1. An isolated nucleic acid molecule comprising a sequence that encodes a protein or polypeptide comprising amino acid sequence of SEQ ID NO:2, a protein or polypeptide sequence that is at least 99%, 98%, 97% 96%, 95%, and 78% homologous to SEQ ID NO:2, or biologically active contiguous portions or variants thereof.
2. The isolated nucleic acid molecule of claim 1, wherein the protein or polypeptide comprises the amino acid sequence of SEQ ID NOS:4, 18, 20 or 22, or biologically active contiguous portions or variants thereof.
3. An isolated nucleic acid molecule comprising a sequence that encodes a protein or polypeptide comprising the amino acid sequence of SEQ ID NO:6, a protein or polypeptide sequence that is at least 99% homologous thereto, or biologically active contiguous portions or variants thereof.
4. The isolated nucleic acid molecule of claim 1, wherein the nucleic acid comprises a sequence selected from SEQ ID NOS:1, 3, 17, 19, 21, a nucleic acid sequence that is at least 99%, 98%, 97% 96%, 95%, or 81% homologous to SEQ ID NOS:1, 3, 17, 19, 21, or contiguous portions thereof.
5. The isolated nucleic acid molecule of claim 3, wherein the nucleic acid comprises a sequence selected from SEQ ID NO:5, a nucleic acid sequence that is at least 99% homologous thereto, or contiguous portions thereof.
6. The isolated nucleic acid molecule of any one of claims 1 and 2, wherein the polypeptide converts p-coumaryl andor coniferyl alcohol esters into the respective allylphenols, chavicol andor eugenol, estragole, anethole or other derivatives.
7. A protein or polypeptide, comprising the amino acid sequence of SEQ ID NO:2, a protein sequence that is at least 99%, 98%, 97% 96%, 95%, or 78% homologous thereto, or biologically active contiguous portions or variants thereof.
8. The protein or polypeptide of claim 7, wherein the protein or polypeptide comprises the amino acid sequence of SEQ ID NOS:4, 18, 20, 22, or biologically active contiguous portions or variants thereof.
9. A protein or polypeptide, comprising the amino acid sequence of SEQ ID NO:6, a protein sequence that is at least 99% homologous thereto, or biologically active contiguous portions or variants thereof.
10. The protein or polypeptide of any one of claims 7 and 9, wherein the polypeptide converts p-coumaryl andor coniferyl alcohol esters into the respective allylphenols, chavicol andor eugenol, estragole, anethole or other derivatives.
11. A recombinant expression vector, comprising at least one nucleic acid sequence that encodes a protein or polypeptide comprising amino acid sequence of SEQ ID NO:2, a protein or polypeptide sequence that is at least 99%, 98%, 97% 96%, 95%, or 78% homologous to SEQ ID NO:2, or a biologically active contiguous portion or variant thereof, the at least one nucleic acid sequence in operative association with transcriptional and translational regulatory regions or sequences suitable to provide for expression of the at least one nucleic sequence and the respective encoded protein or polypeptide in a host cell.
12. The recombinant expression vector of claim 11, wherein the encoded protein or polypeptide wherein the polypeptide comprises the amino acid sequence of SEQ ID NOS:4, 18, 20, 22, or biologically active contiguous portions or variants thereof.
13. The recombinant expression vector of claim 11, wherein the at least one nucleic acid sequence comprises a sequence selected from SEQ ID NOS: 1, 3, 17, 19, 21, and a nucleic acid sequence that is at least 99%, 98%, 97% 96%, 95%, or 81% homologous to SEQ ID NOS:1, 3, 17, 19, 21, or contiguous portions thereof
14. A recombinant expression vector, comprising at least one nucleic acid sequence that encodes a protein or polypeptide comprising the amino acid sequence of SEQ ID NO:6, a protein or polypeptide sequence that is at least 99% homologous thereto, or biologically active contiguous portions or variants thereof, the at least one nucleic acid sequence in operative association with transcriptional and translational regulatory regions or sequences suitable to provide for expression of the at least one nucleic acid sequence and the respective encoded protein or polypeptide in a host cell.
15. The recombinant expression vector of claim 14, wherein the at least one nucleic acid sequence comprises a sequence selected from SEQ ID NO:5, a nucleic acid sequence that is at least 99% homologous thereto, or contiguous portions thereof.
16. The recombinant expression vector of any one of claims 11 and 14, wherein the host cell is a plant cell, yeast cell, bacterial cell or insect cell.
