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Ribulose

Ribulose is a five-carbon sugar that plays a crucial role in the Calvin cycle of photosynthesis.
It serves as the substrate for the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), which catalyzes the first step in carbon fixation.
Ribulose is a key intermediate in the conversion of light energy into chemical energy during the light-independent reactions of photosynthesis.
Reseraching ribulose and its metabolic pathways can provide insights into plant physiology, carbon cycling, and potential applications in bioenergy and agriculture.
PubCompare.ai can help locate the best protocols and products to advance your ribulose research and improve reproducibility.

Most cited protocols related to «Ribulose»

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Publication 2020
Maize or Arabidopsis material was ground to a fine powder by hand in a mortar pre-cooled with liquid N2 or in a cryo-robot (Stitt et al., 2007 ), and stored at –80 °C. Samples were analyzed by LC-MS/MS and GC-MS, with authentic standards for accurate metabolite quantification, as in Heise et al. (2014) (link). We additionally analyzed aspartate, PEP, 2-phosphoglycolate (2PG), ribose-5-phosphate (R5P), and ribulose-5-phosphate+xylulose-5-phosphate (Ru5P+Xu5P) [see Supplementary Tables S1, S2 for the isotopomer-dependent MS parameters used for selected reaction monitoring (SRM) and the corconfig.cfg file used to correct for natural abundance; Heise et al., 2014 (link); Huege et al., 2014 ]. Amounts of the unlabeled form and each 13C isotopomers in maize samples are provided in Supplementary Table S3 and total contents in Supplementary Table S4. Total amounts of 3PGA and PEP were determined enzymatically using a Sigma-22 dual-wavelength photometer (Merlo et al., 1993 ) using freshly prepared extracts for PEP. 13C Enrichment and isotopomer distribution were calculated as in Szecowka et al. (2013) (link) (Supplementary Tables S5, S6). Active and inactive pools were calculated as in Supplementary Table S3, positional 13C enrichment (C4 and C1–C3 positions) of aspartate and malate as in Supplementary Tables S7, S8, and 13C amounts in metabolites as in Supplementary Tables S7, S8.
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Publication 2016
Arabidopsis Aspartate Gas Chromatography-Mass Spectrometry Maize malate phosphoglycolate Powder ribose-5-phosphate ribulose 5-phosphate Tandem Mass Spectrometry Xylulose
The activities of the photosynthetic enzymes Rubisco and PEPC were measured as previously described by Cousins et al. (2007) (link), with some changes. Frozen leaf tissue was processed in ice-cold glass homogenizers with 500 μl of extraction buffer (50 mM HEPES-KOH pH 7.8, 1 mM EDTA, 0.1% Triton-X, 10 mM dithiothreitol, and 1% polyvinylpolypyrrolidone) and 10 μl of protease inhibitor cocktail (Sigma). The homogenate was briefly centrifuged and the supernatant used for assays. For PEPC, 10 μl of leaf extract was combined with 980 μl of assay buffer (50 mM EPPS-NaOH pH 8, 10 mM MgCl2, 0.5 mM EDTA, 0.2 mM NADH, 5 mM glucose-6-phosphate 1 mM NaHCO3, and 1 U ml−1 malate dehydrogenase) and the reaction initiated by the addition of 10 μl of 400 mM PEP. For Rubisco, 10 μl of leaf extract was combined with 970 μl of assay buffer (50 mM EPPS-NaOH pH 8, 10 mM MgCl2, 0.5 mM EDTA, 1 mM ATP, 5 mM phosphocreatine, 20 mM NaHCO3, 0.2 mM NADH, 50 U ml−1 creatine phosphokinase, 0.2 mg carbonic anhydrase, 50 U ml−1 3-phosphoglycerate kinase, 40 U ml−1 glyceraldehyde-3-phosphate dehydrogenase, 113 U m;−1 Triose-phosphate isomerase, 39 U ml−1 glycerol 3 phosphate dehydrogenase) and the reaction initiated by the addition of 20 μl of 21.9 mM ribulose-1, 5-bisphosphate (RuBP). The activity of both enzymes was calculated by monitoring the decrease of NADH absorbance at 340 nm with a diode array spectrophotometer (Hewlett Packard) after initiation of the reaction.
