DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Election/Restriction
Applicant’s election without traverse of Group I (claims 1-18) and SEQ ID NO: 2 in the reply filed on 3/5/2025 is acknowledged.
Claims 19-42 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected Group, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 3/5/2025.
The requirement is still deemed proper and is therefore made FINAL.
Status of Claims
Claims 1-18 are under examination on the merits.
Claims 19-42 are withdrawn.
Nucleotide and/or Amino Acid Sequence Disclosures
This application contains sequence disclosures that are encompassed by the definitions for nucleotide and/or amino acid sequences set forth in 37 CFR 1.831(b). However, this application fails to comply with the requirements of 37 CFR 1.831 through 1.834.
The incorporation of sequence listing (paragraph [02]) provides the size of the file in KB, but the size of the file in bytes is required. See MPEP 1.834(c)(1)(iii).
Full compliance with the sequence rules is required in response to this Office action. A complete response to this Office action must include both compliance with the sequence rules and a response to the issues set forth herein. Failure to fully comply with both of these requirements in the time period set forth in this Office action will be held to be non-responsive.
Specification
The disclosure is objected to because of the following informalities:
The Description of Figure 9 (paragraph [014]) does not match the figure 9 submitted 1/19/2024. Specifically, the description of 9A as a boxplot describes figure 9C, the description of 9B describes 9E, the description of 9C describes 9F, the description of 9D/E as optical sections describes figure 9G, the description of figure F describes 9A, the description of 9G describes 9B, and the description of 9H describes 9D.
Appropriate correction is required.
Claim Objections
Claims 1, 2, 5, 15, & 17-18 are objected to because of the following informalities:
Claims 1, 2, 15, & 17-18: the list items in each claim are presented in the format “a.”, “b.”, etc. Proper structure for a claim is to begin with a capital letter and end with a period. Periods may not be used elsewhere in the claims except for abbreviations. See Fressola v. Manbeck, 36 USPQ2d 1211 (D.D.C. 1995). An alternative format such as --a)-- would be appropriate.
Claim 5 (line 3): “a Escherichia coli” should read --an Escherichia coli--.
Claim 18 (line 2 and 5): the genus name for “S. meliloti” and “R. irregularis” should be written out in full at first reference and may be abbreviated in later usage.
Appropriate correction is required.
Claim Rejections - 35 USC § 112
Indefiniteness
The following is a quotation of 35 U.S.C. 112(b):
(b) CONCLUSION.—The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the inventor or a joint inventor regards as the invention.
The following is a quotation of 35 U.S.C. 112 (pre-AIA ), second paragraph:
The specification shall conclude with one or more claims particularly pointing out and distinctly claiming the subject matter which the applicant regards as his invention.
Claims 1-18 are rejected under 35 U.S.C. 112(b) or 35 U.S.C. 112 (pre-AIA ), second paragraph, as being indefinite for failing to particularly point out and distinctly claim the subject matter which the inventor or a joint inventor (or for applications subject to pre-AIA 35 U.S.C. 112, the applicant), regards as the invention.
The term “about” in claim 1 (lines 6-7 & 13-14) and 17 (lines 4-5 & 7-8) is indefinite. Because it is unclear to one of ordinary skill in the art what lower bound of sequence identity is encompassed by claims 1 and 17, these claims and their dependents are indefinite.
Claim 2 is indefinite as whether it is claiming a method (part a, lines 2-4: “said recombinant DNA molecule is expressed in a plant cell”) or a product (part b, lines 5-7). Dependent claims 6-7 are likewise indefinite.
Claims 7 & 10 require a plant or a plant cell that is ornamental (line 7). No definition is provided for this term in the specification. It would be unclear to one of ordinary skill in the art if an ornamental plant is restricted to a plant currently being grown ornamentally or if this term encompasses plants commonly used for ornamental purposes. Because the bounds of this limitation is unclear, claims 7 & 10 are indefinite.
Claim 15 recites the limitation "the plants" in line 5. There is insufficient antecedent basis for this limitation in the claim. Claim 15 presents a plant in step (b) (line 4). It is unclear if “the plants” of step (c) are intended to refer to the “a plant” of step (b) or another set of plants not presented.
Claim 18 recites a group comprising both S. meliloti (line 2) and Sinorhizobium meliloti (line 3). Because both are provided in the group, a reasonable interpretation would be that S. meliloti and Sinorhizobium meliloti are different rhizobia bacteria and “S.” is short for a genus other than Sinorhizobium. However, another interpretation of claim 18 is that S. meliloti and Sinorhizobium meliloti are the same bacteria listed twice. Because it is not clear what S. meliloti is intended to encompass, claim 18 is indefinite.
Improper Dependency
The following is a quotation of 35 U.S.C. 112(d):
(d) REFERENCE IN DEPENDENT FORMS.—Subject to subsection (e), a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
The following is a quotation of pre-AIA 35 U.S.C. 112, fourth paragraph:
Subject to the following paragraph [i.e., the fifth paragraph of pre-AIA 35 U.S.C. 112], a claim in dependent form shall contain a reference to a claim previously set forth and then specify a further limitation of the subject matter claimed. A claim in dependent form shall be construed to incorporate by reference all the limitations of the claim to which it refers.
Claims 2-7 & 10 are rejected under 35 U.S.C. 112(d) or pre-AIA 35 U.S.C. 112, 4th paragraph, as being of improper dependent form for failing to further limit the subject matter of the claim upon which it depends, or for failing to include all the limitations of the claim upon which it depends.
