DETAILED ACTION
Status of the Application
Claims 1-2, 5-17, 21, 23, 25-26 are pending.
The present application, filed on or after March 16, 2013, is being examined under the first inventor to file provisions of the AIA .
Applicant’s amendment of claims 1, 16 as submitted in a communication filed on 12/10/2025 is acknowledged.
Claims 1-2, 5-15 are withdrawn from further consideration pursuant to 37 CFR 1.142(b) as being drawn to a nonelected invention, there being no allowable generic or linking claim. Election was made without traverse in the reply filed on 12/20/2019. Claims 16-17, 21, 23, 25-26 have been examined only to the extent they encompasses the polypeptide of SEQ ID NO: 591.
The text of those sections of Title 35, U.S. Code not included in this action can be found in a prior Office action.
Rejections and/or objections not reiterated from previous office actions are hereby withdrawn.
Claim Rejections - 35 USC § 112(b) or Second Paragraph (pre-AIA )
Claims 16-17, 21, 23, 25-26 were 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 pre-AIA the applicant regards as the invention. In view of Applicant’s amendment of claim 16, which now recites “at least 95% sequence identity”, this rejection is hereby withdrawn.
Claim Rejections - 35 USC § 112(a) or First Paragraph (pre-AIA )
Claims 16-17, 21, 23, 25-26 remain 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 pre-AIA the inventor(s), at the time the application was filed, had possession of the claimed invention. This rejection is necessitated by the introduction new matter.
As set forth in MPEP 2163 (I)(B), new or amended claims which introduce elements or limitations which are not supported by the as-filed disclosure violate the written description requirement. See, e.g., In re Lukach, 442 F.2d 967, 169 USPQ 795 (CCPA 1971) (subgenus range was not supported by generic disclosure and specific example within the subgenus range); In re Smith, 458 F.2d 1389, 1395, 173 USPQ 679, 683 (CCPA 1972) (a subgenus is not necessarily described by a genus encompassing it and a species upon which it reads). Claim 16 and dependent claims 17, 21, 23, 25-26 as amended now require an engineered composition that consists of four components, a Cas polypeptide, a nucleic acid component that forms a complex with the Cas polypeptide, a nucleic acid that comprises a detectable label which is not complementary to the nucleic acid component that forms a complex with the Cas polypeptide, and a buffer. While the Examiner has found support for an engineered composition that comprises a Cas polypeptide, a nucleic acid component that forms a complex with the Cas polypeptide and a nucleic acid comprising a detectable label which is not complementary to the nucleic acid component that forms a complex with the Cas polypeptide, the Examiner is unable to find support for an engineered composition that consists of four components, namely a Cas polypeptide, a nucleic acid component that forms a complex with the Cas polypeptide, a nucleic acid that comprises a detectable label and is not complementary to the nucleic acid component that forms a complex with the Cas polypeptide, and a buffer. Thus, there is no indication that an engineered composition that consists of four components, wherein said components are a Cas polypeptide, a nucleic acid component that forms a complex with the Cas polypeptide, a nucleic acid that comprises a detectable label and is not complementary to the nucleic acid component, and a buffer, was within the scope of the invention as conceived by Applicant at the time of the invention. Accordingly, Applicant is required to cancel the new matter in the response to this Office Action.
