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 .
This is the First Office Action on the Merits of US 18/469,512 filed on 09/18/2023 which claims US priority benefit of US Provisional 63/376,419 filed on 09/20/2022.
Claims 1-60 are cancelled.
Claims 61-72 are pending and under examination.
Specification
The specification is objected to as failing to provide proper antecedent basis for the claimed subject matter. See 37 CFR 1.75(d)(1) and MPEP § 608.01(o). Correction of the following is required: Table 1.1 (para 571) appears to be missing from the specification. Present claim 62 refers to sequences set forth in TABLE 1.1.
Claim Rejections - 35 USC § 112
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.
Claims 61-72 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.
Claims 62-66, and 69-71 are indefinite because they each depend from a cancelled claim. Claim 72 is indefinite as it depends from claim 71.
Claims 61-63, 67-68, and 72 are indefinite for referring to lists recited in a TABLE in the specification. Where possible, claims are to be complete in themselves. Incorporation by reference to a specific figure or table is permitted only in exceptional circumstances where there is no practical way to define the invention in words and where it is more concise to incorporate by reference than duplicating a drawing or table into the claim. Incorporation by reference is a necessity doctrine, not for applicant’s convenience. Ex parte Fressola, 27 USPQ2d 1608, 1609 (Bd. Pat. App. & Inter. 1993)" MPEP 2173.05(s)) informs that although applications in TC 1600 commonly include tables with large numbers of genes, proteins, small molecule biomarkers, diseases, acceptable excipients, etc., claims cannot refer back to these tables in the specification; e.g., "wherein the biomarkers are selected from the group consisting of those listed in Table 4" or "wherein the cancer is one of those listed in Table 3." Applicants should copy the table contents into the claim itself. There is no limit to the length of a claim. If the subject matter can be listed in the specification, that list can be copied and pasted into a claim.
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.
Claims 61-72 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 full scope of the claimed invention.
Independent claims 61 and 67-68 require the critically essential element of a composition (claim 61), expression vector (claim 67), or system (claim 68) comprising/encoding a polypeptide comprising an amino acid sequence that is an “effector protein” and is at least 75% identical to any one of the sequences shown in Table 1. Claims 61 and 68 also require an engineered guide nucleic acid. Further, in view of the claims drawn to a method of using such critically essential element, it appears that the critically essential product of claims 61 and 67-68 have the intended required functional property of treating a disease associated with any mutation or aberrant expression of a human gene in a subject in need thereof. Dependent claims are not remedial and although they presently depend from cancelled claims, they are included in this rejection for purpose of compact prosecution.
A review of Table 1 of the instant specification shows a list of SEQ ID NO:s 1 to 454 of “Effector Proteins” described only by an “Effector ID” No. However, the instant specification lacks a representative set of species of variants of such effector proteins encompassed by the present claim language “75% identical” so that one of ordinary skill in the art would be able to envision whether a given variant effector protein amino acid sequence would be effective at treating any disease associated with any mutation or aberrant expression of a human gene in a subject in need thereof.
The state of the art teaches the unpredictability of treating a human disease using an effector protein variant and a generic guide nucleic acid. (See US Patent 11,453,866 to Doudna et al (US 20200299660 published 06/09/2020).
Further, the instant specification provided no examples of in vitro or in vivo assays using variants of the sequences shown in Table 1. Further, the examples show nothing regarding treating a disease.
Example 1: Metagenomic Identification of Effector Proteins and Effector Partners
[0631] Genes encoding effector proteins and effector partners were identified by sequence homology and structural analyses of potential CRISPR arrays and cognate proteins. Two groups of proteins emerged: a first group of proteins were identified close to the CRISPR arrays and a second group of proteins were identified close to the first group of proteins. All proteins were sorted by structural similarity into clusters. Through BLAST and HEIPred analysis, the identified proteins were found to be structurally similar to the IS family of transposases. Specifically, the first group of proteins were structurally similar to Ist21 transposases of the IS family of transposases (e.g., as encoded by istA) and identified as effector proteins of interest, and the second group of proteins were structurally similar to the helper proteins (e.g., as encoded by istB) of the IS family of transposases. Of the second group of proteins, two-subgroups of proteins emerged: a first subgroup that was generally found downstream of and typically shared an overlapping ORF with the first group of proteins; and a second subgroup that was found in varying locations. When a protein from the second subgroup was found downstream of the first subgroup, it was typically found to be ˜150 bp away and may have some overlapping ORFs. There were some exceptions, for example, when a protein from the second subgroup was found far downstream, such a protein was found to be about −3.5 kb away. When a protein from the second subgroup was found upstream, the ORF overlapped with the first group of proteins about half the time, otherwise the proteins were found to be within 50 bp of one another. Furthermore, if the ORF of a first subgroup does not overlap with the first group, then the two proteins were found within 50 bp of each other.