17. The recombinant expression vector of claim 16, wherein the the host cell is a plant cell.
18. A host cell, transformed with the recombinant expression vector of any one of claims 11 and 14.
19. The host cell of claim 18, wherein the host cell is a plant cell.
20. A host cell, comprising a first recombinant DNA construct and a second recombinant DNA construct, wherein
the first recombinant DNA construct comprises a first DNA sequence encoding a protein or polypeptide comprising amino acid sequence of SEQ ID NO:2, a protein or polypeptide sequence that is at least 99%, 98%, 97% 96%, 95%, or 78% homologous to SEQ ID NO:2, or a biologically active contiguous portion or variant thereof, the at least one nucleic acid sequence in operative association with transcriptional and translational regulatory regions or sequences suitable to provide for expression of the at least one nucleic sequence and the respective encoded protein or polypeptide in a host cell, and wherein
the second recombinant DNA construct comprises a second DNA sequence encoding an acyl transferase suitable for acylation of monolignols forming esters, the DNA sequence in operative association with transcriptional and translational regulatory regions or sequences suitable to provide for expression of the second DNA sequence and the respective encoded acyl transferase in the host cell.
21. A host cell, comprising a first recombinant DNA construct and a second recombinant DNA construct, wherein
the first recombinant DNA construct comprises a first DNA sequence encoding a protein or polypeptide comprising the amino acid sequence of SEQ ID NO:6, a protein or polypeptide sequence that is at least 99% homologous thereto, or biologically active contiguous portions or variants thereof, the at least one nucleic acid sequence in operative association with transcriptional and translational regulatory regions or sequences suitable to provide for expression of the at least one nucleic sequence and the respective encoded protein or polypeptide in a host cell, and wherein
the second recombinant DNA construct comprises a second DNA sequence encoding an acyl transferase suitable for acylation of monolignols forming esters, the DNA sequence in operative association with transcriptional and translational regulatory regions or sequences suitable to provide for expression of the second DNA sequence and the respective encoded acyl transferase in the host cell.
22. The host cell of any one of claims 20 and 21, wherein the host cell is a plant cell, and wherein the first and second DNA constructs are present as parts of a single recombinant DNA construct, or are present on separate recombinant DNA constructs.
23. The host cell of any one of claims 20 and 21, wherein the host cell is a plant cell, yeast cell, bacterial cell, or insect cell.
24. The recombinant expression vector of claim 23, wherein the host cell is a plant cell.
25. A plant having at least one cell transformed with the recombinant expression vector of any one of claims 11 and 14.
26. A plant seed from a plant according to claim 25.
27. An oil derived from the seed of claim 26.
28. An antibody or epitope-binding fragment thereof specific for an amino acid sequence selected from the group consisting of amino acid sequence of SEQ ID NO:2, and respective epitope-bearing portions thereof.
29. An antibody or epitope-binding fragment thereof specific for an amino acid sequence selected from the group consisting of amino acid sequence of SEQ ID NOS:4, 18, 20, 22, and respective epitope-bearing portions thereof.
30. An antibody or epitope-binding fragment thereof specific for an amino acid sequence selected from the group consisting of amino acid sequence of SEQ ID NO:6, and respective epitope-bearing portions thereof.
31. (canceled)
32. A method for converting monolignols to allylpropenyl phenols or for production of biofuels, comprising:
acylating, using a suitable acyl transferase, at least one monolignol to form at least one respective acyl ester; and
transferring, using an isolated or suitable recombinant regiospecific reductase, a hydride to either the C-7 position, or the C-9 position of the at least one monolignol acyl ester or to a quinone methide derivative thereof, to provide at least one allyl or propenyl phenol derivative, respectively.
33. The method of claim 32, wherein the isolated or suitable recombinant regiospecific reductase comprises a protein or polypeptide comprising the amino acid sequence of SEQ ID NO:2, a protein or polypeptide sequence that is at least 99%, 98%, 97% 96%, 95%, or 78% homologous to SEQ ID NO:2, or a biologically active contiguous portion or variant thereof.
34. The method of claim 33, wherein the protein or polypeptide comprises the amino acid sequence of SEQ ID NOS:4. 18, 20, 22, or a biologically active contiguous portion or variant thereof.
35. The method of claim 32, wherein the isolated or suitable recombinant regiospecific reductase comprises a protein or polypeptide comprising the amino acid sequence of SEQ ID NO:6, a protein or polypeptide sequence that is at least 99% homologous thereto, or a biologically active contiguous portion or variant thereof.
36. The method of claim 32, wherein the at least one acyl ester comprises p-coumaryl alcohol ester or coniferyl alcohol ester, and wherein the at least one allyl or propenyl phenol derivative comprises eugenol, chavicol, estragole, anethole or other derivatives.