With regard to the written description rejection previously raised, Applicant argues that the Office conflates written description with enablement. Applicant states that a composition claim does not require written description support for every possible method in which that composition might be used and that the relevant inquiry is whether the specification demonstrates possession of the claimed composition. Applicant states that the specification’s statement that the composition “comprise at least two components” explicitly means the composition can have “two or more components” and is not limited to exactly two. Applicant states that this statement inherently discloses that the composition can have exactly two, three, or more discrete components. Applicant states that support for the amendment of claim 16, which now requires a composition that consists of four components, is found in paragraphs [01016], [0183]. Applicant states that these multiple paragraphs explicitly demonstrate that the inventors were in possession of compositions consisting of (i) a Cas polypeptide, (ii) a nucleic acid component, (iii) a non-target nucleic acid with detectable label, and (iv) buffers. Applicant states that the specification need not recite every possible claim format or explicitly state “a composition consisting of three components” when it already demonstrate possession through its functional description of those components working in concert. Applicant states that the Office’s argument that the specification’s use of “comprises” precludes written description for “consisting of” claims misunderstand the written description requirement. Applicant is of the opinion that when the specification discloses a composition that comprises specific components working together, one of skill in the art would understand that the inventors possess a composition consisting of those components, even if the specification used “comprises” rather than “consists of”. Applicant refers to paragraphs [01016], [0160], [0183] in support of the argument that the specification demonstrates possession of compositions consisting of the three elements. Applicant further refers to Figures 118 D, 118F and 118H as providing further support that the nucleic acid component is capable of hybridizing to the target nucleic acid as claimed.
Applicant’s arguments as they relate to the rejection set forth above have been fully considered but not deemed persuasive to avoid the rejection of claims 16-17, 21, 23, 25-26. The Examiner acknowledges the amendments made to claim 16. However, the Examiner disagrees with Applicant’s contention that the claimed composition finds support in the specification as originally filed. While it is agreed that the Abstract and the specification refer to compositions for targeting nucleic acids, including a non-naturally occurring or engineered composition comprising a Type VI CRISPR-Cas loci effector protein and one or more nucleic acid components (paragraph [0013]), the issue in the instant case is whether a composition consisting of 4 components, wherein said 4 components are limited to a Cas polypeptide, a nucleic acid component that forms a complex with the Cas polypeptide, a nucleic acid that comprises a detectable label and is not complementary to the nucleic acid component, and a buffer has been disclosed in the specification as originally filed, or has been disclosed as a preferred embodiment of the genus of compositions comprising a Type VI CRISPR-Cas loci effector protein and one or more nucleic acid components. As previously indicated, the term “comprising” is open language while the term “consisting of” is closed language. There is no mention of a composition that only has the recited four components in the specification. Moreover, while Applicant refers to paragraphs [01016], [0160] and [0183] as examples of the claimed composition, it is noted that paragraph [0160] refers to Figure 71 as disclosing the results of an assay where a C2c2 protein from Leptotrichia shahii (Cas polypeptide) was used to cleave an RNA target using two different buffers of different compositions, without any mention of a nucleic acid that comprises a detectable label and is not complementary to the crRNA (nucleic acid component) that forms a complex with the C2c2 protein, paragraph [0183] refers to Figure 94 as disclosing that a C2c2 protein from Leptotrichia shahii processes its own array using two different buffers of different compositions, without any mention of a nucleic acid that comprises a detectable label and is not complementary to the crRNA (nucleic acid component) that forms a complex with the C2c2 protein, and paragraph [01016] discloses nuclease assays performed with labeled target single stranded RNA, a C2c2 protein from Leptotrichia shahii (Cas polypeptide), and crRNA in the presence of a buffer having a specific composition, without any mention of a nucleic acid that comprises a detectable label and is not complementary to the crRNA (nucleic acid component) that forms a complex with the C2c2 protein. The labeled target single stranded RNA is complementary to the crRNA (nucleic acid component). All of the compositions disclosed in these paragraphs require a nucleic acid which is excluded from the 4 components recited in the claims, namely a target RNA, and none of these compositions comprise the required nucleic acid that comprises a detectable label and is not complementary to the crRNA. Furthermore, while these specific compositions as disclosed in paragraphs [0160], [0183] and [01016] comprise a specific Cas polypeptide (from Leptotrichia shahii ), and a specific crRNA in buffers whose components are well defined, the composition of the claims requires a genus of Cas polypeptides and a genus of buffers. With regard to the argument that Figures 118D, 118F and 118H show that the nucleic acid component is capable of hybridizing to the target nucleic acid as claimed, it is noted that the Examiner has not argued that there is no support for a nucleic acid component that is capable of hybridizing to the target nucleic acid.