[0632] Without being bound by theory, it is contemplated that the identified effector proteins function as RNA-guided transposases. Also, without being bound by theory, it is contemplated that the second group of proteins, like the IS helper proteins, are also helper or partner proteins for the identified effector proteins of interest.
[0633] Effector Protein Library: In total, 454 effector proteins (SEQ ID NO: 1 to SEQ ID NO: 454), as set forth in TABLE 1 were selected as candidates.
[0624] TABLE 1 provides illustrative amino acid sequences of effector proteins that are useful in the compositions, systems and methods described herein. (SEQ ID corresponds to Effector ID in column to its immediate right).
Example 2: Activity of Effector Protein and Effector Partner In Vitro
[0637] Effector proteins and effector partner combinations are tested for their ability to guide the direct transposition of a donor nucleic acid into a target plasmid in an in vitro assay. A first plasmid encoding an effector protein, a second plasmid encoding an effector partner, and a third target plasmid. Donor DNA can be generated from a plasmid or a linear double-stranded DNA molecule. The donor DNA contains the spectinomycin resistance gene with a structural motif, inverted terminal repeats (ITRs) that a transposase can recognize. Where more than one effector partner is identified for an effector protein (e.g., comp. no. 436 in TABLE 11 above), the second plasmid encoding the effector partner can further include one or more nucleotide sequences encoding the additional effector partners or the additional effector partners can be encoded by a fourth plasmid. Plasmids encoding the effector protein and effector partner(s) are bacterial nuc-doc expression vectors. A target plasmid containing an 51 spacer (5′-TATTAAATACTCGTATTGCTGTTCGATTAT-3′ (SEQ ID NO: 984) and an ampicillin resistance gene are also generated.
[0638] To test for transposase activity, plasmids encoding the effector proteins and effector partners are contacted with a guide RNA, in combinations for example, as set forth in TABLE 3, along with the donor DNA and the target template. The composition is incubated for a sufficient amount of time to allow the effector protein and/or effector partners to recognize the ITRs and direct transposition of the donor nucleic acid to the 51 spacer in the target plasmid. The insertion of the donor DNA into the target plasmid demonstrates the transposase activity of the effector protein and effector partner combinations. After transposition, the target plasmid will contain the spectinomycin and ampicillin resistance genes. The target plasmid is then transformed into E. coli and screened using spectinomycin and ampicillin. Only target plasmids that have successfully been transposed into will allow transformed bacteria to survive both antibiotics. Next, plasmids from the surviving colonies are sequenced by next generation sequencing (NGS) of PCR amplicons to assess whether the donor DNA was integrated in the target site as directed by the guide RNA, as well as PAM requirements of the same. Controls can include gene products of MuA, MuB, IstA, and IstB.
Example 3: Indel Activity of Effector Proteins and Effector Partners in Lipofected Eukaryotic Cells
[0639] Effector proteins and/or effector partners combinations as described in Example 1 are tested for their ability to form indels within a target nucleic acid (e.g., genomic DNA) in eukaryotic cells (e.g., immune cell, T cell, HEK29 cell, or any other eukaryotic cell). Plasmid pairs co-expressing the effector protein, effector partner(s), and gRNA (1 plasmid/target) are delivered to eukaryotic cells via lipofection using a lipofection reagent. Lipofected cells are incubated to allow for indel formation. Indels are detected by next generation sequencing (NGS) of PCR amplicons at the targeted loci, and indel percentage is calculated as the fraction of sequencing reads containing insertions or deletions relative to an unedited reference sequence.
The number of variants encompassed by the present claim language is extremely large. The specification shows possession of the amino acid sequences shown in Table 1 but shows no functional variant species.
The Court of Appeals for the Federal Circuit has recently held that a "written description of an invention involving a chemical genus, like a description of a chemical species, 'requires a precise definition, such as be structure, formula [or] chemical name,' of the claimed subject matter sufficient to distinguish it from other materials." University of California v. Eli Lilly and Co., 1997 U.S. App. LEXlS 18221, at *23, quoting Fiers v. Revel, 25 USPQ2d 1601, 1606 (Fed. Cir. 1993) (bracketed material in original).