Chlorophyll was extracted from frozen leaf discs in a glass homogenizer with 80% acetone. The chlorophyll a and b contents of extracts were measured in a quartz cuvette at 663.3 nm and 646.6 nm, and calculated according to Porra et al. (1989) .
Publication 2010
Acetone Bicarbonate, Sodium Biological Assay Buffers Chlorophyll Chlorophyll A Cold Temperature Creatine Kinase Dehydratase, Carbonate Dithiothreitol Edetic Acid enzyme activity Freezing Glucose-6-Phosphate Glyceraldehyde-3-Phosphate Dehydrogenases Glycerol-3-Phosphate Dehydrogenase HEPES Magnesium Chloride Malate Dehydrogenase NADH Phosphocreatine Phosphotransferases Photosynthesis Plant Leaves polyvinylpolypyrrolidone Protease Inhibitors Quartz ribulose Ribulose-Bisphosphate Carboxylase Tissues Triose-Phosphate Isomerase
A thorough literature search was performed to obtain an in-depth knowledge of all the major metabolic pathways known to occur in an epithelial cell of the small intestine. We then retrieved the corresponding reactions and genes from the human metabolic reconstruction (13 (link)), which is accessible through the BiGG database (70 (link)), to compile a draft reconstruction. Missing transport and metabolic reactions for peptides and for dietary fibers were added to the initial draft reconstruction upon detailed manual gap analysis and further review of the corresponding literature. Genome annotations from the EntrezGene database (71 (link)) as well as protein information from the UniProt (72 (link)) and BRENDA database (73 (link)) were used in addition to the information retrieved from the scientific literature to assign GPR associations to the reactions not present in Recon 1. For the reactions that were extracted from the Recon 1, GPR associations were kept as reported in Recon 1, since no comprehensive transcriptomic data are available for sIECs. The sIEC metabolic reconstruction was assembled and converted to a mathematical model using rBioNet as a reconstruction environment (74 (link)) and an established protocol (75 ).
We used the global human metabolic network, Recon 1 (13 (link)), as reaction database, but adjusted sub-cellular and extracellular location, reaction stoichiometry and directionality according to literature evidence. Only those reactions and pathways with literature evidence for their occurrence in human small intestinal enterocytes were incorporated into hs_sIEC611 from the global human metabolic reconstruction Recon 1, which captures metabolic capabilities known to occur in any human cell. Moreover, we added 262 transport and 50 metabolic reactions, which were not present in Recon 1, but for which supporting information for their presence in sIECs could be found in the scientific literature (Fig. 1E, Supplementary Material, Table S2). These reactions included many transport systems specific for enterocytes and metabolic pathways for sulfo-cysteine metabolism, dietary fiber metabolism, di- and tri-peptide degradation and cholesterol-ester synthesis (Fig. 1E, Supplementary Material, Table S2). In addition to these reactions, 73 reactions were added from our recently published acylcarnitine/fatty acid oxidation module for the human metabolic reconstruction (20 (link)). We added further 95 reactions, which were present in Recon 1, but for which the compartment was adjusted by placing them into the lumen compartment. The stoichiometry of the reactions catalyzed by the glucose 6-phosphate dehydrogenase (E.C. 1.1.1.49), the 6-phosphogluconolactonase (E.C. 3.1.1.31) and the phosphogluconate dehydrogenase (E.C. 1.1.1.44) was changed to three, since they were required to generate three molecules each