Thus, there is no indication that an engineered composition that consists of four components, namely a Cas polypeptide, a nucleic acid component that forms a complex with the Cas polypeptide, a nucleic acid that comprises a detectable label, wherein the nucleic acid is not complementary to the nucleic acid component, and a buffer was within the scope of the invention as conceived by Applicant at the time of the invention. Accordingly, Applicant is required to cancel the new matter in the response to this Office Action.
Double Patenting
Claims 16-17, 21, 23, 25-26 remain rejected on the ground of nonstatutory double patenting as being unpatentable over claims 7-8 of U.S. Patent No. 11,174,515.
This rejection has been discussed at length in prior Office actions. It is maintained for the reasons of record and those set forth below.
Applicant states that the Office appears to be applying an anticipatory-type double patenting analysis and states that this framework does not apply here. Applicant states that claims 7-8 of the ‘515 patent require nucleic acid amplification reagents which are not recited in the instant claims and that the instant claims require a buffer, which is not required by the claims in the ‘515 patent. Applicant states that the later filed ‘515 does not claim a species. Applicant states that the proper inquiry is whether one of ordinary skill would have been motivated to arrive at the instant composition starting from what is actually claimed in the ‘515 patent and not whether the instant claims might read on embodiments described in the ‘515 patent. Applicant states that the ‘515 claims do not require the recited C2c2 proteins, a buffer or any specific sequence identity percentages. Applicant refers to MPEP § 804(II)(B)(1) in support of the argument that no part of the reference patent or application may be used as if it were prior art. Applicant states that reliance on the specification disclosures to bridge the gap between the generic ‘515 patent claims and the instant specific compositions violates MPEP § 804(II)(B)(1). Applicant states that the claims of the ‘515 require nucleic acid amplification reagents and that starting from the ‘515 patent claims, one of skill in the art would have no reason to eliminate amplification reagents and substitute a buffer because this modification would alter the system’s purpose. Applicant states that the Office cannot dismiss amplification reagents as non-essential when they are claimed for the detection system to operate as intended.
Applicant’s arguments have been fully considered but not deemed persuasive to overcome the instant rejections. Claims 16-17, 21, 23, 25-26 of the instant application are directed in part to an engineered composition that consists of four components, wherein said components are a Cas protein that comprises SEQ ID NO: 591, a nucleic acid component that forms a complex with the Cas polypeptide and directs the complex to bind a target RNA, a nucleic acid that comprises a detectable label and is not complementary to the nucleic acid component, and a buffer, wherein the Cas protein has RNase activity, wherein the Cas protein has two HEPN domains separated by a mixed alpha/beta region, wherein one of the HEPN domains is near the C-terminal end of the Cas protein.
With regard to the argument that the Office appears to be applying an anticipatory-type double patenting analysis, Applicant is reminded that the Examiner has repeatedly indicated that the invention of claims 16-17, 21, 23, 25-26 of the instant application is deemed an obvious variation of the invention of claims 7-8 of U.S. Patent No. 11,174,515. Therefore, the Examiner has not applied an anticipatory-type double patenting analysis as asserted.
Claims 7-8 of U.S. Patent No. 11,174,515 are directed in part to a nucleic acid detection system that has a Cas13 protein which is a C2c2 protein from Leptotrichia shahii or Leptotrichia wadei F0279, one or more guide polynucleotides capable of binding to a target nucleic acid, wherein the target nucleic acid is found in a mammalian cell, an RNA-based masking construct (nucleic acid that does not hybridize to the guide polynucleotide), and nucleic acid amplification reagents.