Claims 3-7 are drawn to the recombinant DNA molecule of claim 1 present within a host cell or expressed in a plant cell. Fundamentally, claims 3-7 are still drawn to the DNA molecule. The species of cell in which a DNA molecule is present or expressed does not provide a patentable distinction over the DNA molecule present or expressed in any other species of cell.
Similarly, claim 2 is drawn in alternative to parts a) and b). Claim 2 part b recites the recombinant DNA molecule in operable linkage with a vector but is still drawn to the DNA molecule itself. Claim 2 part a appears to be claiming a method (lines 2-4: “said recombinant DNA molecule is expressed in a plant cell”). However, if claim 2 part a is to be interpreted as a product and the expression in a plant cell is an intended effect, then claim 2 part a also fails to further limit the DNA molecule of claim 1. Thus, claims 2 and 3-7 do not require any further limitation of the subject matter of claim 1.
Claims 6 and 9 require that the plant or plant cell is dicotyledonous or monocotyledonous. Claim 7, which depends on claim 6, allows for a plant cell that is Douglas fir (line 5), Loblolly pine (line 6), pine (line 7), Radiata pine (line 8), or Southern pine (line 9), which are not dicotyledonous or monocotyledonous plants. Claim 7 also encompasses plant cells that are nut (line 7), ornamental (line 7), rootstocks (line 9) and shrub (line 9) cells. Nuts (which encompasses pine nuts), ornamental plants, rootstocks, and shrubs encompass plants that are not monocot or dicots, such as conifers or magnoliids. Similarly, claim 10, which depends on claim 9, encompasses plants that are Douglas fir (line 5), Loblolly pine (line 6), pine (line 8), Radiata pine (line 8), Southern pine (line 9), nut (line 7), ornamental (line 7), rootstocks (line 9) and shrub (line 9); thus, claim 10 encompasses plants that are not monocots or dicots, as required by claim 9. Claims 7 and 10 fail to include all the limitations of the claims upon which they depend.
Applicant may cancel the claim(s), amend the claim(s) to place the claim(s) in proper dependent form, rewrite the claim(s) in independent form, or present a sufficient showing that the dependent claim(s) complies with the statutory requirements.
Written Description
The following is a quotation of the first paragraph of 35 U.S.C. 112(a):
(a) IN GENERAL.—The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor or joint inventor of carrying out the invention.
The following is a quotation of the first paragraph of pre-AIA 35 U.S.C. 112:
The specification shall contain a written description of the invention, and of the manner and process of making and using it, in such full, clear, concise, and exact terms as to enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make and use the same, and shall set forth the best mode contemplated by the inventor of carrying out his invention.
Claims 1-18 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, as failing to comply with the written description requirement. The claim(s) contains subject matter which was not described in the specification in such a way as to reasonably convey to one skilled in the relevant art that the inventor or a joint inventor, or for applications subject to pre-AIA 35 U.S.C. 112, the inventor(s), at the time the application was filed, had possession of the claimed invention.
Claims 1-16 require a polynucleotide segment encoding a light sensitive short hypocotyl protein or fragment wherein the protein comprises an amino acid sequence of at least about 85% sequence identity to SEQ ID NO: 2 or the polynucleotide segment hybridizes under stringent hybridization conditions to a polynucleotide having at least about 85% sequence identity to SEQ ID NOs: 1, 5 & 7 or a fragment thereof. Claims 17 and 18 require a light sensitive short hypocotyl protein or fragment having at least about 70% identity to SEQ ID NO: 2 or encoded by a nucleic acid sequence having at least about 70% sequence identity to SEQ ID NOs: 1, 5 & 7 or a fragment thereof.
An amino acid sequence of at least 85% identity to SEQ ID NO: 2 encompasses amino acid sequences with 33 substitutions relative to the 222 amino acid-long SEQ ID NO: 2. An amino acid sequence having at least 70% sequence identity to SEQ ID NO: 2 encompasses proteins with 66 substitutions relative to SEQ ID NO: 2.
A polynucleotide segment having 85% sequence identity to SEQ ID NOs: 1, 5 & 7 encompasses polynucleotides with 100 substitutions in the 669 nucleotide-long SEQ ID NOs: 1 & 7 or 182 substitutions in the 1218 nucleotide-long SEQ ID NO: 5. This encompasses sequences in which every substitution results in an amino acid change, which in the case of SEQ ID NO: 1, would result in a protein with 55% sequence identity to SEQ ID NO: 2.
A polynucleotide segment having 70% sequence identity to SEQ ID NOs: 1, 5 & 7 encompasses polynucleotides with 200 substitutions in the 669 nucleotide-long SEQ ID NOs: 1 & 7 or 365 substitutions in the 1218 nucleotide-long SEQ ID NO: 5. This encompasses sequences wherein every nucleotide substitution alters the encoded amino acid, which would result in a protein with 10% sequence identity to SEQ ID NO: 2.
The instant disclosure does not specifically define the length of a fragment of either a polypeptide or polynucleotide sequence and does not require that a fragment have functional activity (paragraphs [063 & 066]). Nor do claims 1-18 require that the encoded polypeptide be a light sensitive short hypocotyl protein but merely a fragment thereof. Thus, claims 1-18 encompass fragments as short as 2 amino acids or nucleotides long.
Additionally, because the instant disclosure does not specifically define “stringent hybridization conditions” but instead provides examples of how stringency many be adjusted (paragraphs [064-065]), a polynucleotide segment that hybridizes under stringent conditions to a fragment of a polynucleotide having at least 85% sequence identity to SEQ ID NOs: 1, 5 & 7 (claim 1, lines 12-15) reads on virtually any polynucleotide segment.
