suggest that the sugarcane harvest management system may cause early changes in arbuscular mycorrhiza development.

Early changes in arbuscular mycorrhiza development in sugarcane under two harvest management systems

PubMed Central

de Azevedo, Lucas Carvalho Basilio; Stürmer, Sidney Luiz; Lambais, Marcio Rodrigues

2014-01-01

Sugarcane (Saccharum spp.) is grown on over 8 million ha in Brazil and is used to produce ethanol and sugar. Some sugarcane fields are burned to facilitate harvesting, which can affect the soil microbial community. However, whether sugarcane pre-harvest burning affects the community of arbuscular mycorrhizal fungi (AMF) and symbioses development is not known. In this study, we investigated the early impacts of harvest management on AMF spore communities and root colonization in three sugarcane varieties, under two harvest management systems (no-burning and pre-harvest burning). Soil and root samples were collected in the field after the first harvest of sugarcane varieties SP813250, SP801842, and RB72454, and AMF species were identified based on spore morphology. Diversity indices were determined based on spore populations and root colonization determined as an indicator of symbioses development. Based on the diversity indices, spore number and species occurrence in soil, no significant differences were observed among the AMF communities, regardless of harvest management type, sugarcane variety or interactions between harvest management type and sugarcane variety. However, mycorrhiza development was stimulated in sugarcane under the no-burning management system. Our data suggest that the sugarcane harvest management system may cause early changes in arbuscular mycorrhiza development. PMID:25477936

Applying functional metagenomics to search for novel lignocellulosic enzymes in a microbial consortium derived from a thermophilic composting phase of sugarcane bagasse and cow manure.

PubMed

Colombo, Lívia Tavares; de Oliveira, Marcelo Nagem Valério; Carneiro, Deisy Guimarães; de Souza, Robson Assis; Alvim, Mariana Caroline Tocantins; Dos Santos, Josenilda Carlos; da Silva, Cynthia Canêdo; Vidigal, Pedro Marcus Pereira; da Silveira, Wendel Batista; Passos, Flávia Maria Lopes

2016-09-01

Environments where lignocellulosic biomass is naturally decomposed are sources for discovery of new hydrolytic enzymes that can reduce the high cost of enzymatic cocktails for second-generation ethanol production. Metagenomic analysis was applied to discover genes coding carbohydrate-depleting enzymes from a microbial laboratory subculture using a mix of sugarcane bagasse and cow manure in the thermophilic composting phase. From a fosmid library, 182 clones had the ability to hydrolyse carbohydrate. Sequencing of 30 fosmids resulted in 12 contigs encoding 34 putative carbohydrate-active enzymes belonging to 17 glycosyl hydrolase (GH) families. One third of the putative proteins belong to the GH3 family, which includes β-glucosidase enzymes known to be important in the cellulose-deconstruction process but present with low activity in commercial enzyme preparations. Phylogenetic analysis of the amino acid sequences of seven selected proteins, including three β-glucosidases, showed low relatedness with protein sequences deposited in databases. These findings highlight microbial consortia obtained from a mixture of decomposing biomass residues, such as sugar cane bagasse and cow manure, as a rich resource of novel enzymes potentially useful in biotechnology for saccharification of lignocellulosic substrate.

Integrated disease management strategies in sugarcane cultivation

USDA-ARS?s Scientific Manuscript database

Sugarcane diseases cause severe losses to sugar production around the world. More than 100 bacterial, fungal, phytoplasma and viral diseases are present in sugarcane growing areas worldwide. Some diseases are present in most sugarcane growing regions while others are confined to specific countries. ...

Sugarcane Water Stress Tolerance Mechanisms and Its Implications on Developing Biotechnology Solutions

PubMed Central

Ferreira, Thais H. S.; Tsunada, Max S.; Bassi, Denis; Araújo, Pedro; Mattiello, Lucia; Guidelli, Giovanna V.; Righetto, Germanna L.; Gonçalves, Vanessa R.; Lakshmanan, Prakash; Menossi, Marcelo

2017-01-01

Sugarcane is a unique crop with the ability to accumulate high levels of sugar and is a commercially viable source of biomass for bioelectricity and second-generation bioethanol. Water deficit is the single largest abiotic stress affecting sugarcane productivity and the development of water use efficient and drought tolerant cultivars is an imperative for all major sugarcane producing countries. This review summarizes the physiological and molecular studies on water deficit stress in sugarcane, with the aim to help formulate more effective research strategies for advancing our knowledge on genes and mechanisms underpinning plant response to water stress. We also overview transgenic studies in sugarcane, with an emphasis on the potential strategies to develop superior sugarcane varieties that improve crop productivity in drought-prone environments. PMID:28690620

KAPOSI’S SARCOMA–ASSOCIATED HERPESVIRUS IMMUNOEVASION AND TUMORIGENESIS: TWO SIDES OF THE SAME COIN?

PubMed Central

Moore, Patrick S.; Chang, Yuan

2013-01-01

Kaposi’s sarcoma–associated herpesvirus (KSHV) [or human herpesvirus 8 (HHV-8)] is the most frequent cause of malignancy among AIDS patients. KSHV and related herpesviruses have extensively pirated cellular cDNAs from the host genome, providing a unique opportunity to examine the range of viral mechanisms for controlling cell proliferation. Many of the viral regulatory homologs encode proteins that directly inhibit host adaptive and innate immunity. Other viral proteins target retinoblastoma protein and p53 control of tumor suppressor pathways, which also play key effector roles in intracellular immune responses. The immune evasion strategies employed by KSHV, by targeting tumor suppressor pathways activated during immune system signaling, may lead to inadvertent cell proliferation and tumorigenesis in susceptible hosts. PMID:14527293

Geranyl diphosphate:4-hydroxybenzoate geranyltransferase from Lithospermum erythrorhizon. Cloning and characterization of a ket enzyme in shikonin biosynthesis.

PubMed

Yazaki, Kazufumi; Kunihisa, Miyuki; Fujisaki, Takahiro; Sato, Fumihiko

2002-02-22

Two cDNAs encoding geranyl diphosphate:4-hy- droxybenzoate 3-geranyltransferase were isolated from Lithospermum erythrorhizon by nested PCR using the conserved amino acid sequences among polyprenyl- transferases for ubiquinone biosynthesis. They were functionally expressed in yeast COQ2 disruptant and showed a strict substrate specificity for geranyl diphosphate as the prenyl donor, in contrast to ubiquinone biosynthetic enzymes, suggesting that they are involved in the biosynthesis of shikonin, a naphthoquinone secondary metabolite. Regulation of their expression by various culture conditions coincided with that of geranyltransferase activity and the secondary metabolites biosynthesized via this enzyme. This is the first established plant prenyltransferase that transfers the prenyl chain to an aromatic substrate.

Isolation of stress responsive Psb A gene from rice (Oryza sativa l.) using differential display.

PubMed

Tyagi, Aruna; Chandra, Arti

2006-08-01

Differential display (DD) experiments were performed on drought-tolerant rice (Oryza sativa L.) genotype N22 to identify both upregulated and downregulated partial cDNAs with respect to moisture stress. DNA polymorphism was detected between drought-stressed and control leaf tissues on the DD gels. A partial cDNA showing differential expression, with respect to moisture stress was isolated from the gel. Northern blotting analysis was performed using this cDNA as a probe and it was observed that mRNA corresponding to this transcript was accumulated to high level in rice leaves under water deficit stress. At the DNA sequence level, the partial cDNA showed homology with psb A gene encoding for Dl protein.

Appalachian spring: variations on ancient gastro-entero-pancreatic themes in New World mammals.

PubMed

Seino, S; Blackstone, C D; Chan, S J; Whittaker, J; Bell, G I; Steiner, D F

1988-07-01

Studies of guinea pig genomic and/or cDNA clones encoding the gastro-entero-pancreatic (GEP) hormones--insulin, glucagon and pancreatic polypeptide--as well as portions of the insulin receptor, are described. Multiple clustered substitutions (localized rapid mutation acceptance) altering the biological properties of both insulin and glucagon have been revealed, but this does not appear to be the case with either pancreatic polypeptide or those regions of guinea pig insulin receptor cDNAs that have been examined thus far. These findings suggest that novel selective pressures operative in the New World environment, in which these animals evolved in isolation from Old World mammalian species, have led to altered solutions to problems related to the regulation of growth and carbohydrate metabolism.

Sandalwood Fragrance Biosynthesis Involves Sesquiterpene Synthases of Both the Terpene Synthase (TPS)-a and TPS-b Subfamilies, including Santalene Synthases*

PubMed Central

Jones, Christopher G.; Moniodis, Jessie; Zulak, Katherine G.; Scaffidi, Adrian; Plummer, Julie A.; Ghisalberti, Emilio L.; Barbour, Elizabeth L.; Bohlmann, Jörg

2011-01-01

Sandalwood oil is one of the worlds most highly prized fragrances. To identify the genes and encoded enzymes responsible for santalene biosynthesis, we cloned and characterized three orthologous terpene synthase (TPS) genes SaSSy, SauSSy, and SspiSSy from three divergent sandalwood species; Santalum album, S. austrocaledonicum, and S. spicatum, respectively. The encoded enzymes catalyze the formation of α-, β-, epi-β-santalene, and α-exo-bergamotene from (E,E)-farnesyl diphosphate (E,E-FPP). Recombinant SaSSy was additionally tested with (Z,Z)-farnesyl diphosphate (Z,Z-FPP) and remarkably, found to produce a mixture of α-endo-bergamotene, α-santalene, (Z)-β-farnesene, epi-β-santalene, and β-santalene. Additional cDNAs that encode bisabolene/bisabolol synthases were also cloned and functionally characterized from these three species. Both the santalene synthases and the bisabolene/bisabolol synthases reside in the TPS-b phylogenetic clade, which is more commonly associated with angiosperm monoterpene synthases. An orthologous set of TPS-a synthases responsible for formation of macrocyclic and bicyclic sesquiterpenes were characterized. Strict functionality and limited sequence divergence in the santalene and bisabolene synthases are in contrast to the TPS-a synthases, suggesting these compounds have played a significant role in the evolution of the Santalum genus. PMID:21454632

Enzymatic breakdown of raffinose oligosaccharides in pea seeds.

PubMed

Blöchl, Andreas; Peterbauer, Thomas; Hofmann, Julia; Richter, Andreas

2008-06-01

Both alkaline and acidic alpha-galactosidases (alpha-D: -galactoside galactohydrolases, E.C.3.2.1.22) isolated from various plant species have been described, although little is known about their co-occurrence and functions in germinating seeds. Here, we report on the isolation of two cDNAs, encoding for alpha-galactosidases from maturing and germinating seeds of Pisum sativum. One was identified as a member of the acidic alpha-galactosidase of the family 27 glycosyl hydrolase cluster and the other as a member of the family of alkaline alpha-galactosidases, which are highly homologous to seed imbibition proteins (SIPs). PsGAL1 transcripts, encoding for the ACIDIC alpha-GALACTOSIDASE, were predominately expressed during seed maturation and acidic enzyme activities were already present in dry seeds, showing little changes during seed germination. Compartmentation studies revealed that acidic alpha-galactosidases were located in protein storage vacuoles (PSVs). PsAGA1, encoding for the ALKALINE alpha-GALACTOSIDASE, was only expressed after radicle protrusion, when about 50% of RFOs have already been broken down. RFO breakdown was markedly decreased when the translation of the alkaline enzyme was inhibited, providing evidence that PsAGA1 indeed functioned in RFO degradation. Based on these data, we present an integrated model of RFO breakdown by two sequentially active alpha-galactosidases in pea seeds.

Chicken genome analysis reveals novel genes encoding biotin-binding proteins related to avidin family

PubMed Central

Niskanen, Einari A; Hytönen, Vesa P; Grapputo, Alessandro; Nordlund, Henri R; Kulomaa, Markku S; Laitinen, Olli H

2005-01-01

Background A chicken egg contains several biotin-binding proteins (BBPs), whose complete DNA and amino acid sequences are not known. In order to identify and characterise these genes and proteins we studied chicken cDNAs and genes available in the NCBI database and chicken genome database using the reported N-terminal amino acid sequences of chicken egg-yolk BBPs as search strings. Results Two separate hits showing significant homology for these N-terminal sequences were discovered. For one of these hits, the chromosomal location in the immediate proximity of the avidin gene family was found. Both of these hits encode proteins having high sequence similarity with avidin suggesting that chicken BBPs are paralogous to avidin family. In particular, almost all residues corresponding to biotin binding in avidin are conserved in these putative BBP proteins. One of the found DNA sequences, however, seems to encode a carboxy-terminal extension not present in avidin. Conclusion We describe here the predicted properties of the putative BBP genes and proteins. Our present observations link BBP genes together with avidin gene family and shed more light on the genetic arrangement and variability of this family. In addition, comparative modelling revealed the potential structural elements important for the functional and structural properties of the putative BBP proteins. PMID:15777476

Subcellular distribution of serine acetyltransferase from Pisum sativum and characterization of an Arabidopsis thaliana putative cytosolic isoform.

PubMed

Ruffet, M L; Lebrun, M; Droux, M; Douce, R

1995-01-15

The intracellular compartmentation of serine acetyltransferase, a key enzyme in the L-cysteine biosynthesis pathway, has been investigated in pea (Pisum sativum) leaves, by isolation of organelles and fractionation of protoplasts. Enzyme activity was mainly located in mitochondria (approximately 76% of total cellular activity). Significant activity was also identified in both the cytosol (14% of total activity) and chloroplasts (10% of total activity). Three enzyme forms were separated by anion-exchange chromatography, and each form was found to be specific for a given intracellular compartment. To obtain cDNA encoding the isoforms, functional complementation experiments were performed using an Arabidopsis thaliana expression library and an Escherichia coli mutant devoid of serine acetyltransferase activity. This strategy allowed isolation of three distinct cDNAs encoding serine acetyltransferase isoforms, as confirmed by enzyme activity measurements, genomic hybridizations, and nucleotide sequencing. The cDNA and related gene for one of the three isoforms have been characterized. The predicted amino acid sequence shows that it encodes a polypeptide of M(r) 34,330 exhibiting 41% amino acid identity with the E. coli serine acetyltransferase. Since none of the general features of transit peptides could be observed in the N-terminal region of this isoform, we assume that it is a cytosolic form.

Characterization of interleukin-8 receptors in non-human primates

DOE Office of Scientific and Technical Information (OSTI.GOV)

Alvarez, V.; Coto, E.; Gonzalez-Roces, S.

Interleukin-8 is a chemokine with a potent neutrophil chemoatractant activity. In humans, two different cDNAs encoding human IL8 receptors designated IL8RA and IL8RB have been cloned. IL8RA binds IL8, while IL8RB binds IL8 as well as other {alpha}-chemokines. Both human IL8Rs are encoded by two genes physically linked on chromosome 2. The IL8RA and IL8RB genes have open reading frames (ORF) lacking introns. By direct sequencing of the polymerase chain reaction products, we sequenced the IL8R genes of cell lines from four non-human primates: chimpanzee, gorilla, orangutan, and macaca. The IL8RB encodes an ORF in the four non-human primates, showingmore » 95%-99% similarity to the human IL8RB sequence. The IL8RA homologue in gorilla and chimpanzee consisted of two ORF 98%-99% identical to the human sequence. The macaca and orangutan IL8RA homologues are pseudogenes: a 2 base pair insertion generated a sequence with several stop codons. In addition, we describe the physical linkage of these genes in the four non-human primates and discuss the evolutionary implications of these findings. 25 refs., 5 figs., 3 tabs.« less

A human systemic lupus erythematosus-related anti-cardiolipin/single-stranded DNA autoantibody is encoded by a somatically mutated variant of the developmentally restricted 51P1 V[sub H] gene

DOE Office of Scientific and Technical Information (OSTI.GOV)

Van Es, J.H.; Aanstoot, H.; Gmelig-Meyling, F.H.J.

1992-09-15

The authors report the Ig H and L chain V region sequences from the cDNAs encoding a monoclonal human IgG anti-cardiolipin/ssDNA autoantibody (R149) derived from a patient with active SLE. Comparison with the germ-line V-gene repertoire of this patient revealed that R149 likely arose as a consequence of an Ag-driven selection process. The Ag-binding portions of the V regions were characterized by a high number of arginine residues, a property that has been associated with anti-dsDNA autoantibodies from lupus-prone mice and patients with SLE. The V[sub H] gene encoding autoantibody R149 was a somatically mutated variant of the 51P1 genemore » segment, which is frequently associated with the restricted fetal B cell repertoire, malignant CD5 B cells, and natural antibodies. These data suggest that in SLE patients a common antigenic stimulus may evoke anti-DNA and anti-cardiolipin autoantibodies and provide further evidence that a small set of developmentally restricted V[sub H] genes can give rise to disease-associated autoantibodies through Ag-selected somatic mutations. 42 refs., 5 figs.« less

Characterization and expression of genes encoding three small heat shock proteins in Sesamia inferens (Lepidoptera: Noctuidae).

PubMed

Sun, Meng; Lu, Ming-Xing; Tang, Xiao-Tian; Du, Yu-Zhou

2014-12-12

The pink stem borer, Sesamia inferens (Walker), is a major pest of rice and is endemic in China and other parts of Asia. Small heat shock proteins (sHSPs) encompass a diverse, widespread class of stress proteins that have not been characterized in S. inferens. In the present study, we isolated and characterized three S. inferens genes that encode members of the α-crystallin/sHSP family, namely, Sihsp21.4, Sihsp20.6, and Sihsp19.6. The three cDNAs encoded proteins of 187, 183 and 174 amino acids with calculated molecular weights of 21.4, 20.6 and 19.6 kDa, respectively. The deduced amino acid sequences of the three genes showed strong similarity to sHSPs identified in other lepidopteran insects. Sihsp21.4 contained an intron, but Sihsp20.6 and Sihsp19.6 lacked introns. Real-time quantitative PCR analyses revealed that Sihsp21.4 was most strongly expressed in S. inferens heads; Whereas expression of Sihsp20.6 and Sihsp19.6 was highest in eggs. The three S. inferens sHSP genes were up-regulated during low temperature stress. In summary, our results show that S. inferens sHSP genes have distinct regulatory roles in the physiology of S. inferens.

Characterization and Expression of Genes Encoding Three Small Heat Shock Proteins in Sesamia inferens (Lepidoptera: Noctuidae)

PubMed Central

Sun, Meng; Lu, Ming-Xing; Tang, Xiao-Tian; Du, Yu-Zhou

2014-01-01

The pink stem borer, Sesamia inferens (Walker), is a major pest of rice and is endemic in China and other parts of Asia. Small heat shock proteins (sHSPs) encompass a diverse, widespread class of stress proteins that have not been characterized in S. inferens. In the present study, we isolated and characterized three S. inferens genes that encode members of the α-crystallin/sHSP family, namely, Sihsp21.4, Sihsp20.6, and Sihsp19.6. The three cDNAs encoded proteins of 187, 183 and 174 amino acids with calculated molecular weights of 21.4, 20.6 and 19.6 kDa, respectively. The deduced amino acid sequences of the three genes showed strong similarity to sHSPs identified in other lepidopteran insects. Sihsp21.4 contained an intron, but Sihsp20.6 and Sihsp19.6 lacked introns. Real-time quantitative PCR analyses revealed that Sihsp21.4 was most strongly expressed in S. inferens heads; Whereas expression of Sihsp20.6 and Sihsp19.6 was highest in eggs. The three S. inferens sHSP genes were up-regulated during low temperature stress. In summary, our results show that S. inferens sHSP genes have distinct regulatory roles in the physiology of S. inferens. PMID:25514417

Phytochemical profile of sugarcane and its potential health aspects

PubMed Central

Singh, Amandeep; Lal, Uma Ranjan; Mukhtar, Hayat Muhammad; Singh, Prabh Simran; Shah, Gagan; Dhawan, Ravi Kumar

2015-01-01

Sugarcane (Saccharum officinarum Linn.) is an important perennial grass of Poaceae family, indigenous to tropical South Asia and Southeast Asia. It is cultivated worldwide due to the economical and medicinal value of its high yielding products. Sugarcane juice is well known as a raw material for the production of refined sugar and its wax is considered as a potential substitute for the expensive carnauba wax, which is of cosmetic and pharmaceutical interest. Refined sugar is the primary product of sugarcane juice, but during its processing, various other valuable products are also obtained in an unrefined form, such as, brown sugar, molasses, and jaggery. Sugarcane juice is widely used in India in the treatment of jaundice, hemorrhage, dysuria, anuria, and other urinary diseases. Herein, we have summarized the different phytoconstituents and health benefits of sugarcane and its valuable products. The phytochemistry of sugarcane wax (obtained from the leaves and stalks of sugarcane), leaves, juice, and its products has revealed the presence of various fatty acid, alcohol, phytosterols, higher terpenoids, flavonoids, -O- and -C-glycosides, and phenolic acids. The future prospective of some of the sugarcane products has been discussed, which needs a phytopharmacological study and has a great potential to be a valuable medicinal product. PMID:26009693

Phytochemical profile of sugarcane and its potential health aspects.

PubMed

Singh, Amandeep; Lal, Uma Ranjan; Mukhtar, Hayat Muhammad; Singh, Prabh Simran; Shah, Gagan; Dhawan, Ravi Kumar

2015-01-01

Sugarcane (Saccharum officinarum Linn.) is an important perennial grass of Poaceae family, indigenous to tropical South Asia and Southeast Asia. It is cultivated worldwide due to the economical and medicinal value of its high yielding products. Sugarcane juice is well known as a raw material for the production of refined sugar and its wax is considered as a potential substitute for the expensive carnauba wax, which is of cosmetic and pharmaceutical interest. Refined sugar is the primary product of sugarcane juice, but during its processing, various other valuable products are also obtained in an unrefined form, such as, brown sugar, molasses, and jaggery. Sugarcane juice is widely used in India in the treatment of jaundice, hemorrhage, dysuria, anuria, and other urinary diseases. Herein, we have summarized the different phytoconstituents and health benefits of sugarcane and its valuable products. The phytochemistry of sugarcane wax (obtained from the leaves and stalks of sugarcane), leaves, juice, and its products has revealed the presence of various fatty acid, alcohol, phytosterols, higher terpenoids, flavonoids, -O- and -C-glycosides, and phenolic acids. The future prospective of some of the sugarcane products has been discussed, which needs a phytopharmacological study and has a great potential to be a valuable medicinal product.

DOE Office of Scientific and Technical Information (OSTI.GOV)

Culbert, A.A.; Wallis, G.A.; Kadler, K.E.

The brittleness of bone in people with lethal (type II) osteogenesis imperfecta, a heritable disorder caused by mutations in the type I collagen genes, arises from the deposition of abnormal collagen in the bone matrix. The inability of the abnormal collagen to participate in mineralization may be caused by its failure to interact with other bone proteins. Here, we have designed a strategy to isolate the genes important for mineralization of collagen during bone formation. Cells isolated from 16-day embryonic chick calvaria and seeded post-confluence in culture deposited a mineralized matrix over a period of 2 weeks. Chick skin fibroblastsmore » seeded and cultured under the same conditions did not mineralize. Using RT-PCR, we prepared short cDNAs ({approximately}300 bp) corresponding to the 3{prime} ends of mRNA from fibroblasts and separately from the mineralizing calvarial cells. Subtractive cDNA hybridization generated a pool of cDNAs that were specific to mineralizing calvarial cells but not to fibroblasts. Screening of 100,000 plaques of a chick bone ZAP Express cDNA library with this pool of mineralizing-specific cDNAs identified ten clones which comprised full-length cDNAs for the bone proteins osteopontin (eight of the ten positives), bone sialoprotein II (one of the ten positives), and cystatin (one of the ten positives). cDNAs for type I collagen, fibronectin, alkaline phosphatase, house-keeping genes, and other genes expressed in fibroblasts were not identified in this preliminary screen. The pool of short cDNAs is likely to comprise cDNAs for further bone-specific genes and will be used to screen the entire bone cDNA library of 4.2 million clones. 30 refs., 4 figs.« less

Controlling sugarcane diseases in Florida: a challenge in constant evolution

USDA-ARS?s Scientific Manuscript database

Diseases are limiting factors for the sugarcane crop in almost any sugarcane growing location. More than 40 diseases have been recorded in Florida, with brown rust, orange rust and yellow leaf currently impacting on sugarcane production. Ideally, these diseases should be controlled using resistant c...

A new virus from the family Tombusviridae infecting sugarcane

USDA-ARS?s Scientific Manuscript database

Sugarcane is an economically important crop cultivated in tropical and sub-tropical regions worldwide. Viral diseases are one of the major constraints for sugarcane production. Total RNA was extracted from leaves exhibiting mosaic symptoms on a sugarcane quarantine accession. A cDNA library was cons...

Controlling sugarcane diseases in Florida: a challenge in constant evolution

USDA-ARS?s Scientific Manuscript database

Diseases are limiting factors for the sugarcane crop in almost any sugarcane growing location. More than 40 diseases have been recorded in Florida, with bown rust, orange rust and yellow leaf currently impacting on sugarcane production. Ideally, these diseases should be controlled using resistant ...

Controlling sugarcane diseases in Florida: a challenge in constant evolution

USDA-ARS?s Scientific Manuscript database

Diseases are limiting factors for the sugarcane crop in almost any sugarcane growing location. More than 40 diseases have been recorded in Florida, with brown rust, orange rust and yellow leaf currently impacting on sugarcane production. Ideally, these diseases should be controlled using resistant...

Alternative cropping systems for sugarcane

USDA-ARS?s Scientific Manuscript database

Planting cover crops during the fallow period prior to planting sugarcane has the potential to influence not only the following sugarcane crop, but the economics of the production system as a whole. Research was conducted at the USDA, ARS, Sugarcane Research Unit at Houma, LA to determine the impac...

Efficacy of Alkali-treated Sugarcane Fiber for Improving Physicochemical and Textural Properties of Meat Emulsions with Different Fat Levels.

PubMed

Kim, Hyun-Wook; Setyabrata, Derico; Lee, Yong-Jae; Brad Kim, Yuan H

2018-04-01

The objective of this study was to evaluate the efficacy of alkaline-treated sugarcane bagasse fiber on physicochemical and textural properties of meat emulsion with different fat levels. Crude sugarcane bagasse fiber (CSF) was treated with calcium hydroxide (Ca(OH 2 )) to obtain alkaline-treated sugarcane bagasse fiber (ASF). The two types of sugarcane bagasse fiber (CSF and ASF) were incorporated at 2% levels in pork meat emulsions prepared with 5%, 10% and 20% fat levels. Alkaline-treatment markedly increased acid detergent fiber content ( p =0.002), but significantly decreased protein, fat, ash and other carbohydrate contents. ASF exhibited significantly higher water-binding capacity, but lower oil-binding and emulsifying capacities than CSF. Meat emulsions formulated with 10% fat and 2% sugarcane bagasse fiber had equivalent cooking loss and textural properties to control meat emulsion (20% fat without sugarcane bagasse fiber). The two types of sugarcane bagasse fiber had similar impacts on proximate composition, cooking yield and texture of meat emulsion at the same fat level, respectively ( p >0.05). Our results confirm that sugarcane bagasse fiber could be a functional food ingredient for improving physicochemical and textural properties of meat emulsion, at 2% addition level. Further, the altered functional properties of alkaline-treated sugarcane bagasse fiber had no impacts on physicochemical and textural properties of meat emulsions, regardless of fat level at 5%, 10% and 20%.

Expansion of Sugarcane area for Ethanol production in Brazil: a Threat to Food Production and Environmental Sustainability?

NASA Astrophysics Data System (ADS)

Monteiro, J. M.; Coutinho, H. L.; Veiga, L. B.

2012-12-01

The raise in fossil fuels prices and the increase in Greenhouse Gas emissions is leading nations to adopt non-fossil fuels based energy sources. Sugarcane crops for biofuel production are expanding fast in Brazil, mainly through land use change (LUC) processes, in substitution of pasturelands and grain crops plantations. Would these changes affect negatively sustainability assessments of bioethanol production in the future? We estimate the extent of sugarcane cropland needed to produce sufficient ethanol to attend to market demands. This work presents a baseline scenario for sugarcane cropping area in Brazil in 2017, taking into account market forces (supply and demand). We also comment on a policy instrument targetting sustainable sugarcane production in Brazil. The expansion scenarios took into account the demand for ethanol from 2008-2017, produced by the Energy Research Corporation, of Brazil. In order to develop the expansion scenario, we estimated the amount of sugarcane needed to attend the ethanol demand. We then calculated the area needed to generate that amount of sugarcane. The analytical parameters were: 1) one tonne of sugarcane produces an average 81.6 liters of ethanol; 2) the average sugarcane crop productivity varied linearly from 81.4 tons/hectare in 2008 to 86.2 tons/hectare in 2017. We also assumed that sugarcane productivity in 2017 as the current average productivity of sugarcane in the State of São Paulo. The results show that the requirement for 3.5 million ha in 2007 will increase to 9 million ha in 2017. The Sugarcane Agroecologic Zoning (ZAECANA), published by Embrapa (2009), is a tool that not only informs the territory occupation and use policies, but also classifies land as qualified, restricted or non-qualified for the plantation of sugarcane crops. The ZAECANA is based on soil and climate suitability assessments, and is presented in a spatially-explicit format. Adopting the precautionary principle, a national policy was established restricting the Amazon and the Pantanal basin to sugarcane expansion. These eco-regions were, therefore, not considered by ZAECANA, which defined pasture lands as preferential for sugarcane crop expansion, since their majority is considered as degraded lands. ZAECANA results show that approximately 64 million ha, currently under pasture and agriculture, are suitable for sugarcane cropping in Brazil, located mainly at the Midwest and Southeast regions (35% of the national territory).Our results indicate that, if the ZAECANA instrument is implemented to drive investments for sugarcane expansion in Brazil, the projected demands for bioethanol could be met without significant impacts to food production, and environmental sustainability could be attained by the adoption of good crop, soil and water management practices.

The antibiotic activity and mechanisms of sugarcane (Saccharum officinarum L.) bagasse extract against food-borne pathogens.

PubMed

Zhao, Yi; Chen, Mingshun; Zhao, Zhengang; Yu, Shujuan

2015-10-15

Sugarcane bagasse contains natural compositions that can significantly inhibit food-borne pathogens growth. In the present study, the phenolic content in sugarcane bagasse was detected as higher than 4 mg/g dry bagasse, with 470 mg quercetin/g polyphenol. The sugarcane bagasse extract showed bacteriostatic activity against the growth of Staphylococcus aureus, Listeria monocytogenes, Escherichia coli and Salomonella typhimurium. Additionally, the sugarcane bagasse extract can increase the electric conductivity of bacterial cell suspensions causing cellular leaking of electrolytes. Results of sodium dodecyl sulfate polyacrylamide gel electrophoresis suggested the antibacterial mechanism was probably due to the damaged cellular proteins by sugarcane bagasse extract. The results of scanning electron microscopy and transmission electron microscopy showed that the sugarcane bagasse extract might change cell morphology and internal structure. Copyright © 2015 Elsevier Ltd. All rights reserved.

Complete Genome Sequence of Sporisorium scitamineum and Biotrophic Interaction Transcriptome with Sugarcane

PubMed Central

Benevenuto, Juliana; Peters, Leila P.; Carvalho, Giselle; Palhares, Alessandra; Quecine, Maria C.; Nunes, Filipe R. S.; Kmit, Maria C. P.; Wai, Alvan; Hausner, Georg; Aitken, Karen S.; Berkman, Paul J.; Fraser, James A.; Moolhuijzen, Paula M.; Coutinho, Luiz L.; Creste, Silvana; Vieira, Maria L. C.; Kitajima, João P.; Monteiro-Vitorello, Claudia B.

2015-01-01

Sporisorium scitamineum is a biotrophic fungus responsible for the sugarcane smut, a worldwide spread disease. This study provides the complete sequence of individual chromosomes of S. scitamineum from telomere to telomere achieved by a combination of PacBio long reads and Illumina short reads sequence data, as well as a draft sequence of a second fungal strain. Comparative analysis to previous available sequences of another strain detected few polymorphisms among the three genomes. The novel complete sequence described herein allowed us to identify and annotate extended subtelomeric regions, repetitive elements and the mitochondrial DNA sequence. The genome comprises 19,979,571 bases, 6,677 genes encoding proteins, 111 tRNAs and 3 assembled copies of rDNA, out of our estimated number of copies as 130. Chromosomal reorganizations were detected when comparing to sequences of S. reilianum, the closest smut relative, potentially influenced by repeats of transposable elements. Repetitive elements may have also directed the linkage of the two mating-type loci. The fungal transcriptome profiling from in vitro and from interaction with sugarcane at two time points (early infection and whip emergence) revealed that 13.5% of the genes were differentially expressed in planta and particular to each developmental stage. Among them are plant cell wall degrading enzymes, proteases, lipases, chitin modification and lignin degradation enzymes, sugar transporters and transcriptional factors. The fungus also modulates transcription of genes related to surviving against reactive oxygen species and other toxic metabolites produced by the plant. Previously described effectors in smut/plant interactions were detected but some new candidates are proposed. Ten genomic islands harboring some of the candidate genes unique to S. scitamineum were expressed only in planta. RNAseq data was also used to reassure gene predictions. PMID:26065709

Effect of foliar application of glyphosate and cobalt on sugarcane yields and quality

USDA-ARS?s Scientific Manuscript database

Sugarcane is one of the principal crops of the world, and is used in the production of sugar, alcohol and clean energy. In many sugarcane producing regions of the world selected herbicides, insecticides and fungicides are being evaluated for their potential bioactivator effects on sugarcane yields. ...

Sugarcane boiler ash as an amendment for soilless growing media

USDA-ARS?s Scientific Manuscript database

In 2016, research was conducted to investigate the use of sugarcane bagasse ash (SBA) as an amendment to soilless planting media for the production of vegetable seedlings. Typically, the eleven Louisiana sugarcane mills use a portion of the sugarcane bagasse for fuel, producing over 60,000 tons of S...

A multi-disciplinary approach to sugarcane research at the USDA, ARS, Sugarcane Research Unit in Houma

USDA-ARS?s Scientific Manuscript database

The mission of the Sugarcane Research Unit (SRU) is to provide research-based solutions that enhance the viability of domestic sugarcane industry. To accomplish this mission, SRU uses a multidisciplinary approach to develop improved varieties and environmentally friendly production strategies. Cons...

GGE analysis of ratooning ability in Louisiana sugarcane breeding

USDA-ARS?s Scientific Manuscript database

Ratooning ability is an important sugarcane growth habit that affects profitability. Ratooning ability is the ability of sugarcane to regrow after harvesting and it is measured in this research as the percentage of second ratoon of a trait to plant cane. In sugarcane breeding programs, it is time co...

Natural infection of Sorghum bicolor germplasm by Sugarcane yellow leaf virus in Florida

USDA-ARS?s Scientific Manuscript database

Sugarcane yellow leaf virus (SCYLV), the causal agent of sugarcane yellow leaf, is vectored by the aphid Melanaphis sacchari. Although sugarcane is the primary host of SCYLV, two new natural hosts were recently identified in Florida: the weed Columbus grass (Sorghum almum) and grain sorghum (Sorghum...

Kenaf and cowpea as sugarcane cover crops

USDA-ARS?s Scientific Manuscript database

The use of cover crops during the fallow period prior to planting sugarcane has the potential to influence not only the following sugarcane crop, but the economics of the production system as a whole. Typically, a Louisiana sugarcane field is replanted every four years due to declining yields, and,...

Louisiana sugarcane entomology: A look at the back and a peek at the future

USDA-ARS?s Scientific Manuscript database

Controlling insect pests is an important consideration for sugarcane farmers seeking to minimize losses and maximize profits. Research in managing insects has been conducted for almost as long as sugarcane has been grown in Louisiana. This presentation reviews Louisiana sugarcane entomology from the...

Clarification Properties of Trash and Stalk Tissues from Sugarcane

USDA-ARS?s Scientific Manuscript database

The effect of the U.S. and world-wide change from burnt to unburnt (green) sugarcane harvesting on processing, and the use of sugarcane leaves and tops as a biomass source has not been fully characterized. Sugarcane whole-stalks were harvested from the first ratoon crop of five commercial, Louisian...

Post-processing, energy production use of sugarcane bagasse ash

USDA-ARS?s Scientific Manuscript database

Sugarcane bagasse ash (SBA) is a multi-process by-product produced from the milling of sugarcane. Bagasse is the fibrous material remaining after removing the sugar, water, and other impurities from the sugarcane delivered to the mill. Louisiana produces an estimated 2.7 mt of bagasse each year. In ...

Post-processing, energy production use of sugarcane bagasse ash

USDA-ARS?s Scientific Manuscript database

Sugarcane bagasse ash (SBA) is a multi-processed by-product produced from the milling of sugarcane. Bagasse is the fibrous material remaining after removing the sugar, water, and other impurities from the sugarcane delivered to the mill. Louisiana produces an estimated 3 million tons of bagasse each...

Saponin Biosynthesis in Saponaria vaccaria. cDNAs Encoding β-Amyrin Synthase and a Triterpene Carboxylic Acid Glucosyltransferase1[OA

PubMed Central

Meesapyodsuk, Dauenpen; Balsevich, John; Reed, Darwin W.; Covello, Patrick S.

2007-01-01

Saponaria vaccaria (Caryophyllaceae), a soapwort, known in western Canada as cowcockle, contains bioactive oleanane-type saponins similar to those found in soapbark tree (Quillaja saponaria; Rosaceae). To improve our understanding of the biosynthesis of these saponins, a combined polymerase chain reaction and expressed sequence tag approach was taken to identify the genes involved. A cDNA encoding a β-amyrin synthase (SvBS) was isolated by reverse transcription-polymerase chain reaction and characterized by expression in yeast (Saccharomyces cerevisiae). The SvBS gene is predominantly expressed in leaves. A S. vaccaria developing seed expressed sequence tag collection was developed and used for the isolation of a full-length cDNA bearing sequence similarity to ester-forming glycosyltransferases. The gene product of the cDNA, classified as UGT74M1, was expressed in Escherichia coli, purified, and identified as a triterpene carboxylic acid glucosyltransferase. UGT74M1 is expressed in roots and leaves and appears to be involved in monodesmoside biosynthesis in S. vaccaria. PMID:17172290

Transcriptional analysis of the R locus: Progress report, September 1986 through October 1987

DOE Office of Scientific and Technical Information (OSTI.GOV)

Wessler, S.R.

1987-11-01

The R locus controls where, when and how much anthocyanins are expressed in at least 11 different tissues of the corn plant and seed. Enormous natural variation has been seen when the phenotypes of different R alleles are compared in a common genetic background. Some alleles have been shown to have a compound structure resulting from gene duplication and divergence. In these complex alleles, each member of the duplication (called R genic elements) has a unique pattern of expression. The function of the R locus is not known; genetic and biochemical analyses suggest that it may encode a protein thatmore » regulates other genes in the anthocyanin pathway. Over the past year we have determined that the genic elements (P), (S), and (Lc) all encode a very rare 2.8 kb transcript that is present in tissue displaying anthocyanin pigmentation. cDNA libraries have been constructed using mRNA isolated from tissues shown by Northern blots to be enriched for the R transcript. Full-length cDNAs will be sequenced and compared to each other.« less

A review of topramezone in sugarcane and potential carryover of post emergence soybean herbicides on plant cane

USDA-ARS?s Scientific Manuscript database

There are approximately 430,000 acres in commercial sugarcane production in Lousiana and methods to control weeds consist primarily of herbicides and tillage. Topramezone, the active ingredient in Armezon® received registration in sugarcane in fall of 2017. Data on sugarcane cultivar tolerance to to...

Sugarcane residue and bagasse as biochar precursors for soil amendment applications and beyond

USDA-ARS?s Scientific Manuscript database

There are two potential untapped resources associated with the harvesting and processing of sugarcane, the trash (leaves and tops) left in the field and the sugarcane bagasse as surplus from the mills. Burning of sugarcane trash in the field has been under scrutiny in recent years due to urban encr...

Solanum nigrescens, a problematic nightshade species in Louisiana sugarcane

USDA-ARS?s Scientific Manuscript database

A large perennial broadleaf weed appearing to be a member of the Solanum genus was observed in a commercial sugarcane (Saccharum spp.) field in Vacherie, LA in 2010. Since then, this weed has spread to sugarcane fields in 17 of the 24 parishes which produce sugarcane. The weed has been identified as...

Field screening of sugarcane varieties for sugarcane yellow leaf in Louisiana

USDA-ARS?s Scientific Manuscript database

The causal agent of sugarcane yellow leaf is the Sugarcane yellow leaf virus (SCYLV), a member of Luteoviridae family. As with other luteoviruses, SCYLV is only transmitted by specific aphids in a circulative, non-propagative manner. In Louisiana, the primary vector of SCYLV is believed to be the su...

Unravel the genetic basis of Sugarcane Yellow Leaf Virus (SCYLV) resistance in Saccharum spp. hybrid

USDA-ARS?s Scientific Manuscript database

Sugarcane (Saccharum Spp.) produces 80% of the world’s table sugar along with several other byproducts. The production of sugarcane is vulnerable due to infestation of sugarcane yellow leaf virus (SCYLV) worldwide. A genetic mapping study was conducted using an F1 segregating population derived from...

First report of Sugarcane yellow leaf virus infecting Columbus Grass (Sorghum almum) in Florida

USDA-ARS?s Scientific Manuscript database

Sugarcane yellow leaf virus (SCYLV) [genus Polerovirus, family Luteoviridae] is the causal agent of sugarcane yellow leaf disease. SCYLV is widespread in Florida where sugarcane was the only known natural host of this virus. During spring 2015, we collected (leaves or stalks) and tested several gras...

Efficacy of Alkali-treated Sugarcane Fiber for Improving Physicochemical and Textural Properties of Meat Emulsions with Different Fat Levels

PubMed Central

Kim, Hyun-Wook; Setyabrata, Derico; Lee, Yong-Jae; Brad Kim, Yuan H.

2018-01-01

Abstract The objective of this study was to evaluate the efficacy of alkaline-treated sugarcane bagasse fiber on physicochemical and textural properties of meat emulsion with different fat levels. Crude sugarcane bagasse fiber (CSF) was treated with calcium hydroxide (Ca(OH2)) to obtain alkaline-treated sugarcane bagasse fiber (ASF). The two types of sugarcane bagasse fiber (CSF and ASF) were incorporated at 2% levels in pork meat emulsions prepared with 5%, 10% and 20% fat levels. Alkaline-treatment markedly increased acid detergent fiber content (p=0.002), but significantly decreased protein, fat, ash and other carbohydrate contents. ASF exhibited significantly higher water-binding capacity, but lower oil-binding and emulsifying capacities than CSF. Meat emulsions formulated with 10% fat and 2% sugarcane bagasse fiber had equivalent cooking loss and textural properties to control meat emulsion (20% fat without sugarcane bagasse fiber). The two types of sugarcane bagasse fiber had similar impacts on proximate composition, cooking yield and texture of meat emulsion at the same fat level, respectively (p>0.05). Our results confirm that sugarcane bagasse fiber could be a functional food ingredient for improving physicochemical and textural properties of meat emulsion, at 2% addition level. Further, the altered functional properties of alkaline-treated sugarcane bagasse fiber had no impacts on physicochemical and textural properties of meat emulsions, regardless of fat level at 5%, 10% and 20%. PMID:29805281

Impacts of sugarcane agriculture expansion over low-intensity cattle ranch pasture in Brazil on greenhouse gases.

PubMed

Bento, Camila Bolfarini; Filoso, Solange; Pitombo, Leonardo Machado; Cantarella, Heitor; Rossetto, Raffaella; Martinelli, Luiz Antonio; do Carmo, Janaina Braga

2018-01-15

Sugarcane is a widespread bioenergy crop in tropical regions, and the growing global demand for renewable energy in recent years has led to a dramatic expansion and intensification of sugarcane agriculture in Brazil. Currently, extensive areas of low-intensity pasture are being converted to sugarcane, while management in the remaining pasture is becoming more intensive, i.e., includes tilling and fertilizer use. In this study, we assessed how such changes in land use and management practices alter emissions of greenhouse gases (GHG) such as CO 2 , N 2 O and CH 4 by measuring in situ fluxes for one year after conversion from low-intensity pasture to conventional sugarcane agriculture and management-intensive pasture. Results show that CO 2 and N 2 O fluxes increased significantly in pasture and sugarcane with tillage, fertilizer use, or both combined. Emissions were highly variable for all GHGs, yet, cumulatively, it was clear that annual emissions in CO 2 -equivalent (CO 2 -eq) were higher in management-intense pasture and sugarcane than in unmanaged pasture. Surprisingly, tilled pasture with fertilizer (management-intensive pasture) resulted in higher CO 2 -eq emissions than conventional sugarcane. We concluded that intensification of pasture management and the conversion of pasture to sugarcane can increase the emission factor (EF) estimated for sugarcane produced in Brazil. The role of management practices and environmental conditions and the potential for reducing emissions are discussed. Copyright © 2017 Elsevier Ltd. All rights reserved.

Identifying Quantitative Trait Loci (QTLs) and Developing Diagnostic Markers Linked to Orange Rust Resistance in Sugarcane (Saccharum spp.).

PubMed

Yang, Xiping; Islam, Md S; Sood, Sushma; Maya, Stephanie; Hanson, Erik A; Comstock, Jack; Wang, Jianping

2018-01-01

Sugarcane ( Saccharum spp.) is an important economic crop, contributing up to 80% of table sugar used in the world and has become a promising feedstock for biofuel production. Sugarcane production has been threatened by many diseases, and fungicide applications for disease control have been opted out for sustainable agriculture. Orange rust is one of the major diseases impacting sugarcane production worldwide. Identifying quantitative trait loci (QTLs) and developing diagnostic markers are valuable for breeding programs to expedite release of superior sugarcane cultivars for disease control. In this study, an F 1 segregating population derived from a cross between two hybrid sugarcane clones, CP95-1039 and CP88-1762, was evaluated for orange rust resistance in replicated trails. Three QTLs controlling orange rust resistance in sugarcane (qORR109, qORR4 and qORR102) were identified for the first time ever, which can explain 58, 12 and 8% of the phenotypic variation, separately. We also characterized 1,574 sugarcane putative resistance ( R ) genes. These sugarcane putative R genes and simple sequence repeats in the QTL intervals were further used to develop diagnostic markers for marker-assisted selection of orange rust resistance. A PCR-based Resistance gene-derived maker, G1 was developed, which showed significant association with orange rust resistance. The putative QTLs and marker developed in this study can be effectively utilized in sugarcane breeding programs to facilitate the selection process, thus contributing to the sustainable agriculture for orange rust disease control.