37. The method of claim 32, wherein at least one of acylating using a suitable acyl transferase, and transfering using a suitable recombinant regiospecific reductase occurs in at least one cell.
38. The method of claim 37, further comprising isolating the at least one allyl or propenyl phenol derivative from the at least one cell to provide for at least one isolated allyl or propenyl phenol derivative, or biofuel.
39. The method of claim 37, where both acylating using a suitable acyl transferase, and transfering using a suitable recombinant regiospecific reductase occur in at least one recombinant cell selected from plant cells, yeast cells, bacterial cells, and insect cells.
40. The method of claim 39, wherein where both acylating using a suitable acyl transferase, and transfering using an isolated or suitable recombinant regiospecific reductase occur in cells of a recombinant plant.
41. The method of claim 40, further comprising isolating the at least one allyl or propenyl phenol derivative from the plant to provide for at least one isolated allyl or propenyl phenol derivative, or biofuel.
42. The method of claim 41, wherein the at least one acyl ester comprises p-coumaryl alcohol ester or coniferyl alcohol ester, and wherein the at least one allyl or propenyl phenol derivative comprises eugenol, chavicol, estragole, anethole or other derivatives.
43. A method for re-engineering the biomass composition or redirecting carbon flow of genetically modified cultured cells or plants, comprising introducing, into at least one cell or plant tissue, a recombinant expression vector to provide for recombinant expression of a regiospecific reductase suitable to transfer a hydride to either the C-7 position, or the C-9 position of at least one monolignol acyl ester or to a quinone methide derivative thereof, to provide at least one allyl or propenyl phenol derivative, respectively, and wherein re-engineering the biomass composition or redirecting carbon flow in cell culture or in genetically modified plants is, at least in part, afforded.
44. The method of claim 43, further comprising recombinant expression of at least one monolignol acyl transferase suitable for acylating at least one monolignol to form the at least one respective monolignol acyl ester.
45. The method of claim 44, wherein the monolignol acyl transferase is that of Larrea tridentata, or a biologically active variant thereof.
46. The method of claim 43, wherein the at least one acyl ester comprises p-coumaryl alcohol ester or coniferyl alcohol ester, and wherein the at least one allyl or propenyl phenol derivative comprises eugenol, chavicol, estragole, anethole or other derivatives.
47. The method of claim 43, wherein re-engineering the biomass composition comprises diverting monolignol carbon flow away from lignin biopolymer formation.
48. The method of claim 43, wherein re-engineering the biomass composition comprises converting monolignols into allylpropenyl phenols in the genetically engineered cells or plants.
49. The method of claim 43, wherein re-engineering the biomass composition comprises re-engineering the amount or composition of lignins of the genetically engineered cells or plants.
50. The method of claim 43, wherein re-engineering the biomass composition comprises altering or re-engineering the dynamic modulus of the genetically engineered cells or plants relative to control cells or plants by re-engineering the amount or composition of lignins of the cells or plants.
51. The method of claim 50, wherein the dynamic modulus is reduced with reduction in the amount of lignins in the cells or plants.
52. The method of claim 43, wherein re-engineering the biomass composition comprises altering or re-engineering the formation of \u2018reaction tissue\u2019 of the genetically engineered cells or plants relative to control cells or plants by re-engineering the amount or composition of lignins of the cells or plants.
53. The method of claim 52, wherein the amount andor composition of \u2018reaction tissue\u2019 is increased or altered with reduction in the amount of lignins in the genetically engineered cells or plants.
54. The method of claim 43, wherein re-engineering the biomass composition comprises altering or re-engineering the antimicrobial or analgesic or plant defense properties of genetically engineered cells or plants relative to control cells or plants by re-engineering the amount or composition of lignins of the cells or plants.
55. The method of claim 54, wherein the amount or composition of antimicrobial or analgesic or plant defense properties is increased or altered with reduction in the amount of lignins in the genetically engineered cells or plants.
56. The method of claim 43, wherein re-engineering the biomass composition comprises altering or re-engineering the flavor or fragrance properties of genetically engineered cells or plants relative to control cells or plants by re-engineering the amount or composition of lignins of the cells or plants.
57. The method of claim 56, wherein the amount or composition of flavor or fragrance properties are increased, altered, or decreased with reduction in the amount of lignins in the genetically engineered cells or plants.
58. The method of claim 43, further comprising isolating the at least one allyl or propenyl phenol derivative from the cell culture or genetically modified plant to provide for at least one of: an isolated allyl or propenyl phenol derivative or biofuel; an allyl or propenyl phenol-depleted cell culture material; and an allyl or propenyl phenol-depleted plant material.
