DETAILED ACTION
Notice of Pre-AIA or AIA Status
The present application is being examined under the pre-AIA first to invent provisions.
Status of Claims
Claims 1-30 are canceled.
Claims 31-50 are pending.
Claims 31-50 are rejected.
Priority
Applicant’s claim for the benefit of a prior-filed application, U.S. 14/378,448 filed 13 Aug. 2014, PCT/US13/26414 filed 15 Feb. 2013, U.S. 61/713,163 filed 12 Oct. 2012, and U.S. 61/599,754 filed 16 Feb. 2012 under 35 U.S.C. 119(e) or under 35 U.S.C. 120, 121, 365(c), or 386(c) is acknowledged.
Accordingly, the effective filing date of the claimed invention is 16 Feb. 2012.
Information Disclosure Statement
The information disclosure statement(s) (IDS) submitted on 25 Aug. 2022 is in compliance with the provisions of 37 CFR 1.97. Accordingly, the list of cited references was considered in full by the examiner.
Nucleotide and/or Amino Acid Sequence Disclosures
The sequence listing filed 16 May 2022 has been entered, and is in compliance with all of the requirements of 37 CFR § 1.821 through 1.825.
Drawings
The drawings filed 16 May 2022 are objected to because:
FIG. 2A-D fail to comply with 37 CFR. 1.84(u)(1), which states the different views must be numbered in consecutive Arabic numerals, starting with 1, independent of the numbering of the sheets and, if possible, in the order in which they appear on the drawing sheet(s), because FIG. 2B appears after FIG. 2C and 2D in the drawing sheet(s). FIG. 2B should e placed following FIG. 2A, or FIG. 2A-D should be relabeled such that current FIG. 2B is relabeled FIG. 2D, while FIG. 2C and 2D are relabeled FIG. 2B and 2C respectively.
FIG. 4A-D fail to comply with 37 CFR. 1.84(u)(1), which states the different views must be numbered in consecutive Arabic numerals, starting with 1, independent of the numbering of the sheets and, if possible, in the order in which they appear on the drawing sheet(s) for the same reasons as discussed above for FIG. 2.
Corrected drawing sheets in compliance with 37 CFR 1.121(d) are required in reply to the Office action to avoid abandonment of the application. Any amended replacement drawing sheet should include all of the figures appearing on the immediate prior version of the sheet, even if only one figure is being amended. The figure or figure number of an amended drawing should not be labeled as “amended.” If a drawing figure is to be canceled, the appropriate figure must be removed from the replacement sheet, and where necessary, the remaining figures must be renumbered and appropriate changes made to the brief description of the several views of the drawings for consistency. Additional replacement sheets may be necessary to show the renumbering of the remaining figures. Each drawing sheet submitted after the filing date of an application must be labeled in the top margin as either “Replacement Sheet” or “New Sheet” pursuant to 37 CFR 1.121(d). If the changes are not accepted by the examiner, the applicant will be notified and informed of any required corrective action in the next Office action. The objection to the drawings will not be held in abeyance.
Claim Interpretation
Claims 31 and 46 recite a “translocase”. Applicant’s specification at para. [0055] (as published), defines the term “protein translocase” to mean a protein-binding peptide, such as a polypeptide which is able to control movement of a protein substrate, for example a an enzyme, enzyme complex, or part of an enzyme complex that operates on a protein and moves it relative to the enzyme in a processive manner. Therefore, the term will be interpreted accordingly.
Claim 43 recites “wherein the protein comprises an exogenous sequence”, which further limits the source of a sequence to have been “exogenous”, which further limits the sequence of the protein to have been developed from external factors (e.g. by a mutagen). This is interpreted as a product by process limitation defining the process in which the protein was previously generated. See MPEP 2113 I, stating "[E]ven though product-by-process claims are limited by and defined by the process, determination of patentability is based on the product itself. The patentability of a product does not depend on its method of production. If the product in the 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.".