Monitoring Freeze Injury and Evaluating Losingto Sugar-Cane Using RS and GPS

NASA Astrophysics Data System (ADS)

Tan, Zongkun; Ding, Meihua; Wang, Longhe; Yang, Xin; Ou, Zhaorong

From Jan 12th to Feb 12th 2008, the most severity cold chilling and freeze injury weather took place during the last 50 years in the southern of China.Sugar-cane was suffered injury severity. However, the losing of sugar-cane which it was aroused by thisweather disaster had not been exactitude evaluated till on Apr 1st, 2008. It was not only affected the sugar-cane ordinary harvesting and crushing, but also affected reserving sugar-cane seed for planting. Freeze injury is common disaster for sugar-cane in southern of China and monitoring freeze injury using RS and GIS are of great economic significance but little research work about it has been done in China Freeze injuring is not only related to crop growth stage and the cold air intension from northern to southern and weather types, but also consanguineous related to land form and physiognomy and geographical latitude and height above sea level etc and crop planting spatial distribution. The case study of Guangxi province which is the biggest region of sugar-cane planting in China in this paper, the values of sugar-cane NDVI among the freeze injury occur former and after in early 2008 and without freeze injury occur in the same term 2007 were analyzed and compared based on the sugar-cane planting spatial distribution information which were carried out by using multi-phase EOS/MODIS data. The result showed that it was not only commendably reflected the spatial distribution of freeze injury but also reflected the sugarcane suffered from degree using the values of sugar-cane NDVIof freeze injury occur former and after. The field sample investigation data of using GPS was integrated with the NDVI, the evaluation of region sugar-cane suffer from freeze injury losing could quickly and exactly realize.

A Comparative Object-Based Sugarcane Classification from Sentinel-2 Data Using Random Forests and Support Vector Machines

NASA Astrophysics Data System (ADS)

Chen, C. R.; Chen, C. F.; Nguyen, S. T.; Lau, K.; Lay, J. G.

2016-12-01

Sugarcane mostly grown in tropical and subtropical regions is one of the important commercial crops worldwide, providing significant employment, foreign exchange earnings, and other social and environmental benefits. The sugar industry is a vital component of Belize's economy as it provides employment to 15% of the country's population and 60% of the national agricultural exports. Sugarcane mapping is thus an important task due to official initiatives to provide reliable information on sugarcane-growing areas in respect to improved accuracy in monitoring sugarcane production and yield estimates. Policymakers need such monitoring information to formulate timely plans to ensure sustainably socioeconomic development. Sugarcane monitoring in Belize is traditionally carried out through time-consuming and costly field surveys. Remote sensing is an indispensable tool for crop monitoring on national, regional and global scales. The use of high and low resolution satellites for sugarcane monitoring in Belize is often restricted due to cost limitations and mixed pixel problems because sugarcane fields are small and fragmental. With the launch of Sentinel-2 satellite, it is possible to collectively map small patches of sugarcane fields over a large region as the data are free of charge and have high spectral, spatial, and temporal resolutions. This study aims to develop an object-based classification approach to comparatively map sugarcane fields in Belize from Sentinel-2 data using random forests (RF) and support vector machines (SVM). The data were processed through four main steps: (1) data pre-processing, (2) image segmentation, (3) sugarcane classification, and (4) accuracy assessment. The mapping results compared with the ground reference data indicated satisfactory results. The overall accuracies and Kappa coefficients were generally higher than 80% and 0.7, in both cases. The RF produced slightly more accurate mapping results than SVM. This study demonstrates the realization of the potential application of Sentinel-2 data for sugarcane mapping in Belize with the aid of RF and SVM methods. The methods are thus proposed for monitoring purposes in the country.

Analysis of the resistance mechanisms in sugarcane during Sporisorium scitamineum infection using RNA-seq and microscopy.

PubMed

McNeil, Meredith D; Bhuiyan, Shamsul A; Berkman, Paul J; Croft, Barry J; Aitken, Karen S

2018-01-01

Smut caused by biotrophic fungus Sporisorium scitamineum is a major disease of cultivated sugarcane that can cause considerable yield losses. It has been suggested in literature that there are at least two types of resistance mechanisms in sugarcane plants: an external resistance, due to chemical or physical barriers in the sugarcane bud, and an internal resistance governed by the interaction of plant and fungus within the plant tissue. Detailed molecular studies interrogating these two different resistance mechanisms in sugarcane are scarce. Here, we use light microscopy and global expression profiling with RNA-seq to investigate these mechanisms in sugarcane cultivar CP74-2005, a cultivar that possibly possesses both internal and external defence mechanisms. A total of 861 differentially expressed genes (DEGs) were identified in a comparison between infected and non-infected buds at 48 hours post-inoculation (hpi), with 457 (53%) genes successfully annotated using BLAST2GO software. This includes genes involved in the phenylpropanoid pathway, cell wall biosynthesis, plant hormone signal transduction and disease resistance genes. Finally, the expression of 13 DEGs with putative roles in S. scitamineum resistance were confirmed by quantitative real-time reverse transcription PCR (qRT-PCR) analysis, and the results were consistent with the RNA-seq data. These results highlight that the early sugarcane response to S. scitamineum infection is complex and many of the disease response genes are attenuated in sugarcane cultivar CP74-2005, while others, like genes involved in the phenylpropanoid pathway, are induced. This may point to the role of the different disease resistance mechanisms that operate in cultivars such as CP74-2005, whereby the early response is dominated by external mechanisms and then as the infection progresses, the internal mechanisms are switched on. Identification of genes underlying resistance in sugarcane will increase our knowledge of the sugarcane-S. scitamineum interaction and facilitate the introgression of new resistance genes into commercial sugarcane cultivars.

Molecular cloning and expressional analysis of five sucrose transporter (SUT) genes in sugarcane

USDA-ARS?s Scientific Manuscript database

The sucrose transport and accumulation in sugarcane internodes are very complicated processes and how sugarcane sucrose transporter (SUT) genes function in these processes remains unclear. In this study, five sugarcane SUT genes, namely, SoSUT1, SoSUT2, SoSUT3, SoSUT4 and SoSUT5, were cloned and the...

Comparative performance of sugarcane bagasse and black polyethylene as mulch for squash (Cucurbita pepo L.) production

USDA-ARS?s Scientific Manuscript database

Louisiana processed 11.6 million mt of sugarcane in 2014, producing 1.36 million mt of raw sugar and an estimated 3.5 million mt of bagasse. Sugarcane bagasse is the fibrous material remaining after removing the sucrose, water, and other impurities (filter mud) from the millable sugarcane. Typically...

Sugarcane bagasse and leaf residue biochars as soil amendment for increased sugar and cane yields

USDA-ARS?s Scientific Manuscript database

There are two potential untapped resources associated with the harvesting and processing of sugarcane, the trash (leaves and tops) left in the field and the sugarcane bagasse as surplus from the mills. Burning of sugarcane trash in the field has been under scrutiny in recent years due to urban encr...

Cross-resistance between the Mexican Rice Borer and the Sugarcane Borer (Lepidoptera: Crambidae): A Case Study Using Sugarcane Breeding Populations

USDA-ARS?s Scientific Manuscript database

The sugarcane borer (SCB) (Diatraea saccharalis) and Mexican rice borer (MRB) (Eoreuma loftini) are two economically important pests of sugarcane in the USA. Because of similarities in larval feeding behavior, selecting for resistance to one species could provide resistance to the other, a phenomeno...

Frequency and distribution of the brown rust resistance gene Bru1 and implications for the Louisiana sugarcane breeding programme

USDA-ARS?s Scientific Manuscript database

Brown rust, caused by the fungus Puccinia melanocephala, is an important disease of sugarcane posing an increasing threat to sugarcane industries worldwide. A major gene, Bru1, has been shown to contribute a significant proportion of brown rust resistance in multiple sugarcane industries. The recent...

Policies, Socioeconomic, Institutional and Biophysical Factors Influencing the Change from Rice to Sugarcane in Nong Bua Lamphu Province, Thailand

NASA Astrophysics Data System (ADS)

Lakapunrat, Narinpat; Thapa, Gopal B.

2017-06-01

For the past decade, Thailand pursued a strategy of promoting biofuel crop production, including sugarcane, to meet the ever increasing energy demand and to increase the income of farmers. This study analyzed the influence of policy instruments implemented to promote the sugarcane cultivation, farm household socioeconomic levels, biophysical, and institutional factors driving the conversion of rice fields into sugarcane farms. Primary information was collected from 230 farm households through a structured questionnaire. Relevant policy documents published by the responsible government agencies were the main sources of secondary information collected for policy analysis. The analyses revealed that farmers in the study area converted 25-75% of their rice fields into sugarcane farms as a result of implementation of policy instruments that made sugarcane financially far more attractive than rice. The results of the regression analysis showed that eight variables were found significant and positively influenced the conversion of rice fields into sugarcane farms. These were access to extension services, information, sugarcane loading stations, and ground water for irrigation, and duration of experience in sugarcane farming as well as household head's age and education. Irrespective of landholding size, the majority of farmers were not concerned about food security. In view of the finding, if feasible, in the form of additional price supports and commercial cane sugar index-based pricing strategies to promote sugarcane production should benefit all concerned farmers. Likewise, attention should be paid to deliver essential extension and marketing services in an effective way, particularly to those farmers who are not receiving such services.

Identifying Quantitative Trait Loci (QTLs) and Developing Diagnostic Markers Linked to Orange Rust Resistance in Sugarcane (Saccharum spp.)

PubMed Central

Yang, Xiping; Islam, Md. S.; Sood, Sushma; Maya, Stephanie; Hanson, Erik A.; Comstock, Jack; Wang, Jianping

2018-01-01

Sugarcane (Saccharum spp.) is an important economic crop, contributing up to 80% of table sugar used in the world and has become a promising feedstock for biofuel production. Sugarcane production has been threatened by many diseases, and fungicide applications for disease control have been opted out for sustainable agriculture. Orange rust is one of the major diseases impacting sugarcane production worldwide. Identifying quantitative trait loci (QTLs) and developing diagnostic markers are valuable for breeding programs to expedite release of superior sugarcane cultivars for disease control. In this study, an F1 segregating population derived from a cross between two hybrid sugarcane clones, CP95-1039 and CP88-1762, was evaluated for orange rust resistance in replicated trails. Three QTLs controlling orange rust resistance in sugarcane (qORR109, qORR4 and qORR102) were identified for the first time ever, which can explain 58, 12 and 8% of the phenotypic variation, separately. We also characterized 1,574 sugarcane putative resistance (R) genes. These sugarcane putative R genes and simple sequence repeats in the QTL intervals were further used to develop diagnostic markers for marker-assisted selection of orange rust resistance. A PCR-based Resistance gene-derived maker, G1 was developed, which showed significant association with orange rust resistance. The putative QTLs and marker developed in this study can be effectively utilized in sugarcane breeding programs to facilitate the selection process, thus contributing to the sustainable agriculture for orange rust disease control. PMID:29616061

Policies, Socioeconomic, Institutional and Biophysical Factors Influencing the Change from Rice to Sugarcane in Nong Bua Lamphu Province, Thailand.

PubMed

Lakapunrat, Narinpat; Thapa, Gopal B

2017-06-01

For the past decade, Thailand pursued a strategy of promoting biofuel crop production, including sugarcane, to meet the ever increasing energy demand and to increase the income of farmers. This study analyzed the influence of policy instruments implemented to promote the sugarcane cultivation, farm household socioeconomic levels, biophysical, and institutional factors driving the conversion of rice fields into sugarcane farms. Primary information was collected from 230 farm households through a structured questionnaire. Relevant policy documents published by the responsible government agencies were the main sources of secondary information collected for policy analysis. The analyses revealed that farmers in the study area converted 25-75% of their rice fields into sugarcane farms as a result of implementation of policy instruments that made sugarcane financially far more attractive than rice. The results of the regression analysis showed that eight variables were found significant and positively influenced the conversion of rice fields into sugarcane farms. These were access to extension services, information, sugarcane loading stations, and ground water for irrigation, and duration of experience in sugarcane farming as well as household head's age and education. Irrespective of landholding size, the majority of farmers were not concerned about food security. In view of the finding, if feasible, in the form of additional price supports and commercial cane sugar index-based pricing strategies to promote sugarcane production should benefit all concerned farmers. Likewise, attention should be paid to deliver essential extension and marketing services in an effective way, particularly to those farmers who are not receiving such services.

Transgenic sugarcane overexpressing CaneCPI-1 negatively affects the growth and development of the sugarcane weevil Sphenophorus levis.

PubMed

Schneider, Vanessa Karine; Soares-Costa, Andrea; Chakravarthi, Mohan; Ribeiro, Carolina; Chabregas, Sabrina Moutinho; Falco, Maria Cristina; Henrique-Silva, Flavio

2017-01-01

Transgenic sugarcane expressing CaneCPI-1 exhibits resistance to Sphenophorus levis larvae. Transgenic plants have widely been used to improve resistance against insect attack. Sugarcane is an economically important crop; however, great losses are caused by insect attack. Sphenophorus levis is a sugarcane weevil that digs tunnels in the stem base, leading to the destruction of the crop. This insect is controlled inefficiently by chemical insecticides. Transgenic plants expressing peptidase inhibitors represent an important strategy for impairing insect growth and development. Knowledge of the major peptidase group present in the insect gut is critical when choosing the most effective inhibitor. S. levis larvae use cysteine peptidases as their major digestive enzymes, primarily cathepsin L-like activity. In this study, we developed transgenic sugarcane plants that overexpress sugarcane cysteine peptidase inhibitor 1 (CaneCPI-1) and assessed their potential through feeding bioassays with S. levis larvae. Cystatin overexpression in the transgenic plants was evaluated using semi-quantitative RT-PCR, RT-qPCR, and immunoblot assays. A 50% reduction of the average weight was observed in larvae that fed on transgenic plants in comparison to larvae that fed on non-transgenic plants. In addition, transgenic sugarcane exhibited less damage caused by larval attack than the controls. Our results suggest that the overexpression of CaneCPI-1 in sugarcane is a promising strategy for improving resistance against this insect.

Development of a reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay for the detection of Sugarcane mosaic virus and Sorghum mosaic virus in sugarcane

USDA-ARS?s Scientific Manuscript database

A reverse transcription loop-mediated isothermal amplification (RT-LAMP) assay was developed for detecting Sugarcane mosaic virus (SCMV) and Sorghum mosaic virus (SrMV) in sugarcane. Six sets of four primers corresponding to the conserved coat protein gene were designed for each virus and their succ...

Direct saponification preparation and analysis of free and conjugated phytosterols in sugarcane (Saccharum officinarum L.) by reversed-phase high-performance liquid chromatography.

PubMed

Feng, Simin; Liu, Songbai; Luo, Zisheng; Tang, Kaichen

2015-08-15

A simple method based on direct saponification followed by RP-HPLC analysis was developed for quantification of free and conjugated sterols in sugarcane. Acid hydrolysis prior to alkaline saponification was used to determined acylated steryl glycoside and steryl glycoside in sugarcane. The applicability and generality of this method were improved with intensive investigation. Compared to traditional solvent extraction method, this method was more time saving and appropriate for characterization of sterol fractions in sugarcane. This method was successfully applied for determination of free and conjugated sterols in different sugarcane samples. The results exhibited that stigmasterol (varied from 883.3 ± 23.5 to 1823.9 ± 24.5 μg/g dry weigh) and β-sitosterol (varied from 117.6 ± 19.9 to 801.4 ± 33.5 μg/g dry weight) were major phytosterols in the sugarcane sample, and their glycosylated forms accounted for almost 87.0% of stigmasterol and 87.5% of β-sitosterol in sugarcane, respectively. In addition, among other parts of sugarcane, tips contained the greatest amount of phytosterols. Copyright © 2015 Elsevier Ltd. All rights reserved.

Identification and expression analysis of genes involved in early ovary development in diploid gynogenetic hybrids of red crucian carp x common carp.

PubMed

Liu, Dong; Liu, Shaojun; You, Cuiping; Chen, Lin; Liu, Zhen; Liu, Liangguo; Wang, Jing; Liu, Yun

2010-04-01

Diploid eggs of allotetraploid hybrids (red crucian carp female symbol x common carp male symbol), when activated by UV-irradiated sperm of scatter scale carp, can develop into diploid progenies without chromosome duplication treatment. Diploid progenies produce diploid eggs, which develop into diploid population by the same way. To understand the molecular mechanism underlying the production of diploid eggs by the diploid fish, we constructed a forward suppression subtractive hybridization complementary DNA (cDNA) library. The cDNAs from the ovary in proliferation phase were employed as the "tester," and those in growth phase were used as the "driver." Seventy-three cDNA clones that are specifically expressed in proliferation phase were detected by dot-blot hybridization. Sequencing analyses revealed that several of these cDNAs have high homologies to the known sequences in the NCBI database. Their encoded proteins include the protein preventing mitosis catastrophe (PMC), the signal recognition particle 9, the ATP-binding cassette transporter, the glucanase-xylanase fusion protein, and others. These genes were confirmed by reverse transcriptase-polymerase chain reaction. The expression profile of the PMC gene at different time points was analyzed by quantitative real-time polymerase chain reaction. The results indicated that the expression of this suppression subtractive hybridization-identified gene changed during the time course, corresponding with the cellular phenomenon in the ovary development. Our studies provide insights into the molecular mechanism underlying the ovary development of diploid gynogenetic fish.

Single cell transcriptomics of hypothalamic warm sensitive neurons that control core body temperature and fever response Signaling asymmetry and an extension of chemical neuroanatomy.

PubMed

Eberwine, James; Bartfai, Tamas

2011-03-01

We report on an 'unbiased' molecular characterization of individual, adult neurons, active in a central, anterior hypothalamic neuronal circuit, by establishing cDNA libraries from each individual, electrophysiologically identified warm sensitive neuron (WSN). The cDNA libraries were analyzed by Affymetrix microarray. The presence and frequency of cDNAs were confirmed and enhanced with Illumina sequencing of each single cell cDNA library. cDNAs encoding the GABA biosynthetic enzyme Gad1 and of adrenomedullin, galanin, prodynorphin, somatostatin, and tachykinin were found in the WSNs. The functional cellular and in vivo studies on dozens of the more than 500 neurotransmitters, hormone receptors and ion channels, whose cDNA was identified and sequence confirmed, suggest little or no discrepancy between the transcriptional and functional data in WSNs; whenever agonists were available for a receptor whose cDNA was identified, a functional response was found. Sequencing single neuron libraries permitted identification of rarely expressed receptors like the insulin receptor, adiponectin receptor 2 and of receptor heterodimers; information that is lost when pooling cells leads to dilution of signals and mixing signals. Despite the common electrophysiological phenotype and uniform Gad1 expression, WSN transcriptomes show heterogeneity, suggesting strong epigenetic influence on the transcriptome. Our study suggests that it is well-worth interrogating the cDNA libraries of single neurons by sequencing and chipping. Copyright © 2010 Elsevier Inc. All rights reserved.

Cytochrome P450-Dependent Metabolism of Oxylipins in Tomato. Cloning and Expression of Allene Oxide Synthase and Fatty Acid Hydroperoxide Lyase1

PubMed Central

Howe, Gregg A.; Lee, Gyu In; Itoh, Aya; Li, Lei; DeRocher, Amy E.

2000-01-01

Allene oxide synthase (AOS) and fatty acid hydroperoxide lyase (HPL) are plant-specific cytochrome P450s that commit fatty acid hydroperoxides to different branches of oxylipin metabolism. Here we report the cloning and characterization of AOS (LeAOS) and HPL (LeHPL) cDNAs from tomato (Lycopersicon esculentum). Functional expression of the cDNAs in Escherichia coli showed that LeAOS and LeHPL encode enzymes that metabolize 13- but not 9-hydroperoxide derivatives of C18 fatty acids. LeAOS was active against both 13S-hydroperoxy-9(Z),11(E),15(Z)-octadecatrienoic acid (13-HPOT) and 13S-hydroperoxy-9(Z),11(E)-octadecadienoic acid, whereas LeHPL showed a strong preference for 13-HPOT. These results suggest a role for LeAOS and LeHPL in the metabolism of 13-HPOT to jasmonic acid and hexenal/traumatin, respectively. LeAOS expression was detected in all organs of the plant. In contrast, LeHPL expression was predominant in leaves and flowers. Damage inflicted to leaves by chewing insect larvae led to an increase in the local and systemic expression of both genes, with LeAOS showing the strongest induction. Wound-induced expression of LeAOS also occurred in the def-1 mutant that is deficient in octadecanoid-based signaling of defensive proteinase inhibitor genes. These results demonstrate that tomato uses genetically distinct signaling pathways for the regulation of different classes of wound responsive genes. PMID:10859201

Identification of human chromosome 22 transcribed sequences with ORF expressed sequence tags

PubMed Central

de Souza, Sandro J.; Camargo, Anamaria A.; Briones, Marcelo R. S.; Costa, Fernando F.; Nagai, Maria Aparecida; Verjovski-Almeida, Sergio; Zago, Marco A.; Andrade, Luis Eduardo C.; Carrer, Helaine; El-Dorry, Hamza F. A.; Espreafico, Enilza M.; Habr-Gama, Angelita; Giannella-Neto, Daniel; Goldman, Gustavo H.; Gruber, Arthur; Hackel, Christine; Kimura, Edna T.; Maciel, Rui M. B.; Marie, Suely K. N.; Martins, Elizabeth A. L.; Nóbrega, Marina P.; Paçó-Larson, Maria Luisa; Pardini, Maria Inês M. C.; Pereira, Gonçalo G.; Pesquero, João Bosco; Rodrigues, Vanderlei; Rogatto, Silvia R.; da Silva, Ismael D. C. G.; Sogayar, Mari C.; de Fátima Sonati, Maria; Tajara, Eloiza H.; Valentini, Sandro R.; Acencio, Marcio; Alberto, Fernando L.; Amaral, Maria Elisabete J.; Aneas, Ivy; Bengtson, Mário Henrique; Carraro, Dirce M.; Carvalho, Alex F.; Carvalho, Lúcia Helena; Cerutti, Janete M.; Corrêa, Maria Lucia C.; Costa, Maria Cristina R.; Curcio, Cyntia; Gushiken, Tsieko; Ho, Paulo L.; Kimura, Elza; Leite, Luciana C. C.; Maia, Gustavo; Majumder, Paromita; Marins, Mozart; Matsukuma, Adriana; Melo, Analy S. A.; Mestriner, Carlos Alberto; Miracca, Elisabete C.; Miranda, Daniela C.; Nascimento, Ana Lucia T. O.; Nóbrega, Francisco G.; Ojopi, Élida P. B.; Pandolfi, José Rodrigo C.; Pessoa, Luciana Gilbert; Rahal, Paula; Rainho, Claudia A.; da Ro's, Nancy; de Sá, Renata G.; Sales, Magaly M.; da Silva, Neusa P.; Silva, Tereza C.; da Silva, Wilson; Simão, Daniel F.; Sousa, Josane F.; Stecconi, Daniella; Tsukumo, Fernando; Valente, Valéria; Zalcberg, Heloisa; Brentani, Ricardo R.; Reis, Luis F. L.; Dias-Neto, Emmanuel; Simpson, Andrew J. G.

2000-01-01

Transcribed sequences in the human genome can be identified with confidence only by alignment with sequences derived from cDNAs synthesized from naturally occurring mRNAs. We constructed a set of 250,000 cDNAs that represent partial expressed gene sequences and that are biased toward the central coding regions of the resulting transcripts. They are termed ORF expressed sequence tags (ORESTES). The 250,000 ORESTES were assembled into 81,429 contigs. Of these, 1,181 (1.45%) were found to match sequences in chromosome 22 with at least one ORESTES contig for 162 (65.6%) of the 247 known genes, for 67 (44.6%) of the 150 related genes, and for 45 of the 148 (30.4%) EST-predicted genes on this chromosome. Using a set of stringent criteria to validate our sequences, we identified a further 219 previously unannotated transcribed sequences on chromosome 22. Of these, 171 were in fact also defined by EST or full length cDNA sequences available in GenBank but not utilized in the initial annotation of the first human chromosome sequence. Thus despite representing less than 15% of all expressed human sequences in the public databases at the time of the present analysis, ORESTES sequences defined 48 transcribed sequences on chromosome 22 not defined by other sequences. All of the transcribed sequences defined by ORESTES coincided with DNA regions predicted as encoding exons by genscan. (http://genes.mit.edu/GENSCAN.html). PMID:11070084

High-throughput protein analysis integrating bioinformatics and experimental assays

PubMed Central

del Val, Coral; Mehrle, Alexander; Falkenhahn, Mechthild; Seiler, Markus; Glatting, Karl-Heinz; Poustka, Annemarie; Suhai, Sandor; Wiemann, Stefan

2004-01-01

The wealth of transcript information that has been made publicly available in recent years requires the development of high-throughput functional genomics and proteomics approaches for its analysis. Such approaches need suitable data integration procedures and a high level of automation in order to gain maximum benefit from the results generated. We have designed an automatic pipeline to analyse annotated open reading frames (ORFs) stemming from full-length cDNAs produced mainly by the German cDNA Consortium. The ORFs are cloned into expression vectors for use in large-scale assays such as the determination of subcellular protein localization or kinase reaction specificity. Additionally, all identified ORFs undergo exhaustive bioinformatic analysis such as similarity searches, protein domain architecture determination and prediction of physicochemical characteristics and secondary structure, using a wide variety of bioinformatic methods in combination with the most up-to-date public databases (e.g. PRINTS, BLOCKS, INTERPRO, PROSITE SWISSPROT). Data from experimental results and from the bioinformatic analysis are integrated and stored in a relational database (MS SQL-Server), which makes it possible for researchers to find answers to biological questions easily, thereby speeding up the selection of targets for further analysis. The designed pipeline constitutes a new automatic approach to obtaining and administrating relevant biological data from high-throughput investigations of cDNAs in order to systematically identify and characterize novel genes, as well as to comprehensively describe the function of the encoded proteins. PMID:14762202

Adult Schistosoma mansoni express cathepsin L proteinase activity.

PubMed

Smith, A M; Dalton, J P; Clough, K A; Kilbane, C L; Harrop, S A; Hole, N; Brindley, P J

1994-09-01

This report presents the deduced amino acid sequence of a novel cathepsin L proteinase from Schistosoma mansoni, and describes cathepsin L-like activity in extracts of adult schistosomes. Using consensus primers specific for cysteine proteinases, gene fragments were amplified from adult S. mansoni cDNA by PCR and cloned. One of these fragments showed marked identity to Sm31, the cathepsin B cysteine proteinase of adult S. mansoni, whereas another differed from Sm31 and was employed as a probe to isolate two cDNAs from an adult S. mansoni gene library. Together these cDNAs encoded a novel preprocathepsin L of 319 amino acids; this zymogen is predicted to be processed in vivo into a mature, active cathepsin L proteinase of 215 amino acids. Closest homologies were with cathepsins L from rat, mouse, and chicken (46-47% identity). Southern hybridization analysis suggested that only one or a few copies of the gene was present per genome, demonstrated that its locus was distinct from that of Sm31, and that a homologous sequence was present in Schistosoma japonicum. Because these results indicated that schistosomes expressed a cathepsin L proteinase, extracts of adult S. mansoni were examined for acidic, cysteine proteinase activity. Based on rates of cleavage of peptidyl substrates employed to discriminate between classes of cysteine proteinases, namely cathepsin L (Z-phe-arg-AMC), cathepsin B (Z-arg-arg-AMC) and cathepsin H (Bz-arg-AMC), the extracts were found to contain vigorous cathepsin L-like activity.(ABSTRACT TRUNCATED AT 250 WORDS)

Scale insects (Hemiptera: Coccomorpha) on sugarcane in Colombia, with description of a new species of Tillancoccus Ben-Dov (Coccidae).

PubMed

Caballero, Alejandro; Ramos-Portilla, Andrea Amalia; Kondo, Takumasa

2017-05-02

Herein we describe a new species, Tillancoccus koreguajae Caballero & Ramos, sp. n. (Hemiptera: Coccidae) from Colombia collected on sugarcane. Pinnaspis strachani (Cooley) is also recorded on sugarcane for the first time worldwide. An updated list of seven species of Coccomorpha on sugarcane in Colombia is provided, including information on its distribution, biology, and mutualistic ants for each species. Seven species of scale insects (Hemiptera: Coccomorpha) have been recorded previously on sugarcane, Saccharum officinarum L. (Poaceae) in Colombia: Pseudococcidae: Dysmicoccus boninsis (Kuwana), D. brevipes (Cockerell), Pseudococcus calceolariae (Maskell), Saccharicoccus sacchari (Cockerell); Coccidae: Pulvinaria elongata Newstead; Diaspididae: Duplachionaspis divergens (Green) and Serenaspis minima (Maskell). However, the record of S. minima in Colombia is considered doubtful as there are no voucher specimens from Colombia and because the distribution of this species is currently limited to the Australasian region. Pseudococcus calceolariae is present in Colombia but its record on sugarcane is also doubtful. A taxonomic key for the identification of scale insects on sugarcane in Colombia is provided.

Differential expression of diacylglycerol acyltransferase (DGAT) genes in olive tissues.

PubMed

Giannoulia, K; Haralampidis, K; Poghosyan, Z; Murphy, D J; Hatzopoulos, P

2000-12-01

Fatty acids are accumulated in triacylglycerols (TAGs), in specialized organelles of seeds named oil bodies. The major site of TAG accumulation is detected in developing seed and mesocarp of certain species. We have isolated two cDNAs encoding DGAT enzymes from olives. The deduced polypeptides differ by 26 amino acids in size. However, they have high homology and almost identical hydropathy profiles. The DGAT gene is expressed in all tissues that synthesize TAGs. However, higher levels of DGAT transcripts have been detected in seed tissues of developing olive drupe. DGAT expression and mRNA accumulation in drupe tissues is developmentally regulated. Each DGAT transcript shows a distinct profile of accumulation. The existence of two different DGAT transcripts might reflect two different enzymes with discrete function and/or localization.

Dendritic cell-targeting DNA-based mucosal adjuvants for the development of mucosal vaccines

PubMed Central

Kataoka, Kosuke; Fujihashi, Kohtaro

2009-01-01

In order to establish effective mucosal immunity against various mucosal pathogens, vaccines must be delivered via the mucosal route and contain effective adjuvant(s). Since mucosal adjuvants can simply mix with the antigen, it is relatively easy to adapt them for different types of vaccine development. Even in simple admixture vaccines, the adjuvant itself must be prepared without any complications. Thus, CpG oligodeoxynucleotides or plasmids encoding certain cDNA(s) would be potent mucosal adjuvant candidates when compared with other substances that can be used as mucosal adjuvants. The strategy of a DNA-based mucosal adjuvant facilitates the targeting of mucosal dendritic cells, and thus is an effective and safe approach. It would also provide great flexibility for the development of effective vaccines for various mucosal pathogens. PMID:19722892

Frost Damage Detection in Sugarcane Crop Using Modis Images and Srtm Data

NASA Astrophysics Data System (ADS)

Rudorff, B.; Alves de Aguiar, D.; Adami, M.

2011-12-01

Brazil is the largest world producer of sugarcane which is used to produce almost equal proportions of either sugar (food) or ethanol (biofuel). In recent years sugarcane crop production has increased fast to meet the growing market demand for sugar and ethanol. This increase has been mainly due to expansion in crop area, but sugarcane production is also subjected to several factors that influence both the agricultural crop yield (tons of stalks/ha) and the industrial yield (kg of sugar/ton of stalks). Sugarcane is a semi-perennial crop that experiences major growth during spring and summer seasons with large demands for water and high temperatures to produce good stalk formation (crop yield). The harvest is performed mainly during fall and winter seasons when water availability and temperature should be low in order to accumulate sucrose in the stalks (industrial yield). These favorable climatic conditions for sugarcane crop are found in several regions in Brazil, particularly in São Paulo state, which is the major sugarcane producer in Brazil being responsible for almost 60% of its production. Despite the favorable climate in São Paulo state there is a certain probability of frost occurrence from time to time that has a negative impact on sugarcane crop, particularly on industrial yield, reducing the amount of sugar in the stalks; having consequences on price increase and product shortage. To evaluate the impact of frost on sugarcane crop, in the field, on a state level, is not a trivial task; however, this information is relevant due to its direct impact on the consumer market. Remote sensing images allow a synoptic view and present great potential to monitor large sugarcane plantations as has been done since 2003 in São Paulo state by the Canasat Project with Landsat type images (http://www.dsr.inpe.br/laf/canasat/en/). Images acquired from sensors with high temporal resolution such as MODIS (Moderate-Resolution Imaging Spectroradiometer) present the potential to detect the impact of climatic effects, such as frost, on crop growth, which is relevant information to evaluate the negative impact on sugarcane production. Thus, the objective of the present study is to detect the impact of the frost occurred on 28 June 2011 in the sugarcane production region of São Paulo state, using MODIS images acquired on board of Terra and Aqua satellites before and after the frost event. Also, Landsat type images were used to map the harvested sugarcane fields up to the frost event based on a sugarcane crop map for year 2011. The remaining sugarcane fields available for harvest in 2011 were monitored with the MODIS images acquired on 17, 19, 27, 28 June and 8 and 9 July, to detect frost damage. Field work was conducted shortly after frost occurrence to identify sugarcane fields with frost damage for training and validation purposes. MODIS images transformed to vegetation indices and morphometric variables extracted from SRTM (Shuttle Radar Topography Mission) data are being analyzed to detect and quantify the damage of the frost from 28 July 2011 on sugarcane crop.

Analysis of the enzymatic formation of citral in the glands of sweet basil.

PubMed

Iijima, Yoko; Wang, Guodong; Fridman, Eyal; Pichersky, Eran

2006-04-15

Basil glands of the Sweet Dani cultivar contain high levels of citral, a mixture of geranial and its cis-isomer neral, as well as low levels of geraniol and nerol. We have previously reported the identification of a cDNA from Sweet Dani that encodes an enzyme responsible for the formation of geraniol from geranyl diphosphate in the glands, and that these glands cannot synthesize nerol directly from geranyl diphosphate. Here, we report the identification of two basil cDNAs encoding NADP+-dependent dehydrogenases that can use geraniol as the substrate. One cDNA, designated CAD1, represents a gene whose expression is highly specific to gland cells of all three basil cultivars examined, regardless of their citral content, and encodes an enzyme with high sequence similarity to known cinnamyl alcohol dehydrogenases (CADs). The enzyme encoded by CAD1 reversibly oxidizes geraniol to produce geranial (which reversibly isomerizes to neral via keto-enol tautomerization) at half the efficiency compared with its activity with cinnamyl alcohol. CAD1 does not use nerol and neral as substrates. A second cDNA, designated GEDH1, encodes an enzyme with sequence similarity to CAD1 that is capable of reversibly oxidizing geraniol and nerol in equal efficiency, and prolonged incubation of geraniol with GEDH1 in vitro produces not only geranial and neral, but also nerol. GEDH1 is also active, although at a lower efficiency, with cinnamyl alcohol. However, GEDH1 is expressed at low levels in glands of all cultivars compared with its expression in leaves. These and additional data presented indicate that basil glands may contain additional dehydrogenases capable of oxidizing geraniol.

2G ethanol from the whole sugarcane lignocellulosic biomass.

PubMed

Pereira, Sandra Cerqueira; Maehara, Larissa; Machado, Cristina Maria Monteiro; Farinas, Cristiane Sanchez

2015-01-01

In the sugarcane industry, large amounts of lignocellulosic residues are generated, which includes bagasse, straw, and tops. The use of the whole sugarcane lignocellulosic biomass for the production of second-generation (2G) ethanol can be a potential alternative to contribute to the economic viability of this process. Here, we conducted a systematic comparative study of the use of the lignocellulosic residues from the whole sugarcane lignocellulosic biomass (bagasse, straw, and tops) from commercial sugarcane varieties for the production of 2G ethanol. In addition, the feasibility of using a mixture of these residues from a selected variety was also investigated. The materials were pretreated with dilute acid and hydrolyzed with a commercial enzymatic preparation, after which the hydrolysates were fermented using an industrial strain of Saccharomyces cerevisiae. The susceptibility to enzymatic saccharification was higher for the tops, followed by straw and bagasse. Interestingly, the fermentability of the hydrolysates showed a different profile, with straw achieving the highest ethanol yields, followed by tops and bagasse. Using a mixture of the different sugarcane parts (bagasse-straw-tops, 1:1:1, in a dry-weight basis), it was possible to achieve a 55% higher enzymatic conversion and a 25% higher ethanol yield, compared to use of the bagasse alone. For the four commercial sugarcane varieties evaluated using the same experimental set of conditions, it was found that the variety of sugarcane was not a significant factor in the 2G ethanol production process. Assessment of use of the whole lignocellulosic sugarcane biomass clearly showed that 2G ethanol production could be significantly improved by the combined use of bagasse, straw, and tops, when compared to the use of bagasse alone. The lower susceptibility to saccharification of sugarcane bagasse, as well as the lower fermentability of its hydrolysates, can be compensated by using it in combination with straw and tops (sugarcane trash). Furthermore, given that the variety was not a significant factor for the 2G ethanol production process within the four commercial sugarcane varieties evaluated here, agronomic features such as higher productivity and tolerance of soil and climate variations can be used as the criteria for variety selection.

Liming in the sugarcane burnt system and the green harvest practice affect soil bacterial community in northeastern São Paulo, Brazil.

PubMed

Val-Moraes, Silvana Pompeia; de Macedo, Helena Suleiman; Kishi, Luciano Takeshi; Pereira, Rodrigo Matheus; Navarrete, Acacio Aparecido; Mendes, Lucas William; de Figueiredo, Eduardo Barretto; La Scala, Newton; Tsai, Siu Mui; de Macedo Lemos, Eliana Gertrudes; Alves, Lúcia Maria Carareto

2016-12-01

Here we show that both liming the burnt sugarcane and the green harvest practice alter bacterial community structure, diversity and composition in sugarcane fields in northeastern São Paulo state, Brazil. Terminal restriction fragment length polymorphism fingerprinting and 16S rRNA gene cloning and sequencing were used to analyze changes in soil bacterial communities. The field experiment consisted of sugarcane-cultivated soils under different regimes: green sugarcane (GS), burnt sugarcane (BS), BS in soil amended with lime applied to increase soil pH (BSL), and native forest (NF) as control soil. The bacterial community structures revealed disparate patterns in sugarcane-cultivated soils and forest soil (R = 0.786, P = 0.002), and overlapping patterns were shown for the bacterial community structure among the different management regimes applied to sugarcane (R = 0.194, P = 0.002). The numbers of operational taxonomic units (OTUs) found in the libraries were 117, 185, 173 and 166 for NF, BS, BSL and GS, respectively. Sugarcane-cultivated soils revealed higher bacterial diversity than NF soil, with BS soil accounting for a higher richness of unique OTUs (101 unique OTUs) than NF soil (23 unique OTUs). Cluster analysis based on OTUs revealed similar bacterial communities in NF and GS soils, while the bacterial community from BS soil was most distinct from the others. Acidobacteria and Alphaproteobacteria were the most abundant bacterial phyla across the different soils with Acidobacteria Gp1 accounting for a higher abundance in NF and GS soils than burnt sugarcane-cultivated soils (BS and BSL). In turn, Acidobacteria Gp4 abundance was higher in BS soils than in other soils. These differential responses in soil bacterial community structure, diversity and composition can be associated with the agricultural management, mainly liming practices, and harvest methods in the sugarcane-cultivated soils, and they can be detected shortly after harvest.

Exchanging physically effective neutral detergent fiber does not affect chewing activity and performance of late-lactation dairy cows fed corn and sugarcane silages.

PubMed

Sá Neto, A; Bispo, A W; Junges, D; Bercht, A K; Zopollatto, M; Daniel, J L P; Nussio, L G

2014-11-01

The objective of this study was to determine whether replacing the physically effective neutral detergent fiber (peNDF) of corn silage with sugarcane silage peNDF would affect performance in dairy cows. Twenty-four late-lactation Holstein cows were assigned to eight 3 × 3 Latin squares with 21-d periods. The dietary treatments were (1) 25% peNDF of corn silage, (2) 25% peNDF of sugarcane silage, and (3) 12.5% peNDF of corn silage + 12.5% peNDF of sugarcane silage. The physical effectiveness factors (pef) were assumed to be 1 for corn silage and 1.2 for sugarcane silage, as measured previously by bioassay. Thus, peNDF was calculated as neutral detergent fiber (NDF) × pef. The concentrate ingredients were finely ground corn, soybean meal, pelleted citrus pulp, and mineral-vitamin premix. Dry matter intake (22.5 ± 0.63 kg/d), 3.5% fat-corrected milk yield (28.8 ± 1.13 kg/d), milk composition (fat, protein, lactose, urea, casein, free fatty acids, and somatic cell count), and blood metabolites (glucose, insulin, and nonesterified fatty acids) were unaffected by the treatments. The time spent eating, ruminating, or chewing was also similar among the diets, as was particle-sorting behavior. By contrast, chewing per kilogram of forage NDF intake was higher for the sugarcane silage (137 min/kg) than the corn silage diet (116 min/kg), indicating the greater physical effectiveness of sugarcane fiber. Based on chewing behavior (min/d), the estimated pef of sugarcane silage NDF were 1.28 in the corn silage plus sugarcane silage diet and 1.29 in the sugarcane silage diet. Formulating dairy rations of equal peNDF content allows similar performance if corn and sugarcane silages are exchanged. Copyright © 2014 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

Species-Specific Detection and Identification of Fusarium Species Complex, the Causal Agent of Sugarcane Pokkah Boeng in China

PubMed Central

Que, Youxiong; Wang, Jihua; Comstock, Jack C.; Wei, Jinjin; McCord, Per H.; Chen, Baoshan; Chen, Rukai; Zhang, Muqing

2014-01-01

Background Pokkah boeng disease caused by the Fusarium species complex results in significant yield losses in sugarcane. Thus, the rapid and accurate detection and identification of the pathogen is urgently required to manage and prevent the spreading of sugarcane pokkah boeng. Methods A total of 101 isolates were recovered from the pokkah boeng samples collected from five major sugarcane production areas in China throughout 2012 and 2013. The causal pathogen was identified by morphological observation, pathogenicity test, and phylogenetic analysis based on the fungus-conserved rDNA-ITS. Species-specific TaqMan real-time PCR and conventional PCR methods were developed for rapid and accurate detection of the causal agent of sugarcane pokkah boeng. The specificity and sensitivity of PCR assay were also evaluated on a total of 84 isolates of Fusarium from China and several isolates from other fungal pathogens of Sporisorium scitamineum and Phoma sp. and sugarcane endophyte of Acremonium sp. Result Two Fusarium species (F. verticillioides and F. proliferatum) that caused sugarcane pokahh boeng were identified by morphological observation, pathogenicity test, and phylogenetic analysis. Species-specific TaqMan PCR and conventional PCR were designed and optimized to target their rDNA-ITS regions. The sensitivity of the TaqMan PCR was approximately 10 pg of fungal DNA input, which was 1,000-fold over conventional PCR, and successfully detected pokkah boeng in the field-grown sugarcane. Conclusions/Significance This study was the first to identify two species, F. verticillioides and F. proliferatum, that were causal pathogens of sugarcane pokkah boeng in China. It also described the development of a species-specific PCR assay to detect and confirm these pathogens in sugarcane plants from mainland China. This method will be very useful for a broad range of research endeavors as well as the regulatory response and management of sugarcane pokkah boeng. PMID:25141192

Physiological and transcriptional analyses of developmental stages along sugarcane leaf.

PubMed

Mattiello, Lucia; Riaño-Pachón, Diego Mauricio; Martins, Marina Camara Mattos; da Cruz, Larissa Prado; Bassi, Denis; Marchiori, Paulo Eduardo Ribeiro; Ribeiro, Rafael Vasconcelos; Labate, Mônica T Veneziano; Labate, Carlos Alberto; Menossi, Marcelo

2015-12-29

Sugarcane is one of the major crops worldwide. It is cultivated in over 100 countries on 22 million ha. The complex genetic architecture and the lack of a complete genomic sequence in sugarcane hamper the adoption of molecular approaches to study its physiology and to develop new varieties. Investments on the development of new sugarcane varieties have been made to maximize sucrose yield, a trait dependent on photosynthetic capacity. However, detailed studies on sugarcane leaves are scarce. In this work, we report the first molecular and physiological characterization of events taking place along a leaf developmental gradient in sugarcane. Photosynthetic response to CO2 indicated divergence in photosynthetic capacity based on PEPcase activity, corroborated by activity quantification (both in vivo and in vitro) and distinct levels of carbon discrimination on different segments along leaf length. Additionally, leaf segments had contrasting amount of chlorophyll, nitrogen and sugars. RNA-Seq data indicated a plethora of biochemical pathways differentially expressed along the leaf. Some transcription factors families were enriched on each segment and their putative functions corroborate with the distinct developmental stages. Several genes with higher expression in the middle segment, the one with the highest photosynthetic rates, were identified and their role in sugarcane productivity is discussed. Interestingly, sugarcane leaf segments had a different transcriptional behavior compared to previously published data from maize. This is the first report of leaf developmental analysis in sugarcane. Our data on sugarcane is another source of information for further studies aiming to understand and/or improve C4 photosynthesis. The segments used in this work were distinct in their physiological status allowing deeper molecular analysis. Although limited in some aspects, the comparison to maize indicates that all data acquired on one C4 species cannot always be easily extrapolated to other species. However, our data indicates that some transcriptional factors were segment-specific and the sugarcane leaf undergoes through the process of suberizarion, photosynthesis establishment and senescence.

Short-term effects of sugarcane waste products from ethanol production plant as soil amendments on sugarcane growth and metal stabilization.