The only species of light sensitive short hypocotyl protein described in the specification are LSH1 (SEQ ID NO: 2, encoded by SEQ ID NOs: 1, 5 & 7) and LSH2 (SEQ ID NO: 4, encoded by SEQ ID NOs: 3, 6 & 8). SEQ ID NO: 5 is the gDNA sequence while SEQ ID NO: 1 is the cDNA sequence of the M. truncatula LSH1 protein. SEQ ID NO: 7, the H. vulgare codon-optimized coding sequence, has 76.8% identity to SEQ ID NO: 1. See alignment below. Similarly, SEQ ID NO: 6 is the gDNA sequence and SEQ ID NO: 3 is the cDNA sequence of the M. truncatula LSH2 protein. SEQ ID NO: 8, the H. vulgare codon-optimized sequence, has 86% identity to SEQ ID NO: 3. The instant specification also describes polypeptide sequences comprising a conserved ALOG domain (SEQ ID NOs: 9-84), of lengths ranging from 137 amino acids (SEQ ID NO: 43) to 436 amino acids (SEQ ID NO:24). The ALOG domain polypeptide sequence with highest similarity to SEQ ID NO: 2 (SEQ ID NO: 24) has just 86.5% sequence identity. See second alignment below. Thus, the specification does not describe species over the full scope of the proteins and does not describe the full scope of the claimed nucleic acids.
US-18-320-150-7
Sequence 7, US/18320150
Publication No. US20240011045A1
GENERAL INFORMATION
APPLICANT: Cambridge Enterprise Limited (en)
TITLE OF INVENTION: PROTEINS FOR REGULATION OF SYMBIOTIC NODULE ORGAN IDENTITY (en)
FILE REFERENCE: AGOE:007US
CURRENT APPLICATION NUMBER: US/18/320,150
CURRENT FILING DATE: 2023-05-18
NUMBER OF SEQ ID NOS: 94
SEQ ID NO 7
LENGTH: 669
TYPE: DNA
FEATURE:
NAME/KEY: source
LOCATION: 1..669
QUALIFIERS: mol_type = other DNA
note = Codon optimized LSH1 protein
organism = Hordeum vulgare
Query Match 76.8%; Score 513.8; Length 669;
Best Local Similarity 85.5%;
Matches 572; Conservative 0; Mismatches 97; Indels 0; Gaps 0;
Qy 1 ATGGATTCAATTCAAGATTTTATGGACTCATGTAACTCTGACAACAGTTGCAGCCTCACC 60
||||||||||| |||||||| ||||||||||||||||| |||||||| ||||||||||||
Db 1 ATGGATTCAATCCAAGATTTCATGGACTCATGTAACTCGGACAACAGCTGCAGCCTCACC 60
Qy 61 AACAGCACCATAACTACCAACAGCAGTAACAACAACATCAGCAACGCCATAGTTGGTAGC 120
||| ||||| || ||||| ||||| ||||||||||||||||||||||| || ||| |
Db 61 AACTCAACCATTACCACCAATAGCAGCAACAACAACATCAGCAACGCCATCGTGGGTTCC 120
Qy 121 TCTTCACCTTCTGGCTCTACCACCACAAGCAGCCGCTATGAAAACCAGAAACGCCGTGAC 180
|| || || || ||| ||||| ||||||||||||||||| |||||||| ||||| |||
Db 121 TCGTCCCCGTCGGGCAGCACCACGACAAGCAGCCGCTATGAGAACCAGAAGCGCCGCGAC 180
Qy 181 TGGAACACTTTTGGCCAGTACCTCAAGAATCACCGTCCTCCTCTCTCCCTCTCCAGATGT 240
|||||||| |||||||||||||||||||||||||||||||| |||||||||||||||||
Db 181 TGGAACACGTTTGGCCAGTACCTCAAGAATCACCGTCCTCCGCTCTCCCTCTCCAGATGC 240
Qy 241 AGCGGTGCTCATGTGCTTGAATTTCTCCGGTACTTGGACCAATTTGGCAAGACAAAAGTG 300
||||||||||||||||| || || ||||||||| |||||||||||||||||||||||||
Db 241 AGCGGTGCTCATGTGCTGGAGTTCCTCCGGTACCTGGACCAATTTGGCAAGACAAAAGTC 300
Qy 301 CACACACCAATTTGTCCATTCTATGGACATCCAAACCCTCCAGCACCATGTCCATGTCCA 360
||||| ||||| || || ||||| |||||||| ||||||||||| || ||||| || ||
Db 301 CACACTCCAATCTGCCCGTTCTACGGACATCCCAACCCTCCAGCCCCCTGTCCTTGCCCC 360
Qy 361 TTAAGACAAGCTTGGGGTAGTCTTGATGCACTGATAGGTCGTTTAAGGGCAGCTTTTGAG 420
||||||||||| ||||| ||||||||||| |||||||| || || |||||||| || |||
Db 361 TTAAGACAAGCATGGGGCAGTCTTGATGCCCTGATAGGGCGGTTGAGGGCAGCGTTCGAG 420
Qy 421 GAAAATGGAGGGAAGCCAGAAACAAATCCATTTGGTGCTAGAGCTGTTAGACTTTACCTT 480
||||||||||||||||| ||||| |||||||| || ||||| || || || || |||||
Db 421 GAAAATGGAGGGAAGCCCGAAACTAATCCATTCGGCGCTAGGGCGGTCAGGCTCTACCTG 480
Qy 481 CGTGAGGTTCGTGATCTTCAATCCAAAGCAAGAGGTATTAGTTATGAGAAGAAGAAAAGG 540
|| |||||||| || ||||| ||||| || |||| |||||||| ||||||||||| |||
