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Tyrosine

Tyrosine is a nonessential amino acid that plays a crucial role in various physiological processes.
It serves as a precursor for the synthesis of important neurotransmitters and hormones, including dopamine, epinephrine, and thyroid hormones.
Tyrosine is involved in melanin production, skin pigmentation, and the regulation of metabolism.
Dietary sources of tyrosine include protein-rich foods such as meat, dairy, eggs, and legumes.
Proper tyrosine levels are essential for maintaining cognitive function, mood, and overall health.
Researchers studying tyrosine's impact on the body can leverage PubCompare.ai's AI-driven platform to easily locate, comapre, and identify the best protocols and products for their experiments, enhancing the reproducibility and accuracy of their tyrosine-related studies.

Most cited protocols related to «Tyrosine»

To maximize transferability of the parameters, multidimensional structure scans were employed to generate conformational diversity. For smaller side chains, grid scans in dihedral space were used to generate side chain variety, including both α and β backbone conformations for each side chain rotamer. Grid scans were generated for Val in one dimension, as it only has χ1, at an interval of 10°. Grids were generated for Asp, Asn, Cys, Phe, His (δ-, ɛ-, and doubly-protonated), Ile, Leu, Ser, Thr, and Trp in two dimensions, as they have χ1 and χ2, at intervals of 20°, yielding 324 structures per amino acid.
We were unable to exhaustively explore side chain conformational space side chains with more than two rotatable bonds. Tyrosine has 3 rotatable χ bonds, but dihedral space is reduced as 180° rotation of either the phenol (χ2) or of the hydroxyl produce the same effect when accounting for symmetry of the ring. We therefore fully scanned each tyrosine dihedral when the other two were at a stable rotamer defined as any instance of that value in the rotamer library for this amino acid, rounded to the nearest 10° and limiting χ2 to (−90°, 90°] to account for symmetry. Stable rotamers for the hydroxyl, not in the rotamer library, were inferred from the QM energy profiles discussed above. Stable rotamers were 180° or ±60° for χ1, ±30° or 90° for χ2, and 0° or 180° for the hydroxyl. Conformations were generated using a full scan for each dihedral (at 20° increments), repeated for every combination of stable rotamer values for the other two dihedrals. As protonated aspartate has nearly the same dihedrals as Tyr (χ1, χ2 and hydroxyl), it was scanned in the same manner, but without χ2 restriction because aspartate does not have the same symmetry properties.
Cysteine presents a special case, as it can form disulfide bonds that bridge two amino acids. In addition to developing parameters for reduced Cys (no disulfide), a pair of Cys dipeptides with a disulfide bond was employed to scan the S-S energy profile. However, a disulfide between CysA and CysB has a total of five dihedrals: χ1A, χ2A, χSS, χ2B, and χ1B. As full sampling across five dihedrals is clearly intractable, conformation space was reduced by applying the same χ1 / χ2 values to both dipeptides. Using this symmetry, a two-dimensional scan was performed for all χ1 / χ2 combinations using 20° spacing; this scan was repeated with χSS restrained to 180°, ±60°, or ±90° (five 2D scans). Separately, the χSS profile was scanned with 20° spacing using χ1 of 180° or ±60° and χ2 of 180° or ±60° (nine 1D scans total). As with the other amino acids, the entire procedure was repeated with the backbone in α and β conformations; here, both dipeptides adopted the same backbone conformation.
The remaining side chains, Arg+, Gln, Glu (protonated), Glu,Lys+, and Met, have at least three side chain dihedrals (Table S1). Rather than performing a grid search, MD simulations were used to generate diverse conformations of these side chains. Each dipeptide was simulated twice, with α or β backbone restraints, for 100 ns each. To overcome kinetic traps, these simulations were performed at 500 K and the dielectric was set to 4r. Next, a diverse subset was generated by mapping each conformation to a multidimensional grid spaced 10° in each χ. The five lowest energy conformations at each grid point were saved. From each simulation grid, five hundred structures were randomly selected (comparable to the number generated by the grid procedure described above for Tyr). Because the longer, more flexible side chains of these amino acids can adopt conformations with strong interactions between backbone and side chain, conformations where we suspected the in vacuo MM description may produce fitting artifacts were excluded, using electrostatic and distance cutoffs defined in the Supporting Information.
Publication 2015
Amino Acids Aspartate Dipeptides Disulfides DNA Library Electrostatics Hydroxyl Radical Kinetics Phenol Radionuclide Imaging Tyrosine Vertebral Column
lDDT measures how well the environment in a reference structure is reproduced in a protein model. It is computed over all pairs of atoms in the reference structure at a distance closer than a predefined threshold Ro (called inclusion radius), and not belonging to the same residue. These atom pairs define a set of local distances L. A distance is considered preserved in the model M if it is, within a certain tolerance threshold, the same as the corresponding distance in . If one or both the atoms defining a distance in the set are not present in M, the distance is considered non-preserved. For a given threshold, the fraction of preserved distances is calculated. The final lDDT score is the average of four fractions computed using the thresholds 0.5 Å, 1 Å, 2 Å and 4 Å, the same ones used to compute the GDT-HA score (Battey et al., 2007 (link)). For partially symmetric residues, where the naming of chemically equivalent atoms can be ambiguous (glutamic acid, aspartic acid, valine, tyrosine, leucine, phenylalaine and arginine), two lDDTs, one for each of the two possible naming schemes, are computed using all non-ambiguous atoms in M in the reference. The naming convention giving the higher score in each case is used for the calculation of the final structure-wide lDDT score.
The lDDT score can be computed using all atoms in the prediction (the default choice), but also using only distances between Cα atoms, or between backbone atoms. Interactions between adjacent residues can be excluded by specifying a minimum sequence separation parameter. Unless explicitly specified, the calculation of the lDDT scores for all experiments described in this article has been performed using default parameters, i.e. Ro = 15 Å, using all atoms at zero sequence separation.
Publication 2013
Arginine Aspartic Acid Conferences Glutamic Acid Immune Tolerance Leucine Radius Staphylococcal Protein A Tyrosine Valine Vertebral Column