The specification of U.S. Patent No. 11,174,515 states that the nucleic acid amplification reagent includes a buffer. The specification of U.S. Patent No. 11,174,515 discloses the amino acid sequence of SEQ ID NO: 477 as the amino acid sequence of the C2c2 protein from Leptotrichia shahii recited in the claims. SEQ ID NO: 477 is identical to SEQ ID NO: 591 of the instant application. The specification of U.S. Patent No. 11,174,515 discloses the amino acid sequence of SEQ ID NO: 12 as the amino acid sequence of the C2c2 protein from Leptotrichia wadei F0279 recited in the claims. SEQ ID NO: 12 is identical to SEQ ID NO: 587 of the instant application. The proteins of SEQ ID NO: 477 and 12 of U.S. Patent No. 11,174,515 are Leptotrichia shahii and Leptotrichia wadei F0279 C2c2 proteins as recited in the claims of U.S. Patent No. 11,174,515. The specification of U.S. Patent No. 11,174,515 also discloses an RNA-based masking construct (nucleic acid that does not hybridize to the nucleic acid component) that comprises an RNA oligonucleotide linked to a detectable ligand (label) as a preferred embodiment of the genus of masking constructs required in the system of claims 7-8 of U.S. Patent No. 11,174,515 as evidenced by claim 13 of U.S. Patent No. 11,174,515. The nucleic acid detection system of claims 7-8 of U.S. Patent No. 11,174,515 requires four components, namely a Cas polypeptide which is a C2c2 protein from Leptotrichia shahii and Leptotrichia wadei F0279 (called CRISPR effector protein in U.S. Patent No. 11,174,515), a nucleic acid component (called guide RNA in U.S. Patent No. 11,174,515), a nucleic acid that is not complementary to the nucleic acid component (called RNA-based masking construct in U.S. Patent No. 11,174,515), and a buffer in view of the fact that the nucleic acid amplification reagent includes a buffer. Therefore, a composition (system) that consists of the Cas polypeptide of SEQ ID NO: 591 (L. shahii C2c2 protein), a nucleic acid component that forms a complex with the Cas polypeptide of SEQ ID NO: 591 (guide polynucleotide), a nucleic acid molecule that comprises a detectable label which is not complementary to the nucleic acid component (RNA-masking construct) and a buffer would be an obvious variation of the system of claims 7-8 of U.S. Patent No. 11,174,515 in view of the fact that the L. shahii C2c2 protein comprises SEQ ID NO: 591 as evidenced by the specification of 11,174,515 and the nucleic acid amplification reagent includes a buffer.
With regard to the argument that MPEP § 804(II)(B)(1) states that no part of the reference patent or application may be used as if it were prior art, and that reliance on the specification disclosures to bridge the gap between the generic ‘515 patent claims and the instant specific compositions violates MPEP § 804(II)(B)(1), it is noted that the Examiner has not used the specification of U.S. Patent No. 11,174,515 as prior art. As stated in MPEP § 804(II)(B)(1), those portions of the specification which provide support for the reference claims may also be examined and considered when addressing the issue of whether a claim in the application defines an obvious variation of an invention claimed in the reference patent or application (as distinguished from an obvious variation of the subject matter disclosed in the reference patent or application). Moreover, MPEP § 804(II)(B)(1) specifically states that one is not precluded from all use of the reference patent or application disclosure to understand the meaning of the reference claims and that the portion of the specification of the reference that describes subject matter that falls within the scope of a reference claim may be relied upon to properly construe the scope of that claim. In the instant case, the Examiner has previously stated that the proteins of SEQ ID NO: 477 and 12 in U.S. Patent No. 11,174,515 provide support to the genus of C2c2 proteins recited in claims 7-8, and that a labeled RNA-masking construct is clearly encompassed by the claims by being disclosed as a preferred embodiment of the genus of RNA-masking constructs. Therefore, for the reasons of record and those set forth above, one would reasonably conclude that the claimed invention is unpatentable over claims 7-8 of U.S. Patent No. 11,174,515 on the ground of nonstatutory double patenting.
Claims 16-17, 21, 23, 25-26 remain rejected on the ground of nonstatutory obviousness-type double patenting as being unpatentable over claims 1-8 of U.S. Patent No. 10,266,886. In the alternative, claims 16-17, 21, 23, 25-26 remain rejected on the ground of nonstatutory obviousness-type double patenting as being unpatentable over claims 1-8 of U.S. Patent No. 10,266,886 in view of Podolska et al. (Journal of Biomolecular Screening 19(3):417-426, first published 8/14/2013).