of 6-phospho-d-glucono-1,5-lactone, 6-Phospho-d-gluconate and ribulose-5-phosphate simultaneously (76 ). The directionality of ATP requiring fatty acid activation reactions catalyzed by the fatty acyl-CoA ligase (E.C. 6.2.1.3) was changed in agreement with a recent report (76 ). Also, the cofactor requirement and sub-cellular localization of reactions included in the cholesterol synthesis pathway, which are catalyzed by the desmosterol reductase (E.C. 1.3.1.72) and HMG-CoA reductase (E.C. 2.3.3.10) reactions, were updated in accordance with the current literature evidence (76 ).
Publication 2013
DNA was isolated from the sample LP01 with a DNeasy Plant Mini Kit (Qiagen). Cells were mechanically disrupted by shaking for 15 min (30 Hz) in the presence of glass beads (3 mm diameter, Sigma–Aldrich) in a Mixer Mill MM 400 (Retsch, Germany). Then, samples were put in freezer at −20 °C for half an hour. Subsequently, DNA was isolated in accordance with the manufacturer’s procedure. Quality and concentration of DNA was measured on the NanoDrop® ND–1000 Spectrophotometer (NanoDrop Technologies, Inc.).
The 18S small subunit ribosomal RNA gene (18S rDNA), internal transcribed spacer regions 1 and 2 (ITS1, ITS2 rDNA) and ribulose–1,5–bisphosphate carboxylase/oxygenase large subunit (rbcL) gene regions were amplified from DNA isolates by PCR using existing primers (Table 2). Amplification reactions for 18S rDNA was performed using cycle parameters according to Katana et al. (2001) with minor modification that duration of initial denaturation was prolonged for 10 min and annealing temperatures were 50 °C, 58 °C and 61 °C. Amplification reactions for rbcL gene were performed using cycle parameters according to Hoham et al. (2002) with minor change that three different annealing temperatures were applied (53 °C, 55 °C, 59 °C). Each 20 μl of PCR reaction for 18S and rbcL amplification contained 5 μl of DNA isolates (diluted to concentration of 5 ng.μl−1), 0.8 μl of each 10 μM primer, 1.6 μl of 25 mM MgCl2, 1.5 μl of 2 mM dNTPs, 2 μl of 10× Taq buffer + KCl–MgCl2, 7.8 μl sterile Milli–Q water, and 0.5 μl of 1U.μl−1 Taq DNA polymerase (Fermentas, USA). Amplification reactions for ITS2 rDNA region were performed using cycle parameters according to Goff & Moon (1993) with minor modification that the gradient of annealing temperature was included (56 °C, 58 °C, 61 °C, 64 °C). Each 35 μl PCR reaction contained 1 μl of DNA isolates (diluted to concentration of 5 ng μl−1), 1.4 μl of each 10 μM primer, 2.8 μl of 25 mM MgCl2, 2.6 μl of 2 mM dNTPs, 3.5 μl of 10× buffer Taq buffer + KCl–MgCl2, 21.8 μl sterile Milli–Q water, and 0.5 μl of 1U.μl−1 Taq DNA polymerase (Fermentas). The PCR products were stained with bromophenol loading dye, quantified on 1.5% agarose gel, stained with GelRed. The amplification products were purified and sequenced using an Applied Biosystems automated sequencer (ABI 3730×l) at Macrogen (Korea). The newly obtained sequences were submitted to NCBI Nucleotide sequence database (accession numbers for Cr. nivalis subsp. tatrae LP01: 18S, ITS1, ITS2 – KY499614, rbcL – KY499615; Cr. nivalis P24/DR4: rbcL – KY499616).
The nuclear rDNA ITS2 region was identified using a web interface at the ITS2 database showing position of 5.8S and 26S motives (http://its2.bioapps.biozentrum.uni–wuerzburg.de/cgi–bin/index.pl?annotator; Koetschan et al. 2010 (link)). The sequence was then folded with 5.8S–LSU stem regions using the Mfold server accessible at http://mfold.rna.albany.edu/?q5mfold (Zuker 2003 (link)). A model of the secondary structure consistent with the specific features of nuclear rDNA ITS2 was selected: four helixes, U–U mismatch in helix II, and the UGGU motif near the 5´–end site apex of helix III (Coleman 2007 (link)).
Publication 2017