Db 481 CGGGAGGTTCGGGACCTTCAGTCCAAGGCCCGAGGCATTAGTTACGAGAAGAAGAAGAGG 540
Qy 541 AAACGTCCACCACAACAACAACCACAACAGCTTCAGCTTCAGCAGCAACAACCAATGCAA 600
||||| || || ||||| || || |||||||| ||||| |||||||| || || |||||
Db 541 AAACGCCCCCCGCAACAGCAGCCGCAACAGCTGCAGCTACAGCAGCAGCAGCCCATGCAG 600
Qy 601 TTGCAATTGCCTCTTCATCTTCATCATCACCATCAACATCAGCTTCCACCTCCAGGTGCA 660
||||||||||||| || ||||| || ||||| ||||||||||| ||||| ||||| ||
Db 601 CTGCAATTGCCTCTACACCTTCACCACCACCACCAACATCAGCTCCCACCGCCAGGGGCG 660
Qy 661 ACTCAATAA 669
|| |||| |
Db 661 ACGCAATGA 669
US-18-320-150-24
Sequence 24, US/18320150
Publication No. US20240011045A1
GENERAL INFORMATION
APPLICANT: Cambridge Enterprise Limited (en)
TITLE OF INVENTION: PROTEINS FOR REGULATION OF SYMBIOTIC NODULE ORGAN IDENTITY (en)
FILE REFERENCE: AGOE:007US
CURRENT APPLICATION NUMBER: US/18/320,150
CURRENT FILING DATE: 2023-05-18
NUMBER OF SEQ ID NOS: 94
SEQ ID NO 24
LENGTH: 436
TYPE: PRT
FEATURE:
NAME/KEY: source
LOCATION: 1..436
QUALIFIERS: mol_type = protein
organism = Pisum sativum
Query Match 86.5%; Score 1043.5; Length 436;
Best Local Similarity 88.8%;
Matches 198; Conservative 9; Mismatches 9; Indels 7; Gaps 4;
Qy 1 MDSIQDFMDSCNSDNSCSLTNSTITTNSSN--NNISNAIVGSSSPSGSTTTSSRYENQKR 58
|||||||||||||||||||||||||||::| |: :||:: |||||||| ||||||||||
Db 1 MDSIQDFMDSCNSDNSCSLTNSTITTNNTNNINHNNNALICSSSPSGSTATSSRYENQKR 60
Qy 59 RDWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQFGKTKVHTPICPFYGHPNPPAPCP 118
||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Db 61 RDWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQFGKTKVHTPICPFYGHPNPPAPCP 120
Qy 119 CPLRQAWGSLDALIGRLRAAFEENGGKPETNPFGARAVRLYLREVRDLQSKARGISYEKK 178
||||||||||||||||||||||||||||:|||||||||||||||||||||||||||||||
Db 121 CPLRQAWGSLDALIGRLRAAFEENGGKPDTNPFGARAVRLYLREVRDLQSKARGISYEKK 180
Qy 179 KRKRPPQQQPQQLQLQQQQPMQ---LQLPLHLHHHHQHQLPPP 218
|||||| || | | || ||:| :|||||| |||||||||
Db 181 KRKRPPPQQQHQ-QQQQHQPLQQLPMQLPLHL-CHHQHQLPPP 221
ARABIDOPSIS LIGHT-DEPENDENT SHORT HYPOCOTYLS 1 and rice G1/LIGHT-DEPENDENT SHORT HYPOCOTYLS (ALOG/LSH) are known in the art as plant specific transcription factors that regulate diverse processes in growth, development, and stress response (Upadhyaya et al 2025 J of Experimental Botany. 76(3): 836–850 (published 2/7/2025 after the priority date of the instant application, hereafter Upadhyaya) page 836, right column, paragraph 1 figure 4).
Upadhyaya discloses that ALOG proteins have a Domain of Unknown Function 640 or an ALOG domain (page 837, left column, paragraph 1) comprising 4 alpha-helices and a zinc-ribbon (page 837, left column, paragraph 2) a C-terminus Nuclear Localization Signal (page 837, right column, paragraph 2). Upadhyaya discloses that the ALOG domain is likely a DNA-binding domain recognizing DNA sequences in gene promoters (page 837, left column, paragraph 2). DNA interactions are mediated by contacts made by 3rd alpha helix and NLS (Upadhyaya page 845, left column, paragraph 3). Although the DNA motif bound by ALOG proteins has been identified, the molecular mode of action of ALOGs is unknown (Upadhyaya page 845, right column, paragraph 1).
Lee et al (2024) Current Biology. 34: 825–840 (published 2/26/2024 after the filing date of the instant application, hereafter Lee 2024) describes the biological function of LSH1 and LSH2 as repressors and activators of transcription (page 831, left column, paragraph 2). Lee 2024 describes LSH1 and LSH2 as having an identical ALOG domain similar to AtLSH3 and Pisum sativum SYMMETRIC PETALS 1 (page 826, left column, paragraph 2), but no other structure is described for these proteins.
