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 .
Response to Arguments
In view of the Appeal Brief filed on 05/07/2026, PROSECUTION IS HEREBY REOPENED. New grounds of rejection are set forth below.
To avoid abandonment of the application, appellant must exercise one of the following two options:
(1) file a reply under 37 CFR 1.111 (if this Office action is non-final) or a reply under 37 CFR 1.113 (if this Office action is final); or,
(2) initiate a new appeal by filing a notice of appeal under 37 CFR 41.31 followed by an appeal brief under 37 CFR 41.37. The previously paid notice of appeal fee and appeal brief fee can be applied to the new appeal. If, however, the appeal fees set forth in 37 CFR 41.20 have been increased since they were previously paid, then appellant must pay the difference between the increased fees and the amount previously paid.
A Supervisory Patent Examiner (SPE) has approved of reopening prosecution by signing below:
/LYLE ALEXANDER/Supervisory Patent Examiner, Art Unit 1797
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.
The factual inquiries for establishing a background for determining obviousness under 35 U.S.C. 103 are summarized as follows:
1. Determining the scope and contents of the prior art.
2. Ascertaining the differences between the prior art and the claims at issue.
3. Resolving the level of ordinary skill in the pertinent art.
4. Considering objective evidence present in the application indicating obviousness or nonobviousness.
Claim(s) 11-16 and 19 is/are rejected under 35 U.S.C. 103 as being unpatentable over Zhang et al. (Quantitative Proteomics Reveals Histone Modifications in Crosstalk with H3 Lysine 27 Methylation), in view of Nelson et al. (Implications of 15N-metabolic labeling for automated peptide identification in Arabidopsis thaliana) and Mylne et al. (15N Cyclotides by Whole Plant Labeling).
Regarding claim 11, Zhang discloses two or more peptides corresponding to peptides that are common between two or more plant species (pg. 750-751/EXPERIMENTAL PROCESURES, see: selected peptides from each of the core histones “AGLQFPVGR” which is identical to the Applicant’s “SEQ ID No. 153”, and “TLYGFGG” which is identical to the Applicant’s “SEQ ID NO. 60”; Regarding the limitations directed towards the peptides being common between two or more plant species, the Applicants explicitly disclose SEQ ID No. 153 and 60 are peptides which are included in the limitation’s scope (see: Claim 14)).
Zhang further discloses preparing core histones as internal standards by metabolically labelling wild-type Tetrahymena cells by feeding on Escherichia coli BL21 cells grown in the [15N] M9 minimal medium supplemented with 15N-substituted Bioexpress, and then purifying the individual histones by centrifugation, extraction, precipitation, and washing the metabolically labeled cells species (pg. 750-751/EXPERIMENTAL PROCESURES, see: Cell Culture, Core Histone Preparation, and HPLC Purification).
Zhang does not explicitly disclose all of the core histones being metabolically labelled.
Nelson teaches it was well known in that the metabolic labeling of plant cells by growing the cells in 15N-labeled media results in 15N-labeled peptides (pg. 1280/col. 1/para. 2, see: “The second approach provides heavy isotopes such as 15N or 13C to the organism in a simpler form, such as isotopically labeled salts or sugars. As the organism grows and metabolizes these labeled salts or sugars, it incorporates the isotopic label into synthesized proteins.”).
Mylne teaches an analogous method of producing of 15N labeled cyclotides by whole plant labeling (pg. 576/Plant Growth and 15N Media, see: “complete method for labeled cyclotide production using an established growth media”).
It would have been obvious to one having ordinary skill in the art, before the effective filing date of the claimed invention, to metabolically label all of the core histones disclosed by Zhang, as taught by Nelson and Mylne, in order to provide for improved mass spectrometry resolution in quantitative proteomic applications.
Regarding the recitation of the two or more labeled peptides being configured as a kit, Zhang further discloses purifying the individual histones by resolving them with an HPLC column, wherein the HPLC fractions containing individual histones are combined after evaluation by SDS-PAGE (pg. 750-751/EXPERIMENTAL PROCESURES, see: Cell Culture, Core Histone Preparation, and HPLC Purification).
It would have been obvious to one having ordinary skill in the art, before the effective filing date of the claimed invention, to arrange the analogous two or more labeled peptides in the device disclosed by modified Zhang in a kit since combining the known chemical components into a packaged collection involves only routine assembly of known items yielding predictable results.
Additionally, it would have been obvious to a person of ordinary skill in the art, before the effective filing date of the claimed invention, to arrange the individual labeled proteins in the device disclosed by modified Zhang into a pre-packaged kit in order to provide user convenience and portability.
Regarding claim 12, Zhang further discloses the peptides common to the two or more plant species are selected from a set of common peptides that are common for the two or more plant species (The instant claims recite peptides selected from the group consisting of SEQ ID NO. 54 through SEQ ID NO. 453 are common between two or more plant species of Rosids (Claims 11 and 15). Since Zhang explicitly discloses the peptides having the same sequence as the instantly claimed SEQ ID NO. 153 and 60 (see: Rejection of Claim 11), it is the position of the Examiner that the peptides disclosed by Zhang would be present in two or more plant species of Rosids)).
Regarding claim 13, Zhang further discloses the peptides common to the two or more plant species are selected using a computational approach, a hybrid approach, and/or an empirical approach (Regarding the method limitations recited in claim 13 the Examiner notes that even though a product-by-process is defined by the process steps by which the product is made, determination of patentability is based on the product itself. In re Thorpe, 777 F.2d 695, 227 USPQ 964 (Fed. Cir. 1985). As the court stated in Thorpe, 777 F.2d at 697, 227 USPQ at 966 (The patentability of a product does not depend on its method of production. In re Pilkington, 411 F.2d 1345, 1348, 162 USPQ 145, 147 (CCPA 1969). If the product in a product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process).