Claim 46 recites “A device for determining one or more characteristics of a protein, the device comprising:….instructions that cause the device to: monitor ionic current changes during translocation of a protein by a protein translocase on the first side…”. The device of claim 46 is interpreted to merely be programmed and able to monitor ionic current changes, but the process in which the ionic current change was generated is not part of the claimed device (i.e. the device does not include a protein translocase). That is, the method in which the device is intended to be operated (i.e. by monitoring currents generated by a translocase) is not part of the device. See MPEP 2114 I. "[A]pparatus claims cover what a device is, not what a device does." Hewlett-Packard Co. v. Bausch & Lomb Inc., 909 F.2d 1464, 1469, 15 USPQ2d 1525, 1528 (Fed. Cir. 1990) (emphasis in original).
Claim Rejections - 35 USC § 112 (pre-AIA ), second paragraph
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 46-50 are rejected under 35 U.S.C. 112(b), 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.
Claim 46, and claims dependent therefrom, are indefinite for recitation of “A device…comprising: a nanopore…; a circuit…; and instructions that cause the device to: monitor…”. When determining the scope of a claim directed to a computer-readable medium containing certain programming, the examiner should first look to the relationship between the programming and the intended computer system. See MPEP 2111.05. In the instant case, the functional relationship between the “instructions that cause the device” and the device itself are unclear. For example it is not clear if the “instructions that cause the device” is intended to be programming in a functional relationship to the nanopore, programming for the circuit, or programming of some other component of the device (e.g. a field-programmable gate array hardware on pg. 35 of the specification). Alternatively it is unclear if the device merely comprises instructions with an intended use of cause the device to perform the functions, such that no functional relationship exists. Clarification is requested regarding the relationship between the instructions and the device. For purpose of examination, the device is interpreted to comprise programming of any hardware of the device.
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 pre-AIA 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) the invention was known or used by others in this country, or patented or described in a printed publication in this or a foreign country, before the invention thereof by the applicant for a patent.
(b) the invention was patented or described in a printed publication in this or a foreign country or in public use or on sale in this country, more than one year prior to the date of application for patent in the United States.
Claims 31-34, 38-43, and 45-50 are rejected under pre-AIA 35 U.S.C. 102(a) as being anticipated by Gundlach (2011), as evidenced by Akeson (2007).
Cited references:
Gundlach et al. WO2011106459 A2; Pub. Date: 01 Sept. 2011; and
Akeson et al., US 7238485 B2, Pub. Date: 03 Jul. 2007.
Regarding claim 31, Gundlach discloses a method for analyte sequencing, including protein sequencing, with nanopores (Abstract; pg. 7, lines 17-26; claims 1-2; Figure 2) comprising the following steps:
Gundlach discloses (a) providing a device for translocating a protein through a nanopore (Figures 2A-D), comprising the following:
Gundlach discloses (i) a nanopore that forms tunnel upon insertion into a membrane, wherein the nanopore is positioned between a cis side (i.e. the second side) comprising a first liquid medium and a trans side (i.e. the first side) comprising a second liquid medium (pg. 1, lines 28-32; pg. 7, lines 17-24).
Gundlach discloses (ii) a patch clamp amplifier, or circuit, providing a voltage between the cis and trans side (pg. 59, lines 13-24; FIG. 2A-C; pg. 5, lines 29-32, e.g. voltage applied) for monitoring ionic current through the nanopore (FIG. 2D, e.g. see monitored current).
Gundlach discloses (b) adding a “molecular motor”, defined as a molecule or enzyme that physically interacts with an analyte, which includes a protein (pg. 7, lines 17-26) and is capable of physically moving the analyte through an opening of a nanopore in a sequential manner, to the trans side (i.e. the first side) of a membrane (pg. 23, line 23 to pg. 24, lines 11). Therefore, the molecular motor of Gundlach is considered a translocase, consistent with Applicant’s definition of a “protein translocase” discussed above in claim interpretation.