This rejection has been discussed at length in prior Office actions. It is maintained for the reasons of record and those set forth below.
Applicant states that the Office appears to be applying an anticipatory-type double patenting analysis and states that this framework does not apply here. Applicant states that claims 1-8 of the ‘886 patent require nucleic acid amplification reagents which are not recited in the instant claims and that the instant claims require a buffer, which is not required by the claims in the ‘886 patent. Applicant states that the later filed ‘886 does not claim a species. Applicant states that the proper inquiry is whether one of ordinary skill would have been motivated to arrive at the instant composition starting from what is actually claimed in the ‘886 patent and not whether the instant claims might read on embodiments described in the ‘886 patent. Applicant states that the ‘886 claims do not require the recited C2c2 proteins, a buffer or any specific sequence identity percentages. Applicant refers to MPEP § 804(II)(B)(1) in support of the argument that no part of the reference patent or application may be used as if it were prior art. Applicant states that reliance on the specification disclosures to bridge the gap between the generic ‘886 patent claims and the instant specific compositions violates MPEP § 804(II)(B)(1). Applicant states that the claims of the ‘886 require nucleic acid amplification reagents and that starting from the ‘886 patent claims, one of skill in the art would have no reason to eliminate amplification reagents and substitute a buffer because this modification would alter the system’s purpose. Applicant states that the Office cannot dismiss amplification reagents as non-essential when they are claimed for the detection system to operate as intended.
Applicant’s arguments have been fully considered but not deemed persuasive to overcome the instant rejections. Claims 16-17, 21, 23, 25-26 of the instant application are directed in part to an engineered composition that consists of four components, wherein said components are a Cas protein that comprises SEQ ID NO: 591, a nucleic acid component that forms a complex with the Cas polypeptide and directs the complex to bind a target RNA, a nucleic acid that comprises a detectable label and is not complementary to the nucleic acid component, and a buffer, wherein the Cas protein has RNase activity, wherein the Cas protein has two HEPN domains separated by a mixed alpha/beta region, wherein one of the HEPN domains is near the C-terminal end of the Cas protein.
With regard to the argument that the Office appears to be applying an anticipatory-type double patenting analysis, Applicant is reminded that the Examiner has repeatedly indicated that the invention of claims 16-17, 21, 23, 25-26 of the instant application is deemed an obvious variation of the invention of claims 1-8 of U.S. Patent No. 10,266,886. Therefore, the Examiner has not applied an anticipatory-type double patenting analysis as asserted.
Claims 1-8 of U.S. Patent No. 10,266,886 are directed in part to a system that comprises reagents for amplifying a target nucleic acid, an RNA construct that comprises a non-target sequence (not complementary to the nucleic acid component), a Cas13a protein (has two HEPN domains), a guide polynucleotide that binds to the Cas13a protein and forms a complex with the Cas13a protein, wherein the Cas13a protein comprises one or more HEPN domains, wherein the Cas13a protein cleaves the RNA construct comprising the non-target sequence, wherein the Cas13a comprises one or more HEPN domains, and wherein the Cas13a protein cleaves the RNA construct that comprises the non-target sequence. According to the specification of U.S. Patent No. 10,266,886, the target RNA is complementary to the guide polynucleotide and the non-target RNA is not complementary to the guide polynucleotide.
