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 / Restrictions
In response to previous restriction requirement, Applicant has chosen SEQ ID NO.1 (i.e. HK1) as the elected species.
Previous restriction requirement among inventive groups is withdrawn, and Groups I & II are rejoined.
Claim Status
Claims 1-2, 4-11 & 33 are under examination on the merits.
Claims 3, 12-16 & 18-19 are withdrawn from examination as reciting non-elected subject matter.
Claims 17 & 20-32 are cancelled.
Priority
Claims 1-2, 5-11 & 33 receive the U.S. effective filing date of 24 Sep 2021.
Specification
The disclosure is objected to because it contains an embedded hyperlink and/or other form of browser-executable code [par.70,71]. Applicant is required to delete the embedded hyperlink and/or other form of browser-executable code; references to websites should be limited to the top-level domain name without any prefix such as http:// or other browser-executable code. See MPEP § 608.01.
Claim Rejections - 35 USC § 112
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 1-2, 5-11 & 33 are rejected on the basis that claim 1 contains an improper Markush grouping of alternatives. See In re Harnisch, 631 F.2d 716, 721-22 (CCPA 1980) and Ex parte Hozumi, 3 USPQ2d 1059, 1060 (Bd. Pat. App. & Int. 1984).
A Markush grouping is proper if the alternatives defined by the Markush group (i.e., alternatives from which a selection is to be made in the context of a combination or process, or alternative chemical compounds as a whole) share a “single structural similarity” and a common use. A Markush grouping meets these requirements in two situations.
First, a Markush grouping is proper if the alternatives are all members of the same recognized physical or chemical class or the same art-recognized class, and are disclosed in the specification or known in the art to be functionally equivalent and have a common use. Second, where a Markush grouping describes alternative chemical compounds, whether by words or chemical formulas, and the alternatives do not belong to a recognized class as set forth above, the members of the Markush grouping may be considered to share a “single structural similarity” and common use where the alternatives share both a substantial structural feature and a common use that flows from the substantial structural feature. See MPEP § 2117.
The Markush grouping of ‘SEQ ID NO.1 or SEQ ID NO.2’ as recited in claim 1 is improper because the alternatives defined by the Markush grouping do not share both a single structural similarity and a common use for the following reasons: the claimed sequences do not have a substantial structural feature described from which their use/function flows. The grouped sequences encode different proteins, with different function (i.e. HK1 vs LRP1). Because claims 2, 5-11 & 33 depend from claim 1, they are also rejected.
To overcome this rejection, Applicant may set forth each alternative (or grouping of patentably indistinct alternatives) within an improper Markush grouping in a series of independent or dependent claims and/or present convincing arguments that the group members recited in the alternative within a single claim in fact share a single structural similarity as well as a common use.
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 1-2, 5-11 & 33 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 claims contain 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.
The claims all require a nucleic acid with at least 85% identity to SEQ ID NO.1, which encodes a HK1 (hexokinase) enzyme responsible for root nodulation.
Nucleic acids with 85% identity to the 990bp long SEQ ID NO.1 would have 148 nucleotide substitutions relative to SEQ ID NO.1. The corresponding protein encoded by a 990bp nucleotide would be 330 residues long, with approximately 49 random amino acid substitutions. These nucleic acids encompass those in which every substitution is in a different codon and in which every substitution results in codon that encodes a different amino acid. Describing a genus of polypeptides with all such possible single amino acid substitutions relative to the 330-amino-acids-long polypeptide encoded by SEQ ID NO.1 would require describing 4920 polypeptide sequences; most of which were not in Applicant’s possession at the time of filing. It is reasonable to consider that such wide breadth of structurally variable proteins would have correspondingly variable functionality.
Thus, all potential nucleic acid variants of this genus would encode a large plurality of potential polypeptides, with correspondingly varying structure(s) and physiological function.
The only species described in the specification is SEQ ID NO.1, which encodes the MtHK1 protein involved in root nodulation. Thus, the specification does not describe species over the full scope of the claimed nucleic acids.
Prior art does not disclose any specific polypeptide structures causative of root nodulation associated with HK1, nor indicate the corresponding encoding nucleic acids. Sequence search of SEQ ID NO.1 reveals the nearest identified sequence is that of genomic DNA from Medicago, with no annotated function [72.4% sequence identity to TIGR sequence: MTYBD43TF; Cheung et al. Construction and analysis of normalized cDNA library from flowers, seeds and stems of Medicago truncatula; Published 15 Dec 2005].