Most recents protocols related to «Ribulose»

To determine the KM(RuBP), photospectrometric reactions were set up with slight adaptations to previously published protocols 38 (link) . Reactions were carried out in 100 mM HEPES-KOH (pH 8.00) and contained 10 mM MgCl2, 2.5 mM ATP, 0.3 mM NADH, 2.5 U/mL pgk, 5 U/mL gapdh, 0.02 mg/mL carbonic anhydrase, 55 mM NaHCO3, varying amounts of RuBP (0 -5 mM), 0.2-2 µM activated Rubisco, and a 5-fold SSU excess, if applicable. Rubisco was activated by a 30-minute pre-incubation in 50 mM HEPES-KOH (pH 8.00), 10 mM MgCl2, 20 mM NaHCO3, and 0.02 mg/mL carbonic anhydrase. Reaction progress was followed by measuring the depletion of NADH at 340 nm (Abs340).
Publication 2024
The N and P concentrations of the dry sample were measured using the micro-Kjeldahl method and the molybdenum blue method, respectively [92 (link),93 (link)].
According to Wang et al., the PNUE was given by: [94 (link)]

Anmax, the maximum net photosynthetic rate; Narea, total foliar N.
N allocation within the photosynthetic apparatus was calculated according to the model from Niinemets et al. [95 (link)].

PNcb, the fraction of nitrogen allocated to the carboxylation system; Vcmax, maximum ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) carboxylation rate; 6.25, 6.25 g Rubisco (g nitrogen in Rubisco)−1 converts nitrogen content to protein content; Vcr, the maximum rate of Ribulose-1,5-bisphosphate (RUBP) carboxylation per unit Rubisco protein (20.8 μmol CO2 (g Rubisco)−1 s−1); Narea, total foliar N.

PNet, the fraction of nitrogen allocated to electron transport components; Jmax, maximum electron transport rate; 8.06, the investment in bioenergetics is at least 8.06 μmol cyt f (g N in bioenergetics)−1; Jmc, the potential rate of photosynthetic electron transport per unit cytochrome f (155.6 μmol electrons (μmol cyt f)−1 s−1); Narea, total foliar N.

PNlc, the fraction of nitrogen allocated to the light capture system; Cc, Total chlorophyll concentration; Narea, total foliar N; CB, chlorophyll-binding (2.15 mmol (g N)−1).

PNnon-psn is the fraction of nitrogen allocated to non-photosynthetic nitrogen.
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Publication 2024
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Gas exchange parameters were measured from 08:00 h to 11:00 h on the rst fully expanded leaf using an infrared gas analyzer (IRGA, Walz -GFS3000) with a coupled uorometer. The analyzed parameters included net photosynthesis (A), transpiration (E), stomatal conductance (gs), and internal CO 2 concentration (Ci). Using the data, the ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) carboxylation e ciency (A/Ci), intrinsic water use e ciency (A/gs), and instantaneous water use e ciency (A/E) were calculated.
Publication 2024
According to the established screening strategy, four target sequences, including P-35S, T-NOS, T-E9 (ribulose-1,5-bisphosphate carboxylase small subunit gene terminator), and T-pin II (protease inhibitor II gene terminator) were inserted, and the corresponding endonuclease-restriction sites were added at the splice sites of various elements; this was followed by the insertion of targeted sequences of Lectin, zssIIb (starch synthase IIb), Cru A (cruciferin A), and SPS (sucrose phosphate synthase) genes. These four genes were used as endogenous reference genes for soybean, maize, canola, and rice, respectively, to determine whether the tested samples contained the corresponding crop species [43 , 44 (link)]. The spliced sequences were artificially synthesized (Sangon Biotech, Shanghai, China) and cloned into the pUC18 vector between the EcoR I and Hind III sites to generate the pGMOIT-1 plasmid. The target sequences of P-AtRbcS4 (the ribulose-1,5-bisphosphate carboxylase small subunit gene promoter), pat (phosphinothricin N-acetyltransferase gene), and the four endogenous reference genes were artificially synthesized (Sangon Biotech) and cloned in the same arrangement described above to generate the pGMOIT-2 plasmid. Escherichia coli TOP10 strains containing plasmids pGMOIT-1 or pGMOIT-2 were named T10pGMOIT-1 and T10pGMOIT-2, respectively, and used for plasmid maintenance or expansion. Positive plasmids pGMOIT-1 and pGMOIT-2 were extracted using the Axygen AxyPrep Plasmid Microprep Kit (Thermo Fisher Scientific, Shanghai, China) following manufacturer instructions and validated using enzymatic digestion with different combinations of restriction endonucleases (Thermo Fisher Scientific).
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Publication 2024
Under a calibrated compound light microscope (Olympus CH20i) with 10 ×, 40 ×, and 100 × immersion lenses, the main morphological characteristics of the isolated algal strain were examined and digital photomicrographs of the specimens were taken. For molecular identification, the genomic DNA extraction method (CTAB) was used to characterize the algal strain, which was then followed by PCR, gel electrophoresis, and algal identification was done by using rbcL (Ribulose bisphosphate Carboxylase Large subunit) gene sequencing. In addition, that sequence was uploaded to the NCBI database to obtain an accession number.
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Publication 2024