PubMed

Akkajit, Pensiri; DeSutter, Thomas; Tongcumpou, Chantra

2013-05-01

Numerous waste products have been widely studied and used as soil amendments and metal immobilizing agents. Waste utilization from ethanol production processes as soil amendments is one of the most promising and sustainable options to help utilize materials effectively, reduce waste disposal, and add value to byproducts. As a consequence, this present work carried out a four-month pot experiment of sugarcane (Saccharum officinarum L.) cultivation in Cd and Zn contaminated soil to determine the effect of three sugarcane waste products (boiler ash, filter cake and vinasse) as soil amendment on sugarcane growth, metal translocation and accumulation in sugarcane, and fractionation of Cd and Zn in soil by the BCR sequential extraction. Four treatments were tested: (1) non-amended soil; (2) 3% w/w boiler ash; (3) 3% w/w filter cake; and (4) a combination of 1.5% boiler ash and 1.5% vinasse (w/w). Our findings showed the improved biomass production of sugarcanes; 6 and 3-fold higher for the above ground parts (from 8.5 to 57.6 g per plant) and root (from 2.1 to 6.59 g per plant), respectively, as compared to non-amended soil. Although there was no significant difference in Cd and Zn uptake in sugarcane (mg kg(-1)) between the non-amended soil and the treated soils (0.44 to 0.52 mg Cd kg(-1) and 39.9 to 48.1 mg Zn kg(-1), respectively), the reduction of the most bioavailable Cd concentration (BCR1 + 2) in the treated soils (35.4-54.5%) and the transformation of metal into an insoluble fraction (BCR3) highlighted the beneficial effects of sugarcane waste-products in promoting the sugarcane growth and Cd stabilization in soil.

Transgenic Sugarcane with a cry1Ac Gene Exhibited Better Phenotypic Traits and Enhanced Resistance against Sugarcane Borer

PubMed Central

Gao, Shiwu; Yang, Yingying; Wang, Chunfeng; Guo, Jinlong; Zhou, Dinggang; Wu, Qibin; Su, Yachun; Xu, Liping

2016-01-01

We developed sugarcane plants with improved resistance to the sugarcane borer, Diatraea saccharalis (F). An expression vector pGcry1Ac0229, harboring the cry1Ac gene and the selectable marker gene, bar, was constructed. This construct was introduced into the sugarcane cultivar FN15 by particle bombardment. Transformed plantlets were identified after selection with Phosphinothricin (PPT) and Basta. Plantlets were then screened by PCR based on the presence of cry1Ac and 14 cry1Ac positive plantlets were identified. Real-time quantitative PCR (RT-qPCR) revealed that the copy number of cry1Ac gene in the transgenic lines varied from 1 to 148. ELISA analysis showed that Cry1Ac protein levels in 7 transgenic lines ranged from 0.85 μg/FWg to 70.92 μg/FWg in leaves and 0.04 μg/FWg to 7.22 μg/FWg in stems, and negatively correlated to the rate of insect damage that ranged from 36.67% to 13.33%, respectively. Agronomic traits of six transgenic sugarcane lines with medium copy numbers were similar to the non-transgenic parental line. However, phenotype was poor in lines with high or low copy numbers. Compared to the non-transgenic control plants, all transgenic lines with medium copy numbers had relatively equal or lower sucrose yield and significantly improved sugarcane borer resistance, which lowered susceptibility to damage by insects. This suggests that the transgenic sugarcane lines harboring medium copy numbers of the cry1Ac gene may have significantly higher resistance to sugarcane borer but the sugarcane yield in these lines is similar to the non-transgenic control thus making them superior to the control lines. PMID:27093437

The type III secretion system is necessary for the development of a pathogenic and endophytic interaction between Herbaspirillum rubrisubalbicans and Poaceae.

PubMed

Schmidt, Maria Augusta; Balsanelli, Eduardo; Faoro, Hellison; Cruz, Leonardo M; Wassem, Roseli; de Baura, Valter A; Weiss, Vinícius; Yates, Marshall G; Madeira, Humberto M F; Pereira-Ferrari, Lilian; Fungaro, Maria H P; de Paula, Francine M; Pereira, Luiz F P; Vieira, Luiz G E; Olivares, Fábio L; Pedrosa, Fábio O; de Souza, Emanuel M; Monteiro, Rose A

2012-06-06

Herbaspirillum rubrisubalbicans was first identified as a bacterial plant pathogen, causing the mottled stripe disease in sugarcane. H. rubrisubalbicans can also associate with various plants of economic interest in a non pathogenic manner. A 21 kb DNA region of the H. rubrisubalbicans genome contains a cluster of 26 hrp/hrc genes encoding for the type three secretion system (T3SS) proteins. To investigate the contribution of T3SS to the plant-bacterial interaction process we generated mutant strains of H. rubrisubalbicans M1 carrying a Tn5 insertion in both the hrcN and hrpE genes. H. rubrisulbalbicans hrpE and hrcN mutant strains of the T3SS system failed to cause the mottled stripe disease in the sugarcane susceptible variety B-4362. These mutant strains also did not produce lesions on Vigna unguiculata leaves. Oryza sativa and Zea mays colonization experiments showed that mutations in hrpE and hrcN genes reduced the capacity of H. rubrisulbalbicans to colonize these plants, suggesting that hrpE and hrcN genes are involved in the endophytic colonization. Our results indicate that the T3SS of H. rubrisubalbicans is necessary for the development of the mottled stripe disease and endophytic colonization of rice.

Sandalwood fragrance biosynthesis involves sesquiterpene synthases of both the terpene synthase (TPS)-a and TPS-b subfamilies, including santalene synthases.

PubMed

Jones, Christopher G; Moniodis, Jessie; Zulak, Katherine G; Scaffidi, Adrian; Plummer, Julie A; Ghisalberti, Emilio L; Barbour, Elizabeth L; Bohlmann, Jörg

2011-05-20

Sandalwood oil is one of the worlds most highly prized fragrances. To identify the genes and encoded enzymes responsible for santalene biosynthesis, we cloned and characterized three orthologous terpene synthase (TPS) genes SaSSy, SauSSy, and SspiSSy from three divergent sandalwood species; Santalum album, S. austrocaledonicum, and S. spicatum, respectively. The encoded enzymes catalyze the formation of α-, β-, epi-β-santalene, and α-exo-bergamotene from (E,E)-farnesyl diphosphate (E,E-FPP). Recombinant SaSSy was additionally tested with (Z,Z)-farnesyl diphosphate (Z,Z-FPP) and remarkably, found to produce a mixture of α-endo-bergamotene, α-santalene, (Z)-β-farnesene, epi-β-santalene, and β-santalene. Additional cDNAs that encode bisabolene/bisabolol synthases were also cloned and functionally characterized from these three species. Both the santalene synthases and the bisabolene/bisabolol synthases reside in the TPS-b phylogenetic clade, which is more commonly associated with angiosperm monoterpene synthases. An orthologous set of TPS-a synthases responsible for formation of macrocyclic and bicyclic sesquiterpenes were characterized. Strict functionality and limited sequence divergence in the santalene and bisabolene synthases are in contrast to the TPS-a synthases, suggesting these compounds have played a significant role in the evolution of the Santalum genus. © 2011 by The American Society for Biochemistry and Molecular Biology, Inc.

Mining secreted proteins that function in pepper fruit development and ripening using a yeast secretion trap (YST)

DOE Office of Scientific and Technical Information (OSTI.GOV)

Lee, Je Min, E-mail: jemin@knu.ac.kr; Department of Horticultural Science, Kyungpook National University, Daegu; Lee, Sang-Jik

Highlights: • Yeast secretion trap (YST) is a valuable tool for mining secretome. • A total of 80 secreted proteins are newly identified via YST in pepper fruits. • The secreted proteins are differentially regulated during pepper development and ripening. • Transient GFP-fusion assay and in planta secretion trap can effectively validate the secretion of proteins. - Abstract: Plant cells secrete diverse sets of constitutively- and conditionally-expressed proteins under various environmental and developmental states. Secreted protein populations, or secretomes have multiple functions, including defense responses, signaling, metabolic processes, and developmental regulation. To identify genes encoding secreted proteins that function inmore » fruit development and ripening, a yeast secretion trap (YST) screen was employed using pepper (Capsicum annuum) fruit cDNAs. The YST screen revealed 80 pepper fruit-related genes (CaPFRs) encoding secreted proteins including cell wall proteins, several of which have not been previously described. Transient GFP-fusion assay and an in planta secretion trap were used to validate the secretion of proteins encoded by selected YST clones. In addition, RNA gel blot analyses provided further insights into their expression and regulation during fruit development and ripening. Integrating our data, we conclude that the YST provides a valuable functional genomics tool for the identification of substantial numbers of novel secreted plant proteins that are associated with biological processes, including fruit development and ripening.« less

Distinct Calcium Signaling Pathways Regulate Calmodulin Gene Expression in Tobacco1

PubMed Central

van der Luit, Arnold H.; Olivari, Claudio; Haley, Ann; Knight, Marc R.; Trewavas, Anthony J.

1999-01-01

Cold shock and wind stimuli initiate Ca2+ transients in transgenic tobacco (Nicotiana plumbaginifolia) seedlings (named MAQ 2.4) containing cytoplasmic aequorin. To investigate whether these stimuli initiate Ca2+ pathways that are spatially distinct, stress-induced nuclear and cytoplasmic Ca2+ transients and the expression of a stress-induced calmodulin gene were compared. Tobacco seedlings were transformed with a construct that encodes a fusion protein between nucleoplasmin (a major oocyte nuclear protein) and aequorin. Immunocytochemical evidence indicated targeting of the fusion protein to the nucleus in these plants, which were named MAQ 7.11. Comparison between MAQ 7.11 and MAQ 2.4 seedlings confirmed that wind stimuli and cold shock invoke separate Ca2+ signaling pathways. Partial cDNAs encoding two tobacco calmodulin genes, NpCaM-1 and NpCaM-2, were identified and shown to have distinct nucleotide sequences that encode identical polypeptides. Expression of NpCaM-1, but not NpCaM-2, responded to wind and cold shock stimulation. Comparison of the Ca2+ dynamics with NpCaM-1 expression after stimulation suggested that wind-induced NpCaM-1 expression is regulated by a Ca2+ signaling pathway operational predominantly in the nucleus. In contrast, expression of NpCaM-1 in response to cold shock is regulated by a pathway operational predominantly in the cytoplasm. PMID:10557218

Sucrose and color profiles in sugarcane (Saccharum sp.) juice analyzed by UFLC-ELSD and Synapt High-Definition Mass Spectrometry during radiation treatment

NASA Astrophysics Data System (ADS)

Lima, Roberta B.; de Aguiar, Claudio Lima; Galaverna, Renan; Baptista, Antonio S.; Eberlin, Marcos N.; Arthur, Valter

2016-04-01

This work evaluated the effect of electron beam irradiation (E-beam) on sugarcane juice and compared the results with preliminary tests performed on sugarcane juice treated with gamma irradiation. The samples were irradiated at 5, 10 and 20 kGy doses and results were compared wile control samples without irradiation. The results showed a significant increase (p≤0.05) of phenolic compounds in both treatments. We also observed increased contents of reducing sugars (glucose and fructose) for the samples irradiated with gamma rays and E-beam measured by the DNS methods. However, there was no significant difference of sugars content measured by chromatographic analyses performed in the sugarcane juice treated with E-beam. Therefore reducing sugars content could be overestimated by the DNS method because salts in sugarcane juice. The treatments were able to reduce sugarcane juice ICUMSA color intensity in both treatments with irradiation. E-beam reduced sugarcane juice color by roughly 49% compared the control, while gamma irradiation reduced it by 30%.

Sugarcane Crop Extraction Using Object-Oriented Method from ZY-3 High Resolution Satellite Tlc Image

NASA Astrophysics Data System (ADS)

Luo, H.; Ling, Z. Y.; Shao, G. Z.; Huang, Y.; He, Y. Q.; Ning, W. Y.; Zhong, Z.

2018-04-01

Sugarcane is one of the most important crops in Guangxi, China. As the development of satellite remote sensing technology, more remotely sensed images can be used for monitoring sugarcane crop. With the help of Three Line Camera (TLC) images, wide coverage and stereoscopic mapping ability, Chinese ZY-3 high resolution stereoscopic mapping satellite is useful in attaining more information for sugarcane crop monitoring, such as spectral, shape, texture difference between forward, nadir and backward images. Digital surface model (DSM) derived from ZY-3 TLC images are also able to provide height information for sugarcane crop. In this study, we make attempt to extract sugarcane crop from ZY-3 images, which are acquired in harvest period. Ortho-rectified TLC images, fused image, DSM are processed for our extraction. Then Object-oriented method is used in image segmentation, example collection, and feature extraction. The results of our study show that with the help of ZY-3 TLC image, the information of sugarcane crop in harvest time can be automatic extracted, with an overall accuracy of about 85.3 %.

The isolation of cDNAs from OATL1 at Xp11.2 using a 480-kb YAC

DOE Office of Scientific and Technical Information (OSTI.GOV)

Geraghty, M.T.; Brody, L.C.; Martin, L.S.

1993-05-01

Using an ornithine-{delta}-aminotransferase (OAT) cDNA, the authors identified five YACs that cover two nonadjacent OAT-related loci in Xp11.2-p11.3, designated OATL1 (distal) and OATL2 (proximal). Because several retinal degenerative disorders map to this region, they used YAC2 (480 kb), which covers the most distal part of OATL1, as a probe to screen a retinal cDNA library. From 8 {times} 10{sup 4} plaques screened, they isolated 13 clones. Two were OAT cDNAs. The remaining 11 were divided into eight groups by cross-hybridization. Groups 1-4 contain cDNAs that originate from single-copy X-linked genes in YAC2. Each has an open reading frame of >500more » bp and detects one or more transcripts on a Northern blot. The gene for each was sublocalized and ordered in YAC2. The cDNAs in groups 5-8 contained two or more Alu sequences, had no open reading frames, and did not detect transcripts. The cDNAs from groups 1-4 provide expressed sequence tags and identify candidate genes for the genetic disorders that map to this region. 28 refs., 5 figs., 1 tab.« less

Expression profiling of Crambe abyssinica under arsenate stress identifies genes and gene networks involved in arsenic metabolism and detoxification

PubMed Central

2010-01-01

Background Arsenic contamination is widespread throughout the world and this toxic metalloid is known to cause cancers of organs such as liver, kidney, skin, and lung in human. In spite of a recent surge in arsenic related studies, we are still far from a comprehensive understanding of arsenic uptake, detoxification, and sequestration in plants. Crambe abyssinica, commonly known as 'abyssinian mustard', is a non-food, high biomass oil seed crop that is naturally tolerant to heavy metals. Moreover, it accumulates significantly higher levels of arsenic as compared to other species of the Brassicaceae family. Thus, C. abyssinica has great potential to be utilized as an ideal inedible crop for phytoremediation of heavy metals and metalloids. However, the mechanism of arsenic metabolism in higher plants, including C. abyssinica, remains elusive. Results To identify the differentially expressed transcripts and the pathways involved in arsenic metabolism and detoxification, C. abyssinica plants were subjected to arsenate stress and a PCR-Select Suppression Subtraction Hybridization (SSH) approach was employed. A total of 105 differentially expressed subtracted cDNAs were sequenced which were found to represent 38 genes. Those genes encode proteins functioning as antioxidants, metal transporters, reductases, enzymes involved in the protein degradation pathway, and several novel uncharacterized proteins. The transcripts corresponding to the subtracted cDNAs showed strong upregulation by arsenate stress as confirmed by the semi-quantitative RT-PCR. Conclusions Our study revealed novel insights into the plant defense mechanisms and the regulation of genes and gene networks in response to arsenate toxicity. The differential expression of transcripts encoding glutathione-S-transferases, antioxidants, sulfur metabolism, heat-shock proteins, metal transporters, and enzymes in the ubiquitination pathway of protein degradation as well as several unknown novel proteins serve as molecular evidence for the physiological responses to arsenate stress in plants. Additionally, many of these cDNA clones showing strong upregulation due to arsenate stress could be used as valuable markers. Further characterization of these differentially expressed genes would be useful to develop novel strategies for efficient phytoremediation as well as for engineering arsenic tolerant crops with reduced arsenic translocation to the edible parts of plants. PMID:20546591

Three cDNAs encoding vitellogenin homologs from Antarctic copepod, Tigriopus kingsejongensis: Cloning and transcriptional analysis in different maturation stages, temperatures, and putative reproductive hormones.

PubMed

Lee, Soo Rin; Lee, Ji-Hyun; Kim, Ah Ran; Kim, Sanghee; Park, Hyun; Baek, Hea Ja; Kim, Hyun-Woo

2016-02-01

Three full-length cDNAs encoding lipoprotein homologs were identified in Tigriopus kingsejongensis, a newly identified copepod from Antarctica. Structural and transcriptional analyses revealed homology with two vitellogenin-like proteins, Tik-Vg1 and Tik-Vg2, which were 1855 and 1795 amino acids in length, respectively, along with a third protein, Tik-MEP, which produced a 1517-residue protein with similarity to a melanin engaging protein (MEP) in insects Phylogenetic analysis showed that Vgs in Maxillopods including two Tik-Vgs belong to the arthropod vitellogenin-like clade, which includes clottable proteins (CPs) in decapod crustaceans and vitellogenins in insects. Tik-MEP clustered together with insect MEPs, which appear to have evolved before the apoB-like and arthropod Vg-like clades. Interestingly, no genes orthologous to those found in the apoB clade were identified in Maxillopoda, suggesting that functions of large lipid transfer proteins (LLTPs) in reproduction and lipid metabolism may be different from those in insect and decapod crustaceans. As suggested by phylogenetic analyses, the two Tik-Vgs belonging to the arthropod Vg-like clade appear to play major roles in oocyte maturation, while Vgs belonging to the apoB clade function primarily in the reproduction of decapod crustaceans. Transcriptional analysis of Tik-Vg expression revealed a 24-fold increase in mature and ovigerous females compared with immature female, whereas expression of Tik-MEP remained low through all reproductive stages. Acute temperature changes did not affect the transcription of Tik-Vg genes, whereas Tik-MEP appeared to be affected by temperature change. Among the three hormones thought to be involved in molting and reproduction in arthropods, only farnesoic acid (FA) induced transcription of the two Tik-Vg genes. Regardless of developmental stage and hormone treatment, Tik-Vg1 and Tik-Vg2 exhibited a strong positive correlation in expression, suggesting that expression of these genes may be regulated by the same transcriptional machinery. Copyright © 2015 Elsevier Inc. All rights reserved.

Molecular cloning and characterization of two novel NAC genes from Mikania micrantha (Asteraceae).

PubMed

Li, D M; Wang, J H; Peng, S L; Zhu, G F; Lü, F B

2012-12-17

NAC proteins, which are plant-specific transcription factors, have been identified to play important roles in plant response to stresses and in plant development. The full-length cDNAs that encode 2 putative NAC proteins, designated as MmATAF1 and MmNAP, respectively, were cloned from Mikania micrantha by rapid amplification of cDNA ends. The full-length cDNAs of MmATAF1 and MmNAP were 1329 and 1072 bp, respectively, and they encoded deduced proteins of 260- and 278-amino acid residues, respectively. The proteins MmATAF1 and MmNAP had a calculated molecular mass of 29.81 and 32.55 kDa and a theoretical isoelectric point of 7.08 and 9.00, respectively. Nucleotide sequence data indicated that both MmATAF1 and MmNAP contained 2 introns and 3 exons and that they shared a conserved genomic organization. Multiple sequence alignments showed that MmATAF1 showed high sequence identity with ATAF1 of Arabidopsis thaliana (61%) and that MmNAP showed high sequence identity with NAP of A. thaliana (67%) and CitNAC of Citrus sinensis Osbeck (62%). Phylogenetic analysis showed that the predicted MmATAF1 and MmNAP proteins were classified into the ATAF and NAP subgroups, respectively. Transient expression analysis of onion epidermal cells indicated nuclear localization of both MmATAF1-GFP and MmNAP-GFP fusion proteins. Semi-quantitative reverse transcription polymerase chain reaction (RT-PCR) analysis indicated that MmATAF1 was expressed in all the tissues tested, but in varying abundance, while MmNAP was specifically expressed in stems, petioles, shoots, and leaves, but not in roots. The transcript levels of MmATAF1 and MmNAP in shoots and in infected stems were induced and strengthened by wounding, exogenous ZnSO(4), abscisic acid, salicylic acid, and Cuscuta campestris infection on the basis of semi-quantitative RT-PCR and real-time PCR analyses, respectively. Collectively, these results indicated that MmATAF1 and MmNAP, besides having roles in M. micrantha adaptation to C. campestris infection and abiotic stresses, also integrated signals derived from both C. campestris infection and abiotic stresses.

Integrated management of bermudagrass (Cynodon dactylon) in sugarcane

USDA-ARS?s Scientific Manuscript database

Bermudagrass is a difficult perennial weed to manage in Louisiana sugarcane. Research was conducted to compare interrow tillage practice, postharvest residue management, and herbicide placement on bermudagrass proliferation and sugarcane yield. Tillage frequencies included conventional (four tillage...

Microarray Analyses of Gene Expression during Adventitious Root Development in Pinus contorta1[w

PubMed Central

Brinker, Monika; van Zyl, Leonel; Liu, Wenbin; Craig, Deborah; Sederoff, Ronald R.; Clapham, David H.; von Arnold, Sara

2004-01-01

In order to investigate the gene expression pattern during adventitious root development, RNA of Pinus contorta hypocotyls, pulse-treated with the auxin indole-3-butyric acid and harvested at distinct developmental time points of root development, was hybridized to microarrays containing 2,178 cDNAs from Pinus taeda. Over the period of observation of root development, the transcript levels of 220 genes changed significantly. During the root initiation phase, genes involved in cell replication and cell wall weakening and a transcript encoding a PINHEAD/ZWILLE-like protein were up-regulated, while genes related to auxin transport, photosynthesis, and cell wall synthesis were down-regulated. In addition, there were changes in transcript abundance of genes related to water stress. During the root meristem formation phase the transcript abundances of genes involved in auxin transport, auxin responsive transcription, and cell wall synthesis, and of a gene encoding a B-box zinc finger-like protein, increased, while those encoding proteins involved in cell wall weakening decreased. Changes of transcript abundance of genes related to water stress during the root meristem formation and root formation phase indicate that the plant roots had become functional in water transport. Simultaneously, genes involved in auxin transport were up-regulated, while genes related to cell wall modification were down-regulated. Finally, during the root elongation phase down-regulation of transcripts encoding proteins involved in cell replication and stress occurred. Based on the observed changes in transcript abundances, we suggest hypotheses about the relative importance of various physiological processes during the auxin-induced development of roots in P. contorta. PMID:15247392

Mites associated with sugarcane crop and with native trees from adjacent Atlantic forest fragment in Brazil.

PubMed

Duarte, Mércia E; Navia, Denise; dos Santos, Lucas R; Rideiqui, Pedro J S; Silva, Edmilson S

2015-08-01

In some Brazilian regions the Atlantic forest biome is currently restrict to fragments occurring amid monocultures, as sugarcane crops in the Northeast region. Important influence of forest remnants over mite fauna of permanent crops have been showed, however it has been poorly explored on annual crops. The first step for understanding ecological relationship in an agricultural systems is known its composition. The objective of this study was to investigate the plant-inhabiting mite fauna associated with sugarcane crop (Saccharum officinarum L.) (Poaceae) and caboatã (Cupania oblongifolia Mart.) (Sapindaceae) trees in the state of Alagoas, Brazil. Sugarcane stalks and sugarcane and caboatã apical, middle and basal leaves were sampled. A total of 2565 mites were collected from sugarcane and classified into seven families of Trombidiformes and Mesostigmata orders, with most individuals belonging to the Eriophyidae, Tetranychidae and Tarsonemidae families. Among predatory mites, the Phytoseiidae were the most common. A total of 1878 mites were found on C. oblongifolia and classified into 13 families of Trombidiformes and Mesostigmata orders. The most abundant phytophagous mite family on caboatã was also Eriophyidae. In contrast to sugarcane, Ascidae was the most common predatory mite family observed in caboatã. No phytophagous species were common to both sugarcane and C. oblongifolia. However two predatory mites were shared between host plants. Although mites associated with only one native species in the forest fragment were evaluated in this study, our preliminary results suggest Atlantic forest native vegetation can present an important role in the sugarcane agricultural system as a source of natural enemies.

DNA damage protection against free radicals of two antioxidant neolignan glucosides from sugarcane molasses.

PubMed

Asikin, Yonathan; Takahashi, Makoto; Mizu, Masami; Takara, Kensaku; Oku, Hirosuke; Wada, Koji

2016-03-15

Sugarcane molasses is a potential by-product of the sugarcane manufacturing industry that is rich in antioxidant materials. The present study aimed to obtain antioxidative compounds from sugarcane molasses and to evaluate their ability to protect DNA from oxidative damage. Two neolignan glucosides were isolated from sugarcane molasses using bioassay and UV spectra monitoring-guided fractionation. The compounds were elucidated as (7R,8S)-dehydrodiconiferyl alcohol-4-O-β-d-glucoside (1) and (7S,8R)-simulanol-9'-O-β-d-glucoside (2). Neolignan glucoside 2 protected against DNA damage caused by free radicals more effectively than did neolignan glucoside 1 (13.62 and 9.08 µmol L(-1) for peroxyl and hydroxyl radicals, respectively, compared to 48.07 and 14.42 µmol L(-1) ). Additionally, neolignan glucoside 2 exhibited superior DNA protection against free radicals compared with various known antioxidative compounds, including p-coumaric acid, ferulic acid, vanillic acid and epigallocatechin gallate. The isolated neolignan glucosides from sugarcane molasses are able to protect DNA from oxidative damage caused by free radicals. This is the first identification of these two compounds in sugarcane molasses. The sugarcane molasses can therefore be used as potential nutraceutical preventative agents, and the findings may foster the utilization of this by-product as a bioresource-based product. © 2015 Society of Chemical Industry. Copyright © 2015 Society of Chemical Industry.

Photosynthetic and Canopy Characteristics of Different Varieties at the Early Elongation Stage and Their Relationships with the Cane Yield in Sugarcane

PubMed Central

Luo, Jun; Pan, Yong-Bao; Xu, Liping; Zhang, Yuye; Zhang, Hua; Chen, Rukai

2014-01-01

During sugarcane growth, the Early Elongation stage is critical to cane yield formation. In this study, parameters of 17 sugarcane varieties were determined at the Early Elongation stage using CI-301 photosynthesis measuring system and CI-100 digital plant canopy imager. The data analysis showed highly significant differences in leaf area index (LAI), mean foliage inclination angle (MFIA), transmission coefficient for diffused light penetration (TD), transmission coefficient for solar beam radiation penetration (TR), leaf distribution (LD), net photosynthetic rate (PN), transpiration rate (E), and stomatal conductance (GS) among sugarcane varieties. Based on the photosynthetic or canopy parameters, the 17 sugarcane varieties were classified into four categories. Through the factor analysis, nine parameters were represented by three principal factors, of which the cumulative rate of variance contributions reached 85.77%. A regression for sugarcane yield, with relative error of yield fitting less than 0.05, was successfully established: sugarcane yield = −27.19 − 1.69 × PN + 0.17 ×  E + 90.43 × LAI − 408.81 × LD + 0.0015 × NSH + 101.38 ×  D (R 2 = 0.928**). This study helps provide a theoretical basis and technical guidance for the screening of new sugarcane varieties with high net photosynthetic rate and ideal canopy structure. PMID:25045742

Potential influence of sugarcane cultivation on estuarine water quality of Louisiana's gulf coast.

PubMed

Southwick, Lloyd M; Grigg, Brandon C; Kornecki, Ted S; Fouss, James L

2002-07-17

Sugarcane is cultivated on some 170000 ha of land in south central and southwestern Louisiana. This acreage drains into bayous and rivers that empty into Louisiana's coastal bays and estuaries. For a number of years the state's Department of Agriculture and Forestry and Department of Environmental Quality have collected water quality data from this sugarcane area. Study of these data shows that approximately one in five detections of atrazine is above the maximum contaminant level (MCL) for drinking water. Currently there is no U.S. atrazine standard for protection of aquatic life. February and October detections of this herbicide are probably due to sugarcane cultivation. Nitrate levels have remained below the MCL for drinking water, but nitrate and phosphorus concentrations may pose a potential for eutrophication problems. The contribution of sugarcane production to the nutrient status of Louisiana's coastal water bodies is difficult to assess because there are other sources of nutrients in the area and native soil phosphorus levels are high. Cultural practices such as subsurface drains, open drainage ditches, and postharvest residue management have potential through enhancement of soil infiltration for decreasing sugarcane's contribution to water quality problems in southern and coastal Louisiana. A new field project is being installed at the Louisiana State University Agricultural Experiment Station's Sugarcane Research Station at St. Gabriel to assess the water quality benefits of these practices with respect to sugarcane cultivation.

Ethanol production potential from AFEX™ and steam-exploded sugarcane residues for sugarcane biorefineries.

PubMed

Mokomele, Thapelo; da Costa Sousa, Leonardo; Balan, Venkatesh; van Rensburg, Eugéne; Dale, Bruce E; Görgens, Johann F

2018-01-01

Expanding biofuel markets are challenged by the need to meet future biofuel demands and mitigate greenhouse gas emissions, while using domestically available feedstock sustainably. In the context of the sugar industry, exploiting under-utilized cane leaf matter (CLM) in addition to surplus sugarcane bagasse as supplementary feedstock for second-generation ethanol production has the potential to improve bioenergy yields per unit land. In this study, the ethanol yields and processing bottlenecks of ammonia fibre expansion (AFEX™) and steam explosion (StEx) as adopted technologies for pretreating sugarcane bagasse and CLM were experimentally measured and compared for the first time. Ethanol yields between 249 and 256 kg Mg -1 raw dry biomass (RDM) were obtained with AFEX™-pretreated sugarcane bagasse and CLM after high solids loading enzymatic hydrolysis and fermentation. In contrast, StEx-pretreated sugarcane bagasse and CLM resulted in substantially lower ethanol yields that ranged between 162 and 203 kg Mg -1 RDM. The ethanol yields from StEx-treated sugarcane residues were limited by the aggregated effect of sugar degradation during pretreatment, enzyme inhibition during enzymatic hydrolysis and microbial inhibition of S. cerevisiae 424A (LNH-ST) during fermentation. However, relatively high enzyme dosages (> 20 mg g -1 glucan) were required irrespective of pretreatment method to reach 75% carbohydrate conversion, even when optimal combinations of Cellic ® CTec3, Cellic ® HTec3 and Pectinex Ultra-SP were used. Ethanol yields per hectare sugarcane cultivation area were estimated at 4496 and 3416 L ha -1 for biorefineries using AFEX™- or StEx-treated sugarcane residues, respectively. AFEX™ proved to be a more effective pretreatment method for sugarcane residues relative to StEx due to the higher fermentable sugar recovery and enzymatic hydrolysate fermentability after high solids loading enzymatic hydrolysis and fermentation by S. cerevisiae 424A (LNH-ST). The identification of auxiliary enzyme activities, adequate process integration and the use of robust xylose-fermenting ethanologens were identified as opportunities to further improve ethanol yields from AFEX™- and StEx-treated sugarcane residues.

Char from sugarcane bagasse

USDA-ARS?s Scientific Manuscript database

Unused sugarcane bagasse represents an underutilized resource in sugarcane growing regions of the world. This is a renewable resource that can be used in a thermochemical process to create chars, which could be incorporated back into agricultural activities. The practice is likely to improve soil ...

PCDD AND PCDF EMISSIONS FROM SIMULATED SUGARCANE FIELD BURNING

EPA Science Inventory

The emissions from simulated sugarcane field burns were sampled and analyzed for polychlorinated dibenzodioxins and dibenzofurans (PCDDs and PCDFs). Sugarcane leaves from Hawaii and Florida were burned in a manner simulating the natural physical dimensions and biomass density fou...

Impact of biotechnology on sugarcane agriculture and industry

USDA-ARS?s Scientific Manuscript database

There are nine key issues that can influence the productivity and sustainability of the sugarcane industry. These include land, soil fertility, water, variety, planting density, crop protection, cultural practices, harvesting and processing, and information technology. To all sugarcane farmers, it r...

Herbicide options for suppressing bermudagrass in sugarcane

USDA-ARS?s Scientific Manuscript database

Bermudagrass is a problematic weed in Louisiana sugarcane. The most effective herbicide options are limited to the fallow period prior to planting. Frequently, efforts to eliminate bermudagrass from fields during the fallow season are unsuccessful. This subjects newly planted sugarcane to competitio...

Molecular cloning and developmental expression of the catalytic and 65-kDa regulatory subunits of protein phosphatase 2A in Drosophila.

PubMed Central

Mayer-Jaekel, R E; Baumgartner, S; Bilbe, G; Ohkura, H; Glover, D M; Hemmings, B A

1992-01-01

cDNA clones encoding the catalytic subunit and the 65-kDa regulatory subunit of protein phosphatase 2A (PR65) from Drosophila melanogaster have been isolated by homology screening with the corresponding human cDNAs. The Drosophila clones were used to analyze the spatial and temporal expression of the transcripts encoding these two proteins. The Drosophila PR65 cDNA clones contained an open reading frame of 1773 nucleotides encoding a protein of 65.5 kDa. The predicted amino acid sequence showed 75 and 71% identity to the human PR65 alpha and beta isoforms, respectively. As previously reported for the mammalian PR65 isoforms, Drosophila PR65 is composed of 15 imperfect repeating units of approximately 39 amino acids. The residues contributing to this repeat structure show also the highest sequence conservation between species, indicating a functional importance for these repeats. The gene encoding Drosophila PR65 was located at 29B1,2 on the second chromosome. A major transcript of 2.8 kilobase (kb) encoding the PR65 subunit and two transcripts of 1.6 and 2.5 kb encoding the catalytic subunit could be detected throughout Drosophila development. All of these mRNAs were most abundant during early embryogenesis and were expressed at lower levels in larvae and adult flies. In situ hybridization of different developmental stages showed a colocalization of the PR65 and catalytic subunit transcripts. The mRNA expression is high in the nurse cells and oocytes, consistent with a high equally distributed expression in early embryos. In later embryonal development, the expression remains high in the nervous system and the gonads but the overall transcript levels decrease. In third instar larvae, high levels of mRNA could be observed in brain, imaginal discs, and in salivary glands. These results indicate that protein phosphatase 2A transcript levels change during development in a tissue and in a time-specific manner. Images PMID:1320961

Molecular cloning and expression of heteromeric ACCase subunit genes from Jatropha curcas.

PubMed

Gu, Keyu; Chiam, Huihui; Tian, Dongsheng; Yin, Zhongchao

2011-04-01

Acetyl-CoA carboxylase (ACCase) catalyzes the biotin-dependent carboxylation of acetyl-CoA to produce malonyl-CoA, which is the essential first step in the biosynthesis of long-chain fatty acids. ACCase exists as a multi-subunit enzyme in most prokaryotes and the chloroplasts of most plants and algae, while it is present as a multi-domain enzyme in the endoplasmic reticulum of most eukaryotes. The heteromeric ACCase of higher plants consists of four subunits: an α-subunit of carboxyltransferase (α-CT, encoded by accA gene), a biotin carboxyl carrier protein (BCCP, encoded by accB gene), a biotin carboxylase (BC, encoded by accC gene) and a β-subunit of carboxyltransferase (β-CT, encoded by accD gene). In this study, we cloned and characterized the genes accA, accB1, accC and accD that encode the subunits of heteromeric ACCase in Jatropha (Jatropha curcas), a potential biofuel plant. The full-length cDNAs of the four subunit genes were isolated from a Jatropha cDNA library and by using 5' RACE, whereas the genomic clones were obtained from a Jatropha BAC library. They encode a 771 amino acid (aa) α-CT, a 286-aa BCCP1, a 537-aa BC and a 494-aa β-CT, respectively. The single-copy accA, accB1 and accC genes are nuclear genes, while the accD gene is located in chloroplast genome. Jatropha α-CT, BCCP1, BC and β-CT show high identity to their homologues in other higher plants at amino acid level and contain all conserved domains for ACCase activity. The accA, accB1, accC and accD genes are temporally and spatially expressed in the leaves and endosperm of Jatropha plants, which are regulated by plant development and environmental factors. Copyright © 2011 Elsevier Ireland Ltd. All rights reserved.

Sequence and pattern of expression of a bovine homologue of a human mitochondrial transport protein associated with Grave's disease.

PubMed

Fiermonte, G; Runswick, M J; Walker, J E; Palmieri, F

1992-01-01

A human cDNA has been isolated previously from a thyroid library with the aid of serum from a patient with Grave's disease. It encodes a protein belonging to the mitochondrial metabolite carrier family, referred to as the Grave's disease carrier protein (GDC). Using primers based on this sequence, overlapping cDNAs encoding the bovine homologue of the GDC have been isolated from total bovine heart poly(A)+ cDNA. The bovine protein is 18 amino acids shorter than the published human sequence, but if a frame shift requiring the removal of one nucleotide is introduced into the human cDNA sequence, the human and bovine proteins become identical in their C-terminal regions, and 308 out of 330 amino acids are conserved over their entire sequences. The bovine cDNA has been used to investigate the expression of the GDC in various bovine tissues. In the tissues that were examined, the GDC is most strongly expressed in the thyroid, but substantial amounts of its mRNA were also detected in liver, lung and kidney, and lesser amounts in heart and skeletal muscle.

Molecular identity and gene expression of aldosterone synthase cytochrome P450

DOE Office of Scientific and Technical Information (OSTI.GOV)

Okamoto, Mitsuhiro; Nonaka, Yasuki; Takemori, Hiroshi

11{beta}-Hydroxylase (CYP11B1) of bovine adrenal cortex produced corticosterone as well as aldosterone from 11-deoxycorticosterone in the presence of the mitochondrial P450 electron transport system. CYP11B1s of pig, sheep, and bullfrog, when expressed in COS-7 cells, also performed corticosterone and aldosterone production. Since these CYP11B1s are present in the zonae fasciculata and reticularis as well as in the zona glomerulosa, the zonal differentiation of steroid production may occur by the action of still-unidentified factor(s) on the enzyme-catalyzed successive oxygenations at C11- and C18-positions of steroid. In contrast, two cDNAs, one encoding 11{beta}-hydroxylase and the other encoding aldosterone synthase (CYP11B2), were isolatedmore » from rat, mouse, hamster, guinea pig, and human adrenals. The expression of CYP11B1 gene was regulated by cyclic AMP (cAMP)-dependent signaling, whereas that of CYP11B2 gene by calcium ion-signaling as well as cAMP-signaling. Salt-inducible protein kinase, a cAMP-induced novel protein kinase, was one of the regulators of CYP11B2 gene expression.« less

A Family of at Least Seven β-Galactosidase Genes Is Expressed during Tomato Fruit Development

PubMed Central

Smith, David L.; Gross, Kenneth C.

2000-01-01

During our search for a cDNA encoding β-galactosidase II, a β-galactosidase/exogalactanase (EC 3.2.1.23) present during tomato (Lycopersicon esculentum Mill.) fruit ripening, a family of seven tomato β-galactosidase (TBG) cDNAs was identified. The shared amino acid sequence identity among the seven TBG clones ranged from 33% to 79%. All contained the putative active site-containing consensus sequence pattern G-G-P-[LIVM]-x-Q-x-E-N-E-[FY] belonging to glycosyl hydrolase family 35. Six of the seven single-copy genes were mapped using restriction fragment length polymorphisms of recombinant inbred lines. RNA gel-blot analysis was used to evaluate TBG mRNA levels throughout fruit development, in different fruit tissues, and in various plant tissues. RNA gel-blot analysis was also used to reveal TBG mRNA levels in fruit of the rin, nor, and Nr tomato mutants. The TBG4-encoded protein, known to correspond to β-galactosidase II, was expressed in yeast and exo-galactanase activity was confirmed via a quantified release of galactosyl residues from cell wall fractions containing β(1→4)-d-galactan purified from tomato fruit. PMID:10889266

Definition of the complete Schistosoma mansoni hemoglobinase mRNA sequence and gene expression in developing parasites.

PubMed

el Meanawy, M A; Aji, T; Phillips, N F; Davis, R E; Salata, R A; Malhotra, I; McClain, D; Aikawa, M; Davis, A H

1990-07-01

Schistosoma mansoni uses a variety of proteases termed hemoglobinases to obtain nutrition from host globin. Previous reports have characterized cDNAs encoding 1 of these enzymes. However, these sequences did not define the primary structures of the mRNA and protein. The complete sequence of the 1390 base mRNA has now been determined. It encodes a 50 kDa primary translation product. In vitro translations coupled with immunoprecipitations and Western blots of parasite lysates allowed visualization of the 50 kDa form. Production of the 31 kDa mature hemoglobinase from the 50 kDa species involves removal of both NH2 and COOH terminal residues from the primary translation product. Expression of hemoglobinase mRNA and protein was examined during larval parasite development. Low levels were observed in young schistosomula. After 6-9 days in culture, high hemoglobinase levels were seen which correlated with the onset of red blood cell feeding. Immunoelectron microscopy was employed to examine hemoglobinase location and function. In adult worms the enzyme was associated with the gut lumen and gut epithelium. In cercariae, the protease was observed in the head gland, suggesting new roles for the protease.

Identification of avian wax synthases

PubMed Central

2012-01-01

Background Bird species show a high degree of variation in the composition of their preen gland waxes. For instance, galliform birds like chicken contain fatty acid esters of 2,3-alkanediols, while Anseriformes like goose or Strigiformes like barn owl contain wax monoesters in their preen gland secretions. The final biosynthetic step is catalyzed by wax synthases (WS) which have been identified in pro- and eukaryotic organisms. Results Sequence similarities enabled us to identify six cDNAs encoding putative wax synthesizing proteins in chicken and two from barn owl and goose. Expression studies in yeast under in vivo and in vitro conditions showed that three proteins from chicken performed WS activity while a sequence from chicken, goose and barn owl encoded a bifunctional enzyme catalyzing both wax ester and triacylglycerol synthesis. Mono- and bifunctional WS were found to differ in their substrate specificities especially with regard to branched-chain alcohols and acyl-CoA thioesters. According to the expression patterns of their transcripts and the properties of the enzymes, avian WS proteins might not be confined to preen glands. Conclusions We provide direct evidence that avian preen glands possess both monofunctional and bifunctional WS proteins which have different expression patterns and WS activities with different substrate specificities. PMID:22305293

Molecular characterization of cDNAs encoding G protein alpha and beta subunits and study of their temporal and spatial expression patterns in Nicotiana plumbaginifolia Viv.

PubMed

Kaydamov, C; Tewes, A; Adler, K; Manteuffel, R

2000-04-25

We have isolated cDNA sequences encoding alpha and beta subunits of potential G proteins from a cDNA library prepared from somatic embryos of Nicotiana plumbaginifolia Viv. at early developmental stages. The predicted NPGPA1 and NPGPB1 gene products are 75-98% identical to the known respective plant alpha and beta subunits. Southern hybridizations indicate that NPGPA1 is probably a single-copy gene, whereas at least two copies of NPGPB1 exist in the N. plumbaginifolia genome. Northern analyses reveal that both NPGPA1 and NPGPB1 mRNA are expressed in all embryogenic stages and plant tissues examined and their expression is obviously regulated by the plant hormone auxin. Immunohistological localization of NPGPalpha1 and NPGPbeta1 preferentially on plasma and endoplasmic reticulum membranes and their immunochemical detection exclusively in microsomal cell fractions implicate membrane association of both proteins. The temporal and spatial expression patterns of NPGPA1 and NPGPB1 show conformity as well as differences. This could account for not only cooperative, but also individual activities of both subunits during embryogenesis and plant development.

Sugarcane straw harvest effects on soil quality and plant growth: preliminary data synthesis of a multi-local project running in Brazil

NASA Astrophysics Data System (ADS)

Cherubin, Maurício; Cerri, Carlos E. P.; Feigl, Brigitte J.; Cerri, Carlos C.

2017-04-01

Brazil is the largest sugarcane producer in the world, and consequently, it is one of major players in the bioenergy production sector. Despite that, growing demands for bioenergies have raised the interest of Brazilian sugarcane industry to harvest the sugarcane straw left on the field for cellulosic ethanol production and/or bioelectricity cogeneration. However, crop residues have a key role in the soil, affecting directly or indirectly multiple soil functions and related ecosystem services. Therefore, indiscriminate straw harvest could jeopardize soil quality, decreasing its capacity to sustain plant productivity over time. In order to evaluate the potential impacts of sugarcane straw harvest on soil quality and plant growth, we are conducting since 2014 a multi-local project across central-southern Brazil, the main core of sugarcane production in the world. A wide range of soil chemical, physical and biological parameters, as well as, plant biomass production has been quantified under increasing straw harvest intensities. Our preliminary findings have showed that short-term straw harvest management did not affect total organic C stocks; however, high straw harvest led to significant reduction in labile C forms (e.g., microbial biomass C and N), and abundance of microbial communities as well. Sugarcane straw harvest affects soil nutrient cycling, since significant amount of nutrients are removed annually by straw, especially in top (green) leaves. In addition, our data show that straw acts as a thermal insulator, decreasing soil temperature amplitude and keeping soil moisture for a longer time. Straw harvest management did not affect sugarcane yields in the first two crop seasons. Based on this first synthesis of the project, we conclude that short-term sugarcane straw harvest led to soil changes, especially in more sensitive and dynamic properties, which did not affect the plant yield. However, long-term impacts should be monitored towards a better understanding about potential trade-offs and synergies associated with sugarcane straw harvest for bioenergy production in Brazil.

[Effects of applying tea seed meal and EDTA on the speciation transformation and phyto-availability of nickel and zinc in soil].

PubMed

Yu, Bin; Xia, Hui-Long

2013-06-01

A pot experiment with sugarcane was conducted to study the effects of applying tea seed meal and EDTA on the speciation transformation and phyto-availability of nickel (Ni) and zinc (Zn) in soil. With the increasing application rate of tea seed meal, the biomass of sugarcane root, stem, and leaf increased gradually, but no significant difference was observed in the stem and leaf biomass between EDTA treatments and the control. Applying tea seed meal and EDTA increased the acid-soluble Ni and Zn contents in soil, and promoted the bioconcentration and translocation of Ni and Zn in sugarcane. Meanwhile, the strengthening effect increased gradually with the increasing application rate of tea seed meal. As compared with EDTA, tea seed meal was more efficient in improving the accumulation of Ni and Zn in sugarcane, and thus, made the sugarcane remove more Ni and Zn from soil. The Ni and Zn contents in sugarcane stem and leaf had significant positive correlations with the application rate of tea seed meal, while the Ni and Zn contents in sugarcane root were significantly negatively correlated with the application rate of tea seed meal.

Herbicide targets and detoxification proteins in sugarcane: from gene assembly to structure modelling.