To fully describe a genus of genetic material, which is a chemical compound, applicants must (1) fully describe at least one species of the claimed genus sufficient to represent said genus whereby a skilled artisan, in view of the prior art, could predict the structure of other species encompassed by the claimed genus and (2) identify the common characteristics of the claimed molecules, e.g., structure, physical and/or chemical characteristics, functional characteristics when coupled with a known or disclosed correlation between function and structure, or a combination of these.
Given this lack of description of representative species encompassed by the genus of the claim, the specification does not sufficiently describe the claimed invention in such full, clear, concise, and exact terms that a skilled artisan would recognize that applicants were in possession of the entire scope of the claimed invention.
For inventions in an unpredictable art, adequate written description of a genus, which embraces widely variant species cannot be achieved by disclosing only one species within the genus. See, e.g., Eli Lilly. Description of a representative number of species does not require the description to be of such specificity that it would provide individual support for each species that the genus embraces. If a representative number of adequately described species are not disclosed for a genus, the claim to that genus must be rejected as lacking adequate written description under 35 U.S.C. 112, first paragraph. In the instant case, the unpredictability of the art is evidenced by the cited references, above. Adequate written description requires more than a mere statement that a compound is part of the invention and reference to a potential method of isolating a compound. The compound itself is required. See Fiers v. Revel, 25 USPQ2d 1601 at 1606 (CAFC 1993) and Amgen Inc. v. Chugai Pharmaceutical Co. Ltd., 18 USPQ2d 1016.
Scope of enablement
Claims 61-72 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 a method of modifying a target nucleic acid within a human gene by contacting the target with a polypeptide having one of the sequences shown in Table 1 and a gRNA, does not reasonably provide enablement for treating any disease associated with a mutation of a human gene in a subject in need thereof by administering to the subject any polypeptide that is at least 75% identical to one of the sequences shown in Table 1 and any gRNA. 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 and use the invention commensurate in scope with these claims.
Factors to be considered in determining whether a disclosure meets the enablement requirement of 35 USC 112, first paragraph, have been described by the court in In re Wands, 8 USPQ2d 1400 (CA FC 1988). Factors to be considered in determining whether a disclosure would require undue experimentation have been summarized by the board in Ex parte Forman. They include (1) the quantity of experimentation necessary, (2) the amount of direction or guidance presented, (3) the presence or absence of working examples, (4) the nature of the invention, (5) the state of the prior art, (6) the relative skill of those in the art, (7) the predictability or unpredictability of the art, and (8) the breadth of the claims.”
The nature of the invention: Present claims are drawn to a method of treating a disease associated with any mutation or aberrant expression of a human gene in a subject in need thereof by administrating to the subject a composition/system comprising a polypeptide comprising an amino acid sequence that is at least 75% identical to one of the sequences shown in Table 1 and any gRNA and has the required functional property of treating a disease associated with any mutation or aberrant expression of a human gene in a subject in need thereof. Thus, the invention is in a class of invention which the CAFC has characterized as “the unpredictable arts such as chemistry and biology.” Mycogen Plant Sci., Inc. v. Monsanto Co., 243 F.3d 1316, 1330 (Fed. Cir. 2001).
Breadth of claims: The claims are broad to treating any disease associated with any mutation or aberrant expression of a human gene in a subject. The claims are broad to a polypeptide comprising an amino acid sequence that is at least 75% identical to one of the sequences shown in Table 1 and to any gRNA.
The unpredictability of the art and the state of the prior art:
The art teaches the unpredictability of treating a human disease using an effector protein variant and a generic guide nucleic acid. (See US Patent 11,453,866 to Doudna et al (US 20200299660 published 06/09/2020).
Guidance in the Specification: The specification provides no evidence that the broad scope of the claims are enabled. The specification shows no working example of administering to a human patient an effector protein of Table 1 being only 75% identical to the instant SEQ ID along with any generic guide nucleic acid to result in treating a disease associated with a mutation or aberrant expression of any human gene. The guidance provided by the specification amounts to an invitation for the skilled artisan to try and follow the disclosed instructions to make and use the claimed invention. For example, the instant specification provided no examples of in vitro or in vivo assays using variants of the sequences shown in Table 1. Further, the examples show nothing regarding treating a disease.