Regarding claim 14, Zhang further discloses the two or more labeled peptides are selected from the group consisting of: SEQ ID NO. 54 through SEQ ID NO. 153, and combinations thereof (pg. 750-751/EXPERIMENTAL PROCESURES, see: selected peptides from each of the core histones “AGLQFPVGR” which is identical to the Applicant’s “SEQ ID No. 153”, and “TLYGFGG” which is identical to the Applicant’s “SEQ ID NO. 60”).
Regarding claim 15, Zhang further discloses the two or more plant species are two or more species of Rosids, and wherein the two or more labeled peptides are selected from the group consisting of: SEQ ID NO. 54 through SEQ ID NO. 453, and combinations thereof (pg. 750-751/EXPERIMENTAL PROCESURES, see: selected peptides from each of the core histones “AGLQFPVGR” which is identical to the Applicant’s “SEQ ID No. 153”, and “TLYGFGG” which is identical to the Applicant’s “SEQ ID NO. 60”).
Regarding claim 16, Zhang further discloses two or more groups of labeled peptides corresponding to the peptides that are common between the two or more species, wherein the two or more groups are in a hierarchical relationship in relation to a taxonomy of species (pg. 750-751/EXPERIMENTAL PROCESURES, see: plurality of selected peptides which grouped into H2A, H3, and H4).
Regarding claim 19, Zhang further discloses the two or more plant species have a common ancestor (The instant claims recite peptides selected from the group consisting of SEQ ID NO. 54 through SEQ ID NO. 453 are common between two or more plant species of Rosids (Claims 11 and 15). Since Zhang explicitly discloses the peptides having the same sequence as the instantly claimed SEQ ID NO. 153 and 60 (see: Rejections of Claims 11 and 15 above), it is the position of the Examiner that the peptides disclosed by Zhang would be present in two or more plant species of Rosids).
Claim(s) 11-13, 16, and 19 is/are rejected under 35 U.S.C. 103 as being unpatentable over Mylne et al. (15N Cyclotides by Whole Plant Labeling).
Regarding claim 11, Mylne discloses two or more labeled peptides corresponding to peptides that are common between two or more plant species (Table II, see: plurality of 15N labeled cyclotides/peptides; pg. 575/INTRODUCTION, see: cyclotides are found in three plant families: the Violaceae (violet family), scattered members of the Rubiaceae (coffee family), and one member of the Cucurbitaceae (cucumbers and gourds) plant families.).
Mylne does not explicitly disclose the two or more labeled peptides being configured as a kit.
It would have been obvious to one having ordinary skill in the art, before the effective filing date of the claimed invention, to arrange the analogous two or more labeled peptides in the device disclosed by Mylne in a kit since combining the known chemical components into a packaged collection involves only routine assembly of known items yielding predictable results.
Additionally, it would have been obvious to a person of ordinary skill in the art, before the effective filing date of the claimed invention, to arrange the individual labeled proteins in the device disclosed by Mylne into a pre-packaged kit in order to provide user convenience and portability.
Regarding claim 12, Mylne further discloses the peptides common to the two or more plant species are selected from a set of common peptides that are common for the two or more plant species (pg. 575/INTRODUCTION, see: cyclotides are found in three plant families: the Violaceae (violet family), scattered members of the Rubiaceae (coffee family), and one member of the Cucurbitaceae (cucumbers and gourds) plant families.).
Regarding claim 13, Mylne further discloses the peptides common to the two or more plant species are selected using a computational approach, a hybrid approach, and/or an empirical approach (Regarding the method limitations recited in claim 13 the Examiner notes that even though a product-by-process is defined by the process steps by which the product is made, determination of patentability is based on the product itself. In re Thorpe, 777 F.2d 695, 227 USPQ 964 (Fed. Cir. 1985). As the court stated in Thorpe, 777 F.2d at 697, 227 USPQ at 966 (The patentability of a product does not depend on its method of production. In re Pilkington, 411 F.2d 1345, 1348, 162 USPQ 145, 147 (CCPA 1969). If the product in a product-by-process claim is the same as or obvious from a product of the prior art, the claim is unpatentable even though the prior product was made by a different process).
Regarding claim 16, Mylne further discloses two or more groups of labeled peptides corresponding to the peptides that are common between the two or more species, wherein the two or more groups are in a hierarchical relationship in relation to a taxonomy of species (pg. 575/INTRODUCTION, see: cyclotides are found in three plant families: the Violaceae (violet family), scattered members of the Rubiaceae (coffee family), and one member of the Cucurbitaceae (cucumbers and gourds) plant families.).
Regarding claim 19, Zhang further discloses the two or more plant species have a common ancestor (pg. 575/INTRODUCTION, see: cyclotides are found in three plant families: the Violaceae (violet family), scattered members of the Rubiaceae (coffee family), and one member of the Cucurbitaceae (cucumbers and gourds) plant families; all plants share a common photosynthetic ancestor)
Conclusion
Any inquiry concerning this communication or earlier communications from the examiner should be directed to ROBERT J EOM whose telephone number is (571)270-7075. The examiner can normally be reached Monday-Friday (9:00AM-5:00PM).
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If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Lyle Alexander can be reached at 5712721254. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
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/ROBERT J EOM/ Primary Examiner, Art Unit 1797
Prosecution Insights