59. The method of claim 58, further comprising making, from the at least one isolated allyl or propenyl phenol derivative, at least one product selected from the group consisting of antibacterials, plant defense agents, analgesic agents, flavoring agents, polymer building blocks, and biofuels.
60. The method of claim 58, further comprising fermenting at least one of the allyl or propenyl phenol-depleted cell culture material and the allyl or propenyl phenol-depleted plant material.
61. The method of claim 59, wherein fermenting comprises fermenting to produce ethanol.
62. The method of claim 58, further comprising producing wood, pulp, or paper products using at least one of the allyl or propenyl phenol-depleted cell culture material and the allyl or propenyl phenol-depleted plant material.
63. The method of claim 43, further comprising making, from the genetically engineered cells or plants, at least one product selected from the group consisting of antibacterials, plant defense agents, analgesic agents, flavoring agents, polymer building blocks, and biofuels.
64. The method of claim 43, further comprising fermenting of the genetically engineered cells andor plants.
65. The method of claim 64, wherein fermenting comprises fermenting to produce ethanol.
66. The method of claim 43, wherein the recombinatnt expression vector comprises at least one nucleic acid sequence that encodes a protein or polypeptide comprising an amino acid sequence selected from the group consisting of SEQ ID NO:2, a protein or polypeptide sequence that is at least 99%, 98%, 97% 96%, 95%, or 78% homologous to SEQ ID NO:2, SEQ ID NO:6, a protein or polypeptide sequence that is at least 99% homologous thereto, or biologically active contiguous portions or variants thereof, the at least one nucleic acid sequence in operative association with transcriptional and translational regulatory regions or sequences suitable to provide for expression of the at least one nucleic acid sequence and the respective encoded protein or polypeptide in a host cell.
The claims below are in addition to those above.
All refrences to claim(s) which appear below refer to the numbering after this setence.
1. A system for registering a floating image with a reference image, the system comprising:
a reference image memory configured to store a reference image voxel set representing the reference image;
a floating image memory configured to store a floating image voxel set the floating image;
a voxel enumerator unit configured to count the voxels in sequential order along an axis of the reference image voxel set;
a voxel coordinate transformation unit configured to transform the voxels of the floating image voxel set with respect to the voxel in the reference image voxel set indicated by the voxel enumerator unit and to produce a transformed floating image voxel set;
a mutual histogram accumulator unit configured to accumulate a mutual histogram representing the transformed floating image voxel set interpolated with the reference image voxel set;
a volumetric interpolator unit configured to store in the mutual histogram accumulator unit the contribution to the mutual histogram of respective voxels of the transformed floating image voxel set interpolated with respective voxels of the reference image voxel set; and
a mutual information calculator unit configured to calculate the mutual information between the reference image voxel set and the transformed floating image voxel set based on the mutual histogram.
2. The system of claim 1, wherein the floating image is obtained utilizing a preoperative PET imaging modality.
3. The system of claim 1, wherein the reference image is obtained utilizing one of a preoperative PET imaging modality, an X-ray imaging modality, an X-ray CT imaging modality, an ultrasound imaging modality, and an MRI imaging modality.
4. The system of claim 1, wherein the floating image memory configured comprises a configuration to store at least four copies of the floating image voxel set and to read a voxel octet from the floating image voxel set corresponding to a voxel in the reference image voxel set.
5. The system of claim 1, wherein the mutual information calculator unit comprises a configuration to calculate the mutual information based on the joint probabilities between the reference image voxel set and the transformed floating image voxel set as an aggregate of the individual probabilities of the reference image voxels with respective transformed floating image voxels.
6. The system of claim 5, wherein the configuration of the mutual information calculator unit further comprises a logarithmic lookup table, and the mutual information calculator unit is configured to consult the logarithmic lookup table to compute logarithmic components of the individual probabilities.
7. The system of claim 1, comprising an image registration control unit comprising a configuration to perform multi-pass registration of the floating image with the reference image until the mutual information between the reference image voxel set and the transformed floating image voxel set is within a desired mutual information range.
8. The system of claim 7, wherein the image registration control unit is configured, before initiating an at least second registration pass, to subdivide the voxels of the transformed floating image voxel set.
9. The system of claim 1, comprising a field-programmable gate array comprising a configuration to represent at least one of the voxel enumerator unit, voxel coordinate transformation unit, the mutual histogram accumulator unit, the volumetric interpolator unit, and the mutual information calculator unit.