PubMed

Lloyd Evans, Dyfed; Joshi, Shailesh Vinay

2017-07-01

In a genome context, sugarcane is a classic orphan crop, in that no genome and only very few genes have been assembled. We have devised a novel exome assembly methodology that has allowed us to assemble and characterize 49 genes that serve as herbicide targets, safener interacting proteins, and members of herbicide detoxification pathways within the sugarcane genome. We have structurally modelled the products of each of these genes, as well as determining allelic, genomic, and RNA-Seq based polymorphisms for each gene. This study provides the largest collection of sugarcane structures modelled to date. We demonstrate that sugarcane genes are highly polymorphic, revealing that each genotype is evolving both uniquely and independently. In addition, we present an exome assembly system for orphan crops that can be executed on commodity infrastructure, making exome assembly practical for any group. In terms of knowledge about herbicide modes of action and detoxification, we have advanced sugarcane from a crop where no information about any herbicide-associated gene was available to the situation where sugarcane is now a species with the single largest collection of known and annotated herbicide-associated genes.

7 CFR 1435.311 - Proportionate shares for sugarcane producers.

Code of Federal Regulations, 2010 CFR

2010-01-01

... CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS SUGAR PROGRAM Flexible Marketing Allotments For Sugar § 1435.311 Proportionate shares for sugarcane producers. (a... sugarcane farms. (b) CCC will determine whether Louisiana sugar production, in the absence of proportionate...

7 CFR 1435.311 - Proportionate shares for sugarcane producers.

Code of Federal Regulations, 2011 CFR

2011-01-01

... CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS SUGAR PROGRAM Flexible Marketing Allotments For Sugar § 1435.311 Proportionate shares for sugarcane producers. (a... sugarcane farms. (b) CCC will determine whether Louisiana sugar production, in the absence of proportionate...

Sugarcane Diseases: Futuristic Management Strategies

USDA-ARS?s Scientific Manuscript database

Sugarcane pathology and disease control practices are changing due to social, economic and technological events. Sugarcane is becoming more important economically because of the increasing price and demand for sugar and its use for bio-energy. These pressures make the control of diseases more import...

7 CFR 1435.311 - Proportionate shares for sugarcane producers.

Code of Federal Regulations, 2012 CFR

2012-01-01

... CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS SUGAR PROGRAM Flexible Marketing Allotments For Sugar § 1435.311 Proportionate shares for sugarcane producers. (a... sugarcane farms. (b) CCC will determine whether Louisiana sugar production, in the absence of proportionate...

7 CFR 1435.311 - Proportionate shares for sugarcane producers.

Code of Federal Regulations, 2014 CFR

2014-01-01

... CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS SUGAR PROGRAM Flexible Marketing Allotments For Sugar § 1435.311 Proportionate shares for sugarcane producers. (a... sugarcane farms. (b) CCC will determine whether Louisiana sugar production, in the absence of proportionate...

7 CFR 1435.311 - Proportionate shares for sugarcane producers.

Code of Federal Regulations, 2013 CFR

2013-01-01

... CREDIT CORPORATION, DEPARTMENT OF AGRICULTURE LOANS, PURCHASES, AND OTHER OPERATIONS SUGAR PROGRAM Flexible Marketing Allotments For Sugar § 1435.311 Proportionate shares for sugarcane producers. (a... sugarcane farms. (b) CCC will determine whether Louisiana sugar production, in the absence of proportionate...

Transgene vaccination using Ulex europaeus agglutinin I (UEA-1) for targeted mucosal immunization against HIV-1 envelope.

PubMed

Wang, Xinhai; Kochetkova, Irina; Haddad, Asmahan; Hoyt, Teri; Hone, David M; Pascual, David W

2005-05-31

Receptor-mediated gene transfer using an M cell ligand has been shown to be an efficient method for mucosal DNA immunization. To investigate further into alternative M cell ligands, the plant lectin, Ulex europaeus agglutinin I (UEA-1), was tested. UEA-1 binds to human intestinal Caco-2 cells, and these cells can be transfected with poly-l-lysine (PL)-conjugated UEA-1 for expression of reporter cDNAs. When tested in vivo, mice nasally immunized with UEA-1-PL complexed to plasmid encoding HIV-1 envelope showed elevated systemic and mucosal antibody responses, and these were supported by tissue antibody-forming cells. Likewise, elevated envelope-specific CTLs were induced. Thus, UEA-1 mediated DNA delivery represents an alternative mucosal formulation for inducing humoral and cellular immunity against HIV-1.

Evaluation of new energy cane varieties for Louisiana

USDA-ARS?s Scientific Manuscript database

Renewed interest in U.S bioenergy markets may offer an alternative source of income for Louisiana sugarcane growers. High-fiber sugarcane or energy cane varieties are currently being developed. As with traditional sugarcane varieties, energy-cane varieties need to be evaluated across the sugarca...

Registration of "CPSG-3481 sugarcane

USDA-ARS?s Scientific Manuscript database

‘CPSG-3481’ (Reg. No. , PI 676023) sugarcane (a complex hybrid of Saccharum spp.) was a new cultivar developed through cooperative research conducted by the Shakarganj Sugar Research Institute in Pakistan and the USDA-ARS Sugarcane Field Station in USA, and released to growers for loam soils...

Sugarcane Genotype Performance in Three Environments (Based on Crop Cycle) at Mardan, Pakistan

USDA-ARS?s Scientific Manuscript database

Sugarcane breeders often face significant genotype x environment interactions in their trials grown under multiple environments. Hence, genotypes need to be tested for their stability across different environments keeping in view the significant interactions. An experiment comprising 28 sugarcane ge...

Proteomic analysis of a compatible interaction between sugarcane and Sporisorium scitamineum.

PubMed

Barnabas, Leonard; Ashwin, N M R; Kaverinathan, K; Trentin, Anna Rita; Pivato, Micaela; Sundar, A Ramesh; Malathi, P; Viswanathan, R; Rosana, O B; Neethukrishna, K; Carletti, Paolo; Arrigoni, Giorgio; Masi, Antonio; Agrawal, Ganesh Kumar; Rakwal, Randeep

2016-04-01

Smut caused by Sporisorium scitamineum is one of the important diseases of sugarcane with global significance. Despite the intriguing nature of sugarcane, S. scitamineum interaction, several pertinent aspects remain unexplored. This study investigates the proteome level alterations occurring in the meristem of a S. scitamineum infected susceptible sugarcane cultivar at whip emergence stage. Differentially abundant proteins were identified by 2DE coupled with MALDI-TOF/TOF-MS. Comprehensively, 53 sugarcane proteins identified were related to defence, stress, metabolism, protein folding, energy, and cell division; in addition, a putative effector of S. scitamineum, chorismate mutase, was identified. Transcript expression vis-à-vis the activity of phenylalanine ammonia lyase was relatively higher in the infected meristem. Abundance of seven candidate proteins in 2D gel profiles was in correlation with its corresponding transcript expression levels as validated by qRT-PCR. Furthermore, this study has opened up new perspectives on the interaction between sugarcane and S. scitamineum. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Analysis of complex repeat sequences within the spinal muscular atrophy (SMA) candidate region in 5q13

DOE Office of Scientific and Technical Information (OSTI.GOV)

Davies, K.E.; Morrison, K.E.; Daniels, R.I.

1994-09-01

We previously reported that the 400 kb interval flanked the polymorphic loci D5S435 and D5S557 contains blocks of a chromosome 5 specific repeat. This interval also defines the SMA candidate region by genetic analysis of recombinant families. A YAC contig of 2-3 Mb encompassing this area has been constructed and a 5.5 kb conserved fragment, isolated from a YAC end clone within the above interval, was used to obtain cDNAs from both fetal and adult brain libraries. We describe the identification of cDNAs with stretches of high DNA sequence homology to exons of {beta} glucuronidase on human chromosome 7. Themore » cDNAs map both to the candidate region and to an area of 5p using FISH and deletion hybrid analysis. Hybridization to bacteriophage and cosmid clones from the YACs localizes the {beta} glucuronidase related sequences within the 400 kb region of the YAC contig. The cDNAs show a polymorphic pattern on hybridization to genomic BamH1 fragments in the size range of 10-250 kb. Further analysis using YAC fragmentation vectors is being used to determine how these {beta} glucuronidase related cDNAs are distributed within 5q13. Dinucleotide repeats within the region are being investigated to determine linkage disequilibrium with the disease locus.« less

Lignification in Sugarcane: Biochemical Characterization, Gene Discovery, and Expression Analysis in Two Genotypes Contrasting for Lignin Content1[W

PubMed Central

Bottcher, Alexandra; Cesarino, Igor; Brombini dos Santos, Adriana; Vicentini, Renato; Mayer, Juliana Lischka Sampaio; Vanholme, Ruben; Morreel, Kris; Goeminne, Geert; Moura, Jullyana Cristina Magalhães Silva; Nobile, Paula Macedo; Carmello-Guerreiro, Sandra Maria; Antonio dos Anjos, Ivan; Creste, Silvana; Boerjan, Wout; Landell, Marcos Guimarães de Andrade; Mazzafera, Paulo

2013-01-01

Sugarcane (Saccharum spp.) is currently one of the most efficient crops in the production of first-generation biofuels. However, the bagasse represents an additional abundant lignocellulosic resource that has the potential to increase the ethanol production per plant. To achieve a more efficient conversion of bagasse into ethanol, a better understanding of the main factors affecting biomass recalcitrance is needed. Because several studies have shown a negative effect of lignin on saccharification yield, the characterization of lignin biosynthesis, structure, and deposition in sugarcane is an important goal. Here, we present, to our knowledge, the first systematic study of lignin deposition during sugarcane stem development, using histological, biochemical, and transcriptional data derived from two sugarcane genotypes with contrasting lignin contents. Lignin amount and composition were determined in rind (outer) and pith (inner) tissues throughout stem development. In addition, the phenolic metabolome was analyzed by ultra-high-performance liquid chromatography-mass spectrometry, which allowed the identification of 35 compounds related to the phenylpropanoid pathway and monolignol biosynthesis. Furthermore, the Sugarcane EST Database was extensively surveyed to identify lignin biosynthetic gene homologs, and the expression of all identified genes during stem development was determined by quantitative reverse transcription-polymerase chain reaction. Our data provide, to our knowledge, the first in-depth characterization of lignin biosynthesis in sugarcane and form the baseline for the rational metabolic engineering of sugarcane feedstock for bioenergy purposes. PMID:24144790

Characterization of zebrafish dysferlin by morpholino knockdown

DOE Office of Scientific and Technical Information (OSTI.GOV)

Kawahara, Genri; Serafini, Peter R.; Myers, Jennifer A.

2011-09-23

Highlights: {yields} cDNAs of zebrafish dysferlin were cloned (6.3 kb). {yields} The dysferlin expression was detected in skeletal muscle, heart and eye. {yields} Injection of antisense morpholinos to dysferlin caused marked muscle disorganization. {yields} Zebrafish dysferlin expression may be involved in stabilizing muscle structures. -- Abstract: Mutations in the gene encoding dysferlin cause two distinct muscular dystrophy phenotypes: limb-girdle muscular dystrophy type 2B (LGMD-2B) and Miyoshi myopathy (MM). Dysferlin is a large transmembrane protein involved in myoblast fusion and membrane resealing. Zebrafish represent an ideal animal model to use for studying muscle disease including abnormalities of dysferlin. cDNAs of zebrafishmore » dysferlin were cloned (6.3 kb) and the predicted amino acid sequences, showed 68% similarity to predicted amino acid sequences of mammalian dysferlin. The expression of dysferlin was mainly in skeletal muscle, heart and eye, and the expression could be detected as early as 11 h post fertilization (hpf). Three different antisense oligonucleotide morpholinos were targeted to inhibit translation of this dysferlin mRNA and the morpholino-injected fish showed marked muscle disorganization which could be detected by birefringence assay. Western blot analysis using dysferlin antibodies showed that the expression of dysferlin was reduced in each of the three morphants. Dysferlin expression was shown to be reduced at the myosepta of zebrafish muscle using immunohistochemistry, although the expression of other muscle membrane components, dystrophin, laminin, {beta}-dystroglycan were detected normally. Our data suggest that zebrafish dysferlin expression is involved in stabilizing muscle structures and its downregulation causes muscle disorganization.« less

Isolation of cDNAs and functional characterisation of two multi-product terpene synthase enzymes from sandalwood, Santalum album L.

PubMed

Jones, Christopher G; Keeling, Christopher I; Ghisalberti, Emilio L; Barbour, Elizabeth L; Plummer, Julie A; Bohlmann, Jörg

2008-09-01

Sandalwood, Santalum album (Santalaceae) is a small hemi-parasitic tropical tree of great economic value. Sandalwood timber contains resins and essential oils, particularly the santalols, santalenes and dozens of other minor sesquiterpenoids. These sesquiterpenoids provide the unique sandalwood fragrance. The research described in this paper set out to identify genes involved in essential oil biosynthesis, particularly terpene synthases (TPS) in S. album, with the long-term aim of better understanding heartwood oil production. Degenerate TPS primers amplified two genomic TPS fragments from S. album, one of which enabled the isolation of two TPS cDNAs, SamonoTPS1 (1731bp) and SasesquiTPS1 (1680bp). Both translated protein sequences shared highest similarity with known TPS from grapevine (Vitis vinifera). Heterologous expression in Escherichia coli produced catalytically active proteins. SamonoTPS1 was identified as a monoterpene synthase which produced a mixture of (+)-alpha-terpineol and (-)-limonene, along with small quantities of linalool, myrcene, (-)-alpha-pinene, (+)-sabinene and geraniol when assayed with geranyl diphosphate. Sesquiterpene synthase SasesquiTPS1 produced the monocyclic sesquiterpene alcohol germacrene D-4-ol and helminthogermacrene, when incubated with farnesyl diphosphate. Also present were alpha-bulnesene, gamma-muurolene, alpha- and beta-selinenes, as well as several other minor bicyclic compounds. Although these sesquiterpenes are present in only minute quantities in the distilled sandalwood oil, the genes and their encoded enzymes described here represent the first TPS isolated and characterised from a member of the Santalaceae plant family and they may enable the future discovery of additional TPS genes in sandalwood.

Quantitative Proteomics of the Root of Transgenic Wheat Expressing TaBWPR-1.2 Genes in Response to Waterlogging.

PubMed

Haque, Emdadul; Abe, Fumitaka; Mori, Masahiko; Nanjo, Yohei; Komatsu, Setsuko; Oyanagi, Atsushi; Kawaguchi, Kentaro

2014-11-04

Once candidate genes are available, the application of genetic transformation plays a major part to study their function in plants for adaptation to respective environmental stresses, including waterlogging (WL). The introduction of stress-inducible genes into wheat remains difficult because of low transformation and plant regeneration efficiencies and expression variability and instability. Earlier, we found two cDNAs encoding WL stress-responsive wheat pathogenesis-related proteins 1.2 ( TaBWPR-1.2 ), TaBWPR-1.2#2 and TaBWPR-1.2# 13. Using microprojectile bombardment, both cDNAs were introduced into "Bobwhite". Despite low transformation efficiency, four independent T₂ homozygous lines for each gene were isolated, where transgenes were ubiquitously and variously expressed. The highest transgene expression was obtained in Ubi: TaBWPR-1.2#2 L#11a and Ubi:TaBWPR-1.2#13 L#4a. Using quantitative proteomics, the root proteins of L#11a were analyzed to explore possible physiological pathways regulated by TaBWPR-1.2 under normal and waterlogged conditions. In L#11a, the abundance of proteasome subunit alpha type-3 decreased under normal conditions, whereas that of ferredoxin precursor and elongation factor-2 increased under waterlogged conditions in comparison with normal plants. Proteomic results suggest that L#11a is one of the engineered wheat plants where TaBWPR-1.2#2 is most probably involved in proteolysis, protein synthesis and alteration in the energy pathway in root tissues via the above proteins in order to gain metabolic adjustment to WL.

Characterization of two rice MADS box genes that control flowering time.

PubMed

Kang, H G; Jang, S; Chung, J E; Cho, Y G; An, G

1997-08-31

Plants contain a variety of the MADS box genes that encode regulatory proteins and play important roles in both the formation of flower meristem and the determination of floral organ identity. We have characterized two flower-specific cDNAs from rice, designated OsMADS7 and OsMADS8. The cDNAs displayed the structure of a typical plant MADS box gene, which consists of the MADS domain, I region, K domain, and C-terminal region. These genes were classified as members of the AGL2 gene family based on sequence homology. The OsMADS7 and 8 proteins were most homologous to OM1 and FBP2, respectively. The OsMADS7 and 8 transcripts were detectable primarily in carpels and also weakly in anthers. During flower development, the OsMADS genes started to express at the young flower stage and the expression continued to the late stage of flower development. The OsMADS7 and 8 genes were mapped on the long arms of the chromosome 8 and 9, respectively. To study the functions of the genes, the cDNA clones were expressed ectopically using the CaMV 35S promoter in a heterologous tobacco plant system. Transgenic plants expressing the OsMADS genes exhibited the phenotype of early flowering and dwarfism. The strength of the phenotypes was proportional to the levels of transgene expression and the phenotypes were co-inherited with the kanamycin resistant gene to the next generation. These results indicate that OsMADS7 and 8 are structurally related to the AGL2 family and are involved in controlling flowering time.

ScMED7, a sugarcane mediator subunit gene, acts as a regulator of plant immunity and is responsive to diverse stress and hormone treatments.

PubMed

Zhang, Xu; Yang, Yuting; Zou, Jiake; Chen, Yun; Wu, Qibin; Guo, Jinlong; Que, Youxiong; Xu, Liping

2017-12-01

The Mediator complex, is an essential component of the RNA polymerase II general transcriptional machinery in eukaryotes. Mediator subunit 7 (MED7), a key subunit in the central module of this complex, plays an important role in gene transcriptional regulation. The present study isolated the full-length cDNA of the MED7 gene of sugarcane, hereby designated as ScMED7, which was characterized to harbor a 525-bp open reading frame that is predicted to encode a 174-amino acid protein with a molecular mass of 19.9 kDa and was localized to the nucleus and cytoplasm. ScMED7 contains one typical conserved domain of MED7 proteins and shares 98% homology with that from Sorghum bicolor (XP_002447862.1). ScMED7 was constitutively expressed, yet significantly higher in bud tissues. ScMED7 transcription was obviously induced by heavy metal (CdCl 2 ), low temperature (4 °C), and hormone (SA and MeJA) treatments, while inhibited by osmotic stresses of NaCl and PEG. The role of ScMED7 in plant immunity was demonstrated by transient overexpression in tobacco, which in turn induces the expression of six out of nine defense-related marker genes, including all the three hypersensitive response genes. The responses of defense-related marker genes in the mock and in the ScMED7 transiently overexpressed leaves challenged by pathogenic Pseudomonas solanacearum and Fusarium solani var. coeruleum suggest that ScMED7 acts as a negative regulator during pathogen infections, whereas only fungal infection was clearly phenotypically expressed. In sum, ScMED7 plays an important role in modulating sugarcane responses to biotic and abiotic stresses, and may have dual roles in hypersensitive responses and basal defense against pathogens.

Next Generation Sequencing: A useful tool for detection of sugarcane viruses in quarantine programs

USDA-ARS?s Scientific Manuscript database

The international exchange of sugarcane germplasm includes the risk of introducing potentially devastating pathogens that may threaten production. The USDA-APHIS Plant Germplasm Quarantine Program (PGQP) imports and tests sugarcane accessions that are used in research, variety development, and comme...

A report on the 2012 outfield variety tests

USDA-ARS?s Scientific Manuscript database

A dependable and sustainable source of new sugarcane varieties is the life-blood of the Louisiana Sugarcane Industry. To that end, the American Sugarcane League, the Louisiana State University AgCenter, and the USDA Agricultural Research Service have joined forces to insure that life-blood continues...

Allelopathic impact of HoCP 96-540 field residue on seed germination

USDA-ARS?s Scientific Manuscript database

Research indicates that sugarcane field residue and sugarcane mill bagasse may be allelopathic. Allelopathy is the chemical interaction between plants, which may result in the inhibition of plant growth and development. Previous research in Louisiana indicated that sugarcane field residue may inhibi...

Sugarcane and Energycane

USDA-ARS?s Scientific Manuscript database

“Energycane” is a term that is used to describe sugarcane grown solely for the production of renewable energy. A Type I energycane has somewhat lower sugar content (10-14%) and higher fiber content (14-20%) than a commercial sugarcane cultivar bred for sugar production. In contrast, a Type II energy...

World Collection of Sugarcane and Related Grasses: Utilizing a Vast Genetic Resource

USDA-ARS?s Scientific Manuscript database

Sugarcane (Saccharum spp.) cultivar improvement programs have not yet systematically utilized most of the genetic sources of yield potential and resistance to biotic and abiotic stresses that may exist in the Saccharum germplasm. Two collections of genetic material potentially useful to sugarcane br...

Soil quality indexing strategies for evaluating sugarcane expansion in Brazil

USDA-ARS?s Scientific Manuscript database

Increasing demands for biofuels have intensified the land use change (LUC) for sugarcane cropping expansion in Brazil. Assessments of LUC-induced changes on soil quality (SQ) are essential for quantifying and monitoring the sustainability of sugarcane production over time. Since there is not a unive...

Free amino acids - determinant of sugarcane resistance/susceptibility to stalk borer and sap feeders

USDA-ARS?s Scientific Manuscript database

Two relatively new key species in Louisiana that conform to the plant stress hypothesis are the Mexican rice borer, Eoreuma loftini (Dyar) and the sugarcane aphid, Melanaphis sacchari (Zehntner). High performance liquid chromatography differentiated insect resistant and susceptible sugarcane cultiva...

Repeatability of Sugarcane Selection on Sand and Organic Soils

USDA-ARS?s Scientific Manuscript database

The Canal Point (CP) Sugarcane Cultivar Development Program (a cooperative program between the USDA-ARS, the University of Florida and the Florida Sugarcane League) has been more successful at breeding for cultivars adapted to organic soils (muck) than for those adapted to sand soils. Currently, onl...

NDVI to detect sugarcane aphid injury to grain sorghum

USDA-ARS?s Scientific Manuscript database

Multispectral remote sensing has potential to provide quick and inexpensive information on sugarcane aphid, Melanaphis sacchari (Zehntner), pest status in sorghum fields. The purpose of this report is to describe a study conducted to determine if injury caused by sugarcane aphid to sorghum plants i...

Independently segregating simple sequence repeats (SSR) alleles in polyploid sugarcane

USDA-ARS?s Scientific Manuscript database

The complex nuclear genomic and flower structures of sugarcane cultivars (Saccharum hybrids spp., 2n = 10x = 100 – 130) render sugarcane a difficult subject for genetics research. Using a capillary electrophoresis- and fluorescence-labeling-based SSR genotyping platform, the segregation of a multi-a...

Registration of ‘CP 09-1822’ Sugarcane

USDA-ARS?s Scientific Manuscript database

‘CP 09-1822’ (Reg. No. __; PI 686942 sugarcane (a complex hybrid of Saccharum spp.) was released in June 2016 for commercial cultivation on sand (mineral) soils in Florida. This cultivar was developed through a collaborative sugarcane cultivar development program of the USDA-ARS, the University of F...

Limiting microbial degradation in Louisiana sugarcane mills: Are biocides effective?

USDA-ARS?s Scientific Manuscript database

Sucrose loss takes place post-harvest in sugarcane, and still represents a significant problem for the global sugar industry. In Louisiana, microorganisms cause the majority of sucrose loss during sugarcane transport to the factory, in cane piles at factory stock yards, and during overnight truck lo...

Identifying a new causal agent of mosaic in Louisiana sugarcane

USDA-ARS?s Scientific Manuscript database

Sugarcane mosaic virus (SCMV) is a pathogen of economic concern that infects maize, sorghum, and sugarcane worldwide. It is a member of the genus Potyvirus in the family Potyviridae and contains a linear, positive sense ssRNA genome 10 kb long. It is transmitted non-persistently via aphids and ...

Genetic diversity of viruses causing mosaic in Louisiana sugarcane

USDA-ARS?s Scientific Manuscript database

Mosaic caused by Sugarcane mosaic virus (SCMV) contributed to the near collapse of Louisiana’s sugarcane industry in the early 20th Century. By the 1950s, the cultivation of resistant cultivars eliminated mosaic as a major disease problem; however, new strains arose among previously resistant cultiv...

Sugarcane field residue and bagasse allelopathic impact on vegetable seed germination

USDA-ARS?s Scientific Manuscript database

The chemical interaction between plants, which is referred to as allelopathy, may result in the inhibition of plant growth and development. The objective of this research was to determine the allelopathic impact of sugarcane (Saccharum officinarum) var. ‘HoCP 96-540’ field residue and sugarcane baga...

A rapid biochemical test to assess postharvest deterioration of sugarcane and milled juice

USDA-ARS?s Scientific Manuscript database

The delivery of consignments of deteriorated sugarcane to factories can detrimentally affect multiple process units, and even lead to a factory shut-down. An enzymatic factory method was used to measure mannitol, a major degradation product of sugarcane Leuconostoc deterioration in the U.S., in pre...

Vegetable seedling production with sugarcane bagasse ash

USDA-ARS?s Scientific Manuscript database

The eleven sugarcane mills in Louisiana processed 380,000 ac and 12.8 million tons of harvested sugarcane in 2014, producing 1.5 million tons of raw sugar (brown sugar), and an estimated 3 million tons of the fibrous plant residue called bagasse. Bagasse is the fibrous material remaining after remov...

Establishing sugarcane (Saccharum spp.) genetic resources for in vitro storage and cryopreservation

USDA-ARS?s Scientific Manuscript database

Sugarcane (Saccharum spp.) is used to produce sugar, a variety of alcoholic beverages, bagasse and industrial ethanol utilized in making fuel. In production fields, sugarcane is propagated vegetatively and currently, the crop’s genetic resources are also preserved as field plantings. The National Pl...

Influence of potential evapotranspiration on the water balance of sugarcane fields in Maui, Hawaii

USDA-ARS?s Scientific Manuscript database

The year-long warm temperatures and other climatic characteristics of the Pacific Ocean Islands have made Hawaii an optimum place for growing sugarcane; however, irrigation is essential to satisfy the large water demand of sugarcane. Under the Hawaiian tropical weather, actual evapotranspiration (A...

Sugarcane straw removal effects on plant growth and stalk yield

USDA-ARS?s Scientific Manuscript database

There is growing interest in sugarcane straw removal from the field to use as raw material for bioenergy production. In contrast, sugarcane straw removal may have negative implications for many soil ecosystem services and subsequent plant growth. A two-year experiment was conducted at Bom Retiro and...

Crop parameters for modeling sugarcane under rainfed conditions in Mexico

USDA-ARS?s Scientific Manuscript database

Crop models with well-tested parameters can improve sugarcane productivity for food and biofuel generation. This study aimed to (i) calibrate the light extinction coefficient (k) and other crop parameters for the sugarcane cultivar CP 72-2086, an early-maturing cultivar grown in Mexico and many oth...

Using normalized difference vegetation index (NDVI) to estimate sugarcane yield and yield components

USDA-ARS?s Scientific Manuscript database

Sugarcane (Saccharum spp.) yield and yield components are important traits for growers and scientists to evaluate and select cultivars. Collection of these yield data would be labor intensive and time consuming in the early selection stages of sugarcane breeding cultivar development programs with a ...

Determining yield loss caused by brown rust in production fields of sugarcane

USDA-ARS?s Scientific Manuscript database

Infections of Puccinia melanocephala, the causal agent of brown rust, appear on Louisiana sugarcane in the spring. Disease expression is usually limited to 2 to 3 months until temperatures exceed those favorable for spore production. The affected sugarcane is harvested 4 to 6 months after rust sympt...

Glyphosate Control of Orange and Brown Rusts in Glyphosate-Sensitive Sugarcane Cultivars

USDA-ARS?s Scientific Manuscript database

Technical Abstract: Brown and orange rust diseases cause substantial yield reductions on sugarcane (Saccharum spp.) in Florida and other regions where sugarcane is grown. Brown rust caused by Puccinia melanocephala Syd. & P. Syd has been present in Florida since 1978 and orange rust caused by Pucci...

Loop-mediated isothermal amplification (LAMP) based detection of Colletotrichum falcatum causing red rot in sugarcane

USDA-ARS?s Scientific Manuscript database

Red rot, caused by Colletotrichum falcatum, is a destructive disease prevalent in most sugarcane-producing countries. Disease-free sugarcane planting materials are essential as the pathogen spreads primarily through infected setts. The present study was undertaken to develop loop-mediated isothermal...

Identification of stable fly attractant compounds in vinasse, a byproduct of sugarcane-ethanol distillation

USDA-ARS?s Scientific Manuscript database

The stable fly, Stomoxys calcitrans (Diptera: Muscidae), is a worldwide pest of livestock. Recent outbreaks of stable flies in sugarcane fields in Brazil have become a serious problem for livestock producers. Larvae and pupae found inside sugarcane stems after harvesting may indicate that stable fli...

The long and short of it: Sugarcane planting systems (whole stalks, billets, and single nodes)

USDA-ARS?s Scientific Manuscript database

Louisiana sugarcane (Saccharum spp.) producers use vegetative cuttings to plant their 100,000 plus acres of their sugarcane crop rotation each year. Researchers with USDA-ARS, LSU AgCenter, American Sugar Cane League, private industry, and producers have conducted cooperative and independent researc...

Sugarcane Genotype Selection for Sand Soils in Florida

USDA-ARS?s Scientific Manuscript database

Selection of high yielding sugarcane (Saccharum spp.) genotypes for organic (muck) soils in Florida has been more successful than for sand soils. The purpose of this study was to compare the performance of 31 sugarcane genotypes on sand soils with and without mill mud added at the rate of 1510 cubic...

Development of Leaf Spectral Models for Evaluating Large Numbers of Sugarcane Genotypes

USDA-ARS?s Scientific Manuscript database

Leaf reflectance has been used to estimate crop leaf chemical and physiological characters. Sugarcane (Saccharum spp.) leaf N, C, and chlorophyll levels are important traits for high yields and perhaps useful for genotype evaluation. The objectives of this study were to identify sugarcane genotypic ...

Introduction of orange rust caused by Puccinia kuehnii into the Louisiana sugarcane industry

USDA-ARS?s Scientific Manuscript database

The first observation of orange rust infecting sugarcane, caused by Puccinia kuehnii, in the Americas was in Florida in 2007. To monitor for the possible introduction of orange rust into Louisiana, visual surveys were initiated throughout the Louisiana sugarcane industry among plantings of cultivar...

Effect of orange rust on sugarcane breeding program at canal Point

USDA-ARS?s Scientific Manuscript database

Orange rust of sugarcane (Saccharum spp. hybrids), caused by Puccinia kuehnii (W. Krüger) E.J. Butler, appeared in the Western Hemisphere ten years ago. Orange rust substantially reduces yields in susceptible sugarcane genotypes. Majority of the commercial cultivars were susceptible at the time of o...

Status of Sugarcane yellow leaf virus and its impact in different progenies

USDA-ARS?s Scientific Manuscript database

Yellow leaf disease caused by Sugarcane yellow leaf virus (SCYLV) a Polerovirus is an important disease for sugarcane industries worldwide. High yield losses up to 50% were reported in susceptible varieties. Most of the commercial cultivars in Florida are infected with SCYLV; therefore, there is a ...

Phenotypic evaluation of the World Collection of Sugarcane and Related Grasses

USDA-ARS?s Scientific Manuscript database

Plants related to sugarcane (Saccharum sp.) produce biomass efficiently and rapidly and therefore may contain useful genes for biofuels. One of the two World Collections of Sugarcane and Related Grasses is located at the USDA-ARS Subtropical Horticulture Research Station in Miami, FL and presumably ...

Building organic matter of long-term sugarcane soils in a temperate environment

USDA-ARS?s Scientific Manuscript database

Mineral soils with a history of sugarcane monoculture cropping contain less soil organic matter (-35%), and plant macro- and micronutrients, including N (-20%), K (-26%), S (-7%), Ca (-8%), B (-33%), Zn (-88%), Mn (-29%), and Cu (-26%), than adjacent non-cultivated soils. Harvesting sugarcane ‘green...

Sugarcane aphid resistance in sorghum and a host range

USDA-ARS?s Scientific Manuscript database

The sugarcane aphid (SCA), Melanaphis sacchari, has been present in the United States primarily on sugarcane in Florida, Hawaii, and Louisiana until 2013 where it was found on grain sorghum near Beaumont, Texas. Since 2013, the SCA has been rapidly spreading and overwintering. Depending on the plant...

Characterizing a shallow groundwater system beneath irrigated sugarcane with electrical resistivity and radon (Rn-222), Puunene, Hawaii

USDA-ARS?s Scientific Manuscript database

In this study, we use a combination of electrical resistivity profiling and radon (222Rn) measurements to characterize a shallow groundwater system beneath the last remaining, large-scale sugarcane plantation on Maui, Hawaii. Hawaiian Commercial & Sugar Company has continuously operated a sugarcane...

Spatial variability of sugarcane yields in relation to soil salinity in Louisiana

USDA-ARS?s Scientific Manuscript database

High soil salinity levels have been documented to negatively impact sugarcane yields. Tests were conducted in commercial sugarcane fields in South Louisiana in 2009-2010 to determine if elevated soil salinity levels resulting from salt water intrusion from several recent hurricanes was having a neg...

Genetic Diversity and Genome Complexity of Sugarcane

USDA-ARS?s Scientific Manuscript database

Sugarcane (Saccharum spp.) as a C4 plant, is one of the most efficient crops in converting solar energy into chemical energy. Sugarcane cultivar improvement programs have not yet systematically utilized the most of the genetic sources of yield potential and resistance to stresses that may exist in t...

Registration of ‘CP 09-1430’ Sugarcane

USDA-ARS?s Scientific Manuscript database

‘CP 09-1430’ (Reg. No. ; PI 686940 sugarcane (a complex hybrid of Saccharum spp.) was developed and released (6 Jun. 2016) through cooperative research conducted by the USDA-ARS Sugarcane Field Station , Canal Point, the University of Florida, and the Florida Sugar Cane League, Inc. for use on ...

Registration of ‘Ho 00-961’ sugarcane

USDA-ARS?s Scientific Manuscript database

‘Ho 00-961’ (Reg. No., PI) sugarcane (a complex hybrid of Saccharum officinarum L., S. spontaneum L., S. barberi Jeswiet, and S. sinense Roxb. amend. Jeswiet) was selected by the USDA-ARS Sugarcane Research Unit, and evaluated cooperatively with the Louisiana State University Agricultural Center, an...

Potential of diazotrophic bacteria associated with sugarcane for energycane production

USDA-ARS?s Scientific Manuscript database

Crosses between sugarcane and wild species of Saccharum and other closely related genera are made to introgress new genes from the wild species into sugarcane. Characteristics of the progeny from these crosses may include increased biomass and the ability to be grown in a broader geographical range ...

Carbon balance of sugarcane agriculture on histosols of the everglades agricultural area: review, analysis, and global energy perspectives

USDA-ARS?s Scientific Manuscript database

Biofuels production from crop products and cellulosic by-products, including sugarcane, has received much attention. In Florida, most sugarcane is produced on drained Histosols (organic soils) of the Everglades Agricultural Area (EAA). Subsidence has occurred via microbial oxidation since drainage i...

Identifying Physiological and Yield Related Traits in Sugarcane and Energy Cane

USDA-ARS?s Scientific Manuscript database

A growing interest of producing sugarcane (Saccharum spp.) for both sugar and bioenergy and saturation of using organic soils provide an opportunity to expand production on mineral (sand) soils. However, sugarcane yields and profits on sand soils are generally low. Energy cane may be an alternative ...

Allelic divergence and cultivar-specific SSR alleles revealed by capillary electrophoresis using fluorescence-labeled SSR markers in sugarcane

USDA-ARS?s Scientific Manuscript database

Though sugarcane cultivars (Saccharum spp. hybrids) are complex aneu-polyploid hybrids, genetic evaluation and tracking of clone- or cultivar-specific alleles become possible due to capillary electrophoregrams (CE) using fluorescence-labeled SSR primer pairs. Twenty-four sugarcane cultivars, 12 each...

Fiber composition of a diversity panel of the world collection of sugarcane (Saccharum sp.) and related grasses

USDA-ARS?s Scientific Manuscript database

The world collection of sugarcane (Saccharum hybrids) and related grasses (WCSRG) is an important genetic resource for sugarcane and energy cane (Saccharum hybrids) breeding. Fiber components and structural carbohydrates in bioenergy feedstocks are utilized for conversion to lignocellulosic biofuel....

Genome-wide identification, characterization and expression profile analysis of expansins gene family in sugarcane (Saccharum spp.).

PubMed

Santiago, Thaís R; Pereira, Valquiria M; de Souza, Wagner R; Steindorff, Andrei S; Cunha, Bárbara A D B; Gaspar, Marília; Fávaro, Léia C L; Formighieri, Eduardo F; Kobayashi, Adilson K; C Molinari, Hugo B

2018-01-01

Expansins refer to a family of closely related non-enzymatic proteins found in the plant cell wall that are involved in the cell wall loosening. In addition, expansins appear to be involved in different physiological and environmental responses in plants such as leaf and stem initiation and growth, stomata opening and closing, reproduction, ripening and stress tolerance. Sugarcane (Saccharum spp.) is one of the main crops grown worldwide. Lignocellulosic biomass from sugarcane is one of the most promising raw materials for the ethanol industry. However, the efficient use of lignocellulosic biomass requires the optimization of several steps, including the access of some enzymes to the hemicellulosic matrix. The addition of expansins in an enzymatic cocktail or their genetic manipulation could drastically improve the saccharification process of feedstock biomass by weakening the hydrogen bonds between polysaccharides present in plant cell walls. In this study, the expansin gene family in sugarcane was identified and characterized by in silico analysis. Ninety two putative expansins in sugarcane (SacEXPs) were categorized in three subfamilies after phylogenetic analysis. The expression profile of some expansin genes in leaves of sugarcane in different developmental stages was also investigated. This study intended to provide suitable expansin targets for genetic manipulation of sugarcane aiming at biomass and yield improvement.

Rational regional distribution of sugarcane cultivars in China

PubMed Central

Luo, Jun; Pan, Yong-Bao; Xu, Liping; Grisham, Michael Paul; Zhang, Hua; Que, Youxiong

2015-01-01

Knowing yield potential and yield stability of sugarcane cultivars is of significance in guiding sugarcane breeding and rationalising regional distribution of sugarcane cultivars. In the present study, a heritability-adjusted genotype main effect plus genotype × environment (HA-GGE) biplot program was used to analyze the cane and sucrose yields of 44 newly released sugarcane cultivars at eight pilot test sites. The cane and sucrose yields of nine cultivars were higher than those of the control cultivar ROC22. From the perspective of cane yield, cultivars FN 40 and YZ 06–407 were well adapted to a wider range of conditions and produced relatively high cane yields in several pilot sites. From the perspective of sucrose yield, cultivars LC 03–1137, FN 38, FN 41, MT 01–77 and LC 05–136 were well adapted to a wide range of conditions and produced relatively high sucrose yields. Based on these results, three high yielding and widely adapted cultivars, namely, FN 39, LC 05–136, and YZ 05–51 were recommended for production in three major Chinese sugarcane planting areas. The results will provide a theoretical basis for recommending the effective use and rational regional distribution of sugarcane cultivars in China. PMID:26499905

Soil Quality Indexing Strategies for Evaluating Sugarcane Expansion in Brazil

PubMed Central

Cherubin, Maurício R.; Karlen, Douglas L.; Cerri, Carlos E. P.; Franco, André L. C.; Tormena, Cássio A.; Davies, Christian A.; Cerri, Carlos C.

2016-01-01

Increasing demand for biofuel has intensified land-use change (LUC) for sugarcane (Saccharum officinarum) expansion in Brazil. Assessments of soil quality (SQ) response to this LUC are essential for quantifying and monitoring sustainability of sugarcane production over time. Since there is not a universal methodology for assessing SQ, we conducted a field-study at three sites within the largest sugarcane-producing region of Brazil to develop a SQ index (SQI). The most common LUC scenario (i.e., native vegetation to pasture to sugarcane) was evaluated using six SQI strategies with varying complexities. Thirty eight soil indicators were included in the total dataset. Two minimum datasets were selected: one using principal component analysis (7 indicators) and the other based on expert opinion (5 indicators). Non-linear scoring curves were used to interpret the indicator values. Weighted and non-weighted additive methods were used to combine individual indicator scores into an overall SQI. Long-term conversion from native vegetation to extensive pasture significantly decreased overall SQ. In contrast, conversion from pasture to sugarcane had no significant impact on overall SQ at the regional scale, but site-specific responses were found. In general, sugarcane production improved chemical attributes (i.e., higher macronutrient levels and lower soil acidity); however it has negative effects on physical and biological attributes (i.e., higher soil compaction and structural degradation as well as lower soil organic carbon (SOC), abundance and diversity of macrofauna and microbial activity). Overall, we found that simple, user-friendly strategies were as effective as more complex ones for identifying SQ changes. Therefore, as a protocol for SQ assessments in Brazilian sugarcane areas, we recommend using a small number of indicators (e.g., pH, P, K, Visual Evaluation of Soil Structure -VESS scores and SOC concentration) and proportional weighting to reflect chemical, physical and biological processes within the soil. Our SQ evaluations also suggest that current approaches for expanding Brazilian sugarcane production by converting degraded pasture land to cropland can be a sustainable strategy for meeting increasing biofuel demand. However, management practices that alleviate negative impacts on soil physical and biological indicators must be prioritized within sugarcane producing areas to prevent unintentional SQ degradation over time. PMID:26938642

Soil Quality Indexing Strategies for Evaluating Sugarcane Expansion in Brazil.

PubMed

Cherubin, Maurício R; Karlen, Douglas L; Cerri, Carlos E P; Franco, André L C; Tormena, Cássio A; Davies, Christian A; Cerri, Carlos C

2016-01-01

Increasing demand for biofuel has intensified land-use change (LUC) for sugarcane (Saccharum officinarum) expansion in Brazil. Assessments of soil quality (SQ) response to this LUC are essential for quantifying and monitoring sustainability of sugarcane production over time. Since there is not a universal methodology for assessing SQ, we conducted a field-study at three sites within the largest sugarcane-producing region of Brazil to develop a SQ index (SQI). The most common LUC scenario (i.e., native vegetation to pasture to sugarcane) was evaluated using six SQI strategies with varying complexities. Thirty eight soil indicators were included in the total dataset. Two minimum datasets were selected: one using principal component analysis (7 indicators) and the other based on expert opinion (5 indicators). Non-linear scoring curves were used to interpret the indicator values. Weighted and non-weighted additive methods were used to combine individual indicator scores into an overall SQI. Long-term conversion from native vegetation to extensive pasture significantly decreased overall SQ. In contrast, conversion from pasture to sugarcane had no significant impact on overall SQ at the regional scale, but site-specific responses were found. In general, sugarcane production improved chemical attributes (i.e., higher macronutrient levels and lower soil acidity); however it has negative effects on physical and biological attributes (i.e., higher soil compaction and structural degradation as well as lower soil organic carbon (SOC), abundance and diversity of macrofauna and microbial activity). Overall, we found that simple, user-friendly strategies were as effective as more complex ones for identifying SQ changes. Therefore, as a protocol for SQ assessments in Brazilian sugarcane areas, we recommend using a small number of indicators (e.g., pH, P, K, Visual Evaluation of Soil Structure -VESS scores and SOC concentration) and proportional weighting to reflect chemical, physical and biological processes within the soil. Our SQ evaluations also suggest that current approaches for expanding Brazilian sugarcane production by converting degraded pasture land to cropland can be a sustainable strategy for meeting increasing biofuel demand. However, management practices that alleviate negative impacts on soil physical and biological indicators must be prioritized within sugarcane producing areas to prevent unintentional SQ degradation over time.

Maize Elongin C interacts with the viral genome-linked protein, VPg, of Sugarcane mosaic virus and facilitates virus infection

PubMed Central

Zhu, Min; Chen, Yuting; Ding, Xin Shun; Webb, Stephen L; Zhou, Tao; Nelson, Richard S; Fan, Zaifeng

2014-01-01

The viral genome-linked protein, VPg, of potyviruses is involved in viral genome replication and translation. To determine host proteins that interact with Sugarcane mosaic virus (SCMV) VPg, a yeast two-hybrid screen was used and a maize (Zea mays) Elongin C (ZmElc) protein was identified. ZmELC transcript was observed in all maize organs, but most highly in leaves and pistil extracts, and ZmElc was present in the cytoplasm and nucleus of maize cells in the presence or absence of SCMV. ZmELC expression was increased in maize tissue at 4 and 6 d post SCMV inoculation. When ZmELC was transiently overexpressed in maize protoplasts the accumulation of SCMV RNA was approximately doubled compared with the amount of virus in control protoplasts. Silencing ZmELC expression using a Brome mosaic virus-based gene silencing vector (virus-induced gene silencing) did not influence maize plant growth and development, but did decrease RNA accumulation of two isolates of SCMV and host transcript encoding ZmeIF4E during SCMV infection. Interestingly, Maize chlorotic mottle virus, from outside the Potyviridae, was increased in accumulation after silencing ZmELC expression. Our results describe both the location of ZmElc expression in maize and a new activity associated with an Elc: support of potyvirus accumulation. PMID:24954157

Maize Elongin C interacts with the viral genome-linked protein, VPg, of Sugarcane mosaic virus and facilitates virus infection.

PubMed

Zhu, Min; Chen, Yuting; Ding, Xin Shun; Webb, Stephen L; Zhou, Tao; Nelson, Richard S; Fan, Zaifeng

2014-09-01

The viral genome-linked protein, VPg, of potyviruses is involved in viral genome replication and translation. To determine host proteins that interact with Sugarcane mosaic virus (SCMV) VPg, a yeast two-hybrid screen was used and a maize (Zea mays) Elongin C (ZmElc) protein was identified. ZmELC transcript was observed in all maize organs, but most highly in leaves and pistil extracts, and ZmElc was present in the cytoplasm and nucleus of maize cells in the presence or absence of SCMV. ZmELC expression was increased in maize tissue at 4 and 6 d post SCMV inoculation. When ZmELC was transiently overexpressed in maize protoplasts the accumulation of SCMV RNA was approximately doubled compared with the amount of virus in control protoplasts. Silencing ZmELC expression using a Brome mosaic virus-based gene silencing vector (virus-induced gene silencing) did not influence maize plant growth and development, but did decrease RNA accumulation of two isolates of SCMV and host transcript encoding ZmeIF4E during SCMV infection. Interestingly, Maize chlorotic mottle virus, from outside the Potyviridae, was increased in accumulation after silencing ZmELC expression. Our results describe both the location of ZmElc expression in maize and a new activity associated with an Elc: support of potyvirus accumulation. © 2014 The Authors. New Phytologist © 2014 New Phytologist Trust.