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Publication 2010
Acyltransferase Amino Acids Anabolism brevianamide F CSF2RB protein, human Dehydrogenase, Aminoadipate-Semialdehyde Dimethylallyltranstransferase Enzymes Genes Genes, Fungal Genome Genome, Fungal Hybrids Lyngbya Toxins Nitric Oxide Synthase non-ribosomal peptide synthase Proteins Protein Subunits SET Domain short chain trans-2-enoyl-CoA reductase Synthase, Polyketide tryptophan dimethylallyltransferase Tyrosine Vertebral Column
The PhosphoBase (6 (link)) consists of 1883 experimentally verified phosphorylation sites within 597 protein entries. The number of serine, threonine and tyrosine sites is 984, 246 and 653, respectively. Swiss-Prot (7 (link)) (release 45 of October 2004) maintains 163 500 protein entries, of which 3614 have phosphorylation annotation. Among these entries, the number of serine, threonine and tyrosine sites was 1005, 281 and 321, respectively. Generally, the serine, threonine and tyrosine, which are not annotated as phosphorylation residues, within the experimentally validated phosphorylated proteins, are selected as negative sets, i.e. the non-phosphorylated sites. Therefore, two negative (non-phosphorylated) datasets were obtained from the PhosphoBase and Swiss-Prot based on the phosphorylation annotation. Because of the absence of good negative dataset exists for non-phosphorylated sites, the residues that had not been previously annotated as phosphorylated in phosphorylation annotated proteins were chosen as a reflection of more general non-phosphorylated sites. Supplementary Table S1 summarizes the statistics of kinase-specific phosphorylated sites used for learning models in the proposed application. This work confirms the existence of two major protein kinases phosphorylating either at serine/threonine residues or at tyrosine residues.
Figure 1 depicts a flowchart of the proposed method. Phosphorylated sites were first extracted as positive sets; non-phosphorylated sites were extracted as negative sets, and the catalytic kinase annotations were obtained from PhosphoBase and Swiss-Prot. The positive sets were then categorized by catalytic kinases. Alternatively, in larger positive groups, the sequences of the phosphorylated sites can be clustered into subgroups by maximal dependence decomposition (MDD) (8 (link)). The MDD was first applied in nucleotides and is a recursive process to divide a sequence set into tree-like subgroups based on the positional dependency of the sequences. Here, we applied the MDD to group protein phosphorylation substrates into subgroups. As the example given in Figure 1, 232 phosphorylation serine substrates are grouped into subgroups. When applying MDD to cluster the sequences of a positive set, a parameter, i.e. the minimum-cluster-size, should be set. If the size of a subgroup is less than the minimum-cluster-size, the subgroup is terminated to be divided. The MDD process terminates until all the subgroup sizes are less than the minimum-cluster-size.
Thereupon, the concept of the profile HMM was adopted to learn computational models from positive sets of phosphorylation sites. To evaluate the learned models, k-fold cross-validation and leave-one-out cross-validation were performed on them. After evaluating the models, the model with highest accuracy in each dataset was chosen.
For each kinase-specific positive set of the phosphorylated sites, the best performed model is selected and used to identify the phosphorylation sites within the input protein sequences by HMMsearch (9 (link)). To search the hits of a model, HMMER returns both a HMMER bit score and an expectation value (E-value). The HMMER bit score is used as the criterion to define a HMM match. We select the HMMER score as the criterion to define a HMM match. A search of a model with the HMMER score greater than the threshold t is defined as a positive prediction, i.e. a HMM recognizes a phosphorylation site. The threshold t of each model is decided by maximizing the accuracy measure during a variety of cross-validations with the HMM bit score value range from 0 to −10. For example, Supplementary Figure S1 depicts the optimization of the threshold of the HMM bit scores in the S_PKA model. The threshold of the S_PKA model is set to −4.5 to maximize the accuracy measure of the model.
When considering a MDD-clustered dataset, for example, MDD-clustered PKA catalytic serine (S_PKA), the HMMs are trained separately from the subgroups of the phosphorylated sites resulted by MDD. Each model is used to search in the given protein sequences for the phosphorylated sites. A positive prediction of a model group is defined by at least one of the models that makes a positive prediction, whereas a negative prediction is defined as all the models that make negative predictions.
Publication 2005
Amino Acid Sequence Base Sequence Catalysis Exhaling Hypertelorism, Severe, With Midface Prominence, Myopia, Mental Retardation, And Bone Fragility Nucleotides Phosphorylation Phosphotransferases Protein Kinases Proteins Reflex Serine Threonine Trees Tyrosine
BY4741 wild-type yeast were grown in yeast extract peptone dextrose media to mid-log phase (OD600 = 0.6). Proteins were chemically extracted with YPer (Thermo Scientific Pierce; Rockford, IL), and digested with Promega sequencing-grade modified trypsin (Madison, WI) at a 1:50 enzyme:substrate ratio at 37 °C overnight and quenched by acidification with TFA. Peptides were desalted and labeled with Thermo Scientific Pierce TMTsixplex (Rockford, IL; lot number KD130680A), with intermittent mixing at room temperature, and quenched following an hour of incubation. Peptides labeled with tags of nominal m/z 126 through 131 were mixed in ratios of 1: 5: 2: 1.5: 1: 3, respectively.
Peptides were separated on a Waters nanoACQUITY UPLC (Milford, MA) with a self-packed 9 cm precolumn (75 μm i.d.) and a 30 cm analytical column (50 μm i.d.), both packed with Alltech Alltima 5 μm C18 particles (Deerfield, IL) [33 (link)]. The peptides were eluted with a gradient of 5 to 30% acetonitrile over two hours at a flow rate of 300 nL/min. The eluent was analyzed with LC–MS/MS on a Thermo Scientific LTQ Orbitrap Velos mass spectrometer (San Jose, CA/Bremen, Germany). The instrument method was 165 minutes and consisted of a 30,000 resolving power MS1 survey scan followed by data-dependent top-10 higher-energy collision dissociation (HCD) MS2 at 7,500 resolving power, all detected in the orbitrap. Precursor charges states that were unknown or +1 were excluded, and dynamic exclusion was enabled after one fragmentation event for 45 seconds.
This dataset was searched against the Saccharomyces Genome Database [36 (link)] (http://www.yeastgenome.org/; January 5, 2010 release; “all” file including verified, uncharacterized, and dubious open reading frames, and pseudogenes). Full trypsin enzymatic specificity was required, allowing up to three missed cleavages. Carbamidomethylation of cysteines (+57 Da) and TMT 6-plex on peptide N-termini and lysines (+229 Da) were specified as fixed modifications, while oxidation of methionines (+16 Da) and TMT 6-plex (+229 Da) on tyrosines were specified as variable modifications. An average mass tolerance of ±5 Da was used for precursors, while a monoisotopic mass tolerance of ±0.01 Da was used for products. For TPP analysis, the data was searched with Sequest (version 27 from the University of Washington) or OMSSA (2.1.9) using either a ±5 Da average precursor mass tolerance or a ±10 ppm monoisotopic precursor mass tolerance and a monoisotopic fragment bin size of 0.01 Da (Sequest) or a monoisotopic product mass tolerance of ±0.01 Da (OMSSA). Results were filtered with PeptideProphet, iProphet and ProteinProphet from TPP 4.3 rev 1. The accurate mass, non-parametric model, and decoy estimation options were used in PeptideProphet. The TPP component Libra was used for isobaric label quantitation.
Publication 2011
acetonitrile Cysteine Cytokinesis Enzymes Genome Glucose Immune Tolerance Lysine Methionine Neoplasm Metastasis Open Reading Frames Peptides Peptones Promega Proteins Pseudogenes Radionuclide Imaging Saccharomyces Saccharomyces cerevisiae Tandem Mass Spectrometry Trypsin Tyrosine