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The LI-6400 is a portable photosynthesis system designed for measuring gas exchange in plants. It is capable of measuring net carbon dioxide and water vapor exchange, as well as environmental conditions such as temperature, humidity, and light levels.
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The LI-6400XT is a portable photosynthesis system designed for measuring gas exchange in plants. It is capable of measuring net photosynthesis, transpiration, stomatal conductance, and other physiological parameters. The system consists of a control unit and a leaf chamber that encloses a portion of a plant leaf.
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The ABI 3730XL is a high-performance, automated DNA sequencing system. It is designed to provide efficient and reliable DNA sequencing capabilities for a wide range of applications, including genetic research, diagnostics, and drug discovery.
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Ribulose-5-phosphate is a chemical compound that serves as an intermediate in the Calvin cycle of photosynthesis. It is a key substrate in the conversion of carbon dioxide to organic compounds within plant cells.
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The Junior-PAM is a compact and portable chlorophyll fluorescence measuring device. It is designed to assess the photosynthetic performance of plants. The instrument provides a non-invasive and reliable method for evaluating various photosynthetic parameters.
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Ribose 5-phosphate is a chemical compound that functions as an important intermediate in several metabolic pathways, including the pentose phosphate pathway and nucleic acid synthesis.
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More about "Ribulose"

Ribulose, a crucial five-carbon sugar, plays a central role in the Calvin cycle of photosynthesis.
It serves as the substrate for the enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (RuBisCO), which catalyzes the first step in carbon fixation.
Ribulose is a key intermediate in the conversion of light energy into chemical energy during the light-independent reactions of photosynthesis.
Researching ribulose and its metabolic pathways can provide invaluable insights into plant physiology, carbon cycling, and potential applications in bioenergy and agriculture.
Tools like the DNeasy Plant Mini Kit, LI-6400 and LI-6400XT gas exchange systems, and the ABI 3730XL DNA Analyzer can be used to study ribulose and related intermediates such as ribulose-5-phosphate and ribose 5-phosphate.
Techniques like Sanger sequencing and fluorescence-based methods using instruments like the Junior-PAM and Dual-PAM-100 can help elucidate the enzymes and pathways involved in ribulose metabolism.
The LA211 leaf chamber can be used to measure photosynthetic parameters related to ribulose utilization.
By leveraging the latest research and technological advancements, scientists can unlock the full potential of ribulose and advance our understanding of plant biology, carbon cycling, and sustainable bioenergy solutions.
PubCompare.ai, an AI-driven platform, can help locate the best protocols and products to imrove the reproducibility and accuracy of ribulose research.