The type III secretion system is necessary for the development of a pathogenic and endophytic interaction between Herbaspirillum rubrisubalbicans and Poaceae

PubMed Central

2012-01-01

Background Herbaspirillum rubrisubalbicans was first identified as a bacterial plant pathogen, causing the mottled stripe disease in sugarcane. H. rubrisubalbicans can also associate with various plants of economic interest in a non pathogenic manner. Results A 21 kb DNA region of the H. rubrisubalbicans genome contains a cluster of 26 hrp/hrc genes encoding for the type three secretion system (T3SS) proteins. To investigate the contribution of T3SS to the plant-bacterial interaction process we generated mutant strains of H. rubrisubalbicans M1 carrying a Tn5 insertion in both the hrcN and hrpE genes. H. rubrisulbalbicans hrpE and hrcN mutant strains of the T3SS system failed to cause the mottled stripe disease in the sugarcane susceptible variety B-4362. These mutant strains also did not produce lesions on Vigna unguiculata leaves. Oryza sativa and Zea mays colonization experiments showed that mutations in hrpE and hrcN genes reduced the capacity of H. rubrisulbalbicans to colonize these plants, suggesting that hrpE and hrcN genes are involved in the endophytic colonization. Conclusions Our results indicate that the T3SS of H. rubrisubalbicans is necessary for the development of the mottled stripe disease and endophytic colonization of rice. PMID:22672506

The Sugarcane Defense Protein SUGARWIN2 Causes Cell Death in Colletotrichum falcatum but Not in Non-Pathogenic Fungi

PubMed Central

Franco, Flávia P.; Santiago, Adelita C.; Henrique-Silva, Flávio; de Castro, Patrícia Alves; Goldman, Gustavo H.; Moura, Daniel S.; Silva-Filho, Marcio C.

2014-01-01

Plants respond to pathogens and insect attacks by inducing and accumulating a large set of defense-related proteins. Two homologues of a barley wound-inducible protein (BARWIN) have been characterized in sugarcane, SUGARWIN1 and SUGARWIN2 (sugarcane wound-inducible proteins). Induction of SUGARWINs occurs in response to Diatraea saccharalis damage but not to pathogen infection. In addition, the protein itself does not show any effect on insect development; instead, it has antimicrobial activities toward Fusarium verticillioides, an opportunistic fungus that usually occurs after D. saccharalis borer attacks on sugarcane. In this study, we sought to evaluate the specificity of SUGARWIN2 to better understand its mechanism of action against phytopathogens and the associations between fungi and insects that affect plants. We used Colletotrichum falcatum, a fungus that causes red rot disease in sugarcane fields infested by D. saccharalis, and Ceratocystis paradoxa, which causes pineapple disease in sugarcane. We also tested whether SUGARWIN2 is able to cause cell death in Aspergillus nidulans, a fungus that does not infect sugarcane, and in the model yeast Saccharomyces cerevisiae, which is used for bioethanol production. Recombinant SUGARWIN2 altered C. falcatum morphology by increasing vacuolization, points of fractures and a leak of intracellular material, leading to germling apoptosis. In C. paradoxa, SUGARWIN2 showed increased vacuolization in hyphae but did not kill the fungi. Neither the non-pathogenic fungus A. nidulans nor the yeast S. cerevisiae was affected by recombinant SUGARWIN2, suggesting that the protein is specific to sugarcane opportunistic fungal pathogens. PMID:24608349

Genome characterization of Sugarcane Yellow Leaf Virus with special reference to RNAi based molecular breeding.

PubMed

Khalil, Farghama; Yueyu, Xu; Naiyan, Xiao; Di, Liu; Tayyab, Muhammad; Hengbo, Wang; Islam, Waqar; Rauf, Saeed; Pinghua, Chen

2018-05-04

Sugarcane is an essential crop for sugar and biofuel. Globally, its production is severely affected by sugarcane yellow leaf disease (SCYLD) caused by Sugarcane Yellow Leaf Virus (SCYLV). Many aphid vectors are involved in the spread of the disease which reduced the effectiveness of cultural and chemical management. Empirical methods of plant breeding such as introgression from wild and cultivated germplasm were not possible or at least challenging due to the absence of resistance in cultivated and wild germplasm of sugarcane. RNA interference (RNAi) transformation is an effective method to create virus-resistant varieties. Nevertheless, limited progress has been made due to lack of comprehensive research program on SCYLV based on RNAi technique. In order to show improvement and to propose future strategies for the feasibility of the RNAi technique to cope SCYLV, genome-wide consensus sequences of SCYLV were analyzed through GenBank. The coverage rates of every consensus sequence in SCYLV isolates were calculated to evaluate their practicability. Our analysis showed that single consensus sequence from SCYLV could not work well for RNAi based sugarcane breeding programs. This may be due to high mutation rate and continuous recombination within and between various viral strains. Alternative multi-target RNAi strategy is suggested to combat several strains of the viruses and to reduce the silencing escape. The multi-target small interfering RNA (siRNA) can be used together to construct RNAi plant expression plasmid, and to transform sugarcane tissues to develop new sugarcane varieties resistant to SCYLV. Copyright © 2018 Elsevier Ltd. All rights reserved.

Identification and differential induction of the expression of aquaporins by salinity in broccoli plants.

PubMed

Muries, Beatriz; Faize, Mohamed; Carvajal, Micaela; Martínez-Ballesta, María Del Carmen

2011-04-01

Plant aquaporins belong to a large superfamily of conserved proteins called the major intrinsic proteins (MIPs). There is limited information about the diversity of MIPs and their water transport capacity in broccoli (Brassica oleracea) plants. In this study, the cDNAs of isoforms of Plasma Membrane Intrinsic Proteins (PIPs), a class of aquaporins, from broccoli roots have been partially sequenced. Thus, sequencing experiments led to the identification of eight PIP1 and three PIP2 genes encoding PIPs in B. oleracea plants. The occurrence of different gene products encoding PIPs suggests that they may play different roles in plants. The screening of their expression as well as the expression of two specific PIP2 isoforms (BoPIP2;2 and BoPIP2;3), in different organs and under different salt-stress conditions in two varieties, has helped to unravel the function and the regulation of PIPs in plants. Thus, a high degree of BoPIP2;3 expression in mature leaves suggests that this BoPIP2;3 isoform plays important roles, not only in root water relations but also in the physiology and development of leaves. In addition, differences between gene and protein patterns led us to consider that mRNA synthesis is inhibited by the accumulation of the corresponding encoded protein. Therefore, transcript levels, protein abundance determination and the integrated hydraulic architecture of the roots must be considered in order to interpret the response of broccoli to salinity.

Subcellular distribution of human RDM1 protein isoforms and their nucleolar accumulation in response to heat shock and proteotoxic stress.

PubMed

Messaoudi, Lydia; Yang, Yun-Gui; Kinomura, Aiko; Stavreva, Diana A; Yan, Gonghong; Bortolin-Cavaillé, Marie-Line; Arakawa, Hiroshi; Buerstedde, Jean-Marie; Hainaut, Pierre; Cavaillé, Jérome; Takata, Minoru; Van Dyck, Eric

2007-01-01

The RDM1 gene encodes a RNA recognition motif (RRM)-containing protein involved in the cellular response to the anti-cancer drug cisplatin in vertebrates. We previously reported a cDNA encoding the full-length human RDM1 protein. Here, we describe the identification of 11 human cDNAs encoding RDM1 protein isoforms. This repertoire is generated by alternative pre-mRNA splicing and differential usage of two translational start sites, resulting in proteins with long or short N-terminus and a great diversity in the exonic composition of their C-terminus. By using tagged proteins and fluorescent microscopy, we examined the subcellular distribution of full-length RDM1 (renamed RDM1alpha), and other RDM1 isoforms. We show that RDM1alpha undergoes subcellular redistribution and nucleolar accumulation in response to proteotoxic stress and mild heat shock. In unstressed cells, the long N-terminal isoforms displayed distinct subcellular distribution patterns, ranging from a predominantly cytoplasmic to almost exclusive nuclear localization, suggesting functional differences among the RDM1 proteins. However, all isoforms underwent stress-induced nucleolar accumulation. We identified nuclear and nucleolar localization determinants as well as domains conferring cytoplasmic retention to the RDM1 proteins. Finally, RDM1 null chicken DT40 cells displayed an increased sensitivity to heat shock, compared to wild-type (wt) cells, suggesting a function for RDM1 in the heat-shock response.

Carbon accumulation in a two year sugarcane rotation in Hawai’i, USA

USDA-ARS?s Scientific Manuscript database

Sugarcane has been examined as a bioenergy feedstock for producing aviation fuel in the Pacific Basin. Hawaii has been a major producer of sugarcane (Saccharum officinarum L.) in the Pacific, with its typical two-year production cycle having some of the highest reported rates of sugar production in...

First report of Sugarcane mosaic virus infecting Columbus Grass (Sorghum almum) in the United States

USDA-ARS?s Scientific Manuscript database

Mosaic symptoms in sorghum can be caused by several potyviruses [family Potyviridae], including Sorghum mosaic virus (SrMV) and Sugarcane mosaic virus (SCMV). SrMV and SCMV are responsible for global economic losses in sorghum, maize, and sugarcane. Ten plants of Columbus grass (Sorghum almum) exhib...

A structured approach to target starch solubilization and hydrolysis for the sugarcane industry

USDA-ARS?s Scientific Manuscript database

In sugarcane processing, starch is considered an impurity that negatively affects processing and reduces the quality of the sugar end-product. In the last decade, there has been a general world-wide increase in starch concentrations in sugarcane. Industrial a-amylases have been used for many years ...

Constructing high-density genetic maps for polypoid sugarcane (Saccharum spp.) and identifying quantitative trait loci controlling brown rust resistance

USDA-ARS?s Scientific Manuscript database

Sugarcane (Saccharum spp.) is an important economic crop for producing edible sugar and bioethanol. Brown rust had long been a major disease impacting sugarcane production world widely. Resistance resource and markers linked to the resistance are valuable tools for disease resistance improvement. An...

Dry mass yield and fiber composition of a diversity panel of the world collection of sugarcane (Saccharum sp.) and related grasses

USDA-ARS?s Scientific Manuscript database

The world collection of sugarcane (Saccharum hybrids) and related grasses (WCSRG) is an important genetic resource for sugarcane and energy cane breeding. Fiber components and structural carbohydrates in bioenergy feedstocks are utilized for conversion to lignocellulosic biofuel. The objective of th...

Sugarcane Responses to Water-Table Depth and Periodic Flood

USDA-ARS?s Scientific Manuscript database

Sugarcane (Saccharum spp.) is routinely exposed to periodic floods and shallow water tables in Florida’s Everglades Agricultural Area (EAA). The purpose of this study was to examine the yields and juice quality of four sugarcane cultivars (CP 88-1762, CP 89-2143, CP 89-2376, and CP 96-1252) maintain...

First year in operating a mechanical detrasher system at a sugarcane factory in Louisiana

USDA-ARS?s Scientific Manuscript database

Over the past 2 years, a new prototype mechanical detrasher system was built at a Louisiana sugarcane factory by American Biocarbon LLC. It was built to remove sugarcane trash (top stalks and leaves) before processing, and for the manufacture and sale of value-added-products from the removed trash,...

Invasion of sorghum in the Americas by a new sugarcane aphid (Melanaphis sacchari) superclone

USDA-ARS?s Scientific Manuscript database

In the United States (U.S.), the sugarcane aphid (SCA) Melanaphis sacchari (Zehnter) (Hemiptera: Aphididae) was introduced in the 1970s, however, at this time it was only considered a pest of sugarcane. In 2013, a massive outbreak of M. sacchari occurred on sorghum, resulting in significant economi...

Discovery of uncharacterized sugarcane viruses by next generation sequencing technology: the case of Ramu stunt

USDA-ARS?s Scientific Manuscript database

Ramu stunt disease of sugarcane was first reported in Papua New Guinea in the mid 1980's. The disease can reduce sugarcane yields significantly and causes severe stunting and mortality in highly susceptible cultivars. The causal agent of Ramu stunt has been investigated but its characterization has ...

Pyraclostrobin wash-off from sugarcane leaves and aerobic dissipation in agricultural soil

USDA-ARS?s Scientific Manuscript database

In order to mitigate damage from the fungal sugarcane pathogen brown rust (Puccinia melanocephala), a Section 18 Emergency Use Label was put in place by the EPA for the application of pyraclostrobin (trade name Headline® SC; produced by BASF) on sugarcane in 2008. In order to assess the dynamics of ...

Genotyping Sugarcane for the Brown Rust Resistance Locus Bru1 Using Unlabeled Probe Melting

USDA-ARS?s Scientific Manuscript database

Brown rust, caused by the fungus Puccinia melanocephala, is a major disease of sugarcane (Saccharum spp.) in Florida, Louisiana, and other sugarcane growing regions. The Bru1 locus has been used as a durable and effective source of resistance, and markers are available to select for the trait. The...

Does fallow planted soybean and sweet sorghum reduce plant cane density?

USDA-ARS?s Scientific Manuscript database

Sugarcane is planted to approximately 172,000 hectares in Louisiana annually and nearly 25% of a sugarcane growers’ land that is to be planted to sugarcane remains fallow 8 to 10 months each year. During the fallow period land is regraded to improve drainage, and weeds are controlled by herbicides a...

Genetic variability among the brown rust resistant and susceptible genotypes of sugarcane by RAPD technique

USDA-ARS?s Scientific Manuscript database

Brown leaf rust in sugarcane is caused by Puccinia melanocephala (Syd. & P. Syd.), which is major cause of cultivar withdrawal. We attempted to analyze the RAPD diversity of two discrete phenotypic classes i.e. rust resistant (R) and rust susceptible (S) of six commercially available sugarcane elite...

Effect of potassium fertilizer application on the yield and quality of current sugarcane varieties in Louisiana

USDA-ARS?s Scientific Manuscript database

For many sugarcane producers in Louisiana the only fertilizer that is routinely applied to their crop is nitrogen that is side-dressed in the spring. This is due, primarily to the high cost of potassium and phosphorus fertilizers. Recent cooperative research conducted between the USDA/ARS Sugarcane ...

Constructing high-density genetic maps for polyploid sugarcane (Saccharum spp.) and identifying quantitative trait loci controlling brown rust resistance

USDA-ARS?s Scientific Manuscript database

Sugarcane (Saccharum spp.) is an important economic crop for producing edible sugar and bioethanol. Brown rust had long been a major disease impacting sugarcane production world widely. Resistance resource and markers linked to the resistance are valuable tools for disease resistance improvement. An...

Development and integration of an SSR-based molecular identity database into sugarcane breeding program

USDA-ARS?s Scientific Manuscript database

Sugarcane breeding is very difficult and it takes 12 to 14 years to develop a new cultivar for commercial production. This is because sugarcane varieties are highly polyploid, inter-specific hybrids with 100 to 130 chromosomes that may vary across geographical areas. Other obstacles/constraints incl...

The latest progress in sugarcane molecular genetics research at the USDA-ARS, Sugarcane Research Laboratory

USDA-ARS?s Scientific Manuscript database

In 2005, two sugar molecular genetics tools were developed in the USDA-ARS, Southeast Area, Sugarcane Research Laboratory at Houma, LA. One is the high throughput fluorescence- and capillary electrophoregrams (CE)-based SSR genotyping tool and the other is single pollen collection and SSR genotyping...

Postharvest accumulation of resveratrol and piceatannol in sugarcane with enhanced antioxidant activity

USDA-ARS?s Scientific Manuscript database

A new plant source, sugarcane, was used to produce the stilbenes piceatannol and resveratrol. Both stilbenes were identified in sugarcane billet stalks (12 mm) after incubation at room temperature for 3 days. Low concentrations of piceatannol (30.6 ug/g) and resveratrol (12.3 ug/g) were detected a...

Diversity and antifungal activity of endophytic diazotrophic bacteria colonizing sugarcane in Egypt

USDA-ARS?s Scientific Manuscript database

The price of nitrogen continues to increase and is a major input in sugarcane production. Sugarcane grown in Egypt was screened for the presence of nitrogen-fixing bacteria. Nitrogen-free medium LGI-P was used to isolate bacteria from cane stalks. Among the 52 isolates subjected to acetylene redu...

Management of Sugarcane Aphid in Sorghum

ERIC Educational Resources Information Center

Zerger, Sarah

2017-01-01

Sugarcane aphids are becoming a more prevalent pest in sorghum in the United States, especially in the south and are making their way north. There are many management practices that can be used on sugarcane aphids, the most important being scouting and maintaining populations. The most common mistake once a pest has been found is to immediately…

77 FR 43593 - Pesticide Emergency Exemptions; Agency Decisions and State and Federal Agency Crisis Declarations

Federal Register 2010, 2011, 2012, 2013, 2014

2012-07-25

... sugarcane to control Orange Rust (Puccinia kuehnii); January 11, 2012 to January 11, 2013. Contact: Libby Pemberton. EPA authorized the use of pyraclostrobin on sugarcane to control Orange Rust (Puccinia kuehnii... sugarcane to control Brown Rust (Puccinia melanocephala); March 22, 2012 to June 30, 2012. Contact: Libby...

Sugarcane Leaf Spectra and Photosynthesis Responses to Millmud Application on a Sand Soil

USDA-ARS?s Scientific Manuscript database

Sugarcane (Saccharum spp.) yields on sand soils in Florida are much lower than on organic soils and have no improvements during a recent 33-year period. A current study suggested that the sand soil with addition of millmud, a by-product from the sugarcane milling process, significantly improved suga...

Sugarcane Leaf Photosynthesis and Growth Characters during Development of Water-Deficit Stress

USDA-ARS?s Scientific Manuscript database

Yield and profitability of sugarcane grown on sand soils are much lower than on organic soils in Florida due to biotic and abiotic stresses. A greenhouse study was conducted using a sand soil to identify effects of water deficit stress (WS) during sugarcane early growth on leaf photosynthetic compon...

Outbreak of sorghum/sugarcane aphid on sorghum: First detections, distribution, and notes on management

USDA-ARS?s Scientific Manuscript database

An outbreak of an invasive aphid was discovered damaging grain sorghum in Texas and neighboring states in 2013. It may be a new variant of sugarcane aphid, Melanaphis sacchari, that has a high preference for sorghum, or a very closely related species (M. sorghi). We designate it sorghum/sugarcane ...

Biology and management of sugarcane yellow leaf virus: an historical overview.

PubMed

ElSayed, Abdelaleim Ismail; Komor, Ewald; Boulila, Moncef; Viswanathan, Rasappa; Odero, Dennis C

2015-12-01

Sugarcane yellow leaf virus (SCYLV) is one of the most widespread viruses causing disease in sugarcane worldwide. The virus has been responsible for drastic economic losses in most sugarcane-growing regions and remains a major concern for sugarcane breeders. Infection with SCYLV results in intense yellowing of the midrib, which extends to the leaf blade, followed by tissue necrosis from the leaf tip towards the leaf base. Such symptomatic leaves are usually characterized by increased respiration, reduced photosynthesis, a change in the ratio of hexose to sucrose, and an increase in starch content. SCYLV infection affects carbon assimilation and metabolism in sugarcane, resulting in stunted plants in severe cases. SCYLV is mainly propagated by planting cuttings from infected stalks. Phylogenetic analysis has confirmed the worldwide distribution of at least eight SCYLV genotypes (BRA, CHN1, CHN3, CUB, HAW, IND, PER, and REU). Evidence of recombination has been found in the SCYLV genome, which contains potential recombination signals in ORF1/2 and ORF5. This shows that recombination plays an important role in the evolution of SCYLV.

Sugarcane and other crops as fuel feedstocks

DOE Office of Scientific and Technical Information (OSTI.GOV)

Irvine, J.E.

1980-07-01

The use of sugarcane as a feedstock for fuel alcohol production in Brazil, and in Zimbabwe Rhodesia and Panama stimulated tremendous interest in the potential of agricultural crops for renewable energy sources. The cost of the feedstock is important. Corn, the current major agricultural feedstock in US fuel alcohol production, costs 60 to 80% of the selling price of the alcohol produced from it. Production costs for sugarcane and sugarbeets are higher than for corn. Sugarcane and sugarbeets, yield more fermentable carbohydrates per acre than any other crop. Sugarcane has the distinct advantage of containing a large amount of fibermore » in the harvested portion. The feedstock cost of sugarcane can be reduced by producing more cane per acre. Sweet sorghum has been discussed as a fuel crop. Cassana, the tapioca source, is thought to be a fuel crop of major potential. Feedstock cost can also be reduced through management decisions that reduce costly practices. Cultivation and fertilizer costs can be reduced. The operating cost of the processing plant is affected by the choice of crops grown for feedstock, both by their cost and by availability. (DP)« less

Study of Structural and Electrical Conductivity of Sugarcane Bagasse-Carbon with Hydrothermal Carbonization

NASA Astrophysics Data System (ADS)

Kurniati, M.; Nurhayati, D.; Maddu, A.

2017-03-01

The important part of fuel cell is the gas diffusion layer who made from carbon based material porous and conductive. The main goal of this research is to obtain carbon material from sugarcane bagasse with hydrothermal carbonization and chemical-physics activation. There were two step methods in this research. The first step was sample preparation which consisted of prepare the materials, hydrothermal carbonization and chemical-physics activation. The second one was analyze character of carbon using EDS, SEM, XRD, and LCR meter. The amount of carbon in sugarcane bagasse-carbon was about 85%-91.47% with pore morphology that already form. The degree of crystallinity of sugarcane bagasse carbon was about 13.06%-20.89%, leaving the remain as the amorphous phase. Electrical conductivity was about 5.36 x 10-2 Sm-1 - 1.11 Sm-1. Sugarcane bagasse-carbon has porous characteristic with electrical conductivity property as semiconductor. Sugarcane bagasse-carbon with hydrothermal carbonization potentially can be used as based material for fuel cell if only time of hydrothermal carbonization hold is increased.

Differential gene expression profiles in the venom gland/sac of Eumenes pomiformis (Hymenoptera: Eumenidae).

PubMed

Baek, Ji Hyeong; Lee, Si Hyeock

2010-06-01

To search for novel transcripts encoding biologically active venom components, a subtractive cDNA library specific to the venom gland and sac (gland/sac) of a solitary hunting wasp species, Eumenes pomiformis Fabricius (1781), was constructed by suppression subtractive hybridization. A total of 541 expressed sequence tags (ESTs) were clustered and assembled into 102 contigs (31 multiple sequences and 71 singletons). In total, 37 cDNAs were found in the library via BLASTx searching and manual annotation. Eight contigs (337 ESTs) encoding short venom peptides (10 to 16 amino acids) occupied 62% of the library. The deduced amino acid sequence (78 amino acids) of a novel venom peptide transcript shared sequence similarity with trypsin inhibitors and dendrotoxin-like venom peptides known to be K(+) channel blockers, implying that this novel peptide may play a role in the paralysis of prey. In addition to phospholipase A2 and hyaluronidase, which are known to be the main components of wasp venoms, several transcripts encoding enzymes, including three metallopeptidases and a decarboxylase likely involved in the processing and activation of venomous proteins, peptides, amines, and neurotransmitters, were also isolated from the library. The presence of a transcript encoding a putative insulin/insulin-like peptide binding protein suggests that solitary hunting wasps use their venom to control their prey, leading to larval growth cessation. The abundance of these venom components in the venom gland/sac and in the alimentary canal was confirmed by quantitative real-time PCR. Discovery of venom gland/sac-specific transcripts should promote further studies on biologically active components in the venom of solitary hunting wasps. Copyright 2010 Elsevier Ltd. All rights reserved.

Dynamics modeling for sugar cane sucrose estimation using time series satellite imagery

NASA Astrophysics Data System (ADS)

Zhao, Yu; Justina, Diego Della; Kazama, Yoriko; Rocha, Jansle Vieira; Graziano, Paulo Sergio; Lamparelli, Rubens Augusto Camargo

2016-10-01

Sugarcane, as one of the most mainstay crop in Brazil, plays an essential role in ethanol production. To monitor sugarcane crop growth and predict sugarcane sucrose content, remote sensing technology plays an essential role while accurate and timely crop growth information is significant, in particularly for large scale farming. We focused on the issues of sugarcane sucrose content estimation using time-series satellite image. Firstly, we calculated the spectral features and vegetation indices to make them be correspondence to the sucrose accumulation biological mechanism. Secondly, we improved the statistical regression model considering more other factors. The evaluation was performed and we got precision of 90% which is about 20% higher than the conventional method. The validation results showed that prediction accuracy using our sugarcane growth modeling and improved mix model is satisfied.

Soil carbon, nitrogen and phosphorus changes under sugarcane expansion in Brazil.

PubMed

Franco, André L C; Cherubin, Maurício R; Pavinato, Paulo S; Cerri, Carlos E P; Six, Johan; Davies, Christian A; Cerri, Carlos C

2015-05-15

Historical data of land use change (LUC) indicated that the sugarcane expansion has mainly displaced pasture areas in Central-Southern Brazil, globally the largest producer, and that those pastures were prior established over native forests in the Cerrado biome. We sampled 3 chronosequences of land use comprising native vegetation (NV), pasture (PA), and sugarcane crop (SC) in the sugarcane expansion region to assess the effects of LUC on soil carbon, nitrogen, and labile phosphorus pools. Thirty years after conversion of NV to PA, we found significant losses of original soil organic matter (SOM) from NV, while insufficient new organic matter was introduced from tropical grasses into soil to offset the losses, reflecting in a net C emission of 0.4 Mg ha(-1)yr(-1). These findings added to decreases in (15)N signal indicated that labile portions of SOM are preserved under PA. Afterwards, in the firsts five years after LUC from PA to SC, sparse variations were found in SOM levels. After more than 20 years of sugarcane crop, however, there were losses of 40 and 35% of C and N stocks, respectively, resulting in a rate of C emission of 1.3 Mg ha(-1)yr(-1) totally caused by the respiration of SOM from C4-cycle plants. In addition, conversion of pastures to sugarcane mostly increased (15)N signal, indicating an accumulation of more recalcitrant SOM under sugarcane. The microbe- and plant-available P showed site-specific responses to LUC as a function of different P-input managements, with the biological pool mostly accounting for more than 50% of the labile P in both anthropic land uses. With the projections of 6.4 Mha of land required by 2021 for sugarcane expansion in Brazil to achieve ethanol's demand, this explanatory approach to the responses of SOM to LUC will contribute for an accurate assessment of the CO₂ balance of sugarcane ethanol. Copyright © 2015 Elsevier B.V. All rights reserved.

Chronic consumption of distilled sugarcane spirit induces anxiolytic-like effects in mice.

PubMed

Sena, Maria Clecia P; Nunes, Fabíola C; Salvadori, Mirian G S Stiebbe; Carvalho, Cleyton Charles D; Morais, Liana Clebia S L; Braga, Valdir A

2011-01-01

Chronic ethanol consumption is a major public health problem throughout the world. We investigated the anxiolytic-like effects and the possible ever injury induced by the chronic consumption of ethanol or sugarcane spirit in mice. Adult mice were exposed to a two-bottle free-choice paradigm for 6 weeks. The mice in Group A (n = 16) had access to sugarcane spirit + distilled water, the mice in Group B (n = 15) had access to ethanol + distilled water, and the mice in Group C (control, n = 14) had access to distilled water + distilled water. The ethanol content in the beverages offered to Groups A and B was 2% for the first week, 5% for the second week and 10% for the remaining four weeks. At the end of the experimental period, the mice were evaluated using the elevated-plus maze and the hole-board test to assess their anxiety-related behaviors. We also determined the serum aspartate aminotransferase and alanine aminotransferase levels. In the elevated-plus maze, the time spent in the open arms was increased in the mice exposed to chronic ethanol (32 ± 8 vs. 7 ± 2 s, n = 9) or sugarcane spirit (36 ± 9 vs. 7 ± 2 s, n = 9) compared to the controls. In the hole-board test, the mice exposed to ethanol or sugarcane spirit displayed increases in their head-dipping frequency (16 ± 1 for the control group, 27 ± 2 for the ethanol group, and 31 ± 3 for the sugarcane-spirit group; n = 9 for each group). In addition, the mice exposed to sugarcane spirit displayed an increase in the aspartate aminotransferase / alanine aminotransferase ratio compared to the ethanol group (1.29 ± 0.17 for the control group and 2.67 ± 0.17 for the sugarcane spirit group; n = 8 for each group). The chronic consumption of sugarcane-spirit produces liver injury and anxiolytic-like effects and the possible liver injury in mice.

Synthetic versions of firefly luciferase and Renilla luciferase reporter genes that resist transgene silencing in sugarcane

PubMed Central

2014-01-01

Background Down-regulation or silencing of transgene expression can be a major hurdle to both molecular studies and biotechnology applications in many plant species. Sugarcane is particularly effective at silencing introduced transgenes, including reporter genes such as the firefly luciferase gene. Synthesizing transgene coding sequences optimized for usage in the host plant is one method of enhancing transgene expression and stability. Using specified design rules we have synthesised new coding sequences for both the firefly luciferase and Renilla luciferase reporter genes. We have tested these optimized versions for enhanced levels of luciferase activity and for increased steady state luciferase mRNA levels in sugarcane. Results The synthetic firefly luciferase (luc*) and Renilla luciferase (Renluc*) coding sequences have elevated G + C contents in line with sugarcane codon usage, but maintain 75% identity to the native firefly or Renilla luciferase nucleotide sequences and 100% identity to the protein coding sequences. Under the control of the maize pUbi promoter, the synthetic luc* and Renluc* genes yielded 60x and 15x higher luciferase activity respectively, over the native firefly and Renilla luciferase genes in transient assays on sugarcane suspension cell cultures. Using a novel transient assay in sugarcane suspension cells combining co-bombardment and qRT-PCR, we showed that synthetic luc* and Renluc* genes generate increased transcript levels compared to the native firefly and Renilla luciferase genes. In stable transgenic lines, the luc* transgene generated significantly higher levels of expression than the native firefly luciferase transgene. The fold difference in expression was highest in the youngest tissues. Conclusions We developed synthetic versions of both the firefly and Renilla luciferase reporter genes that resist transgene silencing in sugarcane. These transgenes will be particularly useful for evaluating the expression patterns conferred by existing and newly isolated promoters in sugarcane tissues. The strategies used to design the synthetic luciferase transgenes could be applied to other transgenes that are aggressively silenced in sugarcane. PMID:24708613

Synthetic versions of firefly luciferase and Renilla luciferase reporter genes that resist transgene silencing in sugarcane.

PubMed

Chou, Ting-Chun; Moyle, Richard L

2014-04-08

Down-regulation or silencing of transgene expression can be a major hurdle to both molecular studies and biotechnology applications in many plant species. Sugarcane is particularly effective at silencing introduced transgenes, including reporter genes such as the firefly luciferase gene.Synthesizing transgene coding sequences optimized for usage in the host plant is one method of enhancing transgene expression and stability. Using specified design rules we have synthesised new coding sequences for both the firefly luciferase and Renilla luciferase reporter genes. We have tested these optimized versions for enhanced levels of luciferase activity and for increased steady state luciferase mRNA levels in sugarcane. The synthetic firefly luciferase (luc*) and Renilla luciferase (Renluc*) coding sequences have elevated G + C contents in line with sugarcane codon usage, but maintain 75% identity to the native firefly or Renilla luciferase nucleotide sequences and 100% identity to the protein coding sequences.Under the control of the maize pUbi promoter, the synthetic luc* and Renluc* genes yielded 60x and 15x higher luciferase activity respectively, over the native firefly and Renilla luciferase genes in transient assays on sugarcane suspension cell cultures.Using a novel transient assay in sugarcane suspension cells combining co-bombardment and qRT-PCR, we showed that synthetic luc* and Renluc* genes generate increased transcript levels compared to the native firefly and Renilla luciferase genes.In stable transgenic lines, the luc* transgene generated significantly higher levels of expression than the native firefly luciferase transgene. The fold difference in expression was highest in the youngest tissues. We developed synthetic versions of both the firefly and Renilla luciferase reporter genes that resist transgene silencing in sugarcane. These transgenes will be particularly useful for evaluating the expression patterns conferred by existing and newly isolated promoters in sugarcane tissues. The strategies used to design the synthetic luciferase transgenes could be applied to other transgenes that are aggressively silenced in sugarcane.

Epicoccum nigrum P16, a Sugarcane Endophyte, Produces Antifungal Compounds and Induces Root Growth

PubMed Central

Fávaro, Léia Cecilia de Lima; Sebastianes, Fernanda Luiza de Souza; Araújo, Welington Luiz

2012-01-01

Background Sugarcane is one of the most important crops in Brazil, mainly because of its use in biofuel production. Recent studies have sought to determine the role of sugarcane endophytic microbial diversity in microorganism-plant interactions, and their biotechnological potential. Epicoccum nigrum is an important sugarcane endophytic fungus that has been associated with the biological control of phytopathogens, and the production of secondary metabolites. In spite of several studies carried out to define the better conditions to use E. nigrum in different crops, little is known about the establishment of an endophytic interaction, and its potential effects on plant physiology. Methodology/Principal Findings We report an approach based on inoculation followed by re-isolation, molecular monitoring, microscopic analysis, plant growth responses to fungal colonization, and antimicrobial activity tests to study the basic aspects of the E. nigrum endophytic interaction with sugarcane, and the effects of colonization on plant physiology. The results indicate that E. nigrum was capable of increasing the root system biomass and producing compounds that inhibit the in vitro growth of sugarcane pathogens Fusarium verticillioides, Colletotrichum falcatum, Ceratocystis paradoxa, and Xanthomomas albilineans. In addition, E. nigrum preferentially colonizes the sugarcane surface and, occasionally, the endophytic environment. Conclusions/Significance Our work demonstrates that E. nigrum has great potential for sugarcane crop application because it is capable of increasing the root system biomass and controlling pathogens. The study of the basic aspects of the interaction of E. nigrum with sugarcane demonstrated the facultative endophytism of E. nigrum and its preference for the phylloplane environment, which should be considered in future studies of biocontrol using this species. In addition, this work contributes to the knowledge of the interaction of this ubiquitous endophyte with the host plant, and also to a better use of microbial endophytes in agriculture. PMID:22675473

Detection of Genetically Modified Sugarcane by Using Terahertz Spectroscopy and Chemometrics

NASA Astrophysics Data System (ADS)

Liu, J.; Xie, H.; Zha, B.; Ding, W.; Luo, J.; Hu, C.

2018-03-01

A methodology is proposed to identify genetically modified sugarcane from non-genetically modified sugarcane by using terahertz spectroscopy and chemometrics techniques, including linear discriminant analysis (LDA), support vector machine-discriminant analysis (SVM-DA), and partial least squares-discriminant analysis (PLS-DA). The classification rate of the above mentioned methods is compared, and different types of preprocessing are considered. According to the experimental results, the best option is PLS-DA, with an identification rate of 98%. The results indicated that THz spectroscopy and chemometrics techniques are a powerful tool to identify genetically modified and non-genetically modified sugarcane.

Study of Sugarcane Pieces as Yeast Supports for Ethanol Production from Sugarcane Juice and Molasses Using Newly Isolated Yeast from Toddy Sap

PubMed Central

Satyanarayana, Botcha; Balakrishnan, Kesavapillai; Raghava Rao, Tamanam; Seshagiri Rao, Gudapaty

2012-01-01

A repeated batch fermentation system was used to produce ethanol using Saccharomyces cerevisiae strain (NCIM 3640) immobilized on sugarcane (Saccharum officinarum L.) pieces. For comparison free cells were also used to produce ethanol by repeated batch fermentation. Scanning electron microscopy evidently showed that cell immobilization resulted in firm adsorption of the yeast cells within subsurface cavities, capillary flow through the vessels of the vascular bundle structure, and attachment of the yeast to the surface of the sugarcane pieces. Repeated batch fermentations using sugarcane supported biocatalyst were successfully carried out for at least ten times without any significant loss in ethanol production from sugarcane juice and molasses. The number of cells attached to the support increased during the fermentation process, and fewer yeast cells leaked into fermentation broth. Ethanol concentrations (about 72.65~76.28 g/L in an average value) and ethanol productivities (about 2.27~2.36 g/L/hr in an average value) were high and stable, and residual sugar concentrations were low in all fermentations (0.9~3.25 g/L) with conversions ranging from 98.03~99.43%, showing efficiency 91.57~95.43 and operational stability of biocatalyst for ethanol fermentation. The results of the work pertaining to the use of sugarcane as immobilized yeast support could be promising for industrial fermentations. PMID:22783132

Biocontrol of Sugarcane Smut Disease by Interference of Fungal Sexual Mating and Hyphal Growth Using a Bacterial Isolate.

PubMed

Liu, Shiyin; Lin, Nuoqiao; Chen, Yumei; Liang, Zhibin; Liao, Lisheng; Lv, Mingfa; Chen, Yufan; Tang, Yingxin; He, Fei; Chen, Shaohua; Zhou, Jianuan; Zhang, Lianhui

2017-01-01

Sugarcane smut is a fungal disease caused by Sporisorium scitamineum , which can cause severe economic losses in sugarcane industry. The infection depends on the mating of bipolar sporida to form a dikaryon and develops into hyphae to penetrate the meristematic tissue of sugarcane. In this study, we set to isolate bacterial strains capable of blocking the fungal mating and evaluate their potential in control of sugarcane smut disease. A bacterial isolate ST4 from rhizosphere displayed potent inhibitory activity against the mating of S. scitamineum bipolar sporida and was selected for further study. Phylogenetic analyses and biochemical characterization showed that the isolate was most similar to Pseudomonas guariconensis . Methanol extracts from minimum and potato dextrose agar (PDA) agar medium, on which strain ST4 has grown, showed strong inhibitory activity on the sexual mating of S. scitamineum sporida, without killing the haploid cells MAT-1 or MAT-2. Further analysis showed that only glucose, but not sucrose, maltose, and fructose, could support strain ST4 to produce antagonistic chemicals. Consistent with the above findings, greenhouse trials showed that addition of 2% glucose to the bacterial inoculum significantly increased the strain ST4 biocontrol efficiency against sugarcane smut disease by 77% than the inoculum without glucose. The results from this study depict a new strategy to screen for biocontrol agents for control and prevention of the sugarcane smut disease.

Identifying quantitative trait loci (QTLs) and developing diagnostic markers linked to orange rust resistance in sugarcane (Saccharum spp.)

USDA-ARS?s Scientific Manuscript database

Sugarcane (Saccharum spp.) is an important economic crop, contributing up to 80% of table sugar used in the world and has become a promising feedstock for biofuel production. Sugarcane production has been threatened by many diseases, and fungicide applications for disease control have been opted ou...

Phenotypic evaluation of a diversity panel selected from the world collection of sugarcane (Saccharum spp.) and related grasses

USDA-ARS?s Scientific Manuscript database

Long-term improvement of sugarcane and energy cane (complex hybrids of Saccharum spp.) cultivars can be enhanced by breeding with the type of diverse germplasm available at the World Collection of Sugarcane and Related Grasses (WCSRG) maintained in Miami, Florida. To evaluate germplasm in the WCSRG ...

Distribution and frequency of Bru1, a major brown rust resistance gene, in the sugarcane world collection

USDA-ARS?s Scientific Manuscript database

Brown rust, caused by Puccinia melanocephala, is an important disease of sugarcane worldwide. Molecular markers for a major brown rust resistance gene, Bru1, were used to screen a total of 1,282 clones in the World Collection of Sugarcane and Related Grasses (WCSRG) to determine the distribution and...

Seasonal Fiber Content of Three Sugarcane Cultivars in Three Crop Cycles on Sand and Muck Soils

USDA-ARS?s Scientific Manuscript database

Accurate seasonal estimates of fiber are needed to maximize profits whether producing sugarcane (Saccharum spp.) for sucrose or ethanol. The main purpose of this study was to determine the effects of sample date and crop cycle on fiber content of three sugarcane cultivars growing on sand and organic...

Plant resistance in sorghums to the sugarcane aphid Melanaphis sacchari (Hemiptera: Aphididae)

USDA-ARS?s Scientific Manuscript database

We evaluated ten sorghum lines that were near or in commercial release with the intent of identifying phenotypic expression of host-plant resistance to the sugarcane aphid. Two of the ten entries OL2042 and SP7715 expressed a high degree of resistance to the sugarcane aphid with damage ratings <3.0...

Detection by next generation sequencing of a multi-segmented viral genome from sugarcane associated with Ramu stunt disease

USDA-ARS?s Scientific Manuscript database

Ramu stunt disease of sugarcane was first reported in Papua New Guinea in the mid 1980's. The disease can reduce sugarcane yields significantly and causes severe stunting and mortality in highly susceptible cultivars. The causal agent of Ramu stunt has been investigated but its characterization has ...

The Sugarcane-Biofuel Expansion and Dairy Farmers' Responses in Brazil

ERIC Educational Resources Information Center

Novo, Andre; Jansen, Kees; Slingerland, Maja

2012-01-01

The expansion of sugarcane for biofuels is a highly contentious issue. The growth of sugarcane area has occurred simultaneously with a reduction of dairy production in Sao Paulo state, the primary production region for sugar and ethanol in Brazil. This paper analyses different dairy farm rationales to continue dairy production in the context of a…

Identifying quantitative trait loci (QTLs) and developing diagnostic markers linked to orange rust resistance in sugarcane (Saccharum spp.)

USDA-ARS?s Scientific Manuscript database

Sugarcane (Saccharum spp.) is an important economic crop, contributing up to 80% of table sugar used in the world and has become a promising feedstock for biofuel production. Sugarcane production has been threatened by many diseases, and fungicide applications for disease control have been opted out...

Spread, genetic variation and methods for the detection of Puccinia kuehnii, the causal agent of sugarcane orange rust.

USDA-ARS?s Scientific Manuscript database

Sugarcane is susceptible to infection by two rust pathogens, Puccinia melanocephala and P. kuehnii, causing brown and orange rust, respectively. Orange rust of sugarcane was first reported in the Western hemisphere in Florida in July 2007. The pathogen was found to be distributed widely throughout t...

Screening for Resistance to Brown Rust of Sugarcane: Use of Bru1 resistance gene prospects and challenges

USDA-ARS?s Scientific Manuscript database

Brown rust of sugarcane caused by, Puccinia melanocephala, is a serious problem in the US sugarcane industry. A major resistance gene, Bru1 was identified and methodology for detecting it was developed by French scientists at CIRAD. The majority of the research resulting in the discovery of Bru1 res...

Length and nucleotide sequence polymorphism at the trnL and trnF non-coding regions of chloroplast genomes among Saccharum and Erianthus species

USDA-ARS?s Scientific Manuscript database

The aneupolyploidy genome of sugarcane (Saccharum hybrids spp.) and lack of a classical genetic linkage map make genetics research most difficult for sugarcane. Whole genome sequencing and genetic characterization of sugarcane and related taxa are far behind other crops. In this study, universal PCR...

The aphid Melanaphis sacchari and the weed Sorghum almum – Partners in crime

USDA-ARS?s Scientific Manuscript database

Sugarcane yellow leaf virus (SCYLV), the causal agent of yellow leaf disease of sugarcane, is widespread in Florida and vectored by the aphid Melanaphis sacchari. Sugarcane was the only known natural host of SCYLV in the USA until 2015 when a new natural host was found for this virus in Florida: Sor...

Comparison of Sugarcane and Energy Cane in Growth and Biomass Production

USDA-ARS?s Scientific Manuscript database

Sugarcane is one of major crops on sand soils in south Florida, but yields and profits are low compared to sugarcane grown on organic soils in the region. Energy cane may be an alternative crop on sand soils in the future to improve profits because of the growing interest of high biomass for energy....

Repeatability and Genotype x Environment Interaction of Intermediate Stage Sugarcane Selection Conducted on Sand and Organic soils

USDA-ARS?s Scientific Manuscript database

The Florida cooperative sugarcane cultivar development program conducts all of its early selection stages on muck (organic) soils at the USDA-ARS Sugarcane Field Station in Canal Point. About 25% of the locations in the final two stages (Stages 3 and 4) are conducted on sand soils, after a reduction...

Molecular cloning, structure, phylogeny and expression analysis of the invertase gene family in sugarcane.

PubMed

Wang, Liming; Zheng, Yuexia; Ding, Shihui; Zhang, Qing; Chen, Youqiang; Zhang, Jisen

2017-06-23

Invertases (INVs) are key enzymes regulating sucrose metabolism and are here revealed to be involved in responses to environmental stress in plants. To date, individual members of the invertase gene family and their expression patterns are unknown in sugarcane due to its complex genome despite their significance in sucrose metabolism. In this study, based on comparative genomics, eleven cDNA and twelve DNA sequences belonging to 14 non-redundant members of the invertase gene family were successfully cloned from sugarcane. A comprehensive analysis of the invertase gene family was carried out, including gene structures, phylogenetic relationships, functional domains, conserved motifs of proteins. The results revealed that the 14 invertase members from sugarcane could be clustered into three subfamilies, including 6 neutral/alkaline invertases (ShN/AINVs), and 8 acid invertases (ShAINVs). Faster divergence occurred in acid INVs than in neutral/alkaline INVs after the split of sugarcane and sorghum. At least a one-time gene duplication event was observed to have occurred in the four groups of acid INVs, whereas ShN/AINV1 and ShN/AINV2 in the β8 lineage were revealed to be the most recently duplicated genes among their paralogous genes in the β group of N/AINVs. Furthermore, comprehensive expression analysis of these genes was performed in sugarcane seedlings subjected to five abiotic stresses (drought, low temperature, glucose, fructose, and sucrose) using Quantitative Real-time PCR. The results suggested a functional divergence of INVs and their potential role in response to the five different treatments. Enzymatic activity in sugarcane seedlings was detected under five abiotic stresses treatments, and showed that the activities of all INVs were significantly inhibited in response to five different abiotic stresses, and that the neutral/alkaline INVs played a more prominent role in abiotic stresses than the acid INVs. In this study, we determined the INV gene family members of sugarcane by PCR cloning using sorghum as a reference, providing the first study of the INV gene family in sugarcane. Combining existing INV gene data from 7 plants with a comparative approach including a series of comprehensive analyses to isolate and identify INV gene family members proved to be highly successful. Moreover, the expression levels of INV genes and the variation of enzymatic activities associated with drought, low temperature, glucose, fructose, and sucrose are reported in sugarcane for the first time. The results offered useful foundation and framework for future research for understanding the physiological roles of INVs for sucrose accumulation in sugarcane.