Gundlach discloses (c) monitoring ion current levels across the membrane during translocation of the analyte protein from the cis side to the trans side (i.e. in a direction toward the first side of the fluid chamber) (pg. 59, lines 19-24; FIG. 2D; claims 1-2).
Gundlach discloses (d) analyzing the ionic current levels to sequence two or more units of the analyte protein (i.e. determine characteristics of the protein) (claims 1-2).
Regarding claims 32-33, Gundlach discloses the nanopore is α-hemolysin (claim 45; pg. 18, lines 18-21; pg. 42, lines 7-9).
Regarding claim 34, Gundlach discloses the molecular motor (i.e. protein translocase) may be immobilized on the trans side of the membrane (pg. 24, lines 1-4), as described in U.S. 7,238,485 (Akson) incorporated by reference into Gundlach. Akeson discloses the molecular motor is attached to the nanopore via a matrix material to prevent to the molecular motor from diffusing away from the nanopore (col. 8, line 63 to col. 9, line 5).
Regarding claim 38, Gundlach discloses the circuit comprises a patch clamp amplifier applying a constant voltage across the bilayer (i.e. between the first and second side of the fluidic chamber) (pg. 6, lines 15-22, e.g. constant 140 mV voltage; pg. 12, line 6; pg. 59, lines 19-28; FIG. 2A).
Regarding claim 39, Gundlach discloses the analyte comprises a protein (pg. 7, lines 17-19), and that in the native state (i.e. non-denatured), the analytes are able to translocate through an opening of a nanopore (pg. 7, lines 16-20), and furthermore that the analyte (i.e. protein) is placed on a cis side (pg. 1, lines 28-30), demonstrating the protein is not required to be denatured.
Regarding claim 40, Gundlach discloses the nanopore is MsPA (pg. 4, lines 1-5; Figure 1).
Regarding claims 41-42, Gundlach discloses the characteristics of the analyte protein include determining the identity of units of a protein to determine the analyte sequence (pg. 6, lines 28-30; pg. 8, lines 4-11), and discloses the sequence of the analyte corresponds to an identify of the analyte (pg. 43, line 19 through pg. 44, line 22).
Regarding claim 43, claim 44 further limits the source of a sequence to have been “exogenous”, which further limits the sequence of the protein to have been developed from external factors (e.g. by a mutagen). This is interpreted as a product by process limitation as discussed above in claim interpretation. Because claim 44 does not require any particular exogenous sequence, the protein analyte of Gundlach is considered to read on the protein of claim 43.
Regarding claim 45, Gundlach discloses the nanopore can be a solid-state pore (pg. 8, lines 17-20; pg. 12, lines 2-4).
Regarding claim 46, Gundlach discloses a device for analyte sequencing, including protein sequencing, with nanopores (Abstract; pg. 7, lines 17-26; claims 1-2; Figure 2) comprising the following:
Gundlach discloses a nanopore that forms a tunnel upon insertion into a membrane, wherein the nanopore is positioned between a cis side (i.e. the second side) comprising a first liquid medium and a trans side (i.e. the first side) comprising a second liquid medium (pg. 1, lines 28-32; pg. 7, lines 17-24).
Gundlach discloses a patch clamp amplifier, or circuit, providing a voltage between the cis and trans side (pg. 59, lines 13-24; FIG. 2A-C; pg. 5, lines 29-32, e.g. voltage applied) for monitoring ionic current through the nanopore (FIG. 2D, e.g. see monitored current).
Gundlach discloses the device is configured to monitor ion current levels across the membrane during translocation of the analyte protein from the cis side to the trans side (i.e. in a direction toward the first side of the fluid chamber) (pg. 59, lines 19-24; FIG. 2D; claims 1-2). Although not considered part of the device as discussed in claim interpretation, it is noted that Gundlach does discloses the translocation is by a protein translocase capable of physically moving the analyte through an opening of a nanopore in a sequential manner, to the trans side (i.e. the first side) of a membrane (pg. 23, line 23 to pg. 24, lines 11).