The instant specification describes Light Sensitive Short Hypocotyl (LSH) proteins as transcription factors and regulators of nodule organ identity (paragraph [049]). The instant specification describes one LSH function to promote NF-YA1 and NOOT1/2 in the cortex (paragraph [050]). The instant specification describes LSH1 and LSH2 as having an ALOG domain (paragraph [0128]). LSH1 and LSH2 are expressed in roots after rhizobial inoculation but not during lateral root development (paragraph [0128]). The instant specification describes loss of function mutants (but not their sequence or the mutation that resulted in the loss of function) and that the loss of function led to an increase in lateral roots (paragraph [0130]). The instant specification describes that NF-YA1 expression can partly rescue lsh1/lsh2 mutants (paragraph [0139]). LSH1 and LSH2 play a role in infectability of cortical tissue and habitability of nodule primordium (paragraph [0132]). The instant specification discloses targets of LSH1 including CRE1, IPT1, RR19, CKX3, PIN1, STYLISH, PINOID, and NOOT1 and that LSH1 binds directly to DNA regions of cytokinin and auxin signaling and biosynthesis genes (paragraph [0144]). No structural features of an LSH protein other than an ALOG domain are described in the instant specification to provide the biological function of the LSH protein. The specification fails to make up for the lack of knowledge in the art.
One of skill in the art would not recognize that Applicant was in possession of the necessary common attributes or features of the genus in view of the disclosed species.
Hence, Applicant has not, in fact, described nucleic acids encoding a light sensitive short hypocotyl protein or fragment thereof over the full scope of the claims, and the specification fails to provide an adequate written description of the claimed invention. Therefore, given the lack of written description in the specification with regard to the structural and functional characteristics of the claimed compositions, Applicant does not appear to have been in possession of the claimed genus at the time this application was filed.
Scope of Enablement
Claims 2 & 6-18 are rejected under 35 U.S.C. 112(a) or 35 U.S.C. 112 (pre-AIA ), first paragraph, because the specification, while being enabling for plants and plant cells comprising a polynucleotide segment encoding a light sensitive short hypocotyl protein of SEQ ID NO: 2 or SEQ ID NO: 4, does not reasonably provide enablement for any fragment of a light sensitive short hypocotyl protein encoded by a polynucleotide that hybridizes under stringent hybridization conditions to a nucleotide sequence of about 85% identity to a fragment of SEQ ID NO: 1, 5, or 7. The specification does not enable any person skilled in the art to which it pertains, or with which it is most nearly connected, to make or use the invention commensurate in scope with these claims.
The claims are broadly drawn to a plant comprising a light sensitive short hypocotyl (LSH) protein or fragment with 85% (claims 8-16) or 70% (claims 17-18) identity to a fragment SEQ ID NO: 2 or encoded by a polynucleotide hybridizing with a polynucleotide having 85% (claims 8-16) or having 70% identity (claims 17-18) to a fragment of SEQ ID NOs: 1, 5, or 7 or a method using said plant. Claims 2, 6 & 7 are drawn to the recombinant DNA molecule expressed in a plant cell to produce an increase in intercellular cortical infection.
The instant specification, however, only provides guidance for the use of plants comprising nucleic acids encoding proteins of SEQ ID NO: 2 that are light sensitive short hypocotyl proteins. The specification also only provides guidance for making light sensitive short hypocotyl proteins that increase intercellular cortical infection that are proteins of SEQ ID NO: 2 or SEQ ID NO: 4.
Light sensitive short hypocotyl proteins have diverse biological functions in plants (Upadhyaya et al 2025 J of Experimental Botany. 76(3): 836–850, 2025 (published 2/7/2025 after the priority date of the instant application) page 836, right column, paragraph 1; figure 4), and it is not apparent from the instant disclosure that all light sensitive short hypocotyl proteins encompassed by claims 8-18 or encoded by the recombinant DNA molecule of claims 2, 6 & 7 would have the function of promoting intercellular cortical infection or intracellular colonization as described in the instant specification for LSH1 and LSH2. Moreover, claims 2, 6, 7 & 8-18 encompass fragments of a light sensitive short hypocotyl protein and claims 8-18 do not require that the protein or protein fragment have any activity at all.
The instant specification does not provide guidance for how to use nucleic acids encoding proteins with 85% (claims 8-16) or 70% (claims 17-18) identity to a fragment of SEQ ID NO: 2 or encoded by a polynucleotide having 70% identity (claims 17-18) or hybridizing with a polynucleotide having 85% identity (claims 8-16) to a fragment of SEQ ID NOs: 1, 5, or 7 that does not encode a functional LSH protein.
The instant specification also does not provide guidance for how to make nucleic acids encoding proteins with 85% identity (claims 2, 6-7 & 16) or 70% (claims 17-18) identity to a fragment of SEQ ID NO: 2 or encoded by a polynucleotide having 70% identity (claims 17-18) or hybridizing with a polynucleotide having 85% identity (claims 2, 6-7 & 16) to a fragment of SEQ ID NOs: 1, 5, or 7 that increases intercellular cortical infection, increases intracellular colonization by nitrogen-fixing bacteria, or increases nitrogen-fixation of bacteria that do not encode the light sensitive short hypocotyl protein of SEQ ID NO: 2 or SEQ ID NO: 4.
As the specification does not describe how to make or use a recombinant DNA molecule or a plant comprising said molecule encoding a protein with 85% (claims 2 & 6-16) or 70% (claims 17-18) identity to a fragment of SEQ ID NO: 2 or encoded by a polynucleotide having 70% identity (claims 17-18) or hybridizing with a polynucleotide having 85% identity (claims 2 & 6-16) to a fragment of SEQ ID NOs: 1, 5, or 7 that does not encode a functional LSH protein of SEQ ID NO: 2 or 4, undue trial and error experimentation would be required to screen through the myriad of nucleic acids encompassed by the claims to try to find a use for a plant comprising such nucleic acids, if such use is even possible.
Given the claim breadth and lack of guidance in the specification as discussed above, the instant invention is not enabled through the full scope of claims 2 & 6-18.