Linking structural biology with genome research: Beamlines for the Berlin ``Protein Structure Factory'' initiative

NASA Astrophysics Data System (ADS)

Illing, Gerd; Saenger, Wolfram; Heinemann, Udo

2000-06-01

The Protein Structure Factory will be established to characterize proteins encoded by human genes or cDNAs, which will be selected by criteria of potential structural novelty or medical or biotechnological usefulness. It represents an integrative approach to structure analysis combining bioinformatics techniques, automated gene expression and purification of gene products, generation of a biophysical fingerprint of the proteins and the determination of their three-dimensional structures either by NMR spectroscopy or by X-ray diffraction. The use of synchrotron radiation will be crucial to the Protein Structure Factory: high brilliance and tunable wavelengths are prerequisites for fast data collection, the use of small crystals and multiwavelength anomalous diffraction (MAD) phasing. With the opening of BESSY II, direct access to a third-generation XUV storage ring source with excellent conditions is available nearby. An insertion device with two MAD beamlines and one constant energy station will be set up until 2001.

RNA extraction from decaying wood for (meta)transcriptomic analyses.

PubMed

Adamo, Martino; Voyron, Samuele; Girlanda, Mariangela; Marmeisse, Roland

2017-10-01

Wood decomposition is a key step of the terrestrial carbon cycle and is of economic importance. It is essentially a microbiological process performed by fungi and to an unknown extent by bacteria. To gain access to the genes expressed by the diverse microbial communities participating in wood decay, we developed an RNA extraction protocol from this recalcitrant material rich in polysaccharides and phenolic compounds. This protocol was implemented on 22 wood samples representing as many tree species from 11 plant families in the Angiosperms and Gymnosperms. RNA was successfully extracted from all samples and converted into cDNAs from which were amplified both fungal and bacterial protein coding genes, including genes encoding hydrolytic enzymes participating in lignocellulose hydrolysis. This protocol applicable to a wide range of decomposing wood types represents a first step towards a metatranscriptomic analysis of wood degradation under natural conditions.

Ribosomal protein S14 transcripts are edited in Oenothera mitochondria.

PubMed Central

Schuster, W; Unseld, M; Wissinger, B; Brennicke, A

1990-01-01

The gene encoding ribosomal protein S14 (rps14) in Oenothera mitochondria is located upstream of the cytochrome b gene (cob). Sequence analysis of independently derived cDNA clones covering the entire rps14 coding region shows two nucleotides edited from the genomic DNA to the mRNA derived sequences by C to U modifications. A third editing event occurs four nucleotides upstream of the AUG initiation codon and improves a potential ribosome binding site. A CGG codon specifying arginine in a position conserved in evolution between chloroplasts and E. coli as a UGG tryptophan codon is not edited in any of the cDNAs analysed. An inverted repeat 3' of an unidentified open reading frame is located upstream of the rps14 gene. The inverted repeat sequence is highly conserved at analogous regions in other Oenothera mitochondrial loci. Images PMID:2326162

Multiple vitellogenins from the Haemaphysalis longicornis tick are crucial for ovarian development.

PubMed

Boldbaatar, Damdinsuren; Umemiya-Shirafuji, Rika; Liao, Min; Tanaka, Tetsuya; Xuan, Xuenan; Fujisaki, Kozo

2010-11-01

Ovarian development and egg maturation are crucial processes for the success of reproduction in ticks. Three full-length cDNAs encoding the precursor of major yolk protein, vitellogenin, were obtained from cDNA libraries of the Haemaphysalis longicornis tick and designated as HlVg-1, HlVg-2 and HlVg-3. The HlVg mRNAs were found in fed females with major expression sites in the midgut, fat body and ovary. Native PAGE and Western blot demonstrated that HlVgs in the hemolymph, fat body and ovary of fed females consisted of four major polypeptides. RNAi results showed that HlVg dsRNA-injected ticks obtained lower body weight, egg weight and showed higher mortality of engorged females after blood sucking than control groups. Our results indicate that all HlVgs are essential for egg development and oviposition. Copyright 2010 Elsevier Ltd. All rights reserved.

Functional cDNA expression cloning: Pushing it to the limit

PubMed Central

OKAYAMA, Hiroto

2012-01-01

The 1970s and the following decade are the era of the birth and early development of recombinant DNA technologies, which have entirely revolutionized the modern life science by providing tools that enable us to know the structures of genes and genomes and to dissect their components and understand their functions at the molecular and submolecular levels. One major objective of the life sciences is to achieve molecular and chemical understandings of the functions of genes and their encoded proteins, which are responsible for the manifestation of all biological phenomena in organisms. In the early 1980s, I developed, together with Paul Berg, a new technique that enables the cloning of full-length complementary DNAs (cDNAs) on the basis of their functional expression in a given cell of interest. I review the development, application and future implications in the life sciences of this gene-cloning technique. PMID:22450538

New endo-beta-1,4-glucanases from the parabasalian symbionts, Pseudotrichonympha grassii and Holomastigotoides mirabile of Coptotermes termites.

PubMed

Watanabe, H; Nakashima, K; Saito, H; Slaytor, M

2002-11-01

Abstract. An endo-beta-1,4-glucanase (EG) was purified from the hindgut of an Australian mound-building termite, Coptotermes lacteus. The hindgut extract had a peak separate from those for extracts obtained from the salivary glands and the midgut based on sephacryl S-200 gel chromatography, and also demonstrated an origin different from the endogenous EGs of the termite itself. The recovery was further purified by SDS-PAGE, and its N-terminal amino acid sequence analyzed. This showed high homology to EGs from glycoside hydrolase family (GHF) 7. PCR-based cloning methods were applied to the hindgut contents of C. lacteus and individual protozoan symbionts from C formosanus. cDNAs encoding putative EGs homologous to GHF7 members were then identified. The functionality of one of the putative proteins was confirmed by its expression in Escherichia coli.

Cloning and characterization of phenylalanine ammonia-lyase and cinnamate 4-hydroxylase and pyranocoumarin biosynthesis in Angelica gigas.

PubMed

Park, Jee Hee; Park, Nam Il; Xu, Hui; Park, Sang Un

2010-08-27

Phenylalanine ammonia-lyase (PAL) and cinnamate 4-hydroxylase (C4H) are important enzymes in the phenylpropanoid pathway and also in the accumulation of decursin (1) and decursinol angelate (2), which are major secondary metabolites in Angelica gigas. Using PCR with degenerate primers targeted to conserved regions of available orthologous PAL and C4H sequences, cDNAs encoding PAL and C4H from A. gigas were isolated. Both genes were used to show the comparative developmental and inducible accumulation of mRNAs in different organs and in suspension cells of A. gigas. PAL and C4H were induced most strongly in response to 300 microM methyl jasmonate treatment at 6 and 12 h, respectively, and were highly expressed in the fine roots of A. gigas. Similarly, the production of 1 and 2 was most prolific in the fine roots of the plant.

Breast Reference Set Application: Karen Anderson-ASU (2014) — EDRN Public Portal

Cancer.gov

In order to increase the predictive value of tumor-specific antibodies for use as immunodiagnostics, our EDRN BDL has developed a novel protein microarray technology, termed Nucleic Acid Protein Programmable Array (NAPPA), which circumvents many of the limitations of traditional protein microarrays. NAPPA arrays are generated by printing full-length cDNAs encoding the target proteins at each feature of the array. The proteins are then transcribed and translated by a cell-free system and immobilized in situ using epitope tags fused to the proteins. Sera are added, and bound IgG is detected by standard secondary reagents. Using a sequential screening strategy to select AAb from 4,988 candidate tumor antigens, we have identified 28 potential AAb biomarkers for the early detection of breast cancer, and here we propose to evaluate these biomarkers using the EDRN Breast Cancer Reference Set.

Characterization of Zea mays endosperm C-24 sterol methyltransferase: one of two types of sterol methyltransferase in higher plants.

PubMed

Grebenok, R J; Galbraith, D W; Penna, D D

1997-08-01

We report the characterization of a higher-plant C-24 sterol methyltransferase by yeast complementation. A Zea mays endosperm expressed sequence tag (EST) was identified which, upon complete sequencing, showed 46% identity to the yeast C-24 methyltransferase gene (ERG6) and 75% and 37% amino acid identity to recently isolated higher-plant sterol methyltransferases from soybean and Arabidopsis, respectively. When placed under GALA regulation, the Z. mays cDNA functionally complemented the erg6 mutation, restoring ergosterol production and conferring resistance to cycloheximide. Complementation was both plasmid-dependent and galactose-inducible. The Z. mays cDNA clone contains an open reading frame encoding a 40 kDa protein containing motifs common to a large number of S-adenosyl-L-methionine methyltransferases (SMTs). Sequence comparisons and functional studies of the maize, soybean and Arabidopsis cDNAs indicates two types of C-24 SMTs exist in higher plants.

Domestication to Crop Improvement: Genetic Resources for Sorghum and Saccharum (Andropogoneae)

PubMed Central

Dillon, Sally L.; Shapter, Frances M.; Henry, Robert J.; Cordeiro, Giovanni; Izquierdo, Liz; Lee, L. Slade

2007-01-01

Background Both sorghum (Sorghum bicolor) and sugarcane (Saccharum officinarum) are members of the Andropogoneae tribe in the Poaceae and are each other's closest relatives amongst cultivated plants. Both are relatively recent domesticates and comparatively little of the genetic potential of these taxa and their wild relatives has been captured by breeding programmes to date. This review assesses the genetic gains made by plant breeders since domestication and the progress in the characterization of genetic resources and their utilization in crop improvement for these two related species. Genetic Resources The genome of sorghum has recently been sequenced providing a great boost to our knowledge of the evolution of grass genomes and the wealth of diversity within S. bicolor taxa. Molecular analysis of the Sorghum genus has identified close relatives of S. bicolor with novel traits, endosperm structure and composition that may be used to expand the cultivated gene pool. Mutant populations (including TILLING populations) provide a useful addition to genetic resources for this species. Sugarcane is a complex polyploid with a large and variable number of copies of each gene. The wild relatives of sugarcane represent a reservoir of genetic diversity for use in sugarcane improvement. Techniques for quantitative molecular analysis of gene or allele copy number in this genetically complex crop have been developed. SNP discovery and mapping in sugarcane has been advanced by the development of high-throughput techniques for ecoTILLING in sugarcane. Genetic linkage maps of the sugarcane genome are being improved for use in breeding selection. The improvement of both sorghum and sugarcane will be accelerated by the incorporation of more diverse germplasm into the domesticated gene pools using molecular tools and the improved knowledge of these genomes. PMID:17766842

Prospecting sugarcane resistance to Sugarcane yellow leaf virus by genome-wide association.

PubMed

Debibakas, S; Rocher, S; Garsmeur, O; Toubi, L; Roques, D; D'Hont, A; Hoarau, J-Y; Daugrois, J H

2014-08-01

Using GWAS approaches, we detected independent resistant markers in sugarcane towards a vectored virus disease. Based on comparative genomics, several candidate genes potentially involved in virus/aphid/plant interactions were pinpointed. Yellow leaf of sugarcane is an emerging viral disease whose causal agent is a Polerovirus, the Sugarcane yellow leaf virus (SCYLV) transmitted by aphids. To identify quantitative trait loci controlling resistance to yellow leaf which are of direct relevance for breeding, we undertook a genome-wide association study (GWAS) on a sugarcane cultivar panel (n = 189) representative of current breeding germplasm. This panel was fingerprinted with 3,949 polymorphic markers (DArT and AFLP). The panel was phenotyped for SCYLV infection in leaves and stalks in two trials for two crop cycles, under natural disease pressure prevalent in Guadeloupe. Mixed linear models including co-factors representing population structure fixed effects and pairwise kinship random effects provided an efficient control of the risk of inflated type-I error at a genome-wide level. Six independent markers were significantly detected in association with SCYLV resistance phenotype. These markers explained individually between 9 and 14 % of the disease variation of the cultivar panel. Their frequency in the panel was relatively low (8-20 %). Among them, two markers were detected repeatedly across the GWAS exercises based on the different disease resistance parameters. These two markers could be blasted on Sorghum bicolor genome and candidate genes potentially involved in plant-aphid or plant-virus interactions were localized in the vicinity of sorghum homologs of sugarcane markers. Our results illustrate the potential of GWAS approaches to prospect among sugarcane germplasm for accessions likely bearing resistance alleles of significant effect useful in breeding programs.

Development and testing of a rural credit supervision system at the level of counties and rural properties utilizing remote sensing techniqes

NASA Technical Reports Server (NTRS)

Batista, G. T. (Principal Investigator); Delima, A. M.; Tardin, A. T.; Rudorff, B. F. T.; Mendonca, F. J.; Dosanjosferreirapinto, S.; Chen, S. C.; Duarte, V.

1984-01-01

Remote sensing techniques for supporting the rural credit supervision system were developed and tested. The test area comprised the counties of Aracatuba and Guararapes, located in the State of Sao Paulo. Aerial photography, LANDSAT images and topographic charts were used. Aerial photographs were extremely useful for the out lining of properties boundaries with financing of sugarcane plantations by the Banco do Brasil S.A.. The percentage of correctly interpreted sugarcane on LANDSAT images, considering the 85 analyzed properties, was of 63.12%. The occurrence of atypical conditions such as excessive raining, sugarcane in bloom, and wind damaged sugarcane and sugarcane not harvested due to planning failures verified during the period the images were obtained, were some of the contributing factors associated with a low interpretation performance. An alternative approach was developed using several LANDSAT overpasses and auxiliary field data, which resulted in 91.77 percent correct.

Utilization of sugarcane industrial residues as animal food and probiotic medium.

PubMed

Apás, Ana Lidia; Arena, Mario Eduardo; Draksler, Diana; González, Silvia Nelina

2008-10-01

Sugar production from sugarcane generates residual products, currently, many of which are waste products. At the same time, introduction of probiotic bacteria to food animals needs an economical production medium. Fermentation of sugarcane blunting, an industrial residue, inoculated with ruminant probiotic bacteria was investigated. Fermentation was carried out using native flora (NF) alone, NF plus a goat probiotic lactic acid bacterium (LAB), and NF plus goat probiotic co-inoculated with two LAB isolated from sugarcane. Survival of microorganisms and metabolite produce were monitored. In the inoculated samples, pH was lower, dry matter was >30%, and Enterobacteriaceae and fungus decreased when compared to natural fermentation. The LAB inoculated grew and multiplied during fermentation. All beneficial changes were more quickly in the co-inoculated samples. The results presented indicate that sugarcane blunting can be used as a medium for introduction of ruminant probiotic bacteria. Fermentation of blunting can prolong shelf life and increase microbiological safety.

Integrated versus stand-alone second generation ethanol production from sugarcane bagasse and trash.

PubMed

Dias, Marina O S; Junqueira, Tassia L; Cavalett, Otávio; Cunha, Marcelo P; Jesus, Charles D F; Rossell, Carlos E V; Maciel Filho, Rubens; Bonomi, Antonio

2012-01-01

Ethanol production from lignocellulosic materials is often conceived considering independent, stand-alone production plants; in the Brazilian scenario, where part of the potential feedstock (sugarcane bagasse) for second generation ethanol production is already available at conventional first generation production plants, an integrated first and second generation production process seems to be the most obvious option. In this study stand-alone second generation ethanol production from surplus sugarcane bagasse and trash is compared with conventional first generation ethanol production from sugarcane and with integrated first and second generation; simulations were developed to represent the different technological scenarios, which provided data for economic and environmental analysis. Results show that the integrated first and second generation ethanol production process from sugarcane leads to better economic results when compared with the stand-alone plant, especially when advanced hydrolysis technologies and pentoses fermentation are included. Copyright © 2011 Elsevier Ltd. All rights reserved.

A plasmid toolkit for cloning chimeric cDNAs encoding customized fusion proteins into any Gateway destination expression vector

PubMed Central

2013-01-01

Background Valuable clone collections encoding the complete ORFeomes for some model organisms have been constructed following the completion of their genome sequencing projects. These libraries are based on Gateway cloning technology, which facilitates the study of protein function by simplifying the subcloning of open reading frames (ORF) into any suitable destination vector. The expression of proteins of interest as fusions with functional modules is a frequent approach in their initial functional characterization. A limited number of Gateway destination expression vectors allow the construction of fusion proteins from ORFeome-derived sequences, but they are restricted to the possibilities offered by their inbuilt functional modules and their pre-defined model organism-specificity. Thus, the availability of cloning systems that overcome these limitations would be highly advantageous. Results We present a versatile cloning toolkit for constructing fully-customizable three-part fusion proteins based on the MultiSite Gateway cloning system. The fusion protein components are encoded in the three plasmids integral to the kit. These can recombine with any purposely-engineered destination vector that uses a heterologous promoter external to the Gateway cassette, leading to the in-frame cloning of an ORF of interest flanked by two functional modules. In contrast to previous systems, a third part becomes available for peptide-encoding as it no longer needs to contain a promoter, resulting in an increased number of possible fusion combinations. We have constructed the kit’s component plasmids and demonstrate its functionality by providing proof-of-principle data on the expression of prototype fluorescent fusions in transiently-transfected cells. Conclusions We have developed a toolkit for creating fusion proteins with customized N- and C-term modules from Gateway entry clones encoding ORFs of interest. Importantly, our method allows entry clones obtained from ORFeome collections to be used without prior modifications. Using this technology, any existing Gateway destination expression vector with its model-specific properties could be easily adapted for expressing fusion proteins. PMID:23957834

A plasmid toolkit for cloning chimeric cDNAs encoding customized fusion proteins into any Gateway destination expression vector.

PubMed

Buj, Raquel; Iglesias, Noa; Planas, Anna M; Santalucía, Tomàs

2013-08-20

Valuable clone collections encoding the complete ORFeomes for some model organisms have been constructed following the completion of their genome sequencing projects. These libraries are based on Gateway cloning technology, which facilitates the study of protein function by simplifying the subcloning of open reading frames (ORF) into any suitable destination vector. The expression of proteins of interest as fusions with functional modules is a frequent approach in their initial functional characterization. A limited number of Gateway destination expression vectors allow the construction of fusion proteins from ORFeome-derived sequences, but they are restricted to the possibilities offered by their inbuilt functional modules and their pre-defined model organism-specificity. Thus, the availability of cloning systems that overcome these limitations would be highly advantageous. We present a versatile cloning toolkit for constructing fully-customizable three-part fusion proteins based on the MultiSite Gateway cloning system. The fusion protein components are encoded in the three plasmids integral to the kit. These can recombine with any purposely-engineered destination vector that uses a heterologous promoter external to the Gateway cassette, leading to the in-frame cloning of an ORF of interest flanked by two functional modules. In contrast to previous systems, a third part becomes available for peptide-encoding as it no longer needs to contain a promoter, resulting in an increased number of possible fusion combinations. We have constructed the kit's component plasmids and demonstrate its functionality by providing proof-of-principle data on the expression of prototype fluorescent fusions in transiently-transfected cells. We have developed a toolkit for creating fusion proteins with customized N- and C-term modules from Gateway entry clones encoding ORFs of interest. Importantly, our method allows entry clones obtained from ORFeome collections to be used without prior modifications. Using this technology, any existing Gateway destination expression vector with its model-specific properties could be easily adapted for expressing fusion proteins.

Green-cane harvested sugarcane crop residue decomposition as a function of temperature, soil moisture, and particle size

USDA-ARS?s Scientific Manuscript database

Sugarcane, a complex hybrid of Saccharum species, is grown on over 170,000 ha in the state of Louisiana. In 2016, the crop was worth $750 million US. Green-cane harvest, widely used in sugarcane producing countries, deposits up to 20 Mg ha-1 of crop residue annually. Green cane harvesting of sugarca...

Biomass Composition and Mineral Removal of Sugarcane and Energy Cane on a Sand Soil in Florida

USDA-ARS?s Scientific Manuscript database

Approximately 20% of Sugarcane is grown on sand soils in south Florida, but yields and profits are lower compared to sugarcane grown on organic soils in the region. Energy cane may be an alternative crop on sand soils in the future to improve profits because of the growing interest of increased biom...

Sugarcane-Biorefinery.

PubMed

Vaz, Sílvio

2017-03-17

Concepts such as biorefinery and green chemistry focus on the usage of biomass, as with the oil value chain. However, it can cause less negative impact on the environment. A biorefinery based on sugarcane (Saccharum spp.) as feedstock is an example, because it can integrate into the same physical space, of processes for obtaining biofuels (ethanol), chemicals (from sugars or ethanol), electricity, and heat.The use of sugarcane as feedstock for biorefineries is dictated by its potential to supply sugars, ethanol, natural polymers or macromolecules, organic matter, and other compounds and materials. By means of conversion processes (chemical, biochemical, and thermochemical), sugarcane biomass can be transformed into high-value bioproducts to replace petrochemicals, as a bioeconomy model.

Ruminal Ca and P Releases from Diets with Different Portion of the Sugarcane Bagasse

NASA Astrophysics Data System (ADS)

Pangestu, E.; Wahyono, F.; Nuswantara, L. K.; Achmadi, J.

2018-02-01

The in sacco technique was used to study the ruminal Ca and P releases from diets with different portion of sugarcane bagasse. Three diets containing 15, 25, and 35% of sugarcane bagase were tested their kinetic of ruminal Ca and P degradabilities. Two adult male sheep fitted with rumen cannula were used in the in sacco technique. In the in sacco experiment, feed samples were placed in the nylon bag and inserted into ruminal cannula for 0, 1, 3, 6, 12, 24, and 48 h. The kinetic of ruminal Ca and P degradabilities were focused on rapidly soluble fraction (fraction a), potentially degradable fraction (fraction b), and the degradation rate of fraction b (c). The data were tested using analyse of variance based on a completely randomized design. While the portion of sugarcane bagasse increased (P<0.05) fraction a of Ca diet, the portion b of P diet was decreased (P<0.05) by the portion of sugarcane bagasse.In conclusion, the effect of increasing portion of sugarcane bagasse in diet on ruminal release of Ca may be differed with that ofthe ruminal P release.

Determination of Genetic Diversity in Chilo partellus, Busseola fusca, and Spodoptera frugiperda Infesting Sugarcane in Southern Malawi Using DNA Barcodes.

PubMed

Kasambala Donga, Trust; Meadow, Richard

2018-06-22

Sugarcane is one of the most valuable crops in the world. Native and exotic Lepidopteran stemborers significantly limit sugarcane production. However, the identity and genetic diversity of stemborers infesting sugarcane in Malawi is unknown. The main objectives for this study were to identify and determine genetic diversity in stemborers infesting sugarcane in Malawi. We conducted field surveys between June 2016 and March 2017 in the Lower Shire Valley district of Chikwawa and Nsanje, southern Malawi. Molecular identification was based amplification the partial cytochrome oxidase subunit I (COI) gene region. Phylogenetic trees for sequences were generated and published GenBank accessions for each species were constructed. We found that Malawi Busseola fusca (Lepidoptera: Noctuidae) specimens belonged to clade II, Spodoptera frugiperda sp. 1 (Lepidoptera: Noctuidae) and Chilo partellus (Lepidoptera: Crambidae) were infesting sugarcane. Interspecific divergence ranged from 8.7% to 15.3%. Intraspecific divergence was highest for B. fusca , 3.6%. There were eight haplotypes for B. fusca , three for S. frugiperda and three for C. partellus . The importance of accurate species identification and genetic diversity on stemborer management is presented.

Simulated hydroclimatic impacts of projected Brazilian sugarcane expansion

NASA Astrophysics Data System (ADS)

Georgescu, M.; Lobell, D. B.; Field, C. B.; Mahalov, A.

2013-03-01

Sugarcane area is currently expanding in Brazil, largely in response to domestic and international demand for sugar-based ethanol. To investigate the potential hydroclimatic impacts of future expansion, a regional climate model is used to simulate 5 years of a scenario in which cerrado and cropland areas (~1.1E6 km2) within south-central Brazil are converted to sugarcane. Results indicate a cooling of up to ~1.0°C during the peak of the growing season, mainly as a result of increased albedo of sugarcane relative to the previous landscape. After harvest, warming of similar magnitude occurs from a significant decline in evapotranspiration and a repartitioning toward greater sensible heating. Overall, annual temperature changes from large-scale conversion are expected to be small because of offsetting reductions in net radiation absorption and evapotranspiration. The decline in net water flux from land to the atmosphere implies a reduction in regional precipitation, which is consistent with progressively decreasing simulated average rainfall for the study period, upon conversion to sugarcane. However, rainfall changes were not robust across three ensemble members. The results suggest that sugarcane expansion will not drastically alter the regional energy or water balance, but could result in important local and seasonal effects.

Lack of Detection of Bt Sugarcane Cry1Ab and NptII DNA and Proteins in Sugarcane Processing Products Including Raw Sugar

PubMed Central

Cheavegatti-Gianotto, Adriana; Gentile, Agustina; Oldemburgo, Danielle Angeloni; Merheb, Graciela do Amaral; Sereno, Maria Lorena; Lirette, Ron Peter; Ferreira, Thais Helena Silva; de Oliveira, Wladecir Salles

2018-01-01

Brazil is the largest sugarcane producer and the main sugar exporter in the world. The industrial processes applied by Brazilian mills are very efficient in producing highly purified sugar and ethanol. Literature presents evidence of lack of DNA/protein in these products, regardless of the nature of sugarcane used as raw material. Recently CTNBio, the Brazilian biosafety authority, has approved the first biotechnology-derived sugarcane variety for cultivation, event CTC175-A, which expresses the Cry1Ab protein to control the sugarcane borer (Diatraea saccharalis). The event also expresses neomycin-phosphotransferase type II (NptII) protein used as selectable marker during the transformation process. Because of the high purity of sugar and ethanol produced from genetically modified sugarcane, these end-products should potentially be classified as “pure substances, chemically defined,” by Brazilian Biosafety Law No. 11.105. If this classification is to be adopted, these substances are not considered as “GMO derivatives” and fall out of the scope of Law No. 11.105. In order to assess sugar composition and quality, we evaluate Cry1Ab and NptII expression in several sugarcane tissues and in several fractions from laboratory-scale processing of event CTC175-A for the presence of these heterologous proteins as well as for the presence of traces of recombinant DNA. The results of these studies show that CTC175-A presents high expression of Cry1Ab in leaves and barely detectable expression of heterologous proteins in stalks. We also evaluated the presence of ribulose-1,5-bisphosphate carboxylase/oxygenase protein and DNA in the fractions of the industrial processing of conventional Brazilian sugarcane cultivars. Results from both laboratory and industrial processing were concordant, demonstrating that DNA and protein are not detected in the clarified juice and downstream processed fractions, including ethanol and raw sugar, indicating that protein and DNA are removed and/or degraded during processing. In conclusion, the processing of conventional sugarcane and CTC175-A Bt event results in downstream products with no detectable concentrations of heterologous DNA or new protein. These results help in the classification of sugar and ethanol derived from CTC175-A event as pure, chemically defined substances in Brazil and may relieve regulatory burdens in countries that import Brazilian sugar. PMID:29637070

Reference genes for normalization of qPCR assays in sugarcane plants under water deficit.

PubMed

de Andrade, Larissa Mara; Dos Santos Brito, Michael; Fávero Peixoto Junior, Rafael; Marchiori, Paulo Eduardo Ribeiro; Nóbile, Paula Macedo; Martins, Alexandre Palma Boer; Ribeiro, Rafael Vasconcelos; Creste, Silvana

2017-01-01

Sugarcane ( Saccharum spp.) is the main raw material for sugar and ethanol production. Among the abiotic stress, drought is the main one that negatively impact sugarcane yield. Although gene expression analysis through quantitative PCR (qPCR) has increased our knowledge about biological processes related to drought, gene network that mediates sugarcane responses to water deficit remains elusive. In such scenario, validation of reference gene is a major requirement for successful analyzes involving qPCR. In this study, candidate genes were tested for their suitable as reference genes for qPCR analyses in two sugarcane cultivars with varying drought tolerance. Eight candidate reference genes were evaluated in leaves sampled in plants subjected to water deficit in both field and greenhouse conditions. In addition, five genes were evaluated in shoot roots of plants subjected to water deficit by adding PEG8000 to the nutrient solution. NormFinder and RefFinder algorithms were used to identify the most stable gene(s) among genotypes and under different experimental conditions. Both algorithms revealed that in leaf samples, UBQ1 and GAPDH genes were more suitable as reference genes, whereas GAPDH was the best reference one in shoot roots. Reference genes suitable for sugarcane under water deficit were identified, which would lead to a more accurate and reliable analysis of qPCR. Thus, results obtained in this study may guide future research on gene expression in sugarcane under varying water conditions.

The retinal rod Na(+)/Ca(2+),K(+) exchanger contains a noncleaved signal sequence required for translocation of the N terminus.

PubMed

McKiernan, C J; Friedlander, M

1999-12-31

The retinal rod Na(+)/Ca(2+),K(+) exchanger (RodX) is a polytopic membrane protein found in photoreceptor outer segments where it is the principal extruder of Ca(2+) ions during light adaptation. We have examined the role of the N-terminal 65 amino acids in targeting, translocation, and integration of the RodX using an in vitro translation/translocation system. cDNAs encoding human RodX and bovine RodX through the first transmembrane domain were correctly targeted and integrated into microsomal membranes; deletion of the N-terminal 65 amino acids (aa) resulted in a translation product that was not targeted or integrated. Deletion of the first 65 aa had no effect on membrane targeting of full-length RodX, but the N-terminal hydrophilic domain no longer translocated. Chimeric constructs encoding the first 65 aa of bovine RodX fused to globin were translocated across microsomal membranes, demonstrating that the sequence could function heterologously. Studies of fresh bovine retinal extracts demonstrated that the first 65 aa are present in the native protein. These data demonstrate that the first 65 aa of RodX constitute an uncleaved signal sequence required for the efficient membrane targeting and proper membrane integration of RodX.

Purification and cDNA cloning of SAPKK3, the major activator of RK/p38 in stress- and cytokine-stimulated monocytes and epithelial cells.

PubMed Central

Cuenda, A; Alonso, G; Morrice, N; Jones, M; Meier, R; Cohen, P; Nebreda, A R

1996-01-01

Two chromatographically distinct stress-activated protein kinase kinases (SAPKKs) have been identified in several mammalian cells, termed SAPKK2 and SAPKK3, which activate the MAP kinase family member RK/p38 but not JNK/SAPK in vitro. Here we demonstrate that SAPKK2 is identical or very closely related to the MAP kinase kinase family member MKK3. However, under our assay conditions, SAPKK3 was the major activator of RK/p38 detected in extracts prepared from stress- or interleukin-1-stimulated epithelial (KB) cells, from bacterial lipopolysaccharide and tumour necrosis factor alpha-stimulated THP1 monocytes or from rabbit skeletal muscle. The activated form of SAPKK3 was purified from muscle to near homogeneity, and tryptic peptide sequences were used to clone human and murine cDNAs encoding this enzyme. Human SAPKK3 comprised 334 amino acids and was 78% identical to MKK3. The murine and human SAPKK3 were 97% identical in their amino acid sequences. We also cloned a different murine cDNA that appears to encode a SAPKK3 protein truncated at the N-terminus. SAPKK3 is identical to the recently cloned MKK6. Images PMID:8861944

Parasitization by Scleroderma guani influences expression of superoxide dismutase genes in Tenebrio molitor.

PubMed

Zhu, Jia-Ying; Ze, Sang-Zi; Stanley, David W; Yang, Bin

2014-09-01

Superoxide dismutase (SOD) is an antioxidant enzyme involved in detoxifying reactive oxygen species. In this study, we identified genes encoding the extracellular and intracellular copper-zinc SODs (ecCuZnSOD and icCuZnSOD) and a manganese SOD (MnSOD) in the yellow mealworm beetle, Tenebrio molitor. The cDNAs for ecCuZnSOD, icCuZnSOD, and MnSOD, respectively, encode 24.55, 15.81, and 23.14 kDa polypeptides, which possess structural features typical of other insect SODs. They showed 20-94% identity to other known SOD sequences from Bombyx mori, Musca domestica, Nasonia vitripennis, Pediculus humanus corporis, and Tribolium castaneum. Expression of these genes was analyzed in selected tissues and developmental stages, and following exposure to Escherichia coli and parasitization by Scleroderma guani. We recorded expression of all three SODs in cuticle, fat body, and hemocytes and in the major developmental stages. Relatively higher expressions were detected in late-instar larvae and pupae, compared to other developmental stages. Transcriptional levels were upregulated following bacterial infection. Analysis of pupae parasitized by S. guani revealed that expression of T. molitor SOD genes was significantly induced following parasitization. We infer that these genes act in immune response and in host-parasitoid interactions. © 2014 Wiley Periodicals, Inc.

Identification of genes from the Treacher Collins candidate region

DOE Office of Scientific and Technical Information (OSTI.GOV)

Dixon, M.; Dixon, J.; Edwards, S.

Treacher Collins syndrome (TCOF1) is an autosomal dominant disorder of craniofacial development. The TCOF1 locus has previously been mapped to chromosome 5q32-33. The candidate gene region has been defined as being between two flanking markers, ribosomal protein S14 (RPS14) and Annexin 6 (ANX6), by analyzing recombination events in affected individuals. It is estimated that the distance between these flanking markers is 500 kb by three separate analysis methods: (1) radiation hybrid mapping; (2) genetic linkage; and (3) YAC contig analysis. A cosmid contig which spans the candidate gene region for TCOF1 has been constructed by screening the Los Alamos Nationalmore » Laboratory flow-sorted chromosome 5 cosmid library. Cosmids were obtained by using a combination of probes generated from YAC end clones, Alu-PCR fragments from YACs, and asymmetric PCR fragments from both T7 and T3 cosmid ends. Exon amplifications, the selection of genomic coding sequences based upon the presence of functional splice acceptor and donor sites, was used to identify potential exon sequences. Sequences found to be conserved between species were then used to screen cDNA libraries in order to identify candidate genes. To date, four different cDNAs have been isolated from this region and are being analyzed as potential candidate genes for TCOF1. These include the genes encoding plasma glutathione peroxidase (GPX3), heparin sulfate sulfotransferase (HSST), a gene with homology to the ETS family of proteins and one which shows no homology to any known genes. Work is also in progress to identify and characterize additional cDNAs from the candidate gene region.« less

Molecular cloning, characterization and expression profiles of thioredoxin 1 and thioredoxin 2 genes in Mytilus galloprovincialis

NASA Astrophysics Data System (ADS)

Wang, Qing; Ning, Xuanxuan; Pei, Dong; Zhao, Jianmin; You, Liping; Wang, Chunyan; Wu, Huifeng

2013-05-01

Thioredoxin (Trx) proteins are involved in many biological processes especially the regulation of cellular redox homeostasis. In this study, two Trx cDNAs were cloned from the mussel Mytilus galloprovincialis using rapid amplifi cation of cDNA ends-polymerase chain reaction (RACE-PCR). The two cDNAs were named MgTrx1 and MgTrx2, respectively. The open reading frames of MgTrx1 and MgTrx2 were 318 and 507 base pairs (bp) and they encoded proteins of 105 and 168 amino acids with estimated molecular masses of 11.45 and 18.93 kDa, respectively. Sequence analysis revealed that both proteins possessed the conserved active site dithiol motif Cys-Gly-Pro-Cys. In addition, MgTrx2 also possessed a putative mitochondrial targeting signal suggesting that it is located in the mitochondria. Quantitative real-time polymerase chain reaction (qPCR) revealed that both MgTrx1 and MgTrx2 were constitutively expressed in all tissues examined. The MgTrx1 transcript was most abundant in hemocytes and gills, whereas the MgTrx2 transcript was most abundant in gonad, hepatopancreas, gill and hemocytes. Following Vibrio anguillarum challenge, the expression of MgTrx1 was up-regulated and reached its peak, at a value 10-fold the initial value, at 24 h. Subsequently, expression returned back to the original level. In contrast, the expression level of MgTrx2 was down-regulated following bacterial stimulation, with one fi fth of the control level evident at 12 h post challenge. These results suggest that MgTrx1 and MgTrx2 may play important roles in the response of M. galloprovincialis to bacterial challenge.

The role of abscisic acid in regulating cucumber fruit development and ripening and its transcriptional regulation.

PubMed

Wang, Yanping; Wang, Ya; Ji, Kai; Dai, Shengjie; Hu, Ying; Sun, Liang; Li, Qian; Chen, Pei; Sun, Yufei; Duan, Chaorui; Wu, Yan; Luo, Hao; Zhang, Dian; Guo, Yangdong; Leng, Ping

2013-03-01

Cucumber (Cucumis sativus L.), a kind of fruit usually harvested at the immature green stage, belongs to non-climacteric fruit. To investigate the contribution of abscisic acid (ABA) to cucumber fruit development and ripening, variation in ABA level was investigated and a peak in ABA level was found in pulp before fruit get fully ripe. To clarify this point further, exogenous ABA was applied to cucumber fruits at two different development stages. Results showed that ABA application at the turning stage promotes cucumber fruit ripening, while application at the immature green stage had inconspicuous effects. In addition, with the purpose of understanding the transcriptional regulation of ABA, two partial cDNAs of CsNCED1 and CsNCED2 encoding 9-cis-epoxycarotenoid dioxygenase (NCED), a key enzyme in ABA biosynthetic pathway; one partial cDNA of CsCYP707A1 for 8'-hydroxylase, a key enzyme in the oxidative catabolism of ABA and two partial cDNAs of CsBG1 and CsBG2 for β-glucosidase (BG) that hydrolyzes ABA glucose ester (ABA-GE) to release active ABA were cloned from cucumber. The DNA and deduced amino acid sequences of these obtained genes respectively showed high similarities to their homologous genes in other plants. Real-time PCR analysis revealed that ABA content may be regulated by its biosynthesis (CsNCEDs), catabolism (CsCYP707A1) and reactivation genes (CsBGs) at the transcriptional level during cucumber fruit development and ripening, in response to ABA application, dehydration and pollination, among which CsNCED1, CsCYP707A1 and CsBG1 were highly expressed in pulp and may play more important roles in regulating ABA metabolism. Copyright © 2013 Elsevier Masson SAS. All rights reserved.

Direct Detection of Alternative Open Reading Frames Translation Products in Human Significantly Expands the Proteome

PubMed Central

Vanderperre, Benoît; Lucier, Jean-François; Bissonnette, Cyntia; Motard, Julie; Tremblay, Guillaume; Vanderperre, Solène; Wisztorski, Maxence; Salzet, Michel; Boisvert, François-Michel; Roucou, Xavier

2013-01-01

A fully mature mRNA is usually associated to a reference open reading frame encoding a single protein. Yet, mature mRNAs contain unconventional alternative open reading frames (AltORFs) located in untranslated regions (UTRs) or overlapping the reference ORFs (RefORFs) in non-canonical +2 and +3 reading frames. Although recent ribosome profiling and footprinting approaches have suggested the significant use of unconventional translation initiation sites in mammals, direct evidence of large-scale alternative protein expression at the proteome level is still lacking. To determine the contribution of alternative proteins to the human proteome, we generated a database of predicted human AltORFs revealing a new proteome mainly composed of small proteins with a median length of 57 amino acids, compared to 344 amino acids for the reference proteome. We experimentally detected a total of 1,259 alternative proteins by mass spectrometry analyses of human cell lines, tissues and fluids. In plasma and serum, alternative proteins represent up to 55% of the proteome and may be a potential unsuspected new source for biomarkers. We observed constitutive co-expression of RefORFs and AltORFs from endogenous genes and from transfected cDNAs, including tumor suppressor p53, and provide evidence that out-of-frame clones representing AltORFs are mistakenly rejected as false positive in cDNAs screening assays. Functional importance of alternative proteins is strongly supported by significant evolutionary conservation in vertebrates, invertebrates, and yeast. Our results imply that coding of multiple proteins in a single gene by the use of AltORFs may be a common feature in eukaryotes, and confirm that translation of unconventional ORFs generates an as yet unexplored proteome. PMID:23950983

Expressed sequence tags from the oomycete fish pathogen Saprolegnia parasitica reveal putative virulence factors

PubMed Central

Torto-Alalibo, Trudy; Tian, Miaoying; Gajendran, Kamal; Waugh, Mark E; van West, Pieter; Kamoun, Sophien

2005-01-01

Background The oomycete Saprolegnia parasitica is one of the most economically important fish pathogens. There is a dramatic recrudescence of Saprolegnia infections in aquaculture since the use of the toxic organic dye malachite green was banned in 2002. Little is known about the molecular mechanisms underlying pathogenicity in S. parasitica and other animal pathogenic oomycetes. In this study we used a genomics approach to gain a first insight into the transcriptome of S. parasitica. Results We generated 1510 expressed sequence tags (ESTs) from a mycelial cDNA library of S. parasitica. A total of 1279 consensus sequences corresponding to 525944 base pairs were assembled. About half of the unigenes showed similarities to known protein sequences or motifs. The S. parasitica sequences tended to be relatively divergent from Phytophthora sequences. Based on the sequence alignments of 18 conserved proteins, the average amino acid identity between S. parasitica and three Phytophthora species was 77% compared to 93% within Phytophthora. Several S. parasitica cDNAs, such as those with similarity to fungal type I cellulose binding domain proteins, PAN/Apple module proteins, glycosyl hydrolases, proteases, as well as serine and cysteine protease inhibitors, were predicted to encode secreted proteins that could function in virulence. Some of these cDNAs were more similar to fungal proteins than to other eukaryotic proteins confirming that oomycetes and fungi share some virulence components despite their evolutionary distance Conclusion We provide a first glimpse into the gene content of S. parasitica, a reemerging oomycete fish pathogen. These resources will greatly accelerate research on this important pathogen. The data is available online through the Oomycete Genomics Database [1]. PMID:16076392

Readthrough of SCN5A Nonsense Mutations p.R1623X and p.S1812X Questions Gene-therapy in Brugada Syndrome.

PubMed

Teng, Siyong; Huang, Jian; Gao, Zhan; Hao, Jie; Yang, Yuejin; Zhang, Shu; Pu, Jielin; Hui, Rutai; Wu, Yongjian; Fan, Zheng

2017-01-01

Nonsense mutation readthrough is used as a gene-specific treatment in some genetic diseases. The response to readthrough treatment is determined by the readthrough efficiency of various nonsense mutations. In this manuscript, we aimed to explore the harmful effects of nonsense mutation suppression. HEK293 cells were transfected with two SCN5A (encode cardiac Na+ channel) nonsense mutations, p.R1623X and p.S1812X. We applied two readthrough-enhancing methods (either aminoglycosides or a siRNA-targeting eukaryotic release factor eRF3a (a GTPase that binds eRF1)) to suppress these SCN5A nonsense mutations. When either of readthrough methods was used, the sodium channel proteins were examined by western blot and immunoblotting and recorded by whole cell patch-clamp to observe the functional characterization of the restored channels. Upon readthrough treatment, the sodium currents were restored to the mutant cDNAs. These mutations reduced full-length sodium channel protein levels, and the sodium currents were reduced to 3% of wild-type. The mutant cDNA sodium currents were increased to 30% of wild-type, and the fulllength proteins also increased. However, the functional characterization of these channels from cDNAs carrying p.R1623X and p.S1812X exhibited abnormal biophysical properties, including a negative shift in steady-state sodium channel inactivation, a positive shift in sodium channel activation and robust late sodium currents. The ramp test showed prolonged QT intervals. These results demonstrated that readthrough-enhancing methods effectively suppressed nonsense mutations in SCN5A and restored the expression of full-length channels. However, the restored channels may increase the risk of arrhythmia. Copyright© Bentham Science Publishers; For any queries, please email at epub@benthamscience.org.

Analysis of the arabinoxylan arabinofuranohydrolase gene family in barley does not support their involvement in the remodelling of endosperm cell walls during development.

PubMed

Laidlaw, Hunter K C; Lahnstein, Jelle; Burton, Rachel A; Fincher, Geoffrey B; Jobling, Stephen A

2012-05-01

Arabinoxylan arabinofuranohydrolases (AXAHs) are family GH51 enzymes that have been implicated in the removal of arabinofuranosyl residues from the (1,4)-β-xylan backbone of heteroxylans. Five genes encoding barley AXAHs range in size from 4.6 kb to 7.1 kb and each contains 16 introns. The barley HvAXAH genes map to chromosomes 2H, 4H, and 5H. A small cluster of three HvAXAH genes is located on chromosome 4H and there is evidence for gene duplication and the presence of pseudogenes in barley. The cDNAs corresponding to barley and wheat AXAH genes were cloned, and transcript levels of the genes were profiled across a range of tissues at different developmental stages. Two HvAXAH cDNAs that were successfully expressed in Nicotiana benthamiana leaves exhibited similar activities against 4-nitrophenyl α-L-arabinofuranoside, but HvAXAH2 activity was significantly higher against wheat flour arabinoxylan, compared with HvAXAH1. HvAXAH2 also displayed activity against (1,5)-α-L-arabinopentaose and debranched arabinan. Western blotting with an anti-HvAXAH antibody was used to define further the locations of the AXAH enzymes in developing barley grain, where high levels were detected in the outer layers of the grain but little or no protein was detected in the endosperm. The chromosomal locations of the genes do not correspond to any previously identified genomic regions shown to influence heteroxylan structure. The data are therefore consistent with a role for AXAH in depolymerizing arabinoxylans in maternal tissues during grain development, but do not provide compelling evidence for a role in remodelling arabinoxylans during endosperm or coleoptile development in barley as previously proposed.

Sugarcane biochar as an amendment for greenhouse growing media for the production of cucurbit seedlings

USDA-ARS?s Scientific Manuscript database

Louisiana sugarcane farmers in 2016 harvested 11.7 million mt millable sugarcane from 163,000 ha, producing 1.47 million mg of raw sugar and an estimated 3.5 million mt of bagasse. Even though Louisiana sugar mills use 80 to 90% of the bagasse for fuel production, another 350,000 to 700,000 mt of ba...

The Influence of Enterprise Diversification on Household Food Security among Small-Scale Sugarcane Farmers: A Case Study of Muhoroni Division, Nyando District, Kenya

ERIC Educational Resources Information Center

Muthoni Thuo, Caroline

2011-01-01

This paper examines the levels of household food security and the influence of enterprise diversification on household food security among small-scale sugarcane farmers in Muhoroni division, Nyando District, Kenya. A cross-sectional research design was used in this study. The population consisted of small-scale sugarcane farmers who grow sugarcane…

Influence of calcium oxide level and time of exposure to sugarcane on in vitro and in situ digestion kinetics

USDA-ARS?s Scientific Manuscript database

Experiments were carried out to evaluate, using in vitro and in situ techniques, the effects of three inclusion levels of calcium oxide (0, 5, and 10 g/kg of sugarcane fresh matter) and four exposure times (0, 24, 48, and 72 h) of sugarcane to calcium oxide on the chemical composition and digestive ...