Gundlach discloses the device analyzes the ionic current levels to sequence two or more units of the analyte protein (i.e. determine characteristics of the protein) (claims 1-2; FIG. 5 and 7, e.g. nanopore perform sequencing).
Regarding claims 47-48, Gundlach discloses the characteristics of the analyte protein include determining the identity of units of a protein to determine the analyte sequence (pg. 6, lines 28-30; pg. 8, lines 4-11), and discloses the sequence of the analyte corresponds to an identify of the analyte (pg. 43, line 19 through pg. 44, line 22).
Regarding claim 49, Gundlach discloses the nanopore is a α-hemolysin pore protein (claim 45; pg. 18, lines 18-21; pg. 42, lines 7-9).
Regarding claim 50, Gundlach discloses the nanopore can be a solid-state pore (pg. 8, lines 17-20; pg. 12, lines 2-4).
Therefore, Gundlach anticipates the claimed invention.
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 pre-AIA 35 U.S.C. 103(a) which forms the basis for all obviousness rejections set forth in this Office action:
(a) A patent may not be obtained though the invention is not identically disclosed or described as set forth in section 102, if the differences between the subject matter sought to be patented and the prior art are such that the subject matter as a whole would have been obvious at the time the invention was made to a person having ordinary skill in the art to which said subject matter 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 under pre-AIA 35 U.S.C. 103(a), the examiner presumes that the subject matter of the various claims was commonly owned at the time any inventions covered therein were made absent any evidence to the contrary. Applicant is advised of the obligation under 37 CFR 1.56 to point out the inventor and invention dates of each claim that was not commonly owned at the time a later invention was made in order for the examiner to consider the applicability of pre-AIA 35 U.S.C. 103(c) and potential pre-AIA 35 U.S.C. 102(e), (f) or (g) prior art under pre-AIA 35 U.S.C. 103(a).
Claims 35-37 and 44 are rejected under pre-AIA 35 U.S.C. 103(a) as being unpatentable over Gundlach (2011) in view of Kravats (2010) and Howorka (2009).
Cited references:
Gundlach et al. WO2011106459 A2; Pub. Date: 01 Sept. 2011;
Kravats et al., Unfolding and translocation pathway of substrate protein controlled by structure in repetitive allosteric cycles of the ClpY ATPase, 2011, PNAS, 108(6), pg. 2234-2239; cited in IDS filed 25 Aug. 2022; and
Howorka et al., Nanopore analytics: sensing of single molecules, 2009, Chem. Soc. Rev., 38, pg. 2360-2384.
Regarding claim 35-37 and 44, Gundlach discloses a method for analyte sequencing, including protein sequencing, with nanopores (Abstract; pg. 7, lines 17-26; claims 1-2; Figure 2) comprising the following steps:
Gundlach discloses (a) providing a device for translocating a protein through a nanopore (Figures 2A-D), comprising the following:
Gundlach discloses (i) a nanopore that forms tunnel upon insertion into a membrane, wherein the nanopore is positioned between a cis side (i.e. the second side) comprising a first liquid medium and a trans side (i.e. the first side) comprising a second liquid medium (pg. 1, lines 28-32; pg. 7, lines 17-24).
Gundlach discloses (ii) a patch clamp amplifier, or circuit, providing a voltage between the cis and trans side (pg. 59, lines 13-24; FIG. 2A-C; pg. 5, lines 29-32, e.g. voltage applied) for monitoring ionic current through the nanopore (FIG. 2D, e.g. see monitored current).