Most recents protocols related to «Tyrosine»

Example 2

A. Seed Treatment with Isolated Microbe

In this example, an isolated microbe from Tables 1-3 will be applied as a seed coating to seeds of corn (Zea mays). Upon applying the isolated microbe as a seed coating, the corn will be planted and cultivated in the standard manner.

A control plot of corn seeds, which did not have the isolated microbe applied as a seed coating, will also be planted.

It is expected that the corn plants grown from the seeds treated with the seed coating will exhibit a quantifiably higher biomass than the control corn plants.

The biomass from the treated plants may be about 1-10% higher, 10-20% higher, 20-30% higher, 30-40% higher, 40-50% higher, 50-60% higher, 60-70% higher, 70-80% higher, 80-90% higher, or more.

The biomass from the treated plants may equate to about a 1 bushel per acre increase over the controls, or a 2 bushel per acre increase, or a 3 bushel per acre increase, or a 4 bushel per acre increase, or a 5 bushel per acre increase, or more.

In some aspects, the biomass increase is statistically significant. In other aspects, the biomass increase is not statistically significant, but is still quantifiable.

B. Seed Treatment with Microbial Consortia

In this example, a microbial consortium, comprising at least two microbes from Tables 1-3 will be applied as a seed coating to seeds of corn (Zea mays). Upon applying the microbial consortium as a seed coating, the corn will be planted and cultivated in the standard manner.

A control plot of corn seeds, which did not have the microbial consortium applied as a seed coating, will also be planted.

It is expected that the corn plants grown from the seeds treated with the seed coating will exhibit a quantifiably higher biomass than the control corn plants.

The biomass from the treated plants may be about 1-10% higher, 10-20% higher, 20-30% higher, 30-40% higher, 40-50% higher, 50-60% higher, 60-70% higher, 70-80% higher, 80-90% higher, or more.

The biomass from the treated plants may equate to about a 1 bushel per acre increase over the controls, or a 2 bushel per acre increase, or a 3 bushel per acre increase, or a 4 bushel per acre increase, or a 5 bushel per acre increase, or more.

In some aspects, the biomass increase is statistically significant. In other aspects, the biomass increase is not statistically significant, but is still quantifiable.

C. Treatment with Agricultural Composition Comprising Isolated Microbe

In this example, an isolated microbe from Tables 1-3 will be applied as an agricultural composition, administered to the corn seed at the time of sowing.

For example, it is anticipated that a farmer will apply the agricultural composition to the corn seeds simultaneously upon planting the seeds into the field. This can be accomplished, for example, by applying the agricultural composition to a hopper/bulk tank on a standard 16 row planter, which contains the corn seeds and which is configured to plant the same into rows. Alternatively, the agricultural composition can be contained in a separate bulk tank on the planter and sprayed into the rows upon planting the corn seed.

A control plot of corn seeds, which are not administered the agricultural composition, will also be planted.

It is expected that the corn plants grown from the seeds treated with the agricultural composition will exhibit a quantifiably higher biomass than the control corn plants.

The biomass from the treated plants may be about 1-10% higher, 10-20% higher, 20-30% higher, 30-40% higher, 40-50% higher, 50-60% higher, 60-70% higher, 70-80% higher, 80-90% higher, or more.

The biomass from the treated plants may equate to about a 1 bushel per acre increase over the controls, or a 2 bushel per acre increase, or a 3 bushel per acre increase, or a 4 bushel per acre increase, or a 5 bushel per acre increase, or more.

In some aspects, the biomass increase is statistically significant. In other aspects, the biomass increase is not statistically significant, but is still quantifiable.

D. Treatment with Agricultural Composition Comprising Microbial Consortia

In this example, a microbial consortium, comprising at least two microbes from Tables 1-3 will be applied as an agricultural composition, administered to the corn seed at the time of sowing.

For example, it is anticipated that a farmer will apply the agricultural composition to the corn seeds simultaneously upon planting the seeds into the field. This can be accomplished, for example, by applying the agricultural composition to a hopper/bulk tank on a standard 16 row planter, which contains the corn seeds and which is configured to plant the same into rows. Alternatively, the agricultural composition can be contained in a separate bulk tank on the planter and sprayed into the rows upon planting the corn seed.

A control plot of corn seeds, which are not administered the agricultural composition, will also be planted.

It is expected that the corn plants grown from the seeds treated with the agricultural composition will exhibit a quantifiably higher biomass than the control corn plants.