Example 1: Metagenomic Identification of Effector Proteins and Effector Partners
[0631] Genes encoding effector proteins and effector partners were identified by sequence homology and structural analyses of potential CRISPR arrays and cognate proteins. Two groups of proteins emerged: a first group of proteins were identified close to the CRISPR arrays and a second group of proteins were identified close to the first group of proteins. All proteins were sorted by structural similarity into clusters. Through BLAST and HEIPred analysis, the identified proteins were found to be structurally similar to the IS family of transposases. Specifically, the first group of proteins were structurally similar to Ist21 transposases of the IS family of transposases (e.g., as encoded by istA) and identified as effector proteins of interest, and the second group of proteins were structurally similar to the helper proteins (e.g., as encoded by istB) of the IS family of transposases. Of the second group of proteins, two-subgroups of proteins emerged: a first subgroup that was generally found downstream of and typically shared an overlapping ORF with the first group of proteins; and a second subgroup that was found in varying locations. When a protein from the second subgroup was found downstream of the first subgroup, it was typically found to be ˜150 bp away and may have some overlapping ORFs. There were some exceptions, for example, when a protein from the second subgroup was found far downstream, such a protein was found to be about −3.5 kb away. When a protein from the second subgroup was found upstream, the ORF overlapped with the first group of proteins about half the time, otherwise the proteins were found to be within 50 bp of one another. Furthermore, if the ORF of a first subgroup does not overlap with the first group, then the two proteins were found within 50 bp of each other.
[0632] Without being bound by theory, it is contemplated that the identified effector proteins function as RNA-guided transposases. Also, without being bound by theory, it is contemplated that the second group of proteins, like the IS helper proteins, are also helper or partner proteins for the identified effector proteins of interest.
[0633] Effector Protein Library: In total, 454 effector proteins (SEQ ID NO: 1 to SEQ ID NO: 454), as set forth in TABLE 1 were selected as candidates.
[0624] TABLE 1 provides illustrative amino acid sequences of effector proteins that are useful in the compositions, systems and methods described herein. (SEQ ID corresponds to Effector ID in column to its immediate right).
Example 2: Activity of Effector Protein and Effector Partner In Vitro
[0637] Effector proteins and effector partner combinations are tested for their ability to guide the direct transposition of a donor nucleic acid into a target plasmid in an in vitro assay. A first plasmid encoding an effector protein, a second plasmid encoding an effector partner, and a third target plasmid. Donor DNA can be generated from a plasmid or a linear double-stranded DNA molecule. The donor DNA contains the spectinomycin resistance gene with a structural motif, inverted terminal repeats (ITRs) that a transposase can recognize. Where more than one effector partner is identified for an effector protein (e.g., comp. no. 436 in TABLE 11 above), the second plasmid encoding the effector partner can further include one or more nucleotide sequences encoding the additional effector partners or the additional effector partners can be encoded by a fourth plasmid. Plasmids encoding the effector protein and effector partner(s) are bacterial nuc-doc expression vectors. A target plasmid containing an 51 spacer (5′-TATTAAATACTCGTATTGCTGTTCGATTAT-3′ (SEQ ID NO: 984) and an ampicillin resistance gene are also generated.
[0638] To test for transposase activity, plasmids encoding the effector proteins and effector partners are contacted with a guide RNA, in combinations for example, as set forth in TABLE 3, along with the donor DNA and the target template. The composition is incubated for a sufficient amount of time to allow the effector protein and/or effector partners to recognize the ITRs and direct transposition of the donor nucleic acid to the 51 spacer in the target plasmid. The insertion of the donor DNA into the target plasmid demonstrates the transposase activity of the effector protein and effector partner combinations. After transposition, the target plasmid will contain the spectinomycin and ampicillin resistance genes. The target plasmid is then transformed into E. coli and screened using spectinomycin and ampicillin. Only target plasmids that have successfully been transposed into will allow transformed bacteria to survive both antibiotics. Next, plasmids from the surviving colonies are sequenced by next generation sequencing (NGS) of PCR amplicons to assess whether the donor DNA was integrated in the target site as directed by the guide RNA, as well as PAM requirements of the same. Controls can include gene products of MuA, MuB, IstA, and IstB.
Example 3: Indel Activity of Effector Proteins and Effector Partners in Lipofected Eukaryotic Cells
[0639] Effector proteins and/or effector partners combinations as described in Example 1 are tested for their ability to form indels within a target nucleic acid (e.g., genomic DNA) in eukaryotic cells (e.g., immune cell, T cell, HEK29 cell, or any other eukaryotic cell). Plasmid pairs co-expressing the effector protein, effector partner(s), and gRNA (1 plasmid/target) are delivered to eukaryotic cells via lipofection using a lipofection reagent. Lipofected cells are incubated to allow for indel formation. Indels are detected by next generation sequencing (NGS) of PCR amplicons at the targeted loci, and indel percentage is calculated as the fraction of sequencing reads containing insertions or deletions relative to an unedited reference sequence.