Gundlach discloses (b) adding a “molecular motor”, defined as a molecule or enzyme that physically interacts with an analyte, which includes a protein (pg. 7, lines 17-26) and is capable of physically moving the analyte through an opening of a nanopore in a sequential manner, to the trans side (i.e. the first side) of a membrane (pg. 23, line 23 to pg. 24, lines 11). Therefore, the molecular motor of Gundlach is considered a translocase, consistent with Applicant’s definition of a “protein translocase” discussed above in claim interpretation.
Gundlach discloses (c) monitoring ion current levels across the membrane during translocation of the analyte protein from the cis side to the trans side (i.e. in a direction toward the first side of the fluid chamber) (pg. 59, lines 19-24; FIG. 2D; claims 1-2).
Gundlach discloses (d) analyzing the ionic current levels to sequence two or more units of the analyte protein (i.e. determine characteristics of the protein) (claims 1-2).
Gundlach does not disclose the following limitations:
Regarding claims 35-37, while Grundlach discloses a molecular motor (i.e. protein translocase) may be used to physically move the protein analyte through an opening of a nanopore in a sequential manner, to the trans side (i.e. the first side) of a membrane (pg. 23, line 23 to pg. 24, lines 11), and further discloses the methods in which the molecular motor (i.e. protein translocase) may be immobilized on the trans side of the membrane (pg. 24, lines 1-4), Grundlach does not disclose the protein translocase is an AAA+ enzyme of ClpX.
Regarding claim 44, while Grundlach does disclose modifying the protein analyte (claim 1), Grundlach further does not disclose the protein comprises an exogenous sequence of a targeting domain for the protein translocase.
However, these limitations were known to one of ordinary skill in the art, as shown by Howorka and Kravats.
First, Howorka overviews nanopore analytics involving passing individual molecules such as peptides through a single nanopore to give rise to detectable temporary blockades in ionic pore current (Abstract). Howorka discloses that peptides and proteins larger than the pore lumen must unfold to pass through the narrow opening and unfolded proteins can be obtained using a denaturing agent (pg. 2375, col. 2, para. 4; Table 1). Howarka further discloses embodiments in which pores can act as a guide which unfold polymeric analytic strands as they enter the pore (pg. 2379, col. 2, para. 3).
Furthermore, Kravats discloses ClpX is an ATpase that translocates proteins through nanopores, and includes a domain which stabilizes unfolded conformations of the protein and makes them competent for translocation through narrow pores (Abstract; pg. 2234, col. 2, para. 3). Kravats further discloses loops of the Clpx involve recognizing peptide specific tags fused to target proteins (pg. 2234, col. 1, para. 2). Kravats further discloses this allosteric pore mechanism has been selected for its ability to effect unfolding and translocation without assistance from cofactors or environmental variations such as an electrostatic gradient (pg. 2238, col. 1, para. 1).
It would have been prima facie obvious to one of ordinary skill in the art, before the effective filing date of the claimed invention, to have modified the molecular motor and protein of Gundlach to have utilized the ClpX unfoldase and a protein with a fused peptide tag recognized by ClpX, shown by Kravats, discussed above. One of ordinary skill in the art would have been motivated to combine the methods of Gundlach and Kravats in order to allow for the unfolding and translocation of proteins through narrow nanopores without assistance from cofactors or environmental variations such as electrostatic gradients, as shown by Kravats (pg. 2238, col. 1, para. 1) or without using denaturing agents (see Howorka pg. 2375, col. 2, para. 4) , given Howorka explains that large proteins must be unfolded to be able to pass through narrow openings (pg. 2375, col. 2, para. 4). This modification would have had a reasonable expectation of success given Gundlach provides methods in which molecular motors can be immobilized near nanopores to facilitate translocation, as discussed above, and Howorka explains pores can act as a guide which unfold polymeric analytic strands as they enter the pore (pg. 2379, col. 2, para. 3), such that the translocase of Kravats is applicable to the method of Gundlach.