The biomass from the treated plants may be about 1-10% higher, 10-20% higher, 20-30% higher, 30-40% higher, 40-50% higher, 50-60% higher, 60-70% higher, 70-80% higher, 80-90% higher, or more.

The biomass from the treated plants may equate to about a 1 bushel per acre increase over the controls, or a 2 bushel per acre increase, or a 3 bushel per acre increase, or a 4 bushel per acre increase, or a 5 bushel per acre increase, or more.

In some aspects, the biomass increase is statistically significant. In other aspects, the biomass increase is not statistically significant, but is still quantifiable.

A. Seed Treatment with Isolated Microbe

In this example, an isolated microbe from Tables 1-3 will be applied as a seed coating to seeds of corn (Zea mays). Upon applying the isolated microbe as a seed coating, the corn will be planted and cultivated in the standard manner.

A control plot of corn seeds, which did not have the isolated microbe applied as a seed coating, will also be planted.

It is expected that the corn plants grown from the seeds treated with the seed coating will exhibit a quantifiable and superior ability to tolerate drought conditions and/or exhibit superior water use efficiency, as compared to the control corn plants.

The drought tolerance and/or water use efficiency can be based on any number of standard tests from the art, e.g leaf water retention, turgor loss point, rate of photosynthesis, leaf color and other phenotypic indications of drought stress, yield performance, and various root morphological and growth patterns.

B. Seed Treatment with Microbial Consortia

In this example, a microbial consortium, comprising at least two microbes from Tables 1-3 will be applied as a seed coating to seeds of corn (Zea mays). Upon applying the microbial consortium as a seed coating, the corn will be planted and cultivated in the standard manner.

A control plot of corn seeds, which did not have the microbial consortium applied as a seed coating, will also be planted.

It is expected that the corn plants grown from the seeds treated with the seed coating will exhibit a quantifiable and superior ability to tolerate drought conditions and/or exhibit superior water use efficiency, as compared to the control corn plants.

The drought tolerance and/or water use efficiency can be based on any number of standard tests from the art, e.g leaf water retention, turgor loss point, rate of photosynthesis, leaf color and other phenotypic indications of drought stress, yield performance, and various root morphological and growth patterns.

C. Treatment with Agricultural Composition Comprising Isolated Microbe

In this example, an isolated microbe from Tables 1-3 will be applied as an agricultural composition, administered to the corn seed at the time of sowing.

For example, it is anticipated that a farmer will apply the agricultural composition to the corn seeds simultaneously upon planting the seeds into the field. This can be accomplished, for example, by applying the agricultural composition to a hopper/bulk tank on a standard 16 row planter, which contains the corn seeds and which is configured to plant the same into rows. Alternatively, the agricultural composition can be contained in a separate bulk tank on the planter and sprayed into the rows upon planting the corn seed.

A control plot of corn seeds, which are not administered the agricultural composition, will also be planted.

It is expected that the corn plants grown from the seeds treated with the with the agricultural composition will exhibit a quantifiable and superior ability to tolerate drought conditions and/or exhibit superior water use efficiency, as compared to the control corn plants.

The drought tolerance and/or water use efficiency can be based on any number of standard tests from the art, e.g leaf water retention, turgor loss point, rate of photosynthesis, leaf color and other phenotypic indications of drought stress, yield performance, and various root morphological and growth patterns.

D. Treatment with Agricultural Composition Comprising Microbial Consortia

In this example, a microbial consortium, comprising at least two microbes from Tables 1-3 will be applied as an agricultural composition, administered to the corn seed at the time of sowing.

For example, it is anticipated that a farmer will apply the agricultural composition to the corn seeds simultaneously upon planting the seeds into the field. This can be accomplished, for example, by applying the agricultural composition to a hopper/bulk tank on a standard 16 row planter, which contains the corn seeds and which is configured to plant the same into rows. Alternatively, the agricultural composition can be contained in a separate bulk tank on the planter and sprayed into the rows upon planting the corn seed.

A control plot of corn seeds, which are not administered the agricultural composition, will also be planted.

It is expected that the corn plants grown from the seeds treated with the with the agricultural composition will exhibit a quantifiable and superior ability to tolerate drought conditions and/or exhibit superior water use efficiency, as compared to the control corn plants.

The drought tolerance and/or water use efficiency can be based on any number of standard tests from the art, e.g leaf water retention, turgor loss point, rate of photosynthesis, leaf color and other phenotypic indications of drought stress, yield performance, and various root morphological and growth patterns.

A. Seed Treatment with Isolated Microbe

In this example, an isolated microbe from Tables 1-3 will be applied as a seed coating to seeds of corn (Zea mays). Upon applying the isolated microbe as a seed coating, the corn will be planted and cultivated in the standard manner.

A control plot of corn seeds, which did not have the isolated microbe applied as a seed coating, will also be planted.

It is expected that the corn plants grown from the seeds treated with the seed coating will exhibit a quantifiable and superior ability to utilize nitrogen, as compared to the control corn plants.

The nitrogen use efficiency can be quantified by recording a measurable change in any of the main nitrogen metabolic pool sizes in the assimilation pathways (e.g., a measurable change in one or more of the following: nitrate, nitrite, ammonia, glutamic acid, aspartic acid, glutamine, asparagine, lysine, leucine, threonine, methionine, glycine, tryptophan, tyrosine, total protein content of a plant part, total nitrogen content of a plant part, and/or chlorophyll content), or where the treated plant is shown to provide the same or elevated biomass or harvestable yield at lower nitrogen fertilization levels compared to the control plant, or where the treated plant is shown to provide elevated biomass or harvestable yields at the same nitrogen fertilization levels compared to a control plant.

B. Seed Treatment with Microbial Consortia

In this example, a microbial consortium, comprising at least two microbes from Tables 1-3 will be applied as a seed coating to seeds of corn (Zea mays). Upon applying the microbial consortium as a seed coating, the corn will be planted and cultivated in the standard manner.

A control plot of corn seeds, which did not have the microbial consortium applied as a seed coating, will also be planted.

It is expected that the corn plants grown from the seeds treated with the seed coating will exhibit a quantifiable and superior ability to utilize nitrogen, as compared to the control corn plants.