Level of Skill in the Art: The level of skill in the art is deemed to be high.
Quantity of Experimentation: The quantity of experimentation in this area is extremely large since there is significant number of parameters which would have to be studied to enable the skilled artisan to practice the claimed invention as broadly as claimed.
Conclusion: In the instant case, in a highly unpredictable art where the prior art and the specification provides insufficient guidance to make and use the broad scope of the present claims it is considered that it would require undue experimentation for one of skill in the art to use the presently claimed invention in the method of the claims as broadly written.
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.
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 61 and 67-68 are rejected under 35 U.S.C. 103 as being unpatentable over US Patent 11,453,866 to Doudna et al (US 20200299660 published 06/09/2020), in view of in view of Watanabe et al (as evidenced by SCV SEQ ID Results herein).
Regarding base claims 61, 67, and 68, Doudna et al teaches a composition or system that comprises:(i) an effector polypeptide such as a CRISPR associated protein (Cas protein) and a gRNA and expression plasmids encoding such. For example, Doudna recite in the Abstract:
Provided are compositions and methods that include one or more of: (1) a “CasZ” protein (also referred to as a CasZ polypeptide), a nucleic acid encoding the CasZ protein, and/or a modified host cell comprising the CasZ protein (and/or a nucleic acid encoding the same); (2) a CasZ guide RNA that binds to and provides sequence specificity to the CasZ protein, a nucleic acid encoding the CasZ guide RNA, and/or a modified host cell comprising the CasZ guide RNA (and/or a nucleic acid encoding the same); and (3) a CasZ transactivating noncoding RNA (trancRNA) (referred to herein as a “CasZ trancRNA”), a nucleic acid encoding the CasZ trancRNA, and/or a modified host cell comprising the CasZ trancRNA (and/or a nucleic acid encoding the same).
Doudna et al disclose that types of chimeric CasZ proteins of interest included proteins having transposase and integrase activity. Further, Doudna et al disclose using metagenomics and metatranscriptomics to find the effector Cas proteins. (See para 543-545).
However, Doudna et al does not disclose an CasZ effector protein comprising the instant SEQ ID NO:10 or SEQ ID NO:5.
Watanabe et al teaches a polypeptide that is an integrase/transposase that is 75.5% identical to instant SEQ ID NO: 5 wherein the polypeptide comprises an amino acid sequence that is at least 75% identical to any one of the sequences set forth in TABLE 1. (See Result from SCV .rup1234 database shown just below.)
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743
699
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604
600
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Greyscale
The level of skill in the art of using metagenomics and metatranscriptomics to find the effector Cas proteins was high before the effective filing date of the presently claimed invention. (See Doudna et al para 543-545).
One of ordinary skill in the art would have been motivated to make a composition of an effector protein and a gRNA for the rationale of finding a tool to modify genomic nucleic acid in an organism for performing gene-editing in such. Further, a skilled artisan would have been motivated to include the integrase/transposase protein of Watanabe et al because Doudna et al disclose that types of chimeric CasZ proteins of interest included proteins having transposase and integrase activity. It would have been obvious to do such because Doudna et al is in the same field of research using metagenomics and metatranscriptomics to find chimeric effector Cas proteins having transposase/integrase activity.
In view of the high skill level in the art before the effective filing date of the presently claimed invention it is considered that one of ordinary skill in the art having the cited references would have had a reasonable expectation of success to combine the elements of the cited references to arrive at the presently claimed invention.
Conclusion
No claim is allowed.
Prior art which may be applied in a future office action if appropriate:
Kucharzyk et al teaches a polypeptide, wherein the polypeptide comprises an amino acid sequence that is at least 75% identical to instant SEQ ID NO: 10 set forth in TABLE 1. (See Result from SCV .rup1234 database.)
Any inquiry concerning this communication or earlier communications from the examiner should be directed to CATHERINE S HIBBERT whose telephone number is (571)270-3053. The examiner can normally be reached M-F 8:00-5:00.
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CATHERINE S. HIBBERT
Primary Examiner
Art Unit 1658
/CATHERINE S HIBBERT/Primary Examiner, Art Unit 1658