Double Patenting
The nonstatutory double patenting rejection is based on a judicially created doctrine grounded in public policy (a policy reflected in the statute) so as to prevent the unjustified or improper timewise extension of the “right to exclude” granted by a patent and to prevent possible harassment by multiple assignees. A nonstatutory double patenting rejection is appropriate where the conflicting claims are not identical, but at least one examined application claim is not patentably distinct from the reference claim(s) because the examined application claim is either anticipated by, or would have been obvious over, the reference claim(s). See, e.g., In re Berg, 140 F.3d 1428, 46 USPQ2d 1226 (Fed. Cir. 1998); In re Goodman, 11 F.3d 1046, 29 USPQ2d 2010 (Fed. Cir. 1993); In re Longi, 759 F.2d 887, 225 USPQ 645 (Fed. Cir. 1985); In re Van Ornum, 686 F.2d 937, 214 USPQ 761 (CCPA 1982); In re Vogel, 422 F.2d 438, 164 USPQ 619 (CCPA 1970); In re Thorington, 418 F.2d 528, 163 USPQ 644 (CCPA 1969).
A timely filed terminal disclaimer in compliance with 37 CFR 1.321(c) or 1.321(d) may be used to overcome an actual or provisional rejection based on nonstatutory double patenting provided the reference application or patent either is shown to be commonly owned with the examined application, or claims an invention made as a result of activities undertaken within the scope of a joint research agreement. See MPEP § 717.02 for applications subject to examination under the first inventor to file provisions of the AIA as explained in MPEP § 2159. See MPEP § 2146 et seq. for applications not subject to examination under the first inventor to file provisions of the AIA . A terminal disclaimer must be signed in compliance with 37 CFR 1.321(b).
The filing of a terminal disclaimer by itself is not a complete reply to a nonstatutory double patenting (NSDP) rejection. A complete reply requires that the terminal disclaimer be accompanied by a reply requesting reconsideration of the prior Office action. Even where the NSDP rejection is provisional the reply must be complete. See MPEP § 804, subsection I.B.1. For a reply to a non-final Office action, see 37 CFR 1.111(a). For a reply to final Office action, see 37 CFR 1.113(c). A request for reconsideration while not provided for in 37 CFR 1.113(c) may be filed after final for consideration. See MPEP §§ 706.07(e) and 714.13.
The USPTO Internet website contains terminal disclaimer forms which may be used. Please visit www.uspto.gov/patent/patents-forms. The actual filing date of the application in which the form is filed determines what form (e.g., PTO/SB/25, PTO/SB/26, PTO/AIA /25, or PTO/AIA /26) should be used. A web-based eTerminal Disclaimer may be filled out completely online using web-screens. An eTerminal Disclaimer that meets all requirements is auto-processed and approved immediately upon submission. For more information about eTerminal Disclaimers, refer to www.uspto.gov/patents/apply/applying-online/eterminal-disclaimer.
Claims 31-50 are rejected on the ground of nonstatutory double patenting as being unpatentable over claims 1-17 of U.S. Patent No. US 11,339,365 B2. Although the claims at issue are not identical, they are not patentably distinct from each other because:
The reference claims disclose a narrower embodiment of the instant claims.
Reference claim 1 discloses the limitations of instant claims 31 and 46.
Reference claims 5-6 disclose the limitations of instant claims 32-33 and 49.
Reference claims 1 and 12 disclose the limitation of instant claims 35-37.
Reference claim 9 discloses the limitation of instant claim 38.
Reference claims 10-11 disclose the limitation of instant claim 39.
Reference claim 13 discloses the limitation of instant claim 40.
Reference claims 14-15 disclose the limitation of instant claims 41-42 and 47-48.
Reference claims 1 and 16 disclose the limitation of instant claims 43-44.
Reference claim 17 disclose the limitation of instant claims 45 and 50.
Conclusion
No claims are allowed.
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/KAITLYN L MINCHELLA/Primary Examiner, Art Unit 1685