The nitrogen use efficiency can be quantified by recording a measurable change in any of the main nitrogen metabolic pool sizes in the assimilation pathways (e.g., a measurable change in one or more of the following: nitrate, nitrite, ammonia, glutamic acid, aspartic acid, glutamine, asparagine, lysine, leucine, threonine, methionine, glycine, tryptophan, tyrosine, total protein content of a plant part, total nitrogen content of a plant part, and/or chlorophyll content), or where the treated plant is shown to provide the same or elevated biomass or harvestable yield at lower nitrogen fertilization levels compared to the control plant, or where the treated plant is shown to provide elevated biomass or harvestable yields at the same nitrogen fertilization levels compared to a control plant.

C. Treatment with Agricultural Composition Comprising Isolated Microbe

In this example, an isolated microbe from Tables 1-3 will be applied as an agricultural composition, administered to the corn seed at the time of sowing.

For example, it is anticipated that a farmer will apply the agricultural composition to the corn seeds simultaneously upon planting the seeds into the field. This can be accomplished, for example, by applying the agricultural composition to a hopper/bulk tank on a standard 16 row planter, which contains the corn seeds and which is configured to plant the same into rows. Alternatively, the agricultural composition can be contained in a separate bulk tank on the planter and sprayed into the rows upon planting the corn seed.

A control plot of corn seeds, which are not administered the agricultural composition, will also be planted.

It is expected that the corn plants grown from the seeds treated with the agricultural composition will exhibit a quantifiable and superior ability to utilize nitrogen, as compared to the control corn plants.

The nitrogen use efficiency can be quantified by recording a measurable change in any of the main nitrogen metabolic pool sizes in the assimilation pathways (e.g., a measurable change in one or more of the following: nitrate, nitrite, ammonia, glutamic acid, aspartic acid, glutamine, asparagine, lysine, leucine, threonine, methionine, glycine, tryptophan, tyrosine, total protein content of a plant part, total nitrogen content of a plant part, and/or chlorophyll content), or where the treated plant is shown to provide the same or elevated biomass or harvestable yield at lower nitrogen fertilization levels compared to the control plant, or where the treated plant is shown to provide elevated biomass or harvestable yields at the same nitrogen fertilization levels compared to a control plant.

D. Treatment with Agricultural Composition Comprising Microbial Consortia

In this example, a microbial consortium, comprising at least two microbes from Tables 1-3 will be applied as an agricultural composition, administered to the corn seed at the time of sowing.

For example, it is anticipated that a farmer will apply the agricultural composition to the corn seeds simultaneously upon planting the seeds into the field. This can be accomplished, for example, by applying the agricultural composition to a hopper/bulk tank on a standard 16 row planter, which contains the corn seeds and which is configured to plant the same into rows. Alternatively, the agricultural composition can be contained in a separate bulk tank on the planter and sprayed into the rows upon planting the corn seed.

A control plot of corn seeds, which are not administered the agricultural composition, will also be planted.

It is expected that the corn plants grown from the seeds treated with the agricultural composition will exhibit a quantifiable and superior ability to utilize nitrogen, as compared to the control corn plants.

The nitrogen use efficiency can be quantified by recording a measurable change in any of the main nitrogen metabolic pool sizes in the assimilation pathways (e.g., a measurable change in one or more of the following: nitrate, nitrite, ammonia, glutamic acid, aspartic acid, glutamine, asparagine, lysine, leucine, threonine, methionine, glycine, tryptophan, tyrosine, total protein content of a plant part, total nitrogen content of a plant part, and/or chlorophyll content), or where the treated plant is shown to provide the same or elevated biomass or harvestable yield at lower nitrogen fertilization levels compared to the control plant, or where the treated plant is shown to provide elevated biomass or harvestable yields at the same nitrogen fertilization levels compared to a control plant.

The inoculants were prepared from isolates grown as spread plates on R2A incubated at 25° C. for 48 to 72 hours. Colonies were harvested by blending with sterile distilled water (SDW) which was then transferred into sterile containers. Serial dilutions of the harvested cells were plated and incubated at 25° C. for 24 hours to estimate the number of colony forming units (CFU) in each suspension. Dilutions were prepared using individual isolates or blends of isolates (consortia) to deliver 1×105 cfu/microbe/seed and seeds inoculated by either imbibition in the liquid suspension or by overtreatment with 5% vegetable gum and oil.

Seeds corresponding to the plants of table 15 were planted within 24 to 48 hours of treatment in agricultural soil, potting media or inert growing media. Plants were grown in small pots (28 mL to 200 mL) in either a controlled environment or in a greenhouse. Chamber photoperiod was set to 16 hours for all experiments on all species. Air temperature was typically maintained between 22-24° C.

Unless otherwise stated, all plants were watered with tap water 2 to 3 times weekly. Growth conditions were varied according to the trait of interest and included manipulation of applied fertilizer, watering regime and salt stress as follows:

    • Low N—seeds planted in soil potting media or inert growing media with no applied N fertilizer
    • Moderate N—seeds planted in soil or growing media supplemented with commercial N fertilizer to equivalent of 135 kg/ha applied N
    • Insol P—seeds planted in potting media or inert growth substrate and watered with quarter strength Pikovskaya's liquid medium containing tri-calcium phosphate as the only form phosphate fertilizer.
    • Cold Stress—seeds planted in soil, potting media or inert growing media and incubated at 10° C. for one week before being transferred to the plant growth room.
    • Salt stress—seeds planted in soil, potting media or inert growing media and watered with a solution containing between 100 to 200 mg/L NaCl.

Untreated (no applied microbe) controls were prepared for each experiment. Plants were randomized on trays throughout the growth environment. Between 10 and 30 replicate plants were prepared for each treatment in each experiment. Phenotypes were measured during early vegetative growth, typically before the V3 developmental stage and between 3 and 6 weeks after sowing. Foliage was cut and weighed. Roots were washed, blotted dry and weighed. Results indicate performance of treatments against the untreated control.