Claim Rejections - 35 USC § 102
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of the appropriate paragraphs of 35 U.S.C. 102 that form the basis for the rejections under this section made in this Office action:
A person shall be entitled to a patent unless –
(a)(1) the claimed invention was patented, described in a printed publication, or in public use, on sale, or otherwise available to the public before the effective filing date of the claimed invention.
Claims 1-10 & 16-18 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Lei et al (2019) J of Integrative Plant Biology. 61(4): 463–477 (available 8/21/2018, hereafter Lei; appended PDF includes the supplement).
Claims 1-10 & 16-18 are drawn to a recombinant DNA molecule encoding an LSH protein or fragment, present within a host bacteria or plant cell, the plant comprising said molecule, and a method for increasing intracellular colonization by nitrogen-fixing bacteria in a plant.
Lei discloses an overexpression plasmid with a pCAMBIA 1302 backbone comprising an LjALOG1 cDNA molecule fused to red florescence protein driven by CaMV 35S promoter (page 473, right column, paragraph 4). Lei discloses transformation of L. japonicus seedlings via Agrobacterium rhizogenes inoculation (page 473, right column, paragraph 5-page 474, left column, paragraph 1). Overexpression of LjALOG1 in transgenic L. japonicus increased nodule number (page 468, right column, paragraph 2).
Lei discloses that the sequence of the L. japonicus ALOG1 gene was from the Lj5g3v1083950.1 record found on the miyakogusa.jp 3.0 release (figure 1; page 473, left column, paragraph 4). Lei discloses the sequence of the LjALOG1 protein (Figure S1), which has 84% sequence identity to SEQ ID NO: 2. The sequence of LjALOG1 disclosed by Lei also comprises a fragment of 78 amino acids with 100% sequence identity to SEQ ID NO: 2 positions 105-183. See alignment below.
Range 1: 1 to 207GraphicsNext MatchPrevious Match
Alignment statistics for match #1
Score
Expect
Method
Identities
Positives
Gaps
313 bits(802)
3e-114
Compositional matrix adjust.
188/224(84%)
198/224(88%)
20/224(8%)
Query 1 MDSIQDFMDSCNS-DNS-CSLTNSTITTNSSNNNISNAIVGSSSPSGS-TTTSSRYENQK 57
MDSIQ+FM+SCNS DN+ CSL+N+T +NS IVG SSPS S TTTSSRYENQK
Sbjct 1 MDSIQEFMESCNSHDNTNCSLSNTT--SNS-------LIVGGSSPSASVTTTSSRYENQK 51
Query 58 RRDWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQFGKTKVHTPICPFYGHPNPPAPC 117
RRDWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQFGKTKVHTP+CPFYGHPNPPAPC
Sbjct 52 RRDWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQFGKTKVHTPMCPFYGHPNPPAPC 111
Query 118 PCPLRQAWGSLDALIGRLRAAFEENGGKPETNPFGARAVRLYLREVRDLQSKARGISYEK 177
PCPLRQAWGSLDALIGRLRAAFEENGGKPETNPFGARAVRLYLREVRDLQSKARGISYEK
Sbjct 112 PCPLRQAWGSLDALIGRLRAAFEENGGKPETNPFGARAVRLYLREVRDLQSKARGISYEK 171
Query 178 KKRKRPPQQQPQQLQLQQQQPMQLQLPLHLHHHHQHQLPPPGAT 221
KKRKRP PQQ Q QQQQP+Q+ LP HHHHQ QLPPPGA+
Sbjct 172 KKRKRP---HPQQ-QQQQQQPLQV-LP---HHHHQLQLPPPGAS 207
The overexpression plasmid of Lei anticipates a recombinant DNA molecule comprising a heterologous promoter operably linked to a polynucleotide segment encoding a LSH protein or fragment wherein said protein comprises an amino acid sequence having at least about 85% identity to SEQ ID NO: 2 (claim 1), and wherein said recombinant DNA molecule is in operable linkage with a plasmid (claim 2, lines 5-6), and wherein the recombinant DNA molecule is present within an Agrobacterium host cell (claims 3-4). Because the DNA molecule within a different host cell is not patentably distinct from the DNA molecule within an Agrobacterium host cell, Lei anticipates claim 5 as well.
The hairy roots of lotus transformed with an overexpression plasmid of LjALOG1 anticipate the recombinant DNA expressed in a plant cell to increase intracellular colonization by nitrogen-fixing bacteria (claim 2) wherein the plant cell is a dicot (claim 6) and lotus (claim 7, line 6), as well as a lotus plant, which is a dicot, comprising the DNA molecule (claims 8-10). The transgenic lotus roots also anticipate a plant susceptible to intracellular colonization by nitrogen-fixing bacteria comprising the recombinant DNA molecule (claim 16).
Finally, Lei discloses nodulation experiments comprising inoculating plants with Mesorhizobium loti strain MAFF303099 (page 473, left column, paragraph 2). Lei discloses that M. loti are rhizobia capable of infecting cortical cells (page 467, left column). Lei discloses increased expression of LjALOG1 after inoculation with M. loti in wild type plants (page 467, right column, paragraph 1; figure 6b). Because the language of claim 17 does not impose a specific order on the performance of the method steps and it would be improper to import limitations from the specification (MPEP 2111.01 (II)), claim 17 may be interpreted to encompass a method wherein the plant is contacted with an effective amount of rhizobia bacterium prior to expressing a LSH protein in the plant. Therefore, the expression of LjALOG1 in L. japonicus plants after inoculation with M. loti anticipates claims 17-18 under broadest reasonable interpretation. Lei also discloses inoculating with M. loti after transforming with an overexpression construct (page 473, right column, paragraph 5-page 474, left column, paragraph 1), which also anticipates claims 17-18.