Further sequence search of the protein encoded by SEQ ID NO.1 against protein databases reveals 99% sequence identity to a protein described by Young et al. [Nature 480, 520–524 (2011); Published 16 Nov 2011]. However, even though this protein sequence is provided in the context of a genomic survey of genes involved in rhizobial symbiosis in Medicago, neither HK1 or hexokinases in general are indicated in the author’s description of various groups or classes of proteins important to nodulation [p.522, col.2, par.2; p.523, col.1, par.3].
Applicant describes that the function of SEQ ID NO.1 is detected via expression analysis, cloning and genetic transformation of plant material [Specification, par.55]. These are methods focused on genomic (i.e. nucleotide-based) rather than proteomic methods and descriptions. No protein structural or functional motif data is provided by the specification. Applicant is silent as to the required functional motifs required of the encoded HK1 protein to achieve nodulation and prior art does not teach such HK1 features relevant to effective nodule formation. Therefore, the specification fails to make up for the lack of knowledge on the art.
There is no description in the specification of how the structure of SEQ ID NO.1 relates to the structure of alternate hexokinases involved in root nodulation, or to proteins of less than 100% sequence identity to the native MtHK1. Sequences of as little as 85% identity to SEQ ID NO.1 would encode as many as 4920 polypeptide sequences. Further, Applicant does not provide any guidance on the critical functional motifs required among such vast array of proteins. 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 singular species disclosed.
Hence, Applicant has not, in fact, described representative nucleic acids that encode HK1 proteins involved in root nodulation 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.
Because claims 2, 5-11 & 33 rely on the recited 85% sequence identity limitation of claim 1, they too are rejected for lack of full written description.
Claim Rejections - 35 USC § 101
35 U.S.C. 101 reads as follows:
Whoever invents or discovers any new and useful process, machine, manufacture, or composition of matter, or any new and useful improvement thereof, may obtain a patent therefor, subject to the conditions and requirements of this title.
Claim 33 is rejected under 35 U.S.C. 101 because the claimed invention is directed to a naturally occurring seed or grain without significantly more. This judicial exception is not integrated into a practical application because the seed of claim 33 is not limited to transgenic progeny, or otherwise required to carry the transgene relevant to Applicant’s claimed invention. The claim does not include additional elements that are sufficient to amount to significantly more than the judicial exception because claim language does not specify that seed is transgenic or exhibits the transgenic characteristics of the parent plant of claim 1.
Claim 33 recites ‘a seed produced by the plant’ of claim 1. Claim 1 recites a transgenic plant with a specific heterologous sequence involved in root nodulation. However, claim 33 does not limit the claim to seed comprising the nucleic acid sequence (transgene) of SEQ ID NO.1 and it is not specified that the parent plant of claim 1 is homozygous or otherwise stably transmits the transgene. Thus, the claim reads on wild-type seed that contain any amount of DNA of the parent plant but lack a transgene. It is known that during sexual (i.e. seed) reproduction of plants that recombination occurs via meiosis. Therefore, not all progeny of a transgenic plant will always inherit the transgene recited in claim 1. Not all plants pollinated by said parent plant would necessarily produce seed or progeny with SEQ ID NO.1.
Given broadest reasonable interpretation of claim 33, as written, it would encompass any seed of a plant involved in reproducing with the parent plant of claim 1, including those progeny (i.e. seed) that have not inherited the heterologous gene or associated sequence of claim 1. Thus, the claim would encompass wild-type seeds from plants pollinated by the parent plant of claim 1, but lacking the transgene. This would also include commercial grain produced by unintentional pollen drift from the parent plant of claim 1, but lacking the transgene and/or not grown into a transgenic plant (as in claim 1).
Because of this, such a claim is drawn to a natural phenomenon and/or product of nature, that of being claim to production of potentially any wild-type, non-transgenic seed or grain, generally.
Conclusion
No claims are allowed.
Contact Information
Any inquiry concerning this communication or earlier communications from the examiner should be directed to KEITH R WILLIAMS whose telephone number is (571)272-3911. The examiner can normally be reached Mon - Fri, 9:30 - 5:30 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, Amjad Abraham can be reached on (571)270-7058. 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.
/KEITH R. WILLIAMS/Examiner, Art Unit 1663
/Anne Kubelik/Primary Examiner, Art Unit 1663