The specification of U.S. Patent No. 10,266,886 states that the nucleic acid amplification reagent includes a buffer. The specification of US Patent No. 10,266,886 discloses a. L. shahii DSM 19757 C2c2 protein that comprises SEQ ID NO: 591 as one of the preferred embodiment of the genus of Cas proteins in the systems (SEQ ID NO: 591 in the instant application is identical to SEQ ID NO: 591 in U.S. Patent No. 10,266,886). Furthermore, the specification of US Patent No. 10,266,886 discloses a labeled non-target RNA as a preferred embodiment of the genus of RNA constructs comprising a non-target sequence. The system of claims 1-8 of U.S. Patent No. 10,266,886 has four components, namely a Cas polypeptide (Cas13a in claim 6 in U.S. Patent No. 10,266,886), a nucleic acid component (called guide polynucleotide in U.S. Patent No. 10,266,886), a nucleic acid that does not hybridize to the nucleic acid component (called RNA construct that has a non-target sequence in U.S. Patent No. 10,266,886), and a buffer in view of the fact that the nucleic acid amplification reagent includes a buffer according to the specification of U.S. Patent No. 10,266,886. Therefore, a composition (system) that consists of the Cas polypeptide of SEQ ID NO: 591, a nucleic acid component that forms a complex with the Cas polypeptide of SEQ ID NO: 591 (guide polynucleotide), a nucleic acid molecule that comprises a detectable label which is not complementary to the nucleic acid component (RNA construct that comprises a non-target sequence) and a buffer would be an obvious variation of the system of claims 1-8 of U.S. Patent No. 10,266,886 in view of the fact that the protein of SEQ ID NO: 591 is a species disclosed in U.S. Patent No. 10,266,886 that provides support to the genus of Cas13 recited in the claims, a labeled RNA construct that has a non-target sequence is a preferred embodiment of the genus of RNA constructs that have a non-target sequence, and the nucleic acid amplification reagent includes a buffer.
With regard to the argument that MPEP § 804(II)(B)(1) states that no part of the reference patent or application may be used as if it were prior art, and that reliance on the specification disclosures to bridge the gap between the generic ‘886 patent claims and the instant specific compositions violates MPEP § 804(II)(B)(1), it is noted that the Examiner has not used the specification of U.S. Patent No. 10,266,886 as prior art. As stated in MPEP § 804(II)(B)(1), those portions of the specification which provide support for the reference claims may also be examined and considered when addressing the issue of whether a claim in the application defines an obvious variation of an invention claimed in the reference patent or application (as distinguished from an obvious variation of the subject matter disclosed in the reference patent or application). Moreover, MPEP § 804(II)(B)(1) specifically states that one is not precluded from all use of the reference patent or application disclosure to understand the meaning of the reference claims and that the portion of the specification of the reference that describes subject matter that falls within the scope of a reference claim may be relied upon to properly construe the scope of that claim. In the instant case, the Examiner has previously stated that the protein of SEQ ID NO: 591 in U.S. Patent No. 10,266,886 provide support to the genus of C2c2 proteins recited in claims 1-8, and that a labeled RNA construct that has a non-target sequence is clearly encompassed by the claims as a preferred embodiment. Therefore, for the reasons of record and those set forth above, one would reasonably conclude that the claimed invention is unpatentable over claims 1-8 of U.S. Patent No. 10,266,886 on the ground of nonstatutory double patenting.
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Conclusion
No claim is in condition for allowance.
Applicant's amendment necessitated the new ground(s) of rejection presented in this Office action. Accordingly, THIS ACTION IS MADE FINAL. See MPEP § 706.07(a). Applicant is reminded of the extension of time policy as set forth in 37 CFR 1.136(a). A shortened statutory period for reply to this final action is set to expire THREE MONTHS from the mailing date of this action. In the event a first reply is filed within TWO MONTHS of the mailing date of this final action and the advisory action is not mailed until after the end of the THREE-MONTH shortened statutory period, then the shortened statutory period will expire on the date the advisory action is mailed, and any extension fee pursuant to 37 CFR 1.136(a) will be calculated from the mailing date of the advisory action. In no event, however, will the statutory period for reply expire later than SIX MONTHS from the date of this final action.
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Any inquiry concerning this communication or earlier communications from the examiner should be directed to DELIA M RAMIREZ, Ph.D., whose telephone number is (571) 272-0938. The examiner can normally be reached on Monday-Friday from 8:30 AM to 5:00 PM. If attempts to reach the examiner by telephone are unsuccessful, the examiner’s supervisor, Robert B. Mondesi, can be reached at (408) 918-7584. The fax phone number for the organization where this application or proceeding is assigned is 571-273-8300.
/DELIA M RAMIREZ/Primary Examiner, Art Unit 1652
DR
March 2, 2026