Chronic consumption of distilled sugarcane spirit induces anxiolytic-like effects in mice

PubMed Central

Sena, Maria Clécia P; Nunes, Fabíola C; Stiebbe Salvadori, Mirian G S; Carvalho, Cleyton Charles D; Morais, Liana Clébia S L; Braga, Valdir A

2011-01-01

OBJECTIVE: Chronic ethanol consumption is a major public health problem throughout the world. We investigated the anxiolytic-like effects and the possible ever injury induced by the chronic consumption of ethanol or sugarcane spirit in mice. METHOD: Adult mice were exposed to a two-bottle free-choice paradigm for 6 weeks. The mice in Group A (n  =  16) had access to sugarcane spirit + distilled water, the mice in Group B (n  =  15) had access to ethanol + distilled water, and the mice in Group C (control, n  =  14) had access to distilled water + distilled water. The ethanol content in the beverages offered to Groups A and B was 2% for the first week, 5% for the second week and 10% for the remaining four weeks. At the end of the experimental period, the mice were evaluated using the elevated-plus maze and the hole-board test to assess their anxiety-related behaviors. We also determined the serum aspartate aminotransferase and alanine aminotransferase levels. RESULTS: In the elevated-plus maze, the time spent in the open arms was increased in the mice exposed to chronic ethanol (32 ± 8 vs. 7 ± 2 s, n  =  9) or sugarcane spirit (36 ± 9 vs. 7 ± 2 s, n  =  9) compared to the controls. In the hole-board test, the mice exposed to ethanol or sugarcane spirit displayed increases in their head-dipping frequency (16 ± 1 for the control group, 27 ± 2 for the ethanol group, and 31 ± 3 for the sugarcane-spirit group; n  =  9 for each group). In addition, the mice exposed to sugarcane spirit displayed an increase in the aspartate aminotransferase / alanine aminotransferase ratio compared to the ethanol group (1.29 ± 0.17 for the control group and 2.67 ± 0.17 for the sugarcane spirit group; n  =  8 for each group). CONCLUSION: The chronic consumption of sugarcane-spirit produces liver injury and anxiolytic-like effects and the possible liver injury in mice. PMID:21789394

CfPDIP1, a novel secreted protein of Colletotrichum falcatum, elicits defense responses in sugarcane and triggers hypersensitive response in tobacco.

PubMed

Ashwin, N M R; Barnabas, Leonard; Ramesh Sundar, Amalraj; Malathi, Palaniyandi; Viswanathan, Rasappa; Masi, Antonio; Agrawal, Ganesh Kumar; Rakwal, Randeep

2018-07-01

Colletotrichum falcatum, a hemibiotrophic fungal pathogen, causes one of the major devastating diseases of sugarcane-red rot. C. falcatum secretes a plethora of molecular signatures that might play a crucial role during its interaction with sugarcane. Here, we report the purification and characterization of a novel secreted protein of C. falcatum that elicits defense responses in sugarcane and triggers hypersensitive response (HR) in tobacco. The novel protein purified from the culture filtrate of C. falcatum was identified by MALDI TOF/TOF MS and designated as C. falcatum plant defense-inducing protein 1 (CfPDIP1). Temporal transcriptional profiling showed that the level of CfPDIP1 expression was greater in incompatible interaction than the compatible interaction until 120 h post-inoculation (hpi). EffectorP, an in silico tool, has predicted CfPDIP1 as a potential effector. Functional characterization of full length and two other domain deletional variants (CfPDIP1ΔN1-21 and CfPDIP1ΔN1-45) of recombinant CfPDIP1 proteins has indicated that CfPDIP1ΔN1-21 variant elicited rapid alkalinization and induced a relatively higher production of hydrogen peroxide (H 2 O 2 ) in sugarcane suspension culture. However, in Nicotiana tabacum, all the three forms of recombinant CfPDIP1 proteins triggered HR along with the induction of H 2 O 2 production and callose deposition. Further characterization using detached leaf bioassay in sugarcane revealed that foliar priming with CfPDIP1∆1-21 has suppressed the extent of lesion development, even though the co-infiltration of CfPDIP1∆1-21 with C. falcatum on unprimed leaves increased the extent of lesion development than control. Besides, the foliar priming has induced systemic expression of major defense-related genes with the concomitant reduction of pathogen biomass and thereby suppression of red rot severity in sugarcane. Comprehensively, the results have suggested that the novel protein, CfPDIP1, has the potential to trigger a multitude of defense responses in sugarcane and tobacco upon priming and might play a potential role during plant-pathogen interactions.

Production of sugarcane bagasse-based activated carbon for formaldehyde gas removal from potted plants exposure chamber.

PubMed

Mohamed, Elham F; El-Hashemy, Mohammed A; Abdel-Latif, Nasser M; Shetaya, Waleed H

2015-12-01

Agricultural wastes such as rice straw, sugar beet, and sugarcane bagasse have become a critical environmental issue due to growing agriculture demand. This study aimed to investigate the valorization possibility of sugarcane bagasse waste for activated carbon preparation. It also aimed to fully characterize the prepared activated carbon (BET surface area) via scanning electron microscope (SEM) and in terms of surface functional groups to give a basic understanding of its structure and to study the adsorption capacity of the sugarcane bagasse-based activated carbon using aqueous methylene blue (MB). The second main objective was to evaluate the performance of sugarcane bagasse-based activated carbon for indoor volatile organic compounds removal using the formaldehyde gas (HCHO) as reference model in two potted plants chambers. The first chamber was labeled the polluted chamber (containing formaldehyde gas without activated carbon) and the second was taken as the treated chamber (containing formaldehyde gas with activated carbon). The results indicated that the sugarcane bagasse-based activated carbon has a moderate BET surface area (557 m2/g) with total mesoporous volume and microporous volume of 0.310 and 0.273 cm3/g, respectively. The prepared activated carbon had remarkable adsorption capacity for MB. Formaldehyde removal rate was then found to be more than 67% in the treated chamber with the sugarcane bagasse-based activated carbon. The plants' responses for this application as dry weight, chlorophyll contents, and protein concentration were also investigated. Preparation of activated carbon from sugarcane bagasse (SCBAC) is a promising approach to produce cheap and efficient adsorbent for gas pollutants removal. It may be also a solution for the agricultural wastes problems in big cities, particularly in Egypt. MB adsorption tests suggest that the SCBAC have high adsorption capacity. Formaldehyde gas removal in the plant chambers indicates that the SCBAC have potential to recover volatile gases. The results confirmed that the activated carbon produced from sugarcane bagasse waste raw materials can be used as an applicable adsorbent for treating a variety of gas pollutants from the indoor environment.

Sugarcane Initial Growth with Vinasse Application in Latosol under Gradual Aluminum Stress

NASA Astrophysics Data System (ADS)

Marques Viglio, Larissa; Leal Varanda, Leticia; Soares, Marcio Roberto; Casagrande, José Carlos

2015-04-01

One of the strategies for overcoming the high acidity of soils and the consequent toxicity of aluminum (Al) is based on the use of varieties adapted to these conditions. In Brazil, the application of vinasse is routine practice in the cultivation of sugarcane due to its fertilizing effect, mainly because of high potassium content. However, the vinasse may also attenuate the toxic effects of Al in the soil by forming complexes with low molecular weight organic acids providing greater depth of the root of sugarcane. The aim of this work was to evaluate the effect of vinasse on the initial growth of three cultivars of sugarcane (RB855453, RB966928 and RB867515), as well as its influence on root depth in a Dystrophic Red-Yellow Latosol (Typic Hapludox) with gradient of saturation by Al. The experiment was conducted in a greenhouse, in totally randomized design with factorial arrangement and three replications. Seedlings of sugarcane were transplanted to PVC columns 0.8 m high, built by stacking four rings (0.2 m high), filled with soil samples, which offered an increasing gradient of saturation by Al (m%) at depth (0-0.2 m (m% = 0,7); 0.2-0.4 m (m% = 7,9); 0.4-0.6 m (m %= 40.8); 0.6-0.8 m (m%= 62.6)). The collection of the experiment was conducted 120 days after planting, with the determination of the stalk diameter (DC), plant height (ALT), leaf nutrient content, dry matter of the aerial part (MSPA) and dry matter of the root system (MSSR). Cultivars of sugarcane and the application of vinasse had effect on DC and the MSSR. Cultivar RB867515 showed higher DC than in other cultivars, with 20.8 mm. The increase of MSSR by sugarcane cultivars varied due to depth. There were no effects of sugarcane cultivars and vinasse application in MSPA. The vinasse application resulted in plants with higher ALT. With the exception of the foliar content of Fe, the N, Ca, Mg, S and Mn content were below those considered appropriate for sugarcane. Unlike other cultivars, the application of vinasse provided adequate foliar content of P for RB867515.

Fusion of the Human Gene for the Polyubiquitination Coeffector UEV1 with Kua, a Newly Identified Gene

PubMed Central

Thomson, Timothy M.; Lozano, Juan José; Loukili, Noureddine; Carrió, Roberto; Serras, Florenci; Cormand, Bru; Valeri, Marta; Díaz, Víctor M.; Abril, Josep; Burset, Moisés; Merino, Jesús; Macaya, Alfons; Corominas, Montserrat; Guigó, Roderic

2000-01-01

UEV proteins are enzymatically inactive variants of the E2 ubiquitin-conjugating enzymes that regulate noncanonical elongation of ubiquitin chains. In Saccharomyces cerevisiae, UEV is part of the RAD6-mediated error-free DNA repair pathway. In mammalian cells, UEV proteins can modulate c-FOS transcription and the G2-M transition of the cell cycle. Here we show that the UEV genes from phylogenetically distant organisms present a remarkable conservation in their exon–intron structure. We also show that the human UEV1 gene is fused with the previously unknown gene Kua. In Caenorhabditis elegans and Drosophila melanogaster, Kua and UEV are in separated loci, and are expressed as independent transcripts and proteins. In humans, Kua and UEV1 are adjacent genes, expressed either as separate transcripts encoding independent Kua and UEV1 proteins, or as a hybrid Kua–UEV transcript, encoding a two-domain protein. Kua proteins represent a novel class of conserved proteins with juxtamembrane histidine-rich motifs. Experiments with epitope-tagged proteins show that UEV1A is a nuclear protein, whereas both Kua and Kua–UEV localize to cytoplasmic structures, indicating that the Kua domain determines the cytoplasmic localization of Kua–UEV. Therefore, the addition of a Kua domain to UEV in the fused Kua–UEV protein confers new biological properties to this regulator of variant polyubiquitination. [Kua cDNAs isolated by RT-PCR and described in this paper have been deposited in the GenBank data library under accession nos. AF1155120 (H. sapiens) and AF152361 (D. melanogaster). Genomic clones containing UEV genes: S. cerevisiae, YGL087c (accession no. Z72609); S. pombe, c338 (accession no. AL023781); P. falciparum, MAL3P2 (accession no. AL034558); A. thaliana, F26F24 (accession no. AC005292); C. elegans, F39B2 (accession no. Z92834); D. melanogaster, AC014908; and H. sapiens, 1185N5 (accession no. AL034423). Accession numbers for Kua cDNAs in GenBank dbEST: M. musculus, AA7853; T. cruzi, AI612534. Other Kua-containing sequences: A. thaliana genomic clones F10M23 (accession no. AL035440), F19K23 (accession no. AC000375), and T20K9 (accession no. AC004786).] PMID:11076860

Cloning of stanniocalcin (STC) cDNAs of divergent teleost species: Monomeric STC supports monophyly of the ancient teleosts, the osteoglossomorphs.

PubMed

Amemiya, Yutaka; Irwin, David M; Youson, John H

2006-10-01

Molecular cloning of teleost stanniocalcin (STC) cDNAs was undertaken in two species of order Osteoglossiformes of subdivision Osteoglossomorpha and one species of each of orders Cypriniformes and Perciformes within the subdivision Euteleostei. The elephantnose (Gnathonemus petersii) and the butterflyfish (Pantadon buchholzi) are basal teleosts in different osteoglossiforme suborders yet their 218 amino acid (aa) mature hormones, from prehormones of 249 and 251aa, respectively, have only 10 cysteine residues. A substitution for cysteine at the intermonomeric disulfide linkage site, implies that their STCs exist as monomeric peptides, as is the case with STC from another osteoglossormorph, arawana [Amemiya, Y., Marra, L.E., Reyhani, N., Youson, J.H., 2002. Stanniocalcin from an ancient teleost: a monomeric form of the hormone and a possible extracorpuscular distribution. Mol. Cell. Endocrinol. 188, 141-150]. The STC cDNA of the generalized teleost and cyprinid, the white sucker (Catostomus commersoni), encodes a prehormone of 249aa with a signal peptide of 31aa and a mature protein of 218aa that possesses 11 cysteine residues. The latter feature is consistent with a previous analysis that white sucker mature STC is a glycosylated, homodimeric peptide [Amemiya, Y., Marra, L.E., Reyhani, N., Youson, J.H., 2002. Stanniocalcin from an ancient teleost: a monomeric form of the hormone and a possible extracorpuscular distribution. Mol. Cell. Endocrinol. 188, 141-150]. An open reading frame of the STC cDNA of the derived teleost and perciforme, the smallmouth bass (Micropterus dolomieui), encodes a prehormone of 255aa with a signal peptide of 33aa and a mature protein of 222aa. The position of the 11 cysteines in smallmouth bass STC suggests that it exists as a homodimeric peptide. A phylogenetic analysis, using the new STC-1 amino acid sequences and those in the gene data base provided strong support for monophyly of the Osteoglossomorpha and indicated, with positioning of white sucker and smallmouth bass, that this molecule has some utility as a taxonomic marker. This analysis also suggested that two STC-1 gene sequences exist in multiple fish genomes, and that they may be a product of the fish-specific genome duplication. The mutation in the osteoglossomorph STC likely occurred after the appearance of the first teleosts and before movement of the tectonic plates.

Defense-related proteins involved in sugarcane responses to biotic stress

PubMed Central

Souza, Thais P.; Dias, Renata O.; Silva-Filho, Marcio C.

2017-01-01

Abstract Sugarcane is one of the most important agricultural crops in the world. However, pathogen infection and herbivore attack cause constant losses in yield. Plants respond to pathogen infection by inducing the expression of several protein types, such as glucanases, chitinases, thaumatins, peptidase inhibitors, defensins, catalases and glycoproteins. Proteins induced by pathogenesis are directly or indirectly involved in plant defense, leading to pathogen death or inducing other plant defense responses. Several of these proteins are induced in sugarcane by different pathogens or insects and have antifungal or insecticidal activity. In this review, defense-related proteins in sugarcane are described, with their putative mechanisms of action, pathogen targets and biotechnological perspectives. PMID:28222203

Nitrous oxide emissions from sugarcane straw left on the soil surface in Brazil

NASA Astrophysics Data System (ADS)

Galdos, M. V.; Cerri, C. E.; Carvalho, J. L.; Cerri, C. C.

2012-12-01

In Brazil, the largest exporter of ethanol from sugarcane in the world, burning the dry leaves and tops in order to facilitate the harvest and transportation of the stalks is still a common practice. Burning plant residues causes emissions of greenhouse gases (GHGs) such as CO2, CH4 and N2O, besides the release of charcoal particles into the atmosphere. Due to a combination of pressure from changes in the public opinion and economical reasons, in Brazil sugarcane harvest is changing from a burned into an unburned system. Since manual harvest of sugarcane without burning is not economically feasible, mechanical harvesters have been developed that can take the stalk and leave the residues on the field, forming a mulch, in a system called green cane management. It is expected that 80% of the cane harvested in the main producing regions in Brazil will be harvested without burning by 2014. The conversion from burning sugarcane to green management of sugarcane will have impacts on the biogeochemical cycling of carbon and nitrogen in the plant soil system. The green cane management results in the deposition of large amounts of plant litter on the soil surface after harvest, ranging from 10 to 20 tons per hectare, which impact the whole production process of sugarcane, influencing yields, fertilizer management and application, soil erosion, soil organic matter dynamics as well as greenhouse gas emissions (CO2, N2O, CH4). From a GHG perspective, the conservation of sugarcane residues prevents emissions from the burning process, may promote carbon sequestration in soils and releases nitrogen during the decomposition process replacing the need for, and GHG emissions from, fossil fuel based nitrogen fertilizer sources. Measurements of soil C and N stocks and associated greenhouse gas emissions from the burned and unburned sugarcane systems and in the sugarcane expansion areas are still scarce. Therefore, the main objective of this work was to quantify the nitrous oxide emissions from the sugarcane straw left on the soil surface in Brazil. To do so, we evaluated three rates of sugarcane straw,1/3, 2/3 and 3/3 of the total amount left on the field, which corresponds to 15,226 kg of dry matter per hectare. Nitrous oxide fluxes were measured using a two-piece static chamber (45cm x 70cm) about once a week in the period of August 2010 till July 2012. Gas samples were returned to the laboratory and analyzed using gas chromatography. There were no significant difference between straw doses and the N2O emission rate ranged from -45 to 120 μg N-N2O m-2 h-1. Those emission values are relatively low, which might be related to the low precipitation and soil water content in the first few months after deposition of straw on the field, since the harvest takes place in the dry season in this region. The present text is a piece of contribution in the effort to develop an accurate 'field-to-wheels' assessment of sugarcane-derived ethanol production in Brazil. N2O from straw decomposition is of key relevance, given that the GHG offset value is one of the primary environmental indicators of biofuel product quality.

Growth and metal uptake of energy sugarcane (Saccharum spp.) in different metal mine tailings with soil amendments.

PubMed

Zhang, Xin; Zhu, Yongguan; Zhang, Yuebin; Liu, Yunxia; Liu, Shaochun; Guo, Jiawen; Li, Rudan; Wu, Songlin; Chen, Baodong

2014-05-01

A pot experiment was conducted to investigate the feasibility of growing energy sugarcane (Saccharum spp.) in three different metal mine tailings (Cu, Sn and Pb/Zn tailings) amended with uncontaminated soil at different mixing ratios. The results indicated that sugarcane was highly tolerant to tailing environments. Amendments of 20% soil to Sn tailings and 30% soil to Cu tailings could increase the biomass of cane-stem for use as the raw material for bioethanol production. Heavy metals were mostly retained in roots, which indicated that sugarcane was useful for the stabilization of the tailings. Bagasse and juice, as the most valuable parts to produce bioethanol, only accounted for 0.6%-3% and 0.6%-7% of the total metal content. Our study supported the potential use of sugarcane for tailing phytostabilization and bioenergy production. Copyright © 2014 The Research Centre for Eco-Environmental Sciences, Chinese Academy of Sciences. Published by Elsevier B.V. All rights reserved.

Improvement of gaseous energy recovery from sugarcane bagasse by dark fermentation followed by biomethanation process.

PubMed

Kumari, Sinu; Das, Debabrata

2015-10-01

The aim of the present study was to enhance the gaseous energy recovery from sugarcane bagasse. The two stage (biohydrogen and biomethanation) batch process was considered under mesophilic condition. Alkali pretreatment (ALP) was used to remove lignin from sugarcane bagasse. This enhanced the enzymatic digestibility of bagasse to a great extent. The maximum lignin removal of 60% w/w was achieved at 0.25 N NaOH concentration (50°C, 30 min). The enzymatic hydrolysis efficiency was increased to about 2.6-folds with alkali pretreated sugarcane bagasse as compared to untreated one. The maximum hydrogen and methane yields from the treated sugarcane bagasse by biohydrogen and biomethanation processes were 93.4 mL/g-VS and 221.8 mL/g-VS respectively. This process resulted in significant increase in energy conversion efficiency (44.8%) as compared to single stage hydrogen production process (5.4%). Copyright © 2015 Elsevier Ltd. All rights reserved.

Butanol production in a first-generation Brazilian sugarcane biorefinery: technical aspects and economics of greenfield projects.

PubMed

Mariano, Adriano Pinto; Dias, Marina O S; Junqueira, Tassia L; Cunha, Marcelo P; Bonomi, Antonio; Filho, Rubens Maciel

2013-05-01

The techno-economics of greenfield projects of a first-generation sugarcane biorefinery aimed to produce ethanol, sugar, power, and n-butanol was conducted taking into account different butanol fermentation technologies (regular microorganism and mutant strain with improved butanol yield) and market scenarios (chemicals and automotive fuel). The complete sugarcane biorefinery with the batch acetone-butanol-ethanol (ABE) fermentation process was simulated using Aspen Plus®. The biorefinery was designed to process 2 million tonne sugarcane per year and utilize 25%, 50%, and 25% of the available sugarcane juice to produce sugar, ethanol, and butanol, respectively. The investment on a biorefinery with butanol production showed to be more attractive [14.8% IRR, P(IRR>12%)=0.99] than the conventional 50:50 (ethanol:sugar) annexed plant [13.3% IRR, P(IRR>12%)=0.80] only in the case butanol is produced by an improved microorganism and traded as a chemical. Copyright © 2012 Elsevier Ltd. All rights reserved.

Air Emissions and Health Benefits from Using Sugarcane Waste as a Cellulosic Ethanol Feedstock

NASA Astrophysics Data System (ADS)

Tsao, C.; Campbell, E.; Chen, Y.; Carmichael, G.; Mena-Carrasco, M.; Spak, S.

2010-12-01

Brazil, as the largest ethanol exporter in the world, faces rapid expansion of ethanol production due to the increase of global biofuels demand. Current production of Brazilian sugarcane ethanol causes significant air emissions mainly from the open burning phase of agriculture wastes (i.e. sugarcane straws and leaves) resulting in potential health impacts. One possible measure to avoid undesired burning practices is to increase the utilization of unburned sugarcane residues as a feedstock for cellulosic ethanol. To explore the benefits of this substitution, here we first apply a bottom-up approach combining agronomic data and life-cycle models to investigate spatially and temporally explicit emissions from sugarcane waste burning. We further quantify the health benefits from preventing burning practices using the CMAQ regional air quality model and the BenMAP health benefit analysis tool adapted for Brazilian applications. Furthermore, the health impacts will be converted into monetary values which provide policymakers useful information for the development of cellulosic ethanol.

Reducing dissolved inorganic nitrogen in surface runoff water from sugarcane production systems.

PubMed

Webster, A J; Bartley, R; Armour, J D; Brodie, J E; Thorburn, P J

2012-01-01

Nitrogen (N) lost from farms, especially as the highly bioavailable dissolved inorganic form, may be damaging Australia's Great Barrier Reef (GBR). As sugarcane is the dominant cropping system in GBR catchments, its N management practises are coming under increasing scrutiny. This study measured dissolved inorganic N lost in surface runoff water and sugarcane productivity over 3 years. The experiment compared the conventional fertiliser N application rate to sugarcane (average 180kg N/ha/year) and a rate based on replacing N exported in the previous crop (average 94kg N/ha/year). Dissolved inorganic N losses in surface water were 72%, 48% and 66% lower in the three monitored years in the reduced N fertiliser treatment. There was no significant difference in sugarcane yield between the two fertiliser N treatments, nor any treatment difference in soil mineral N - both of these results are indicators of the sustainability of the lower fertiliser N applications. Copyright © 2012 Elsevier Ltd. All rights reserved.

Polyphasic characterization of Gluconacetobacter diazotrophicus isolates obtained from different sugarcane varieties

PubMed Central

Guedes, Helma V.; dos Santos, Samuel T.; Perin, Liamara; Teixeira, Kátia R. dos S.; Reis, Veronica M.; Baldani, José I.

2008-01-01

A polyphasic approach was applied to characterize 35 G. diazotrophicus isolates obtained from sugarcane varieties cultivated in Brazil. The isolates were analyzed by phenotypic (use of different carbon sources) and genotypic tests (ARDRA and RISA–RFLP techniques). Variability among the isolates was observed in relation to the carbon source use preference. Glucose and sucrose were used by all isolates in contrast to myo-inositol, galactose and ribose that were not metabolized. The results of the analysis showed the presence of two groups clustered at 68% of similarity. The genetic distance was higher when RISA-RFLP analysis was used. Analysis of 16S rDNA sequences from isolates showed that all of them belonged to the G. diazotrophicus species. Neither effect of the plant part nor sugarcane variety was observed during the cluster analysis. The observed metabolic and genetic variability will be helpful during the strain selection studies for sugarcane inoculation in association with sugarcane breeding programs. PMID:24031296

A proposed model for the flowering signaling pathway of sugarcane under photoperiodic control.

PubMed

Coelho, C P; Costa Netto, A P; Colasanti, J; Chalfun-Júnior, A

2013-04-25

Molecular analysis of floral induction in Arabidopsis has identified several flowering time genes related to 4 response networks defined by the autonomous, gibberellin, photoperiod, and vernalization pathways. Although grass flowering processes include ancestral functions shared by both mono- and dicots, they have developed their own mechanisms to transmit floral induction signals. Despite its high production capacity and its important role in biofuel production, almost no information is available about the flowering process in sugarcane. We searched the Sugarcane Expressed Sequence Tags database to look for elements of the flowering signaling pathway under photoperiodic control. Sequences showing significant similarity to flowering time genes of other species were clustered, annotated, and analyzed for conserved domains. Multiple alignments comparing the sequences found in the sugarcane database and those from other species were performed and their phylogenetic relationship assessed using the MEGA 4.0 software. Electronic Northerns were run with Cluster and TreeView programs, allowing us to identify putative members of the photoperiod-controlled flowering pathway of sugarcane.

Sugarcane and pine biochar as amendments for greenhouse growing media for the production of bean (Phaseolus vulgaris L.) seedlings

USDA-ARS?s Scientific Manuscript database

Louisiana sugarcane farmers in 2016 harvested 11.7 million Mg of millable sugarcane from 163,000 ha, producing 1.47 million Mg of raw sugar and an estimated 3.5 million Mg of bagasse. Even though Louisiana sugar mills use 80% to 90% of the bagasse for fuel production, another 350,000 to 700,000 Mg o...

Estimating sugarcane yield potential using an in-season determination of normalized difference vegetative index.

PubMed

Lofton, Josh; Tubana, Brenda S; Kanke, Yumiko; Teboh, Jasper; Viator, Howard; Dalen, Marilyn

2012-01-01

Estimating crop yield using remote sensing techniques has proven to be successful. However, sugarcane possesses unique characteristics; such as, a multi-year cropping cycle and plant height-limiting for midseason fertilizer application timing. Our study objective was to determine if sugarcane yield potential could be estimated using an in-season estimation of normalized difference vegetative index (NDVI). Sensor readings were taken using the GreenSeeker® handheld sensor from 2008 to 2011 in St. Gabriel and Jeanerette, LA, USA. In-season estimates of yield (INSEY) values were calculated by dividing NDVI by thermal variables. Optimum timing for estimating sugarcane yield was between 601-750 GDD. In-season estimated yield values improved the yield potential (YP) model compared to using NDVI. Generally, INSEY value showed a positive exponential relationship with yield (r(2) values 0.48 and 0.42 for cane tonnage and sugar yield, respectively). When models were separated based on canopy structure there was an increase the strength of the relationship for the erectophile varieties (r(2) 0.53 and 0.47 for cane tonnage and sugar yield, respectively); however, the model for planophile varieties weakened slightly. Results of this study indicate using an INSEY value for predicting sugarcane yield shows potential of being a valuable management tool for sugarcane producers in Louisiana.

Differential expression profiles and pathways of genes in sugarcane leaf at elongation stage in response to drought stress

PubMed Central

Li, Changning; Nong, Qian; Solanki, Manoj Kumar; Liang, Qiang; Xie, Jinlan; Liu, Xiaoyan; Li, Yijie; Wang, Weizan; Yang, Litao; Li, Yangrui

2016-01-01

Water stress causes considerable yield losses in sugarcane. To investigate differentially expressed genes under water stress, a pot experiment was performed with the sugarcane variety GT21 at three water-deficit levels (mild, moderate, and severe) during the elongation stage and gene expression was analyzed using microarray technology. Physiological parameters of sugarcane showed significant alterations in response to drought stress. Based on the expression profile of 15,593 sugarcane genes, 1,501 (9.6%) genes were differentially expressed under different water-level treatments; 821 genes were upregulated and 680 genes were downregulated. A gene similarity analysis showed that approximately 62.6% of the differentially expressed genes shared homology with functional proteins. In a Gene Ontology (GO) analysis, 901 differentially expressed genes were assigned to 36 GO categories. Moreover, 325 differentially expressed genes were classified into 101 pathway categories involved in various processes, such as the biosynthesis of secondary metabolites, ribosomes, carbon metabolism, etc. In addition, some unannotated genes were detected; these may provide a basis for studies of water-deficit tolerance. The reliability of the observed expression patterns was confirmed by RT-PCR. The results of this study may help identify useful genes for improving drought tolerance in sugarcane. PMID:27170459

Biplot evaluation of test environments and identification of mega-environment for sugarcane cultivars in China

PubMed Central

Luo, Jun; Pan, Yong-Bao; Que, Youxiong; Zhang, Hua; Grisham, Michael Paul; Xu, Liping

2015-01-01

Test environments and classification of regional ecological zones into mega environments are the two key components in regional testing of sugarcane cultivars. This study aims to provide the theoretical basis for test environment evaluation and ecological zone division for sugarcane cultivars. In the present study, sugarcane yield data from a three-year nationwide field trial involving 21 cultivars and 14 pilot test locations were analysed using both analysis of variance (ANOVA) and heritability adjusted-genotype main effect plus genotype-environment interaction (HA-GGE) biplot. The results showed that among the interactive factors, the GE interaction had the greatest impact, while the genotype and year interaction showed the lowest impact. Kaiyuan, Lincang and Baoshan of Yunnan, Zhangzhou and Fuzhou of Fujian, and Hechi, Liuzhou and Chongzuo of Guangxi, and Lingao of Hainan were ideal test environments with a demonstrated high efficiency in selecting new cultivars with a wide adaptability, whereas Baise of Guangxi was not. Based on HA-GGE biplot analysis, there are three ecological sugarcane production zones in China, the Southern China Inland Zone, the Southwestern Plateau Zone, and the Southern Coastal Zone. The HA-GGE biplot analysis here presents the ideal test environments and also identifies the mega-environment for sugarcane cultivars in China. PMID:26489689

RNA Interference of Endochitinases in the Sugarcane Endophyte Trichoderma virens 223 Reduces Its Fitness as a Biocontrol Agent of Pineapple Disease

PubMed Central

Romão-Dumaresq, Aline S.; de Araújo, Welington Luiz; Talbot, Nicholas J.; Thornton, Christopher R.

2012-01-01

The sugarcane root endophyte Trichoderma virens 223 holds enormous potential as a sustainable alternative to chemical pesticides in the control of sugarcane diseases. Its efficacy as a biocontrol agent is thought to be associated with its production of chitinase enzymes, including N-acetyl-ß-D-glucosaminidases, chitobiosidases and endochitinases. We used targeted gene deletion and RNA-dependent gene silencing strategies to disrupt N-acetyl-ß-D-glucosaminidase and endochitinase activities of the fungus, and to determine their roles in the biocontrol of soil-borne plant pathogens. The loss of N-acetyl-ß-D-glucosaminidase activities was dispensable for biocontrol of the plurivorous damping-off pathogens Rhizoctonia solani and Sclerotinia sclerotiorum, and of the sugarcane pathogen Ceratocystis paradoxa, the causal agent of pineapple disease. Similarly, suppression of endochitinase activities had no effect on R. solani and S. sclerotiorum disease control, but had a pronounced effect on the ability of T. virens 223 to control pineapple disease. Our work demonstrates a critical requirement for T. virens 223 endochitinase activity in the biocontrol of C. paradoxa sugarcane disease, but not for general antagonism of other soil pathogens. This may reflect its lifestyle as a sugarcane root endophyte. PMID:23110120

A pilot field evaluation on heat stress in sugarcane workers in Costa Rica: What to do next?

PubMed Central

Crowe, Jennifer; van Wendel de Joode, Berna; Wesseling, Catharina

2009-01-01

Background Climate change is producing major impacts including increasing temperatures in tropical countries, like Costa Rica, where the sugarcane industry employs thousands of workers who are exposed to extreme heat. Objectives This article outlines a pilot qualitative evaluation of working conditions and heat in the sugarcane industry. Design A literature review, direct observations and exploratory interviews with workers were conducted to reach a preliminary understanding of the dimensions of heat-related health issues in the sugarcane industry, as a basis for the design of future studies. Results The industry employs temporary workers from Nicaragua and Costa Rica as well as year-round employees. Temporary employees work 12-hour shifts during the harvest and processing (‘zafra’) season. In many cases, sugarcane field workers are required to carry their own water and often have no access to shade. Sugar mill workers are exposed to different levels of heat stress depending upon their job tasks, with the most intense heat and workload experienced by the oven (‘caldera’) cleaners. Conclusions Research is needed to achieve better understanding of the multiple factors driving and interacting with heat exposures in the sugarcane industry in order to improve the health and safety of workers while maintaining worker productivity. PMID:20052430

Biplot evaluation of test environments and identification of mega-environment for sugarcane cultivars in China.

PubMed

Luo, Jun; Pan, Yong-Bao; Que, Youxiong; Zhang, Hua; Grisham, Michael Paul; Xu, Liping

2015-10-22

Test environments and classification of regional ecological zones into mega environments are the two key components in regional testing of sugarcane cultivars. This study aims to provide the theoretical basis for test environment evaluation and ecological zone division for sugarcane cultivars. In the present study, sugarcane yield data from a three-year nationwide field trial involving 21 cultivars and 14 pilot test locations were analysed using both analysis of variance (ANOVA) and heritability adjusted-genotype main effect plus genotype-environment interaction (HA-GGE) biplot. The results showed that among the interactive factors, the GE interaction had the greatest impact, while the genotype and year interaction showed the lowest impact. Kaiyuan, Lincang and Baoshan of Yunnan, Zhangzhou and Fuzhou of Fujian, and Hechi, Liuzhou and Chongzuo of Guangxi, and Lingao of Hainan were ideal test environments with a demonstrated high efficiency in selecting new cultivars with a wide adaptability, whereas Baise of Guangxi was not. Based on HA-GGE biplot analysis, there are three ecological sugarcane production zones in China, the Southern China Inland Zone, the Southwestern Plateau Zone, and the Southern Coastal Zone. The HA-GGE biplot analysis here presents the ideal test environments and also identifies the mega-environment for sugarcane cultivars in China.

Nitrate Paradigm Does Not Hold Up for Sugarcane

PubMed Central

Robinson, Nicole; Brackin, Richard; Vinall, Kerry; Soper, Fiona; Holst, Jirko; Gamage, Harshi; Paungfoo-Lonhienne, Chanyarat; Rennenberg, Heinz; Lakshmanan, Prakash; Schmidt, Susanne

2011-01-01

Modern agriculture is based on the notion that nitrate is the main source of nitrogen (N) for crops, but nitrate is also the most mobile form of N and easily lost from soil. Efficient acquisition of nitrate by crops is therefore a prerequisite for avoiding off-site N pollution. Sugarcane is considered the most suitable tropical crop for biofuel production, but surprisingly high N fertilizer applications in main producer countries raise doubt about the sustainability of production and are at odds with a carbon-based crop. Examining reasons for the inefficient use of N fertilizer, we hypothesized that sugarcane resembles other giant tropical grasses which inhibit the production of nitrate in soil and differ from related grain crops with a confirmed ability to use nitrate. The results of our study support the hypothesis that N-replete sugarcane and ancestral species in the Andropogoneae supertribe strongly prefer ammonium over nitrate. Sugarcane differs from grain crops, sorghum and maize, which acquired both N sources equally well, while giant grass, Erianthus, displayed an intermediate ability to use nitrate. We conclude that discrimination against nitrate and a low capacity to store nitrate in shoots prevents commercial sugarcane varieties from taking advantage of the high nitrate concentrations in fertilized soils in the first three months of the growing season, leaving nitrate vulnerable to loss. Our study addresses a major caveat of sugarcane production and affords a strong basis for improvement through breeding cultivars with enhanced capacity to use nitrate as well as through agronomic measures that reduce nitrification in soil. PMID:21552564

Burnt sugarcane harvesting is associated with rhinitis symptoms and inflammatory markers.

PubMed

Trevisan, Iara Buriola; Santos, Ubiratan de Paula; Leite, Marceli Rocha; Ferreira, Aline Duarte; Silva, Bruna Spolador de Alencar; Freire, Ana Paula Coelho Figueira; Brigida, Gabriel Faustino Santa; Ramos, Ercy Mara Cipulo; Ramos, Dionei

2018-04-05

Burnt sugarcane harvesting requires intense physical exertion in an environment with high temperatures and exposure to particulate matter. To evaluate the effects of burnt sugarcane harvesting on rhinitis symptoms and inflammatory markers in sugarcane workers. 32 male sugarcane workers were evaluated with questionnaire for rhinitis symptoms, and for inflammatory markers on peripheral blood and nasal lavage, in the non-harvesting, and 3 and 6 months into the sugarcane harvesting period. Weather data and particulate matter fine concentrations were measured in the same day. The particulate matter concentrations in sugarcane harvesting were 27 (23-33μg/m 3 ), 112 (96-122μg/m 3 ), and 63 (17-263μg/m 3 ); 24h temperatures were 32.6 (25.4-37.4°C), 32.3 (26.7-36.7°C) and 29.7 (24.1-34.0°C) and relative humidities were 45.4 (35.0-59.7%), 47.9 (39.1-63.0%), and 59.9 (34.7-63.2%) in the non-harvesting period, three and 6 months of the harvesting period. The age was 37.4±10.9 years. The prevalence of rhinitis symptoms was significantly higher at 3 months of the harvesting period (53.4%), compared to non-harvesting period (26.7%; p=0.039) and at 6 months into the harvesting period (20%; p=0.006). Concentrations of interleukin 6 (IL-6) in nasal lavage increased after 3 months of the harvesting period compared to the non-harvesting period (p=0.012). The presence of rhinitis symptoms, after 3 months of the harvesting period, was directly associated with blood eosinophils and inversely associated with neutrophils. After 3 months of work in burnt sugarcane harvesting the prevalence of rhinitis symptoms and IL-6 in nasal lavage increased. Furthermore, eosinophil counts were directly associated with the rhinitis symptoms in the period of higher concentration of particulate matter. Copyright © 2018. Published by Elsevier Editora Ltda.

Landsat-Based Detection and Severity Analysis of Burned Sugarcane Plots in Tarlac, Philippines Using Differenced Normalized Burn Ratio (dNBR)

NASA Astrophysics Data System (ADS)

Baloloy, A. B.; Blanco, A. C.; Gana, B. S.; Sta. Ana, R. C.; Olalia, L. C.

2016-09-01

The Philippines has a booming sugarcane industry contributing about PHP 70 billion annually to the local economy through raw sugar, molasses and bioethanol production (SRA, 2012). Sugarcane planters adapt different farm practices in cultivating sugarcane, one of which is cane burning to eliminate unwanted plant material and facilitate easier harvest. Information on burned sugarcane extent is significant in yield estimation models to calculate total sugar lost during harvest. Pre-harvest burning can lessen sucrose by 2.7% - 5% of the potential yield (Gomez, et al 2006; Hiranyavasit, 2016). This study employs a method for detecting burn sugarcane area and determining burn severity through Differenced Normalized Burn Ratio (dNBR) using Landsat 8 Images acquired during the late milling season in Tarlac, Philippines. Total burned area was computed per burn severity based on pre-fire and post-fire images. Results show that 75.38% of the total sugarcane fields in Tarlac were burned with post-fire regrowth; 16.61% were recently burned; and only 8.01% were unburned. The monthly dNBR for February to March generated the largest area with low severity burn (1,436 ha) and high severity burn (31.14 ha) due to pre-harvest burning. Post-fire regrowth is highest in April to May when previously burned areas were already replanted with sugarcane. The maximum dNBR of the entire late milling season (February to May) recorded larger extent of areas with high and low post-fire regrowth compared to areas with low, moderate and high burn severity. Normalized Difference Vegetation Index (NDVI) was used to analyse vegetation dynamics between the burn severity classes. Significant positive correlation, rho = 0.99, was observed between dNBR and dNDVI at 5% level (p = 0.004). An accuracy of 89.03% was calculated for the Landsat-derived NBR validated using actual mill data for crop year 2015-2016.

Climate change and sugarcane expansion increase Hantavirus infection risk.

PubMed

Prist, Paula Ribeiro; Uriarte, María; Fernandes, Katia; Metzger, Jean Paul

2017-07-01

Hantavirus Cardiopulmonary Syndrome (HCPS) is a disease caused by Hantavirus, which is highly virulent for humans. High temperatures and conversion of native vegetation to agriculture, particularly sugarcane cultivation can alter abundance of rodent generalist species that serve as the principal reservoir host for HCPS, but our understanding of the compound effects of land use and climate on HCPS incidence remains limited, particularly in tropical regions. Here we rely on a Bayesian model to fill this research gap and to predict the effects of sugarcane expansion and expected changes in temperature on Hantavirus infection risk in the state of São Paulo, Brazil. The sugarcane expansion scenario was based on historical data between 2000 and 2010 combined with an agro-environment zoning guideline for the sugar and ethanol industry. Future evolution of temperature anomalies was derived using 32 general circulation models from scenarios RCP4.5 and RCP8.5 (Representative greenhouse gases Concentration Pathways adopted by IPCC). Currently, the state of São Paulo has an average Hantavirus risk of 1.3%, with 6% of the 645 municipalities of the state being classified as high risk (HCPS risk ≥ 5%). Our results indicate that sugarcane expansion alone will increase average HCPS risk to 1.5%, placing 20% more people at HCPS risk. Temperature anomalies alone increase HCPS risk even more (1.6% for RCP4.5 and 1.7%, for RCP8.5), and place 31% and 34% more people at risk. Combined sugarcane and temperature increases led to the same predictions as scenarios that only included temperature. Our results demonstrate that climate change effects are likely to be more severe than those from sugarcane expansion. Forecasting disease is critical for the timely and efficient planning of operational control programs that can address the expected effects of sugarcane expansion and climate change on HCPS infection risk. The predicted spatial location of HCPS infection risks obtained here can be used to prioritize management actions and develop educational campaigns.

microRNAs Associated with Drought Response in the Bioenergy Crop Sugarcane (Saccharum spp.)

PubMed Central

Vilela, Romel Duarte; Costa, Gustavo Gilson Lacerda; Dias, Lara Isys; Endres, Laurício; Menossi, Marcelo

2012-01-01

Sugarcane (Saccharum spp.) is one of the most important crops in the world. Drought stress is a major abiotic stress factor that significantly reduces sugarcane yields. However the gene network that mediates plant responses to water stress remains largely unknown in several crop species. Although several microRNAs that mediate post-transcriptional regulation during water stress have been described in other species, the role of the sugarcane microRNAs during drought stress has not been studied. The objective of this work was to identify sugarcane miRNAs that are differentially expressed under drought stress and to correlate this expression with the behavior of two sugarcane cultivars with different drought tolerances. The sugarcane cultivars RB867515 (higher drought tolerance) and RB855536 (lower drought tolerance) were cultivated in a greenhouse for three months and then subjected to drought for 2, 4, 6 or 8 days. By deep sequencing of small RNAs, we were able to identify 18 miRNA families. Among all of the miRNAs thus identified, seven were differentially expressed during drought. Six of these miRNAs were differentially expressed at two days of stress, and five miRNAs were differentially expressed at four days. The expression levels of five miRNAs (ssp-miR164, ssp-miR394, ssp-miR397, ssp-miR399-seq 1 and miR528) were validated by RT-qPCR (quantitative reverse transcriptase PCR). Six precursors and the targets of the differentially expressed miRNA were predicted using an in silico approach and validated by RT-qPCR; many of these targets may play important roles in drought tolerance. These findings constitute a significant increase in the number of identified miRNAs in sugarcane and contribute to the elucidation of the complex regulatory network that is activated by drought stress. PMID:23071617

Water sustainability assessment in Brazilian sugarcane expansion area

NASA Astrophysics Data System (ADS)

Scarpare, F. V.; Ruiz-Correa, S. T.; Hernandes, T. A.; Scanlon, B. R.; Picoli, M. C. A.; Bonomi, A.

2016-12-01

Due to the increasing demand for ethanol, sugarcane is expanding into Cerrado (Savannahs), where edaphoclimatic characteristics differ significantly from traditional areas in South-eastern Brazil. It is expected that the sugarcane will be irrigated in those areas to increase yields and ensure stable production. The main objective is to assess the sugarcane land occupation and its dynamics relating its occurrence with the potential and actual yields, the irrigation needs, the production costs, and the water footprint in Paranaíba watershed (222,593 km2 drainage area). The Agroecological Zone Model - FAO was used in order to provide essential data for yield and water requirement assessment. For sugarcane stalk yield estimation, several improvements have been made allowing this tool to assess different irrigation scenarios. In this study, full irrigation which aims to replace 100% of the water deficit until senescence period was considered. The sugarcane occupation and expansion was assessed through EVI approach from 2009/2010 to 2012/2013 crop seasons. It was possible to identify that most part of sugarcane occupation is concentrated in the central area, which presents less potential for yield gain through irrigation and significant water availability issues. With regard to the expansion, an increase of 54% of cane occupation (from 616,899 to 946,589 ha) was detected during the assessed period showing that the main dynamic occurred in central part towards west side and at less extent, to southeaster side. The irrigation management were responsible for increase, on average, 108% of yields while decreasing 42% of water footprints. Simulated yields combine with CanaSoft model estimated a 30% decline in production cost. Although several aspects such as land price and infrastructure must to be considered, in conclusion, the expansion dynamic agrees to the areas with greater yield gain potential through irrigation, lower sugarcane production costs and water footprint values.