10. A system for displaying a composite image from a floating image and a reference image, the system comprising:
a reference image memory configured to store a reference image voxel set representing the reference image;
a floating image memory configured to store a floating image voxel set the floating image;
a voxel enumerator unit configured to count the voxels in sequential order along an axis of the reference image voxel set;
a voxel coordinate transformation unit configured to transform the voxels of the floating image voxel set with respect to the voxel in the reference image voxel set indicated by the voxel enumerator unit and to produce a transformed floating image voxel set;
a mutual histogram accumulator unit configured to accumulate a mutual histogram representing the transformed floating image voxel set interpolated with the reference image voxel set;
a volumetric interpolator unit configured to store in the mutual histogram accumulator unit the contribution to the mutual histogram of respective voxels of the transformed floating image voxel set interpolated with respective voxels of the reference image voxel set;
a mutual information calculator unit configured to calculate the mutual information between the reference image voxel set and the transformed floating image voxel set based on the mutual histogram;
an image registration control unit configured to perform multi-pass registration of the floating image with the reference image until the mutual information between the reference image voxel set and the transformed floating image voxel set is within a desired mutual information range;
a composite image generating component configured to generate a composite image from the reference image voxel set and the transformed floating image voxel set; and
a display unit configured to display the composite image.
11. The system of claim 10, the floating image utilizing a preoperative PET imaging modality.
12. The system of claim 10, the reference image utilizing at least one of a preoperative PET imaging modality, an X-ray imaging modality, an X-ray CT imaging modality, an ultrasound imaging modality, and an MRI imaging modality.
13. The system of claim 10, comprising an imaging unit configured to generate at least one of the reference image and the floating image.
14. The system of claim 10, comprising a field-programmable gate array configured to represent at least one of the voxel enumerator unit, voxel coordinate transformation unit, the mutual histogram accumulator unit, the volumetric interpolator unit, and the mutual information calculator unit.
15. A method of targeting an anatomic feature of an individual pertaining to a medical procedure illustrated in a reference image of the individual utilizing a first imaging modality and a floating image of the individual utilizing a floating imaging modality, the method comprising:
generating a composite image from the reference image and the floating image; and
targeting the anatomic feature using the composite image in furtherance of the medical procedure.
16. The method of claim 15, wherein said targeting comprises evaluating at least one of the presence, the location, the size, and the condition of the anatomic feature in relation to the health state of the individual.
17. The method of claim 15, wherein said medical procedure comprises a surgical procedure, and the targeting comprises using the composite image to guide the identification and localization of the anatomic feature in a surgical procedure.
18. The method of claim 17, wherein using the composite image to guide comprises:
detecting the position of a surgical probe within the surgical site, and
displaying the position of the surgical probe coordinated with the composite image.
19. The method of claim 15, comprising generating at least one of the reference image and the floating image with an imaging component.
20. The method of claim 19, wherein the medical procedure comprising a surgical procedure comprises at least one of the reference image and the floating image generated intraoperatively.
21. The method of claim 15, wherein at least one of the reference imaging modality and the floating imaging modality comprises a PET imaging modality.
22. The method of claim 15, wherein generating a composite image comprises applying a system of generating a composite image to the reference image and the floating image.
23. The method of claim 22, wherein the system comprises a configuration to generate the composite image in at least a near-realtime performance.
24. The method of claim 23, wherein the system comprises:
a reference image memory configured to store a reference image voxel set representing the reference image;
a floating image memory configured to store a floating image voxel set the floating image;
a voxel enumerator unit configured to count the voxels in sequential order along an axis of the reference image voxel set;
a voxel coordinate transformation unit configured to transform the voxels of the floating image voxel set with respect to the voxel in the reference image voxel set indicated by the voxel enumerator unit and to produce a transformed floating image voxel set;
a mutual histogram accumulator unit configured to accumulate a mutual histogram representing the transformed floating image voxel set interpolated with the reference image voxel set;
a volumetric interpolator unit configured to store in the mutual histogram accumulator unit the contribution to the mutual histogram of respective voxels of the transformed floating image voxel set interpolated with respective voxels of the reference image voxel set;
a mutual information calculator unit configured to calculate the mutual information between the reference image voxel set and the transformed floating image voxel set based on the mutual histogram;
an image registration control unit configured to perform multi-pass registration of the floating image with the reference image until the mutual information between the reference image voxel set and the transformed floating image voxel set is within a desired mutual information range; and
a composite image generating component configured to generate a composite image from the reference image voxel set and the transformed floating image voxel set.
25. The method of claim 24, wherein the system comprises a field-programmable gate array comprising a configuration to represent at least one of the voxel enumerator unit, voxel coordinate transformation unit, the mutual histogram accumulator unit, the volumetric interpolator unit, and the mutual information calculator unit.