TABLE 15
StrainShootRoot
Microbe sp.IDCropAssayIOC (%)IOC (%)
Bosea thiooxidans123EfficacyEfficacy
overall100%100%
Bosea thiooxidans54522WheatEarly vigor - insol P30-40 
Bosea thiooxidans54522RyegrassEarly vigor50-60 50-60 
Bosea thiooxidans54522RyegrassEarly vigor - moderate P0-100-10
Duganella violaceinigra111EfficacyEfficacy
overall100%100%
Duganella violaceinigra66361TomatoEarly vigor0-100-10
Duganella violaceinigra66361TomatoEarly vigor30-40 40-50 
Duganella violaceinigra66361TomatoEarly vigor20-30 20-30 
Herbaspirillum huttiense222Efficacy
overall100%
Herbaspirillum huttiense54487WheatEarly vigor - insol P30-40 
Herbaspirillum huttiense60507MaizeEarly vigor - salt stress0-100-10
Janthinobacterium sp.222Efficacy
Overall100%
Janthinobacterium sp.54456WheatEarly vigor - insol P30-40 
Janthinobacterium sp.54456WheatEarly vigor - insol P0-10
Janthinobacterium sp.63491RyegrassEarly vigor - drought0-100-10
stress
Massilia niastensis112EfficacyEfficacy
overall80%80%
Massilia niastensis55184WheatEarly vigor - salt stress0-1020-30 
Massilia niastensis55184WinterEarly vigor - cold stress0-1010-20 
wheat
Massilia niastensis55184WinterEarly vigor - cold stress20-30 20-30 
wheat
Massilia niastensis55184WinterEarly vigor - cold stress10-20 10-20 
wheat
Massilia niastensis55184WinterEarly vigor - cold stress<0<0
wheat
Novosphingobium rosa211EfficacyEfficacy
overall100%100%
Novosphingobium rosa65589MaizeEarly vigor - cold stress0-100-10
Novosphingobium rosa65619MaizeEarly vigor - cold stress0-100-10
Paenibacillus amylolyticus111EfficacyEfficacy
overall100%100%
Paenibacillus amylolyticus66316TomatoEarly vigor0-100-10
Paenibacillus amylolyticus66316TomatoEarly vigor10-20 10-20 
Paenibacillus amylolyticus66316TomatoEarly vigor0-100-10
Pantoea agglomerans323EfficacyEfficacy
33%50%
Pantoea agglomerans54499WheatEarly vigor - insol P40-50 
Pantoea agglomerans57547MaizeEarly vigor - low N<00-10
Pantoea vagans55529MaizeEarly vigor<0<0
(formerly P. agglomerans)
Polaromonas ginsengisoli111EfficacyEfficacy
66%100%
Polaromonas ginsengisoli66373TomatoEarly vigor0-100-10
Polaromonas ginsengisoli66373TomatoEarly vigor20-30 30-40 
Polaromonas ginsengisoli66373TomatoEarly vigor<010-20 
Pseudomonas fluorescens122Efficacy
100%
Pseudomonas fluorescens54480WheatEarly vigor - insol P>100 
Pseudomonas fluorescens56530MaizeEarly vigor - moderate N0-10
Rahnella aquatilis334EfficacyEfficacy
80%63%
Rahnella aquatilis56532MaizeEarly vigor - moderate N10-20 
Rahnella aquatilis56532MaizeEarly vigor - moderate N0-100-10
Rahnella aquatilis56532WheatEarly vigor - cold stress0-1010-20 
Rahnella aquatilis56532WheatEarly vigor - cold stress<00-10
Rahnella aquatilis56532WheatEarly vigor - cold stress10-20 <0
Rahnella aquatilis57157RyegrassEarly vigor<0
Rahnella aquatilis57157MaizeEarly vigor - low N0-100-10
Rahnella aquatilis57157MaizeEarly vigor - low N0-10<0
Rahnella aquatilis58013MaizeEarly vigor0-1010-20 
Rahnella aquatilis58013MaizeEarly vigor - low N0-10<0
Rhodococcus erythropolis313Efficacy
66%
Rhodococcus erythropolis54093MaizeEarly vigor - low N40-50 
Rhodococcus erythropolis54299MaizeEarly vigor - insol P>100 
Rhodococcus erythropolis54299MaizeEarly vigor<0<0
Stenotrophomonas chelatiphaga611EfficacyEfficacy
60%60%
Stenotrophomonas chelatiphaga54952MaizeEarly vigor0-100-10
Stenotrophomonas chelatiphaga47207MaizeEarly vigor<0 0
Stenotrophomonas chelatiphaga64212MaizeEarly vigor0-1010-20 
Stenotrophomonas chelatiphaga64208MaizeEarly vigor0-100-10
Stenotrophomonas chelatiphaga58264MaizeEarly vigor<0<0
Stenotrophomonas maltophilia612EfficacyEfficacy
43%66%
Stenotrophomonas maltophilia54073MaizeEarly vigor - low N50-60 
Stenotrophomonas maltophilia54073MaizeEarly vigor<00-10
Stenotrophomonas maltophilia56181MaizeEarly vigor0-10<0
Stenotrophomonas maltophilia54999MaizeEarly vigor0-100-10
Stenotrophomonas maltophilia54850MaizeEarly vigor 00-10
Stenotrophomonas maltophilia54841MaizeEarly vigor<00-10
Stenotrophomonas maltophilia46856MaizeEarly vigor<0<0
Stenotrophomonas rhizophila811EfficacyEfficacy
12.5%37.5%
Stenotrophomonas rhizophila50839MaizeEarly vigor<0<0
Stenotrophomonas rhizophila48183MaizeEarly vigor<0<0
Stenotrophomonas rhizophila45125MaizeEarly vigor<0<0
Stenotrophomonas rhizophila46120MaizeEarly vigor<00-10
Stenotrophomonas rhizophila46012MaizeEarly vigor<0<0
Stenotrophomonas rhizophila51718MaizeEarly vigor0-100-10
Stenotrophomonas rhizophila66478MaizeEarly vigor<0<0
Stenotrophomonas rhizophila65303MaizeEarly vigor<00-10
Stenotrophomonas terrae221EfficacyEfficacy
50%50%
Stenotrophomonas terrae68741MaizeEarly vigor<0<0
Stenotrophomonas terrae68599MaizeEarly vigor<00-10
Stenotrophomonas terrae68599Capsicum *Early vigor20-30 20-30 
Stenotrophomonas terrae68741Capsicum *Early vigor10-20 20-30 

The data presented in table 15 describes the efficacy with which a microbial species or strain can change a phenotype of interest relative to a control run in the same experiment. Phenotypes measured were shoot fresh weight and root fresh weight for plants growing either in the absence of presence of a stress (assay). For each microbe species, an overall efficacy score indicates the percentage of times a strain of that species increased a both shoot and root fresh weight in independent evaluations. For each species, the specifics of each independent assay is given, providing a strain ID (strain) and the crop species the assay was performed on (crop). For each independent assay the percentage increase in shoot and root fresh weight over the controls is given.