Claims 1-6, 8-9 & 14 are rejected under 35 U.S.C. 102(a)(1) as being anticipated by Lee et al (2020) Genes & Genomics. 42:1151–1162 (published 8/16/2020, hereafter Lee).
Claims 1-6, 8-9 & 14 are drawn to are drawn to a recombinant DNA molecule encoding an LSH protein or fragment, present within a host bacteria or plant cell and the plant comprising said molecule.
Lee discloses cDNA of two LSH genes in Arabidopsis, LSH1 and LSH2, cloned into a pCAMBIA3300 binary vector under control of the CaMV 35S promoter and introduced in Agrobacterium tumefaciens (page 1152, right column, paragraph 2).
Lee discloses that the amino acid sequences for AtLSH1-AtLSH10 were obtained from the NCBI database (page 1153, right column, paragraph 4) and also teaches the sequences themselves in Figure 1B. The sequence for AtLSH1 has 82% sequence similarity to SEQ ID NO: 2, and 100% sequence similarity to fragments of SEQ ID NO: 2. See alignment below; SEQ ID NO: 2 is on the top.
Score
Expect
Method
Identities
Positives
Gaps
206 bits(523)
2e-72
Compositional matrix adjust.
110/134(82%)
121/134(90%)
1/134(0%)
Query 49 TSSRYENQKRRDWNTFGQYLKNHRPPLSLSRCSGAHVLEFLRYLDQFG-KTKVHTPICPF 107
+SSRYENQKRRDWNTF QYL+NHRPPLSL CSGAHVLEFLRYLDQFG KTKVH C F
Sbjct 22 SSSRYENQKRRDWNTFCQYLRNHRPPLSLPSCSGAHVLEFLRYLDQFGGKTKVHHQNCAF 81
Query 108 YGHPNPPAPCPCPLRQAWGSLDALIGRLRAAFEENGGKPETNPFGARAVRLYLREVRDLQ 167
+G PNPPAPCPCPLRQA GSLDALIGRLRAA+EENGG PE NPFG+RAVRL+LREVRD Q
Sbjct 82 FGLPNPPAPCPCPLRQAVGSLDALIGRLRAAYEENGGPPEANPFGSRAVRLFLREVRDFQ 141
Query 168 SKARGISYEKKKRK 181
+KARG+SYEKK+++
Sbjct 142 AKARGVSYEKKRKR 155
The binary vector comprising a cDNA sequence for LSH1 and the CaMV35S promoter present with A. tumefaciens anticipates claims 1-4. Although Lee does not teach the plasmid within a Bacillus, Brevibacillus, or Escherchia bacteria, claim 5 is drawn to the recombinant DNA molecule itself and therefore is anticipated by Lee.
Lee discloses Arabidopsis transformed via flora dip with the constructs comprising the LSH cDNAs as well as homozygous T3 seeds of the transformants (page 1152, right column, paragraph 2). This anticipates transgenic seed comprising the recombinant DNA molecule (claim 14) as well as a dicot plant comprising the recombinant DNA molecule (claims 8-9) and the recombinant DNA molecule present in a dicotyledonous or monocotyledonous plant (claim 6). The limitation that the expression in the plant cell is to increase intracellular colonization by nitrogen-fixing bacteria (claim 2, lines 3-4) is an intended result and doesn’t provide additional patentable weight.
Thus, Lee anticipates claims 1-6, 8-9 & 14.
Claim Rejections - 35 USC § 103
In the event the determination of the status of the application as subject to AIA 35 U.S.C. 102 and 103 (or as subject to pre-AIA 35 U.S.C. 102 and 103) is incorrect, any correction of the statutory basis (i.e., changing from AIA to pre-AIA ) for the rejection will not be considered a new ground of rejection if the prior art relied upon, and the rationale supporting the rejection, would be the same under either status.
The following is a quotation of 35 U.S.C. 103 which forms the basis for all obviousness rejections set forth in this Office action:
A patent for a claimed invention may not be obtained, notwithstanding that the claimed invention is not identically disclosed as set forth in section 102, if the differences between the claimed invention and the prior art are such that the claimed invention as a whole would have been obvious before the effective filing date of the claimed invention to a person having ordinary skill in the art to which the claimed invention pertains. Patentability shall not be negated by the manner in which the invention was made.
This application currently names joint inventors. In considering patentability of the claims the examiner presumes that the subject matter of the various claims was commonly owned as of the effective filing date of the claimed invention(s) absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and effective filing dates of each claim that was not commonly owned as of the effective filing date of the later invention in order for the examiner to consider the applicability of 35 U.S.C. 102(b)(2)(C) for any potential 35 U.S.C. 102(a)(2) prior art against the later invention.
Claims 1-11 & 14-15 are rejected under 35 U.S.C. 103 as being unpatentable over Lee et al (2020) Genes & Genomics. 42:1151–1162 (published 8/16/2020, hereafter Lee) in view of Dong et al (2014) Plant Breed. Biotech. 2(2):126-138 (published June 2014, hereafter Dong).
Claims 1-10 & 14-15 are drawn to a recombinant DNA molecule comprising a heterologous promoter operably linked to a polynucleotide segment encoding a LSH protein or fragment thereof, plants comprising said molecule, and a method of producing progeny seed comprising the recombinant DNA molecule.