Climate change and sugarcane expansion increase Hantavirus infection risk

PubMed Central

Uriarte, María; Fernandes, Katia; Metzger, Jean Paul

2017-01-01

Hantavirus Cardiopulmonary Syndrome (HCPS) is a disease caused by Hantavirus, which is highly virulent for humans. High temperatures and conversion of native vegetation to agriculture, particularly sugarcane cultivation can alter abundance of rodent generalist species that serve as the principal reservoir host for HCPS, but our understanding of the compound effects of land use and climate on HCPS incidence remains limited, particularly in tropical regions. Here we rely on a Bayesian model to fill this research gap and to predict the effects of sugarcane expansion and expected changes in temperature on Hantavirus infection risk in the state of São Paulo, Brazil. The sugarcane expansion scenario was based on historical data between 2000 and 2010 combined with an agro-environment zoning guideline for the sugar and ethanol industry. Future evolution of temperature anomalies was derived using 32 general circulation models from scenarios RCP4.5 and RCP8.5 (Representative greenhouse gases Concentration Pathways adopted by IPCC). Currently, the state of São Paulo has an average Hantavirus risk of 1.3%, with 6% of the 645 municipalities of the state being classified as high risk (HCPS risk ≥ 5%). Our results indicate that sugarcane expansion alone will increase average HCPS risk to 1.5%, placing 20% more people at HCPS risk. Temperature anomalies alone increase HCPS risk even more (1.6% for RCP4.5 and 1.7%, for RCP8.5), and place 31% and 34% more people at risk. Combined sugarcane and temperature increases led to the same predictions as scenarios that only included temperature. Our results demonstrate that climate change effects are likely to be more severe than those from sugarcane expansion. Forecasting disease is critical for the timely and efficient planning of operational control programs that can address the expected effects of sugarcane expansion and climate change on HCPS infection risk. The predicted spatial location of HCPS infection risks obtained here can be used to prioritize management actions and develop educational campaigns. PMID:28727744

Sugarcane Elongin C is involved in infection by sugarcane mosaic disease pathogens

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhai, Yushan; Deng, Yuqing; Cheng, Guangyuan

Sugarcane (Saccharum sp. hybrid) provides the main source of sugar for humans. Sugarcane mosaic disease (SMD) is a major threat to sugarcane production. Currently, control of SMD is mainly dependent on breeding resistant cultivars through hybridization, which is time-consuming. Understanding the mechanism of viral infection may facilitate novel strategies to breed cultivars resistant to SMD and to control the disease. In this study, a wide interaction was detected between the viral VPg protein and host proteins. Several genes were screened from sugarcane cDNA library that could interact with Sugarcane streak mosaic virus VPg, including SceIF4E1 and ScELC. ScELC was predictedmore » to be a cytoplasmic protein, but subcellular localization analysis showed it was distributed both in cytoplasmic and nuclear, and interactions were also detected between ScELC and VPg of SCMV or SrMV that reveal ScELC was widely used in the SMD pathogen infection process. ScELC and VPgs interacted in the nucleus, and may function to enhance the viral transcription rate. ScELC also interacted with SceIF4E2 both in the cytoplasm and nucleus, but not with SceIF4E1 and SceIF4E3. These results suggest that ScELC may be essential for the function of SceIF4E2, an isomer of eIF4E. - Highlights: • We cloned ScELC, SceIF4E1, SceIF4E2 and SceIF4E3 from sugarcane accession Badila. • We examined interactions among VPg, ScELC, SceIF4E1, SceIF4E2 and SceIF4E3. • We proofed that ScELC interacted with VPgs of SCMV, SrMV and SCSMV. • We proofed that ScELC interacted with SceIF4E2 but not SceIF4E1 or SceIF4E3.« less

Field Performance of Transgenic Sugarcane Lines Resistant to Sugarcane Mosaic Virus

PubMed Central

Yao, Wei; Ruan, Miaohong; Qin, Lifang; Yang, Chuanyu; Chen, Rukai; Chen, Baoshan; Zhang, Muqing

2017-01-01

Sugarcane mosaic disease is mainly caused by the sugarcane mosaic virus (SCMV), which can significantly reduce stalk yield and sucrose content of sugarcane in the field. Coat protein mediated protection (CPMP) is an effective strategy to improve virus resistance. A 2-year field study was conducted to compare five independent transgenic sugarcane lines carrying the SCMV-CP gene (i.e., B2, B36, B38, B48, and B51) with the wild-type parental clone Badila (WT). Agronomic performance, resistance to SCMV infection, and transgene stability were evaluated and compared with the wild-type parental clone Badila (WT) at four experimental locations in China across two successive seasons, i.e., plant cane (PC) and 1st ratoon cane (1R). All transgenic lines derived from Badila had significantly greater tons of cane per hectare (TCH) and tons of sucrose per hectare (TSH) as well as lower SCMV disease incidence than those from Badila in the PC and 1R crops. The transgenic line B48 was highly resistant to SCMV with less than 3% incidence of infection. The recovery phenotype of transgenic line B36 was infected soon after virus inoculation, but the subsequent leaves showed no symptoms of infection. Most control plants developed symptoms that persisted and spread throughout the plant with more than 50% incidence. B48 recorded an average of 102.72 t/ha, which was 67.2% more than that for Badila. The expression of the transgene was stable over many generations with vegetative propagation. These results show that SCMV-resistant transgenic lines derived from Badila can provide resistant germplasm for sugarcane breeding and can also be used to study virus resistance mechanisms. This is the first report on the development and field performance of transgenic sugarcane plants that are resistant to SCMV infection in China. PMID:28228765

Field Performance of Transgenic Sugarcane Lines Resistant to Sugarcane Mosaic Virus.

PubMed

Yao, Wei; Ruan, Miaohong; Qin, Lifang; Yang, Chuanyu; Chen, Rukai; Chen, Baoshan; Zhang, Muqing

2017-01-01

Sugarcane mosaic disease is mainly caused by the sugarcane mosaic virus (SCMV), which can significantly reduce stalk yield and sucrose content of sugarcane in the field. Coat protein mediated protection (CPMP) is an effective strategy to improve virus resistance. A 2-year field study was conducted to compare five independent transgenic sugarcane lines carrying the SCMV-CP gene (i.e., B2, B36, B38, B48, and B51) with the wild-type parental clone Badila (WT). Agronomic performance, resistance to SCMV infection, and transgene stability were evaluated and compared with the wild-type parental clone Badila (WT) at four experimental locations in China across two successive seasons, i.e., plant cane (PC) and 1st ratoon cane (1R). All transgenic lines derived from Badila had significantly greater tons of cane per hectare (TCH) and tons of sucrose per hectare (TSH) as well as lower SCMV disease incidence than those from Badila in the PC and 1R crops. The transgenic line B48 was highly resistant to SCMV with less than 3% incidence of infection. The recovery phenotype of transgenic line B36 was infected soon after virus inoculation, but the subsequent leaves showed no symptoms of infection. Most control plants developed symptoms that persisted and spread throughout the plant with more than 50% incidence. B48 recorded an average of 102.72 t/ha, which was 67.2% more than that for Badila. The expression of the transgene was stable over many generations with vegetative propagation. These results show that SCMV-resistant transgenic lines derived from Badila can provide resistant germplasm for sugarcane breeding and can also be used to study virus resistance mechanisms. This is the first report on the development and field performance of transgenic sugarcane plants that are resistant to SCMV infection in China.

Manganese Toxicity in Sugarcane Plantlets Grown on Acidic Soils of Southern China

PubMed Central

Huang, Yu Lan; Yang, Shu; Long, Guang Xia; Zhao, Zun Kang; Li, Xiao Feng; Gu, Ming Hua

2016-01-01

Ratoon sugarcane plantlets in southern China have suffered a serious chlorosis problem in recent years. To reveal the causes of chlorosis, plant nutrition in chlorotic sugarcane plantlets and the role of manganese (Mn) in this condition were investigated. The study results showed that the pH of soils growing chlorotic plantlets ranged from 3.74 to 4.84. The symptoms of chlorosis were similar to those of iron (Fe) deficiency while the chlorotic and non-chlorotic plantlets contained similar amount of Fe. Chlorotic plantlets had 6.4-times more Mn in their leaf tissues compared to the control plants. There was a significantly positive correlation between Mn concentration in the leaves and the exchangeable Mn concentration in the soils. Moreover, leaf Mn concentration was related to both seasonal changes in leaf chlorophyll concentration and to the occurrence of chlorosis. Basal stalks of mature sugarcanes contained up to 564.36 mg·kg-1 DW Mn. Excess Mn in the parent stalks resulted in a depress of chlorophyll concentration in the leaves of sugarcanes as indicated by lower chlorophyll concentration in the leaves of plantlets emerged from basal stalks. Ratoon sugarcane plantlets were susceptible to chlorosis due to high Mn accumulation in their leaves (456.90–1626.95 mg·kg-1 DW), while in planted canes chlorosis did not occur because of low Mn accumulation (94.64–313.41mg·kg-1 DW). On the other hand, active Fe content in chlorotic plantlets (3.39 mg kg-1 FW) was only equivalent to 28.2% of the concentration found in the control. These results indicate that chlorosis in ratoon sugarcane plantlets results from excessive Mn accumulated in parent stalks of planted cane sugarcanes grown on excessive Mn acidic soils, while active Fe deficiency in plantlets may play a secondary role in the chlorosis. PMID:27023702

Sugarcane White Leaf Disease Incidences and Population Dynamic of Leafhopper Insect Vectors in Sugarcane Plantations in Northeast Thailand.

PubMed

Rattanabunta, Chiranan; Hanboonsong, Yupa

2015-04-01

The work consisted of two experiments, i.e. Experiment 1 was conducted under controlled environments where sugarcane plants were used as hosts. This investigation aimed to monitor the occurrence of the Sugarcane White Leaf disease and the abundance of Leafhopper insect vectors and also the work aimed to provide useful information in understanding some aspects on epidemiology of the Sugarcane White Leaf disease. A Completely Randomized Design with three replications was used to justify growth and development of Leafhopper insects as affected by different temperatures: 20 (T1), 25 (T2), 30 (T3) and 35 degrees C (T4). Experiment 2 was carried out to determine the numbers of Leafhopper insects with the use of light traps in the sugarcane Field 1 (ratoon plants), Field 2 (newly planted), Field 3 (newly planted) and Field 4 (ratoon plants). The results of Experiment 1 showed that growth and development of Leafhopper insects were highly affected by temperatures i.e. the higher the environmental temperature the faster the growth and development of the insects to reach its full adulthood. At 20 degrees C, Leafhopper insects took 12 days to lay eggs whereas at 25 degrees C the insects took only 6 days. Male reached its adulthood approximately 9 days earlier than female when cultured at 25 degrees C and became approximately one week at 30 degrees C or higher. The results of Experiment 2 showed that the majority of Leafhopper insects were found within the months of June and July for both newly planted and ratoon crops. A small amount was found in May and August with an exceptional case of Field 4 where the highest number of Leafhopper insects was found in April followed by June and July. For Sugarcane White Leaf disease, the disease was found in all months of the year except February for Fields 2 and 3. Newly planted sugarcane plants attained much smaller percentages of disease than those of the ratoon plants.

Loss of soil (macro)fauna due to the expansion of Brazilian sugarcane acreage.

PubMed

Franco, André L C; Bartz, Marie L C; Cherubin, Maurício R; Baretta, Dilmar; Cerri, Carlos E P; Feigl, Brigitte J; Wall, Diana H; Davies, Christian A; Cerri, Carlos C

2016-09-01

Land use changes (LUC) from pasture to sugarcane (Saccharum spp.) crop are expected to add 6.4Mha of new sugarcane land by 2021 in the Brazilian Cerrado and Atlantic Forest biomes. We assessed the effects of these LUC on the abundance and community structure of animals that inhabit soils belowground through a field survey using chronosequences of land uses comprising native vegetation, pasture, and sugarcane along a 1000-km-long transect across these two major tropical biomes in Brazil. Macrofauna community composition differed among land uses. While most groups were associated with samples taken in native vegetation, high abundance of termites and earthworms appeared associated with pasture soils. Linear mixed effects analysis showed that LUC affected total abundance (X(2)(1)=6.79, p=0.03) and taxa richness (X(2)(1)=6.08, p=0.04) of soil macrofauna. Abundance increased from 411±70individualsm(-2) in native vegetation to 1111±202individualsm(-2) in pasture, but decreased sharply to 106±24individualsm(-2) in sugarcane soils. Diversity decreased 24% from native vegetation to pasture, and 39% from pasture to sugarcane. Thus, a reduction of ~90% in soil macrofauna abundance, besides a loss of ~40% in the diversity of macrofauna groups, can be expected when sugarcane crops replace pasture in Brazilian tropical soils. In general, higher abundances of major macrofauna groups (ants, coleopterans, earthworms, and termites) were associated with higher acidity and low contents of macronutrients and organic matter in soil. This study draws attention for a significant biodiversity loss belowground due to tropical LUC in sugarcane expansion areas. Given that many groups of soil macrofauna are recognized as key mediators of ecosystem processes such as soil aggregation, nutrients cycling and soil carbon storage, our results warrant further efforts to understand the impacts of altering belowground biodiversity and composition on soil functioning and agriculture performance across LUC in the tropics. Copyright © 2016 Elsevier B.V. All rights reserved.

Selection of suitable endogenous reference genes for relative copy number detection in sugarcane.

PubMed

Xue, Bantong; Guo, Jinlong; Que, Youxiong; Fu, Zhiwei; Wu, Luguang; Xu, Liping

2014-05-19

Transgene copy number has a great impact on the expression level and stability of exogenous gene in transgenic plants. Proper selection of endogenous reference genes is necessary for detection of genetic components in genetically modification (GM) crops by quantitative real-time PCR (qPCR) or by qualitative PCR approach, especially in sugarcane with polyploid and aneuploid genomic structure. qPCR technique has been widely accepted as an accurate, time-saving method on determination of copy numbers in transgenic plants and on detection of genetically modified plants to meet the regulatory and legislative requirement. In this study, to find a suitable endogenous reference gene and its real-time PCR assay for sugarcane (Saccharum spp. hybrids) DNA content quantification, we evaluated a set of potential "single copy" genes including P4H, APRT, ENOL, CYC, TST and PRR, through qualitative PCR and absolute quantitative PCR. Based on copy number comparisons among different sugarcane genotypes, including five S. officinarum, one S. spontaneum and two S. spp. hybrids, these endogenous genes fell into three groups: ENOL-3--high copy number group, TST-1 and PRR-1--medium copy number group, P4H-1, APRT-2 and CYC-2--low copy number group. Among these tested genes, P4H, APRT and CYC were the most stable, while ENOL and TST were the least stable across different sugarcane genotypes. Therefore, three primer pairs of P4H-3, APRT-2 and CYC-2 were then selected as the suitable reference gene primer pairs for sugarcane. The test of multi-target reference genes revealed that the APRT gene was a specific amplicon, suggesting this gene is the most suitable to be used as an endogenous reference target for sugarcane DNA content quantification. These results should be helpful for establishing accurate and reliable qualitative and quantitative PCR analysis of GM sugarcane.

Characterization of the gene encoding serine acetyltransferase, a regulated enzyme of cysteine biosynthesis from the protist parasites Entamoeba histolytica and Entamoeba dispar. Regulation and possible function of the cysteine biosynthetic pathway in Entamoeba.

PubMed

Nozaki, T; Asai, T; Sanchez, L B; Kobayashi, S; Nakazawa, M; Takeuchi, T

1999-11-05

The enteric protist parasites Entamoeba histolytica and Entamoeba dispar possess a cysteine biosynthetic pathway, unlike their mammalian host, and are capable of de novo production of L-cysteine. We cloned and characterized cDNAs that encode the regulated enzyme serine acetyltransferase (SAT) in this pathway from these amoebae by genetic complementation of a cysteine-auxotrophic Escherichia coli strain with the amoebic cDNA libraries. The deduced amino acid sequences of the amoebic SATs exhibited, within the most conserved region, 36-52% identities with the bacterial and plant SATs. The amoebic SATs contain a unique insertion of eight amino acids, also found in the corresponding region of a plasmid-encoded SAT from Synechococcus sp., which showed the highest overall identities to the amoebic SATs. Phylogenetic reconstruction also revealed a close kinship of the amoebic SATs with cyanobacterial SATs. Biochemical characterization of the recombinant E. histolytica SAT revealed several enzymatic features that distinguished the amoebic enzyme from the bacterial and plant enzymes: 1) inhibition by L-cysteine in a competitive manner with L-serine; 2) inhibition by L-cystine; and 3) no association with cysteine synthase. Genetically engineered amoeba strains that overproduced cysteine synthase and SAT were created. The cysteine synthase-overproducing amoebae had a higher level of cysteine synthase activity and total thiol content and revealed increased resistance to hydrogen peroxide. These results indicate that the cysteine biosynthetic pathway plays an important role in antioxidative defense of these enteric parasites.

A Novel Kinesin-Like Protein with a Calmodulin-Binding Domain

NASA Technical Reports Server (NTRS)

Wang, W.; Takezawa, D.; Narasimhulu, S. B.; Reddy, A. S. N.; Poovaiah, B. W.

1996-01-01

Calcium regulates diverse developmental processes in plants through the action of calmodulin. A cDNA expression library from developing anthers of tobacco was screened with S-35-labeled calmodulin to isolate cDNAs encoding calmodulin-binding proteins. Among several clones isolated, a kinesin-like gene (TCK1) that encodes a calmodulin-binding kinesin-like protein was obtained. The TCK1 cDNA encodes a protein with 1265 amino acid residues. Its structural features are very similar to those of known kinesin heavy chains and kinesin-like proteins from plants and animals, with one distinct exception. Unlike other known kinesin-like proteins, TCK1 contains a calmodulin-binding domain which distinguishes it from all other known kinesin genes. Escherichia coli-expressed TCK1 binds calmodulin in a Ca(2+)-dependent manner. In addition to the presence of a calmodulin-binding domain at the carboxyl terminal, it also has a leucine zipper motif in the stalk region. The amino acid sequence at the carboxyl terminal of TCK1 has striking homology with the mechanochemical motor domain of kinesins. The motor domain has ATPase activity that is stimulated by microtubules. Southern blot analysis revealed that TCK1 is coded by a single gene. Expression studies indicated that TCKI is expressed in all of the tissues tested. Its expression is highest in the stigma and anther, especially during the early stages of anther development. Our results suggest that Ca(2+)/calmodulin may play an important role in the function of this microtubule-associated motor protein and may be involved in the regulation of microtubule-based intracellular transport.

[Cloning and expressing of cyclophilin B gene from Schistosoma japonnicum and the analysis of immunoprotective effect].

PubMed

Peng, Jinbiao; Han, Hongxiao; Hong, Yang; Wang, Yan; Guo, Fanji; Shi, Yaojun; Fu, Zhiqiang; Liu, Jinming; Cheng, Guofeng; Lin, Jiaojiao

2010-03-01

The present study was intend to clone and express the cDNA encoding Cyclophilin B (CyPB) of Schistosoma japonicum, its preliminary biological function and further immunoprotective effect against schistosome infection in mice. RT-PCR technique was applied to amplify a full-length cDNA encoding protein Cyclophilin B (Sj CyPB) from schistosomula cDNA. The expression profiles of Sj CyPB were determined by Real-time PCR using the template cDNAs isolated from 7, 13, 18, 23, 32 and 42 days parasites. The cDNA containing the Open Reading Frame of CyPB was then subcloned into a pGEX-6P-1 vector and transformed into competent Escherichia coli BL21 for expressing. The recombinant protein was renaturated, purified and its antigenicity were detected by Western blotting, and the immunoprotective effect induced by recombinant Sj CyPB was evaluated in Balb/C mice. The cDNA containing the ORF of Sj CyPB was cloned with the length of 672 base pairs, encoding 223 amino acids. Real-time PCR analysis revealed that the gene had the highest expression in 18-day schistosomula, suggesting that Sj CyPB was schistosomula differentially expressed gene. The recombinant protein showed a good antigenicity detected by Western blotting. Animal experiment indicated that the vaccination of recombinant CyPB protein in mice led to 31.5% worm and 41.01% liver egg burden reduction, respectively, compared with those of the control. A full-length cDNA differentially expressed in schistosomula was obtained. The recombinant Sj CyPB protein could induce partial protection against schistosome infection.

Three new members of the RNP protein family in Xenopus.

PubMed Central

Good, P J; Rebbert, M L; Dawid, I B

1993-01-01

Many RNP proteins contain one or more copies of the RNA recognition motif (RRM) and are thought to be involved in cellular RNA metabolism. We have previously characterized in Xenopus a nervous system specific gene, nrp1, that is more similar to the hnRNP A/B proteins than to other known proteins (K. Richter, P. J. Good, and I. B. Dawid (1990), New Biol. 2, 556-565). PCR amplification with degenerate primers was used to identify additional cDNAs encoding two RRMs in Xenopus. Three previously uncharacterized genes were identified. Two genes encode hnRNP A/B proteins with two RRMs and a glycine-rich domain. One of these is the Xenopus homolog of the human A2/B1 gene; the other, named hnRNP A3, is similar to both the A1 and A2 hnRNP genes. The Xenopus hnRNP A1, A2 and A3 genes are expressed throughout development and in all adult tissues. Multiple protein isoforms for the hnRNP A2 gene are predicted that differ by the insertion of short peptide sequences in the glycine-rich domain. The third newly isolated gene, named xrp1, encodes a protein that is related by sequence to the nrp1 protein but is expressed ubiquitously. Despite the similarity to nuclear RNP proteins, both the nrp1 and xrp1 proteins are localized to the cytoplasm in the Xenopus oocyte. The xrp1 gene may have a function in all cells that is similar to that executed by nrp1 specifically within the nervous system. Images PMID:8451200

Isolation of genes negatively or positively co-expressed with human recombination activating gene 1 (RAG1) by differential display PCR (DD RT-PCR).

PubMed

Verkoczy, L K; Berinstein, N L

1998-10-01

Differential display PCR (DD RT-PCR) has been extensively used for analysis of differential gene expression, but continues to be hampered by technical limitations that impair its effectiveness. In order to isolate novel genes co-expressing with human RAG1, we have developed an effective, multi-tiered screening/purification approach which effectively complements the standard DD RT-PCR methodology. In 'primary' screens, standard DD RT-PCR was used, detecting 22 reproducible differentially expressed amplicons between clonally related cell variants with differential constitutive expression of RAG mRNAs. 'Secondary' screens used differential display (DD) amplicons as probes in low and high stringency northern blotting. Eight of 22 independent DD amplicons detected nine independent differentially expressed transcripts. 'Tertiary' screens used reconfirmed amplicons as probes in northern analysis of multiple RAG-and RAG+sources. Reconfirmed DD amplicons detected six independent RAG co-expressing transcripts. All DD amplicons reconfirmed by northern blot were a heterogeneous mixture of cDNAs, necessitating further purification to isolate single cDNAs prior to subcloning and sequencing. To effectively select the appropriate cDNAs from DD amplicons, we excised and eluted the cDNA(s) directly from regions of prior northern blots in which differentially expressed transcripts were detected. Sequences of six purified cDNA clones specifically detecting RAG co-expressing transcripts included matches to portions of the human RAG2 and BSAP regions and to four novel partial cDNAs (three with homologies to human ESTs). Overall, our results also suggest that even when using clonally related variants from the same cell line in addition to all appropriate internal controls previously reported, further screening and purification steps are still required in order to efficiently and specifically isolate differentially expressed genes by DD RT-PCR.

[Frontier, sugarcane and trafficking: slavery, disease and death in Capivari, São Paulo, 1821-1869].

PubMed

Lima, Carlos A M

2015-01-01

The deaths and diseases of slaves in the São Paulo State sugarcane municipality of Capivari are addressed, associating the causes attributed to these deaths to the social and economic context and characteristics of the local slave communities. The impact of malaria, relating it to the age brackets, the environment created by work on the sugarcane plantations and the evolution of the occupation of the area, initially by expanding frontiers, is emphasized. The relationship between illness and work processes, as well as the post-disembarkation mortality of Africans and the possibility of mortality crises among the sugarcane captives is explored. The results lead to a discussion of the impact of habitat and Atlantic displacement and the difficulty in acclimatizing.

Source apportionment of atmospheric polycyclic aromatic hydrocarbons (PAHs) in Palm Beach County, Florida.

PubMed

Afshar-Mohajer, Nima; Wilson, Christina; Wu, Chang-Yu; Stormer, James E

2016-04-01

Due to concerns about adverse health effects associated with inhalation of atmospheric polycyclic aromatic hydrocarbons (PAHs), 30 ambient air samples were obtained at an air quality monitoring station in Palm Beach County, Florida, from March 2013 to March 2014. The ambient PAH concentration measurements and fractional emission rates of known sources were incorporated into a chemical mass balance model, CMB8.2, developed by EPA, to apportion contributions of three major PAH sources including preharvest sugarcane burning, mobile vehicles, and wildland fires. Strong association between the number of benzene rings and source contribution was found, and mobile vehicles were identified to be the prevailing source (contribution≥56%) for the observed PAHs concentration with lower molecular weights (four or fewer benzene rings) throughout the year. Preharvest sugarcane burning was the primary contributing source for PAHs with relatively higher molecular weights (five or more benzene rings) during the sugarcane burning season (from October to May of the next year). Source contribution of wildland fires varied among PAH compounds but was consistently lower than for sugarcane burning during the sugarcane harvest season. Determining the major sources responsible for ground-level PAHs serves as a tool to improving management strategies for PAH emitting sources and a step toward better protection of the health of residents in terms of exposure to PAHs. The results obtain insight into temporal dominance of PAH polluting sources for those residential areas located near sugarcane burning facilities and have implications beyond Palm Beach County, in areas with high concerns of PAHs and their linked sources. Source apportionment of atmospheric polycyclic hydrocarbons (PAHs) in Palm Beach County, Florida, meant to estimate contributions of major sources in PAH concentrations measured at Belle Glade City of Palm Beach County. Number of benzene rings was found to be the key parameter in determining the source with the prevailing contribution. Mobile vehicle sources showed a higher contribution for species with four or fewer benzene rings, whereas sugarcane burning contributed more for species with five or more benzene rings. Results from this study encourage more control for sugarcane burns and help to better manage authorization of the sugarcane burning incidents and more restrictive transportation plans to limit PAH emissions from mobile vehicles.

Comparison Between Ground Ant (Hymenoptera: Formicidae) Communities Foraging in the Straw Mulch of Sugarcane Crops and in the Leaf Litter of Neighboring Forests.

PubMed

Silva, N S; Saad, L P; Souza-Campana, D R; Bueno, O C; Morini, M S C

2017-02-01

In many sugarcane plantations in Brazil, the straw is left on the soil after harvesting, and vinasse, a by-product of the production of sugar and ethanol, is used for fertigation. Our goal was to compare ant community composition and species richness in the straw mulch of sugarcane crops with the leaf litter of neighboring forests. We tested the hypothesis that ant communities in the straw mulch of vinasse-irrigated sugarcane crops and in the forest leaf litter were similar, because the combination of straw mulching and vinasse irrigation has a positive effect on soil fauna. Straw mulch and leaf litter were collected from 21 sites and placed in Berlese funnels. In total, 61 species were found in the forest leaf litter, whereas 34 and 28 species were found in the straw mulch of sugarcane fields with and without vinasse, respectively. Ant communities differed between forest and crop fields, but the species in the sugarcane straw mulch were a subset of the species found in the forest leaf litter. Although vinasse is rich in organic matter, it did not increase ant diversity. Seven feeding and/or foraging types were identified and, among the different types, surface-foraging omnivorous ants were the most prevalent in all habitats. Vinasse-irrigated sugarcane straw mulch had more predatory species than mulch from vinasse-free fields, but fewer than forest leaf litter. However, this positive effect of vinasse irrigation should be carefully evaluated because vinasse has negative effects on the environment. © The Authors 2017. Published by Oxford University Press on behalf of Entomological Society of America. All rights reserved. For Permissions, please email: journals.permissions@oup.com.

Precision breeding for RNAi suppression of a major 4-coumarate:coenzyme A ligase gene improves cell wall saccharification from field grown sugarcane.

PubMed

Jung, Je Hyeong; Kannan, Baskaran; Dermawan, Hugo; Moxley, Geoffrey W; Altpeter, Fredy

2016-11-01

Sugarcane (Saccharum spp. hybrids) is a major feedstock for commercial bioethanol production. The recent integration of conversion technologies that utilize lignocellulosic sugarcane residues as well as sucrose from stem internodes has elevated bioethanol yields. RNAi suppression of lignin biosynthetic enzymes is a successful strategy to improve the saccharification of lignocellulosic biomass. 4-coumarate:coenzyme A ligase (4CL) is a key enzyme in the biosynthesis of phenylpropanoid metabolites, such as lignin and flavonoids. Identifying a major 4CL involved in lignin biosynthesis among multiple isoforms with functional divergence is key to manipulate lignin biosynthesis. In this study, two full length 4CL genes (Sh4CL1 and Sh4CL2) were isolated and characterized in sugarcane. Phylogenetic, expression and RNA interference (RNAi) analysis confirmed that Sh4CL1 is a major lignin biosynthetic gene. An intragenic precision breeding strategy may facilitate the regulatory approval of the genetically improved events and was used for RNAi suppression of Sh4CL1. Both, the RNAi inducing cassette and the expression cassette for the mutated ALS selection marker consisted entirely of DNA sequences from sugarcane or the sexually compatible species Sorghum bicolor. Field grown sugarcane with intragenic RNAi suppression of Sh4CL1 resulted in reduction of the total lignin content by up to 16.5 % along with altered monolignol ratios without reduction in biomass yield. Mature, field grown, intragenic sugarcane events displayed 52-76 % improved saccharification efficiency of lignocellulosic biomass compared to wild type (WT) controls. This demonstrates for the first time that an intragenic approach can add significant value to lignocellulosic feedstocks for biofuel and biochemical production.

Preparation and application of nanocrystalline cellulose derived from sugarcane waste as filler modified alkanolamide on crosslink of natural rubber latex film

NASA Astrophysics Data System (ADS)

Harahap, Hamidah; Hayat, Nuim; Lubis, Marfuah

2017-07-01

Sugarcane waste is abundant sources of cellulose and it has potential to reutilize. Cellulose from sugarcane waste can be derived into nanocystalline cellulose (NCC) from crystalline region. The NCC as a filler has capability to reinforce natural rubber latex product. The crosslink in vulcanized natural rubber latex film influences several properties of product. In this work, we extracted NCC from sugarcane waste then added into natural rubber latex as filler modified alkanolamide (ALK) and also studied the crosslink of natural rubber latex films. NCC were produced from sugarcane waste by hydrolysis process with sulfuric acid 45%. The obtained NCC was characterized by using x-ray diffraction (XRD), transmission electron microscopy (TEM), and fourier transform infra red (FTIR). NCC was modified by alkanolamide and dispersed in water with filler concentration of 10%. Then the dispersion were added into latex system followed by pre-vulcanization at 70 °C. The films were prepared by coagulant dipping method and dried at 100 °C and 120 °C for 20 minutes. Characterization of NCC from sugarcane waste by using FTIR was done, it clearly showed the functional groups of cellulose. TEM showed the obtained NCC were rod-shaped with about 40-160 nm in diameter and several hundred nm in length, and XRD showed that the degree of crystalinity of NCC from sugarcane waste is 92.33%. The crosslink of natural rubber films were studied by measure the crosslink density for different filler loading by using swelling measurement with toluene solution. The result show that the crosslink density increased in line with amount of filler which added into the system, and also the crosslink density that obtained from vulcanization at 120 °C were higher than 100 °C.

Selection and evaluation of reference genes for RT-qPCR expression studies on Burkholderia tropica strain Ppe8, a sugarcane-associated diazotrophic bacterium grown with different carbon sources or sugarcane juice.

PubMed

da Silva, Paula Renata Alves; Vidal, Marcia Soares; de Paula Soares, Cleiton; Polese, Valéria; Simões-Araújo, Jean Luís; Baldani, José Ivo

2016-11-01

Among the members of the genus Burkholderia, Burkholderia tropica has the ability to fix nitrogen and promote sugarcane plant growth as well as act as a biological control agent. There is little information about how this bacterium metabolizes carbohydrates as well as those carbon sources found in the sugarcane juice that accumulates in stems during plant growth. Reverse transcription quantitative PCR (RT-qPCR) can be used to evaluate changes in gene expression during bacterial growth on different carbon sources. Here we tested the expression of six reference genes, lpxC, gyrB, recA, rpoA, rpoB, and rpoD, when cells were grown with glucose, fructose, sucrose, mannitol, aconitic acid, and sugarcane juice as carbon sources. The lpxC, gyrB, and recA were selected as the most stable reference genes based on geNorm and NormFinder software analyses. Validation of these three reference genes during strain Ppe8 growth on the same carbon sources showed that genes involved in glycogen biosynthesis (glgA, glgB, glgC) and trehalose biosynthesis (treY and treZ) were highly expressed when Ppe8 was grown in aconitic acid relative to other carbon sources, while otsA expression (trehalose biosynthesis) was reduced with all carbon sources. In addition, the expression level of the ORF_6066 (gluconolactonase) gene was reduced on sugarcane juice. The results confirmed the stability of the three selected reference genes (lpxC, gyrB, and recA) during the RT-qPCR and also their robustness by evaluating the relative expression of genes involved in glycogen and trehalose biosynthesis when strain Ppe8 was grown on different carbon sources and sugarcane juice.

Introduction of Pea DNA Helicase 45 Into Sugarcane (Saccharum spp. Hybrid) Enhances Cell Membrane Thermostability And Upregulation Of Stress-responsive Genes Leads To Abiotic Stress Tolerance.

PubMed

Augustine, Sruthy Maria; Ashwin Narayan, J; Syamaladevi, Divya P; Appunu, C; Chakravarthi, M; Ravichandran, V; Tuteja, Narendra; Subramonian, N

2015-05-01

DNA helicases are motor proteins that play an essential role in nucleic acid metabolism, by providing a duplex-unwinding function. To improve the drought and salinity tolerance of sugarcane, a DEAD-box helicase gene isolated from pea with a constitutive promoter, Port Ubi 2.3 was transformed into the commercial sugarcane variety Co 86032 through Agrobacterium-mediated transformation, and the transgenics were screened for tolerance to soil moisture stress and salinity. The transgene integration was confirmed through polymerase chain reaction, and the V 0 transgenic events showed significantly higher cell membrane thermostability under normal irrigated conditions. The V 1 transgenic events were screened for tolerance to soil moisture stress and exhibited significantly higher cell membrane thermostability, transgene expression, relative water content, gas exchange parameters, chlorophyll content, and photosynthetic efficiency under soil moisture stress compared to wild-type (WT). The overexpression of PDH45 transgenic sugarcane also led to the upregulation of DREB2-induced downstream stress-related genes. The transgenic events demonstrated higher germination ability and better chlorophyll retention than WT under salinity stress. Our results suggest the possibility for development of increased abiotic stress tolerant sugarcane cultivars through overexpression of PDH45 gene. Perhaps this is the first report, which provides evidence for increased drought and salinity tolerance in sugarcane through overexpression of PDH45.

Separation of phenolic acids from sugarcane rind by online solid-phase extraction with high-speed counter-current chromatography.

PubMed

Geng, Ping; Fang, Yingtong; Xie, Ronglong; Hu, Weilun; Xi, Xingjun; Chu, Qiao; Dong, Genlai; Shaheen, Nusrat; Wei, Yun

2017-02-01

Sugarcane rind contains some functional phenolic acids. The separation of these compounds from sugarcane rind is able to realize the integrated utilization of the crop and reduce environment pollution. In this paper, a novel protocol based on interfacing online solid-phase extraction with high-speed counter-current chromatography (HSCCC) was established, aiming at improving and simplifying the process of phenolic acids separation from sugarcane rind. The conditions of online solid-phase extraction with HSCCC involving solvent system, flow rate of mobile phase as well as saturated extent of absorption of solid-phase extraction were optimized to improve extraction efficiency and reduce separation time. The separation of phenolic acids was performed with a two-phase solvent system composed of butanol/acetic acid/water at a volume ratio of 4:1:5, and the developed online solid-phase extraction with HSCCC method was validated and successfully applied for sugarcane rind, and three phenolic acids including 6.73 mg of gallic acid, 10.85 mg of p-coumaric acid, and 2.78 mg of ferulic acid with purities of 60.2, 95.4, and 84%, respectively, were obtained from 150 mg sugarcane rind crude extracts. In addition, the three different elution methods of phenolic acids purification including HSCCC, elution-extrusion counter-current chromatography and back-extrusion counter-current chromatography were compared. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

Object-Oriented Classification of Sugarcane Using Time-Series Middle-Resolution Remote Sensing Data Based on AdaBoost

PubMed Central

Zhou, Zhen; Huang, Jingfeng; Wang, Jing; Zhang, Kangyu; Kuang, Zhaomin; Zhong, Shiquan; Song, Xiaodong

2015-01-01

Most areas planted with sugarcane are located in southern China. However, remote sensing of sugarcane has been limited because useable remote sensing data are limited due to the cloudy climate of this region during the growing season and severe spectral mixing with other crops. In this study, we developed a methodology for automatically mapping sugarcane over large areas using time-series middle-resolution remote sensing data. For this purpose, two major techniques were used, the object-oriented method (OOM) and data mining (DM). In addition, time-series Chinese HJ-1 CCD images were obtained during the sugarcane growing period. Image objects were generated using a multi-resolution segmentation algorithm, and DM was implemented using the AdaBoost algorithm, which generated the prediction model. The prediction model was applied to the HJ-1 CCD time-series image objects, and then a map of the sugarcane planting area was produced. The classification accuracy was evaluated using independent field survey sampling points. The confusion matrix analysis showed that the overall classification accuracy reached 93.6% and that the Kappa coefficient was 0.85. Thus, the results showed that this method is feasible, efficient, and applicable for extrapolating the classification of other crops in large areas where the application of high-resolution remote sensing data is impractical due to financial considerations or because qualified images are limited. PMID:26528811

Object-Oriented Classification of Sugarcane Using Time-Series Middle-Resolution Remote Sensing Data Based on AdaBoost.

PubMed

Zhou, Zhen; Huang, Jingfeng; Wang, Jing; Zhang, Kangyu; Kuang, Zhaomin; Zhong, Shiquan; Song, Xiaodong

2015-01-01

Most areas planted with sugarcane are located in southern China. However, remote sensing of sugarcane has been limited because useable remote sensing data are limited due to the cloudy climate of this region during the growing season and severe spectral mixing with other crops. In this study, we developed a methodology for automatically mapping sugarcane over large areas using time-series middle-resolution remote sensing data. For this purpose, two major techniques were used, the object-oriented method (OOM) and data mining (DM). In addition, time-series Chinese HJ-1 CCD images were obtained during the sugarcane growing period. Image objects were generated using a multi-resolution segmentation algorithm, and DM was implemented using the AdaBoost algorithm, which generated the prediction model. The prediction model was applied to the HJ-1 CCD time-series image objects, and then a map of the sugarcane planting area was produced. The classification accuracy was evaluated using independent field survey sampling points. The confusion matrix analysis showed that the overall classification accuracy reached 93.6% and that the Kappa coefficient was 0.85. Thus, the results showed that this method is feasible, efficient, and applicable for extrapolating the classification of other crops in large areas where the application of high-resolution remote sensing data is impractical due to financial considerations or because qualified images are limited.

The effect of w/c ratio on microstructure of self-compacting concrete (SCC) with sugarcane bagasse ash (SCBA)

NASA Astrophysics Data System (ADS)

Hanafiah, Saloma, Victor, Amalina, Khoirunnisa Nur

2017-11-01

Self-Compacting Concrete (SCC) is a concrete that can flow and compact by itself without vibrator. The ability of SCC to flow by itself makes this concrete very suitable for construction that has very small reinforcement gaps. In this study, SCC was designed to get a compressive strength above 60 MPa at the age of 28 days. Sugarcane bagasse ash was used as substitution material for cement replacement. Percentages of sugarcane bagasse ash used were 10%, 15%, and 20%. There were three w/c values that vary from 0.275, 0.300, and 0.325. Testing standards referred to ASTM, EFNARC and ACI. The fresh concrete test was slump flow, L-box and V-funnel. The maximum compressive strength was in the mixture with the sugarcane bagasse ash composition of 15% and w/c=0.275 which was 67.24 MPa. The result of SEM test analysis found that the mixture composition with 15% sugarcane bagasse ash has solid CSH structure, small amount of pores, and smaller pore diameter than other mixtures.

Utilization of pentoses from sugarcane biomass: techno-economics of biogas vs. butanol production.

PubMed

Mariano, Adriano Pinto; Dias, Marina O S; Junqueira, Tassia L; Cunha, Marcelo P; Bonomi, Antonio; Filho, Rubens Maciel

2013-08-01

This paper presents the techno-economics of greenfield projects of an integrated first and second-generation sugarcane biorefinery in which pentose sugars obtained from sugarcane biomass are used either for biogas (consumed internally in the power boiler) or n-butanol production via the ABE batch fermentation process. The complete sugarcane biorefinery was simulated using Aspen Plus®. Although the pentoses stream available in the sugarcane biorefinery gives room for a relatively small biobutanol plant (7.1-12 thousand tonnes per year), the introduction of butanol and acetone to the product portfolio of the biorefinery increased and diversified its revenues. Whereas the IRR of the investment on a biorefinery with biogas production is 11.3%, IRR varied between 13.1% and 15.2% in the butanol production option, depending on technology (regular or engineered microorganism with improved butanol yield and pentoses conversion) and target market (chemicals or automotive fuels). Additional discussions include the effects of energy-efficient technologies for butanol processing on the profitability of the biorefinery. Copyright © 2013 Elsevier Ltd. All rights reserved.

The influence of sugarcane bagasse ash as fly ash on cement quality

NASA Astrophysics Data System (ADS)

Rauf, N.; Damayanti, M. C.; Pratama, S. W. I.

2017-01-01

Fly ash often is used as the third material for cement. The fly ash from sugarcane bagasse is usually considered as industrial waste material that can be added to the base material of cement (clinker, trash, gypsum and lime stone) for economic and environment reason. The amount of fly ash usually up to 30 % of cement material, but in this research the percentage of sugarcane bagasse ash (SBA) is added to cement material is up to 15% total weight. Then the x-rays fluorescence (XRF) was used to determine its chemical composition of raw material and cement samples. The physical properties of cement such as fineness, setting time, expansion, and compressive strength were measured using Automatic Blaine, Vicat, Autoclave, respectively. The result show that the percentage of sugarcane bagasse ash influences the quality of cement and concrete, and this is confirmed with Indonesia National Standard (SNI). It is showed that the sugarcane bagasse ash could be use as material to improve the quality of cement and will solve the environment waste material

Fusarium sacchari, a cause of mycotic keratitis among sugarcane farmers - a series of four cases from North India.

PubMed

Bansal, Yashik; Chander, Jagdish; Kaistha, Neelam; Singla, Nidhi; Sood, Sunandan; van Diepeningen, Anne D

2016-11-01

The two most common filamentous fungi causing mycotic keratitis are Aspergillus and Fusarium spp. Around 70 Fusarium spp. are involved in causing human infections. In this study, four cases of keratitis in sugarcane farmers in India are being reported, caused by the sugar cane pathogen Fusarium sacchari, a species of the Fusarium fujikuroi species complex. Fusarial keratitis was established by potassium hydroxide/Calcofluor white wet mounts and fungal culture of corneal scrapings on conventional media. Final identification was done by genetic sequencing at CBS-KNAW, Utrecht, The Netherlands. The antifungal susceptibility testing was done using broth microdilution method as per CLSI document M38-A2. Four cases of F. sacchari keratitis were identified. Three of them had trauma with sugarcane leaves, whereas one sugarcane farmer reported trauma by vegetative matter. The morphological similarities among various Fusarium species warrant use of molecular methods for identification of cryptic species. A wide distribution of sugarcane farming could be the possible explanation for emergence of F. sacchari keratitis in India. © 2016 Blackwell Verlag GmbH.

Characteristics and oil sorption effectiveness of kapok fibre, sugarcane bagasse and rice husks: oil removal suitability matrix.

PubMed

Ali, Norizan; El-Harbawi, Mohanad; Jabal, Ayman Abo; Yin, Chun-Yang

2012-01-01

The characteristics and water/oil sorption effectiveness ofkapok fibre, sugarcane bagasse and rice husks have been compared. The three biomass types were subjected to field emission scanning electron microscopy-energy dispersive X-ray spectroscopy and surface tension analyses for liquid-air and oil-water systems were conducted. Both kapok fibre and sugarcane bagasse exhibit excellent oil sorption capabilities for diesel, crude, new engine and used engine oils as their oil sorption capacities all exceed 10 g/g. The synthetic sorbent exhibits oil sorption capacities comparable with sugarcane bagasse, while rice husks exhibit the lowest oil sorption capacities among all the sorbents. Kapok fibre shows overwhelmingly high oil-to-water sorption (O/W) ratios ranging from 19.35 to 201.53 while sugarcane bagasse, rice husks and synthetic sorbent have significantly lower O/W ratios (0.76-2.69). This suggests that kapok fibre is a highly effective oil sorbent even in well-mixed oil-water media. An oil sorbent suitability matrix is proposed to aid stakeholders in evaluating customized oil removal usage of the natural sorbents.

Fungal pretreatment improves amenability of lignocellulosic material for its saccharification to sugars.

PubMed

Deswal, Deepa; Gupta, Rishi; Nandal, Preeti; Kuhad, Ramesh Chander

2014-01-01

The sugarcane bagasse was biologically pretreated with three white-rot fungi; Pleurotus florida, Coriolopsis caperata RCK 2011 and Ganoderma sp. rckk-02, individually under solid-state fermentation. P. florida, C. caperata RCK 2011 and Ganoderma sp. rckk-02 degraded lignin up to 7.91, 5.48 and 5.58%, respectively. The lignocellulolytic enzymes produced by these fungi were also monitored during solid state fermentation of sugarcane bagasse. The fungal fermented sugarcane bagasse when hydrolyzed with crude cellulases from brown-rot fungus, Fomitopsis sp. RCK2010, released comparatively 1.5-2.4 fold higher sugars than in case of untreated sugarcane bagasse. The study demonstrated that white-rot fungal pretreatment improved the amenability of plant material for enzymatic hydrolysis. Copyright © 2013 Elsevier Ltd. All rights reserved.

La Roya naranja de la caña de azúcar, una enfermedad emergente: su impacto y comparación con la roya marrón English Translation: Orange rust of sugarcane, an emerging disease: its impact and comparison to brown rust.

USDA-ARS?s Scientific Manuscript database

Sugarcane orange rust, caused by Puccinia kuehnii, was first detected in Florida in 2007, the first for Western Hemisphere. Subsequently, it has spread to the majority of sugarcane producing countries in the hemisphere. Orange rust is distinguished from brown rust its pustule size which is slightl...

7 CFR 457.116 - Sugarcane crop insurance provisions.

Code of Federal Regulations, 2010 CFR

2010-01-01

... was harvested the previous crop year. Sugarcane. The grass, Saccharum officinarum, that is grown to...; (e) Wildlife; (f) Earthquake; (g) Volcanic eruption; or (h) Failure of the irrigation water supply...