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Patent 2024
Ammonia Asparagine Aspartic Acid Biological Assay Bosea thiooxidans Calcium Phosphates Capsicum Cells Chlorophyll Cold Shock Stress Cold Temperature Crop, Avian Dietary Fiber DNA Replication Droughts Drought Tolerance Embryophyta Environment, Controlled Farmers Fertilization Glutamic Acid Glutamine Glycine Growth Disorders Herbaspirillum Herbaspirillum huttiense Leucine Lolium Lycopersicon esculentum Lysine Maize Massilia niastensis Methionine Microbial Consortia Nitrates Nitrites Nitrogen Novosphingobium rosa Paenibacillus Paenibacillus amylolyticus Pantoea agglomerans Pantoea vagans Phenotype Phosphates Photosynthesis Plant Development Plant Embryos Plant Leaves Plant Proteins Plant Roots Plants Polaromonas ginsengisoli Pseudoduganella violaceinigra Pseudomonas Pseudomonas fluorescens Rahnella Rahnella aquatilis Retention (Psychology) Rhodococcus erythropolis Rosa Salt Stress Sodium Chloride Sodium Chloride, Dietary Stenotrophomonas chelatiphaga Stenotrophomonas maltophilia Stenotrophomonas rhizophila Stenotrophomonas terrae Sterility, Reproductive Strains Technique, Dilution Threonine Triticum aestivum Tryptophan Tyrosine Vegetables Zea mays

Example 3

Effectiveness of Newly Evolved TpH Background Strain Using Schistosoma mansoni TpH

One of the 7 evolved high 5HTP-producers was selected to further evaluate if the mutations identified were only specifically beneficial to hsTpH2 or could be widely applicable to others. The chosen evolved strain was first cured to lose the evolution plasmid (e.g. the hsTpH gene) and this was immediately followed by re-introducing the E. coli tyrA gene. Upon restoration of the strain's tyrosine auxotrophy, the resulting strain was transformed with pHM2, which is identical to pHM1 used in the earlier evolution study except that the hsTpH gene was replaced with a Schistosoma mansoni TpH gene (SEQ ID NO:9). The 5HTP production of the resulting strain was compared to a wild-type strain carrying pHM2 in the presence of 100 mg/l tryptophan. Results showed the wild-type transformants could only produce ˜0.05 mg/l 5HTP while the newly evolved background strain transformants accumulated >20 mg/l. These production results demonstrated that the mutations acquired in the evolved background strain were not only beneficial to hsTpH but also to other TpHs; possibly applicable also to other aromatic amino acid hydroxylases (e.g. tyrosine hydroxylase).

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Patent 2024
5-Hydroxytryptophan Aromatic Amino Acids Biological Evolution Cells Escherichia coli Genes Melatonin Mixed Function Oxygenases Mutation Plasmids Schistosoma mansoni Strains Tryptophan Tyrosine Tyrosine 3-Monooxygenase

Example 5

FIG. 16 illustrates (A) a biosynthetic scheme for conversion of L-tyrosine to bisBlAs and (B) yeast strains engineered to biosynthesize bisBlAs, in accordance with embodiments of the invention. In particular, FIG. 16 illustrates (A) a pathway that is used to produce bisBlAs berbamunine and guattegaumerine. FIG. 16 provides the use of the enzymes ARO9, aromatic aminotransferase; ARO10, phenylpyruvate decarboxlase; TyrH, tyrosine hydroxylase; DODC, DOPA decarboxylase; NCS, norcoclaurine synthase; 6OMT, 6-O-methyltransferase; CNMT, coclaurine N-methyltransferase; CYP80A1, cytochrome P450 80A1; CPR, cytochrome P450 NADPH reductase. Of the metabolites provided in FIG. 16, 4-HPA, 4-HPP, and L-tyrosine are naturally synthesized in yeast. Other metabolites that are shown in FIG. 16 are not naturally produced in yeast.

In examples of the invention, a bisBIA-producing yeast strain, that produces bisBlAs such as those generated using the pathway illustrated in (A), is engineered by integration of a single construct into locus YDR514C. Additionally, FIG. 16 provides (B) example yeast strains engineered to synthesize bisBlAs. Ps6OMT, PsCNMT, PsCPR, and BsCYP80A1 were integrated into the yeast genome at a single locus (YDR514C). Each enzyme was expressed from a constitutive promoter. The arrangement and orientation of gene expression cassettes is indicated by arrows in the schematic. These strains convert (R)- and (S)-norcoclaurine to coclaurine and then to N-methylcoclaurine. In one example, the strains may then conjugate one molecule of (R)—N-methylcoclaurine and one molecule of (S)—N-methylcoclaurine to form berbamunine. In another example, the strains may conjugate two molecules of (R)—N-methylcoclaurine to form guattegaumerine. In another example, the strains may conjugate one molecule of (R)—N-methylcoclaurine and one molecule of (S)-coclaurine to form 2′-norberbamunine. In another embodiment, the strain may be engineered to supply the precursors (R)- and (S)-norcoclaurine from L-tyrosine, as provided in FIG. 5.