The teachings of Lee are presented above. Lee does not explicitly teach the method of producing progeny seed comprising the recombinant DNA molecule, Lee does not teach the recombinant DNA molecule in a plant listed in claims 7 or 10, and Lee does not teach that expression of the polynucleotide segment varies over a 24-hour period.
Dong teaches LSH genes in Brassica, including BrLSH2 genes similar to AtLSH2 (table 1, figure 2). Dong teaches that the expression of Brassica rapa (Chinese cabbage) LSH2 transcripts vary throughout the day (figure 1B).
Before the filing date of the instant application, it would have been obvious to one of ordinary skill in the art to substitute a B. rapa LSH2 promoter for the native promoter of the Arabidopsis LSH2 gene in the construct taught by Lee and a B. rapa for Arabidopsis as the transformed plant. One of ordinary skill in the art would have been motivated to substitute a known promoter for another known promoter of a homologous gene as a design choice. One of ordinary skill in the art would have had reasonable expectation of success, because B. rapa and Arabidopsis are closely related species.
Therefore, claims 1, 2, 6 & 7, drawn to the recombinant DNA expressed within a Chinese cabbage plant cell, is obvious in view of Dong and Lee. The limitation that the expression in the plant cell is to increase intracellular colonization by nitrogen-fixing bacteria (claim 2, lines 3-4) is an intended result and doesn’t provide additional patentable weight.
Likewise, the plant of claims 8-10 are obvious in view of Dong and Lee. Because the expression of BrLSH2 varies through a day, it would be obvious that expression of the polynucleotide segment in linkage with this promoter would vary over a 24-hour period (claim 11).
Before the filing date of the instant application, the method of producing progeny seed of claim 15 would have been obvious to one of ordinary skill in the art. The existence of homozygous T3 seed inherently teaches that a T0 transgenic seed was planted, the plant was grown, and progeny seed comprising the recombinant DNA molecule was harvested from the plant, and that this process was repeated twice. Thus, claim 15 is obvious over Lee.
In addition, claims 3-5 & 14 are obvious over Lee as presented above.
Claims 1-6, 8-9 & 11-14 are rejected under 35 U.S.C. 103 as being unpatentable over Lee et al (2020) Genes & Genomics. 42:1151–1162 (published 8/16/2020, hereafter Lee) in view of Repetti et al US 2012/0131691 A1 (published 5/24/2012, hereafter Repetti) taken with the evidence of Ito et al (2005) Biosci. Biotechnol. Biochem. 69 (2), 382–390 (available online 5/22/2014, hereafter Ito).
Claims 1-6, 8-9 & 11-14 are drawn to a recombinant DNA molecule encoding a LSH protein or fragment thereof and a plant comprising said molecule wherein expression is increased during the first 6 or 12 hours of a 12 hour/12 hour light/dark cycle.
The teachings of Lee are presented above. Lee does not teach a heterologous promoter wherein expression varies over a 24-hour period and is increased during the fist 12 or 6 hours of a 12 hour/12 hour light/dark cycle.
Repetti teaches APRR9 as a light-inducible promoter (paragraph [0081]) and teaches the sequence of the Arabidopsis APRR9 promoter (Repetti SEQ ID NO: 6). Repetti teaches transformation of Arabidopsis with constructs driven by light-inducible promoters (paragraphs [0091-0095]). Repetti teaches that crop species such as soybean expressing polypeptides of interest may have improved traits when a sequence encoding the polypeptide is placed under regulatory control of light-responsive promoters (paragraph [0098]). Repetti teaches that a light-inducible promoter can regulate and optimize overexpression of genes in plants (paragraph [003]).
Ito provides evidence that the promoter of APRR9 in Arabidopsis has diurnal oscillation and is rapidly induced by light. When grown under 12 light/12h dark cycles, APRR9 expression increased sharply in the morning (page 384, left column, paragraph 4-right column, paragraph 1), and was highest in the first 6 hours in the light (fig 1A).
Before the filing date of the instant application, it would have been obvious to one of ordinary skill in the art to substitute the CaMV 35S promoter used by Lee for the light inducible APRR9 promoter taught by Repetti. One would have been motivated to use a light-inducible promoter instead of a constitutive promoter in order to optimize expression in a transgenic plant. One would have had reasonable expectation of success, because APRR9 in an endogenous Arabidopsis promoter.
Conclusion
No claims are allowed.
Any inquiry concerning this communication or earlier communications from the examiner should be directed to Victoria L DeLeo whose telephone number is (703)756-5998. The examiner can normally be reached M-Th 7:30am-5pm EST; F 7:30am-12pm EST.
Examiner interviews are available via telephone, in-person, and video conferencing using a USPTO supplied web-based collaboration tool. To schedule an interview, applicant is encouraged to use the USPTO Automated Interview Request (AIR) at http://www.uspto.gov/interviewpractice.
If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Shubo (Joe) Zhou can be reached on (571) 272-0724. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
Information regarding the status of published or unpublished applications may be obtained from Patent Center. Unpublished application information in Patent Center is available to registered users. To file and manage patent submissions in Patent Center, visit: https://patentcenter.uspto.gov. Visit https://www.uspto.gov/patents/apply/patent-center for more information about Patent Center and https://www.uspto.gov/patents/docx for information about filing in DOCX format. For additional questions, contact the Electronic Business Center (EBC) at 866-217-9197 (toll-free). If you would like assistance from a USPTO Customer Service Representative, call 800-786-9199 (IN USA OR CANADA) or 571-272-1000.
/VICTORIA L DELEO/Examiner, Art Unit 1662
/Anne Kubelik/Primary Examiner, Art Unit 1662
Prosecution Insights