The construct includes expression cassettes for P. somniferum enzymes 6OMT and CNMT expressed as their native plant nucleotide sequences. A third enzyme from P. somniferum, CPR, is codon optimized for expression in yeast. The PsCPR supports the activity of a fourth enzyme, Berberis stolonifera CYP80A1, also codon optimized for expression in yeast. The expression cassettes each include unique yeast constitutive promoters and terminators. Finally, the integration construct includes a LEU2 selection marker flanked by loxP sites for excision by Cre recombinase.

A yeast strain expressing Ps6OMT, PsCNMT, BsCYP80A1, and PsCPR is cultured in selective medium for 16 hours at 30° C. with shaking. Cells are harvested by centrifugation and resuspended in 400 μL breaking buffer (100 mM Tris-HCl, pH 7.0, 10% glycerol, 14 mM 2-mercaptoethanol, protease inhibitor cocktail). Cells are physically disrupted by the addition of glass beads and vortexing. The liquid is removed and the following substrates and cofactors are added to start the reaction: 1 mM (R,S)-norcoclaurine, 10 mM S-adenosyl methionine, 25 mM NADPH. The crude cell lysate is incubated at 30° C. for 4 hours and then quenched by the 1:1 addition of ethanol acidified with 0.1% acetic acid. The reaction is centrifuged and the supernatant analyzed by liquid chromatography mass spectrometry (LC-MS) to detect bisBlA products berbamunine, guattegaumerine, and 2′-norberbamunine by their retention and mass/charge.

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Patent 2024
2-Mercaptoethanol 3-phenylpyruvate Acetic Acid Allopurinol Anabolism Barberry Base Sequence berbamunine Buffers Cells Centrifugation coclaurine Codon Cre recombinase Culture Media Cytochrome P450 Dopa Decarboxylase enzyme activity Enzymes Ethanol Gene Expression Genome Glycerin guatteguamerine higenamine Liquid Chromatography Mass Spectrometry Methyltransferase NADP NADPH-Ferrihemoprotein Reductase norcoclaurine synthase Plants Protease Inhibitors Retention (Psychology) S-adenosyl-L-methionine coclaurine N-methyltransferase S-Adenosylmethionine Saccharomyces cerevisiae Strains Transaminases Tromethamine Tyrosine Tyrosine 3-Monooxygenase
HPLC-ESI-MS/MS was performed in positive ion mode on a Thermo Fisher Scientific Orbitrap Fusion Lumos tribrid mass spectrometer fitted with an EASY-Spray Source as previously described (Parker et al., 2019 (link)). NanoLC was performed using a Thermo Fisher Scientific UltiMate 3000 RSLCnano System with an EASY Spray C18 LC column (Thermo Fisher Scientific, 50 cm × 75 μm inner diameter, packed with PepMap RSLC C18 material, 2 μm, cat. # ES803); loading phase for 15 min; mobile phase, linear gradient of 1–47% ACN in 0.1% FA for 106 min, followed by a step to 95% ACN in 0.1% FA over 5 min, hold 10 min, and then a step to 1% ACN in 0.1% FA over 1 min and a final hold for 19 min (total run 156 min); Buffer A = 100% H2O in 0.1% FA; Buffer B = 80% ACN in 0.1% FA; flow rate, 250–300 nl/min. All solvents were liquid chromatography mass spectrometry grade. Spectra were acquired using XCalibur, version 2.1.0 (Thermo Fisher Scientific). A “top 15” data-dependent MS/MS analysis was performed (acquisition of a full scan spectrum followed by collision-induced dissociation mass spectra of the 15 most abundant ions in the survey scan). Dynamic exclusion was enabled with a repeat count of 1, a repeat duration of 30 s, an exclusion list size of 500, and an exclusion duration of 40 s. Tandem mass spectra were extracted from Xcalibur ‘RAW’ files and charge states were assigned using the ProteoWizard 2.1.x msConvert script using the default parameters. The fragment mass spectra were searched against the 2016 Mus musculus SwissProt database (16838 entries) using Mascot (Matrix Science; version 2.4) using the default probability cut-off score. The search variables that were used were: 10 ppm mass tolerance for precursor ion masses and 0.5 Da for product ion masses; digestion with trypsin; a maximum of two missed tryptic cleavages; variable modifications of oxidation of methionine and phosphorylation of serine, threonine, and tyrosine. Cross-correlation of Mascot search results with X! Tandem was accomplished with Scaffold (version Scaffold_4.8.7; Proteome Software). Probability assessment of peptide assignments and protein identifications were made using Scaffold. Only peptides with ≥95% probability were considered.
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Publication 2023
Buffers Cytokinesis Digestion High-Performance Liquid Chromatographies Immune Tolerance Liquid Chromatography Mass Spectrometry Methionine Mice, House Peptides Phosphorylation Proteins Proteome Radionuclide Imaging Serine Solvents Tandem Mass Spectrometry Threonine Trypsin Tyrosine
The proteolytic activity was assessed by mixing 1 mL of culture supernatant and 1 mL of 1% (w/v) azocasein solution dissolved in 0.2 M Tris–HCl buffer of pH 7.0. The enzyme–substrate reaction was allowed to proceed for 30 min at 37 °C and was ended through the addition of 2 mL of 10% (w/v) trichloroacetic acid solution. Thence, incubation for 60 min in a crushed ice bath. The amount of soluble degradation proteins (C) was measured (mg/mL) following this calculation; C (mg/mL) = 1.55 OD280 − 0.76 OD260. One unit (1 U) of proteolytic enzyme activity was equivalent to one microgram of released l-tyrosine per milliliter per minute of the reaction at the standard conditions of experimentations.
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Publication 2023
azocasein Bath enzyme activity Enzymes Peptide Hydrolases Proteolysis Trichloroacetic Acid Tromethamine Tyrosine

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More about "Tyrosine"

Tyrosine, a non-essential amino acid, plays a crucial role in various physiological processes.
It serves as a precursor for the synthesis of important neurotransmitters and hormones, including dopamine, epinephrine, and thyroid hormones.
Tyrosine is also involved in melanin production, skin pigmentation, and the regulation of metabolism.
Dietary sources of tyrosine include protein-rich foods such as meat, dairy, eggs, and legumes.
Proper tyrosine levels are essential for maintaining cognitive function, mood, and overall health.
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